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

PubMed

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

2018-07-01

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

Growth factor effects on costal chondrocytes for tissue engineering fibrocartilage

PubMed Central

Johns, D.E.; Athanasiou, K.A.

2010-01-01

Tissue engineered fibrocartilage could become a feasible option for replacing tissues like the knee meniscus or temporomandibular joint disc. This study employed five growth factors insulin-like growth factor-I, transforming growth factor-β1, epidermal growth factor, platelet-derived growth factor-BB, and basic fibroblast growth factor in a scaffoldless approach with costal chondrocytes, attempting to improve biochemical and mechanical properties of engineered constructs. Samples were quantitatively assessed for total collagen, glycosaminoglycans, collagen type I, collagen type II, cells, compressive properties, and tensile properties at two time points. Most treated constructs were worse than the no growth factor control, suggesting a detrimental effect, but the IGF treatment tended to improve the constructs. Additionally, the 6wk time point was consistently better than 3wks, with total collagen, glycosaminoglycans, and aggregate modulus doubling during this time. Further optimization of the time in culture and exogenous stimuli will be important in making a more functional replacement tissue. PMID:18597118

Integration of Basic Knowledge Models for the Simulation of Cereal Foods Processing and Properties.

PubMed

Kristiawan, Magdalena; Kansou, Kamal; Valle, Guy Della

Cereal processing (breadmaking, extrusion, pasting, etc.) covers a range of mechanisms that, despite their diversity, can be often reduced to a succession of two core phenomena: (1) the transition from a divided solid medium (the flour) to a continuous one through hydration, mechanical, biochemical, and thermal actions and (2) the expansion of a continuous matrix toward a porous structure as a result of the growth of bubble nuclei either by yeast fermentation or by water vaporization after a sudden pressure drop. Modeling them is critical for the domain, but can be quite challenging to address with mechanistic approaches relying on partial differential equations. In this chapter we present alternative approaches through basic knowledge models (BKM) that integrate scientific and expert knowledge, and possess operational interest for domain specialists. Using these BKMs, simulations of two cereal foods processes, extrusion and breadmaking, are provided by focusing on the two core phenomena. To support the use by non-specialists, these BKMs are implemented as computer tools, a Knowledge-Based System developed for the modeling of the flour mixing operation or Ludovic ® , a simulation software for twin screw extrusion. They can be applied to a wide domain of compositions, provided that the data on product rheological properties are available. Finally, it is stated that the use of such systems can help food engineers to design cereal food products and predict their texture properties.

The biochemical properties of antibodies and their fragments

USDA-ARS?s Scientific Manuscript database

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

Mechanics and morphogenesis of fission yeast cells.

PubMed

Davì, Valeria; Minc, Nicolas

2015-12-01

The integration of biochemical and biomechanical elements is at the heart of morphogenesis. While animal cells are relatively soft objects which shape and mechanics is mostly regulated by cytoskeletal networks, walled cells including those of plants, fungi and bacteria are encased in a rigid cell wall which resist high internal turgor pressure. How these particular mechanical properties may influence basic cellular processes, such as growth, shape and division remains poorly understood. Recent work using the model fungal cell fission yeast, Schizosaccharomyces pombe, highlights important contribution of cell mechanics to various morphogenesis processes. We envision this genetically tractable system to serve as a novel standard for the mechanobiology of walled cell. Copyright © 2015 Elsevier Ltd. All rights reserved.

Some Biochemical Properties of an Acido-Thermophilic Archae-Bacterium Sulfolobus Acidocaldarius

NASA Astrophysics Data System (ADS)

Oshima, Tairo; Ohba, Masayuki; Wagaki, Takayoshi

1984-12-01

To elucidate the phylogenic status of archaebacteria, some basic cellular components of an acido-thermophilic archaebacterium,Sulfolobus acidocaldarius, were studied. Poly(A) containing RNA was present in the cells, and performed the role of mRNA in a cell-free extract of reticulocyte or the archaebacteria. Poly(A) containing RNA was also found in other archaebacterial cells. The absence of cap structure was suggested in these RNAs. The cell-free protein synthesis using the archaebacterial extract was inhibited by anisomycin, a specific inhibitor for eukaryotic ribosomes. Two unique membrane-bound ATPases were detected. Based on resistance to H+-ATPase inhibitors, these enzymes seemed not to be F0F1-ATPase.

Gravitational Biology: The Rat Model

NASA Technical Reports Server (NTRS)

1997-01-01

In this session, Session JP3, the discussion focuses on the following topics: Morphology of brain, pituitary and thyroid in the rats exposed to altered gravity; Biochemical Properties of B Adrenoceptors After Spaceflight (LMS-STS78) or Hindlimb Suspension in Rats; Influence of Hypergravity on the Development of Monoaminergic Systems in the Rat Spinal Cord; A Vestibular Evoked Potentials (VsEPs) Study of the Function of the Otolith Organs in Different Head Orientations with respect to Earth Gravity Vector in the Rat; Quantitative Observations on the Structure of Selected Proprioceptive Components in Adult Rats that Underwent About Half of their Fetal Development in Space; Effects of a Nine-Day Shuttle Mission on the Development of the Neonatal Rat Nervous System, A Behavioral Study; Muscle Atrophy Associated to Microgravity in Rat, Basic Data For Countermeasures; Simulated Weightlessness by Unloading in the Rat, Results of a Time Course Study of Biochemical Events Occurring During Unloading and Lack of Effect of a rhBNP-2 Treatment on Bone Formation and Bone Mineral Content in Unloading Rats; and Cytological Mechanism of the Osteogenesis Under Microgravity Conditions.

Potential Tools for Phenotyping for Physical Characteristics of Plants, Pods, and Seed

USDA-ARS?s Scientific Manuscript database

Advances in phenotyping are a key factor for success in modern breeding as well as for basic plant research. Phenotyping provides a critical means to understand morphological, biochemical, physiological principles in the control of basic plant functions as well as for selecting superior genotypes in...

Thermodynamic properties of an emerging chemical disinfectant, peracetic acid.

PubMed

Zhang, Chiqian; Brown, Pamela J B; Hu, Zhiqiang

2018-04-15

Peracetic acid (PAA or CH 3 COOOH) is an emerging disinfectant with a low potential to form carcinogenic disinfection by-products (DBPs). Basic thermodynamic properties of PAA are, however, absent or inconsistently reported in the literature. This review aimed to summarize important thermodynamic properties of PAA, including standard Gibbs energy of formation and oxidation-reduction (redox) potential. The standard Gibbs energies of formation of CH 3 COOOH (aq) , CH 3 COOOH (g) , CH 3 COOOH (l) , and CH 3 COOO (aq) - are -299.41kJ·mol -1 , -283.02kJ·mol -1 , -276.10kJ·mol -1 , and -252.60kJ·mol -1 , respectively. The standard redox potentials of PAA are 1.748V and 1.005V vs. standard hydrogen electrode (SHE) at pH 0 and pH 14, respectively. Under biochemical standard state conditions (pH 7, 25°C, 101,325Pa), PAA has a redox potential of 1.385V vs. SHE, higher than many disinfectants. Finally, the environmental implications of the thermodynamic properties of PAA were systematically discussed. Those properties can be used to predict the physicochemical and biological behavior of aquatic systems exposed to PAA. Copyright © 2017 Elsevier B.V. All rights reserved.

Detection of early changes in lung cell cytology by flow-systems analysis techniques

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

Steinkamp, J.A.; Hansen, K.M.; Wilson, J.S.

1976-12-01

This report summarizes results of continuing experiments to develop cytological and biochemical indicators for estimating damage to respiratory cells in test animals exposed by inhalation to toxic agents associated with nonnuclear energy production, the specific goal being the application of advanced multiparameter flow-systems technologies to the detection of early atypical cellular changes in lung epithelium. Normal Syrian hamster lung cell samples composed of macrophages, leukocytes, ciliated columnar cells, and epithelial cells were stained with fluorescent dyes specific for different biochemical parameters and were analyzed in liquid suspension as they flowed through a chamber intersecting a laser beam of exciting light.more » Multiple sensors measured the total or two-color fluorescence and light scatter on a cell-by-cell basis. Cellular parameters proportional to optical measurements (i.e., cell size, DNA content, total protein, nonspecific esterase activity, nuclear and cytoplasmic diameters) were displayed as frequency distribution histograms. Lung cell samples were also separated according to various cytological parameters and identified microscopically. The basic operating features of the methodology are discussed briefly, along with specific examples of preliminary results illustrating the initial characterization of exfoliated pulmonary cells from normal hamsters. As the flow technology is adapted further to the analysis of respiratory cells, measurements of changes in physical and biochemical properties as a function of exposure to toxic agents will be performed.« less

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

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.

Avocado oil supplementation modifies cardiovascular risk profile markers in a rat model of sucrose-induced metabolic changes.

PubMed

Carvajal-Zarrabal, Octavio; Nolasco-Hipolito, Cirilo; Aguilar-Uscanga, M Guadalupe; Melo-Santiesteban, Guadalupe; Hayward-Jones, Patricia M; Barradas-Dermitz, Dulce M

2014-01-01

The purpose of this study was to evaluate the effects of avocado oil administration on biochemical markers of cardiovascular risk profile in rats with metabolic changes induced by sucrose ingestion. Twenty-five rats were divided into five groups: a control group (CG; basic diet), a sick group (MC; basic diet plus 30% sucrose solution), and three other groups (MCao, MCac, and MCas; basic diet plus 30% sucrose solution plus olive oil and avocado oil extracted by centrifugation or using solvent, resp.). Glucose, total cholesterol, triglycerides, phospholipids, low- and high-density lipoproteins (LDL, HDL), very low-density lipoprotein (VLDL), lactic dehydrogenase, creatine kinase, and high sensitivity C-reactive protein concentration were analyzed. Avocado oil reduces TG, VLDL, and LDL levels, in the LDL case significantly so, without affecting HDL levels. An effect was exhibited by avocado oil similar to olive oil, with no significant difference between avocado oil extracted either by centrifugation or solvent in myocardial injury biochemical indicators. Avocado oil decreased hs-CRP levels, indicating that inflammatory processes were partially reversed. These findings suggested that avocado oil supplementation has a positive health outcome because it reduces inflammatory events and produces positive changes in the biochemical indicators studied, related to the development of metabolic syndrome.

Structural modification of polysaccharides: A biochemical-genetic approach

NASA Technical Reports Server (NTRS)

Kern, Roger G.; Petersen, Gene R.

1991-01-01

Polysaccharides have a wide range of industrial and biomedical applications. An industry trend is underway towards the increased use of bacteria to produce polysaccharides. Long term goals of this work are the adaptation and enhancement of saccharide properties for electronic and optic applications. In this report we illustrate the application of enzyme-bearing bacteriophage on strains of the enteric bacterium Klebsiella pneumoniae, which produces a polysaccharide with the relatively rare rheological property of drag-reduction. This has resulted in the production of new polysaccharides with enhanced rheological properties. Our laboratory is developing techniques for processing and structurally modifying bacterial polysaccharides and oligosaccharides which comprise their basic polymeric repeat units. Our research has focused on bacteriophage which produce specific polysaccharide degrading enzymes. This has lead to the development of enzymes generated by bacteriophage as tools for polysaccharide modification and purification. These enzymes were used to efficiently convert the native material to uniform-sized high molecular weight polymers, or alternatively into high-purity oligosaccharides. Enzyme-bearing bacteriophage also serve as genetic selection tools for bacteria that produce new families of polysaccharides with modified structures.

Kombucha tea fermentation: Microbial and biochemical dynamics.

PubMed

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

2016-03-02

Kombucha tea, a non-alcoholic beverage, is acquiring significant interest due to its claimed beneficial properties. The microbial community of Kombucha tea consists of bacteria and yeast which thrive in two mutually non-exclusive compartments: the soup or the beverage and the biofilm floating on it. The microbial community and the biochemical properties of the beverage have so far mostly been described in separate studies. This, however, may prevent understanding the causal links between the microbial communities and the beneficial properties of Kombucha tea. Moreover, an extensive study into the microbial and biochemical dynamics has also been missing. In this study, we thus explored the structure and dynamics of the microbial community along with the biochemical properties of Kombucha tea at different time points up to 21 days of fermentation. We hypothesized that several biochemical properties will change during the course of fermentation along with the shifts in the yeast and bacterial communities. The yeast community of the biofilm did not show much variation over time and was dominated by Candida sp. (73.5-83%). The soup however, showed a significant shift in dominance from Candida sp. to Lachancea sp. on the 7th day of fermentation. This is the first report showing Candida as the most dominating yeast genus during Kombucha fermentation. Komagateibacter was identified as the single largest bacterial genus present in both the biofilm and the soup (~50%). The bacterial diversity was higher in the soup than in the biofilm with a peak on the seventh day of fermentation. The biochemical properties changed with the progression of the fermentation, i.e., beneficial properties of the beverage such as the radical scavenging ability increased significantly with a maximum increase at day 7. We further observed a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations. Our data thus indicate that the microbial community structure and dynamics play an important role in the biochemistry of the fermentation of the beverage. We envisage that combined molecular and biochemical analyses like in our study will provide valuable insights for better understanding the role of the microbial community for the beneficial properties of the beverage. Copyright © 2016 Elsevier B.V. All rights reserved.

A Study of the Competency of Third Year Medical Students to Interpret Biochemically Based Clinical Scenarios Using Knowledge and Skills Gained in Year 1 and 2

ERIC Educational Resources Information Center

Gowda, Veena Bhaskar S.; Nagaiah, Bhaskar Hebbani; Sengodan, Bharathi

2016-01-01

Medical students build clinical knowledge on the grounds of previously obtained basic knowledge. The study aimed to evaluate the competency of third year medical students to interpret biochemically based clinical scenarios using knowledge and skills gained during year 1 and 2 of undergraduate medical training. Study was conducted on year 3 MBBS…

A homeostatic-driven turnover remodelling constitutive model for healing in soft tissues

PubMed Central

Gasser, T. Christian; Bellomo, Facundo J.

2016-01-01

Remodelling of soft biological tissue is characterized by interacting biochemical and biomechanical events, which change the tissue's microstructure, and, consequently, its macroscopic mechanical properties. Remodelling is a well-defined stage of the healing process, and aims at recovering or repairing the injured extracellular matrix. Like other physiological processes, remodelling is thought to be driven by homeostasis, i.e. it tends to re-establish the properties of the uninjured tissue. However, homeostasis may never be reached, such that remodelling may also appear as a continuous pathological transformation of diseased tissues during aneurysm expansion, for example. A simple constitutive model for soft biological tissues that regards remodelling as homeostatic-driven turnover is developed. Specifically, the recoverable effective tissue damage, whose rate is the sum of a mechanical damage rate and a healing rate, serves as a scalar internal thermodynamic variable. In order to integrate the biochemical and biomechanical aspects of remodelling, the healing rate is, on the one hand, driven by mechanical stimuli, but, on the other hand, subjected to simple metabolic constraints. The proposed model is formulated in accordance with continuum damage mechanics within an open-system thermodynamics framework. The numerical implementation in an in-house finite-element code is described, particularized for Ogden hyperelasticity. Numerical examples illustrate the basic constitutive characteristics of the model and demonstrate its potential in representing aspects of remodelling of soft tissues. Simulation results are verified for their plausibility, but also validated against reported experimental data. PMID:27009177

A homeostatic-driven turnover remodelling constitutive model for healing in soft tissues.

PubMed

Comellas, Ester; Gasser, T Christian; Bellomo, Facundo J; Oller, Sergio

2016-03-01

Remodelling of soft biological tissue is characterized by interacting biochemical and biomechanical events, which change the tissue's microstructure, and, consequently, its macroscopic mechanical properties. Remodelling is a well-defined stage of the healing process, and aims at recovering or repairing the injured extracellular matrix. Like other physiological processes, remodelling is thought to be driven by homeostasis, i.e. it tends to re-establish the properties of the uninjured tissue. However, homeostasis may never be reached, such that remodelling may also appear as a continuous pathological transformation of diseased tissues during aneurysm expansion, for example. A simple constitutive model for soft biological tissues that regards remodelling as homeostatic-driven turnover is developed. Specifically, the recoverable effective tissue damage, whose rate is the sum of a mechanical damage rate and a healing rate, serves as a scalar internal thermodynamic variable. In order to integrate the biochemical and biomechanical aspects of remodelling, the healing rate is, on the one hand, driven by mechanical stimuli, but, on the other hand, subjected to simple metabolic constraints. The proposed model is formulated in accordance with continuum damage mechanics within an open-system thermodynamics framework. The numerical implementation in an in-house finite-element code is described, particularized for Ogden hyperelasticity. Numerical examples illustrate the basic constitutive characteristics of the model and demonstrate its potential in representing aspects of remodelling of soft tissues. Simulation results are verified for their plausibility, but also validated against reported experimental data. © 2016 The Author(s).

The 5 Alpha-Reductase Isozyme Family: A Review of Basic Biology and Their Role in Human Diseases

PubMed Central

Azzouni, Faris; Godoy, Alejandro; Li, Yun; Mohler, James

2012-01-01

Despite the discovery of 5 alpha-reduction as an enzymatic step in steroid metabolism in 1951, and the discovery that dihydrotestosterone is more potent than testosterone in 1968, the significance of 5 alpha-reduced steroids in human diseases was not appreciated until the discovery of 5 alpha-reductase type 2 deficiency in 1974. Affected males are born with ambiguous external genitalia, despite normal internal genitalia. The prostate is hypoplastic, nonpalpable on rectal examination and approximately 1/10th the size of age-matched normal glands. Benign prostate hyperplasia or prostate cancer does not develop in these patients. At puberty, the external genitalia virilize partially, however, secondary sexual hair remains sparse and male pattern baldness and acne develop rarely. Several compounds have been developed to inhibit the 5 alpha-reductase isozymes and they play an important role in the prevention and treatment of many common diseases. This review describes the basic biochemical properties, functions, tissue distribution, chromosomal location, and clinical significance of the 5 alpha-reductase isozyme family. PMID:22235201

Preparative two-step purification of recombinant H1.0 linker histone and its domains.

PubMed

Ivic, Nives; Bilokapic, Silvija; Halic, Mario

2017-01-01

H1 linker histones are small basic proteins that have a key role in the formation and maintenance of higher-order chromatin structures. Additionally, many examples have shown that linker histones play an important role in gene regulation, modulated by their various subtypes and posttranslational modifications. Obtaining high amounts of very pure linker histones, especially for efficient antibody production, remains a demanding and challenging procedure. Here we present an easy and fast method to purify human linker histone H1.0 overexpressed in Escherichia coli, as well as its domains: N-terminal/globular domain and C-terminal intrinsically disordered domain. This purification protocol relies on a simple affinity chromatography step followed by cation exchange due to the highly basic properties of histone proteins. Therefore, this protocol can also be applied to other linker histones. Highly pure proteins in amounts sufficient for most biochemical experiments can be obtained. The functional quality of purified H1.0 histone and its domains has been confirmed by pull-down, gel-mobility shift assays and the nuclear import assay.

Electrical coupling in ensembles of nonexcitable cells: modeling the spatial map of single cell potentials.

PubMed

Cervera, Javier; Manzanares, Jose Antonio; Mafe, Salvador

2015-02-19

We analyze the coupling of model nonexcitable (non-neural) cells assuming that the cell membrane potential is the basic individual property. We obtain this potential on the basis of the inward and outward rectifying voltage-gated channels characteristic of cell membranes. We concentrate on the electrical coupling of a cell ensemble rather than on the biochemical and mechanical characteristics of the individual cells, obtain the map of single cell potentials using simple assumptions, and suggest procedures to collectively modify this spatial map. The response of the cell ensemble to an external perturbation and the consequences of cell isolation, heterogeneity, and ensemble size are also analyzed. The results suggest that simple coupling mechanisms can be significant for the biophysical chemistry of model biomolecular ensembles. In particular, the spatiotemporal map of single cell potentials should be relevant for the uptake and distribution of charged nanoparticles over model cell ensembles and the collective properties of droplet networks incorporating protein ion channels inserted in lipid bilayers.

Triatominae Biochemistry Goes to School: Evaluation of a Novel Tool for Teaching Basic Biochemical Concepts of Chagas Disease Vectors

ERIC Educational Resources Information Center

Cunha, Leonardo Rodrigues; de Oliveria Cudischevitch, Cecília; Carneiro, Alan Brito; Macedo, Gustavo Bartholomeu; Lannes, Denise; da Silva-Neto, Mário Alberto Cardoso

2014-01-01

We evaluate a new approach to teaching the basic biochemistry mechanisms that regulate the biology of Triatominae, major vectors of "Trypanosoma cruzi," the causative agent of Chagas disease. We have designed and used a comic book, "Carlos Chagas: 100 years after a hero's discovery" containing scientific information obtained by…

Potato tuber cytokinin oxidase/dehydrogenase genes: Biochemical properties, activity, and expression during tuber dormancy progression

USDA-ARS?s Scientific Manuscript database

The enzymatic and biochemical properties of the proteins encoded by five potato cytokinin oxidase/dehydrogenase (CKX)-like genes functionally expressed in yeast and the effects of tuber dormancy progression on StCKX expression and cytokinin metabolism were examined in meristems isolated from field-g...

A Review on the Role of Vibrational Spectroscopy as An Analytical Method to Measure Starch Biochemical and Biophysical Properties in Cereals and Starchy Foods

PubMed Central

Cozzolino, D.; Degner, S.; Eglinton, J.

2014-01-01

Starch is the major component of cereal grains and starchy foods, and changes in its biophysical and biochemical properties (e.g., amylose, amylopectin, pasting, gelatinization, viscosity) will have a direct effect on its end use properties (e.g., bread, malt, polymers). The use of rapid and non-destructive methods to study and monitor starch properties, such as gelatinization, retrogradation, water absorption in cereals and starchy foods, is of great interest in order to improve and assess their quality. In recent years, near infrared reflectance (NIR) and mid infrared (MIR) spectroscopy have been explored to predict several quality parameters, such as those generated by instrumental methods commonly used in routine analysis like the rapid visco analyser (RVA) or viscometers. In this review, applications of both NIR and MIR spectroscopy to measure and monitor starch biochemical (amylose, amylopectin, starch) and biophysical properties (e.g., pasting properties) will be presented and discussed. PMID:28234340

Determination of the floral origin of some Romanian honeys on the basis of physical and biochemical properties

NASA Astrophysics Data System (ADS)

Cimpoiu, Claudia; Hosu, Anamaria; Miclaus, Vasile; Puscas, Anitta

The aim of this study was to determine the physical and biochemical properties of some Romanian honeys in order to discriminate between their floral origins. The evaluated properties were total phenolic content, total protein content, total free amino acids content, color intensity (ABS450), pH, ash content, antioxidant activity. Twenty-six commercial honeys from six types of flowers (acacia, sunflower, forest, polyfloral, lime and Sea Buckthorn) were investigated. All samples showed considerable variations with reference to their properties. The properties values were in the range of approved limits (according to EU legislation). The total phenolic, total protein and total free amino acids contents and color intensity varied considerably. Similarly, forest honey had the highest antioxidant activity while the lowest was found in acacia honey. Correlation between the floral origin of honeys and the physical and biochemical properties, respectively, was observed. Moreover, this study demonstrates remarkable variation in DPPH scavenging activity and content of total phenols in honey, depending on its botanic source.

Hydrophilic Dogwood Extracts as Materials for Reducing the Skin Irritation Potential of Body Wash Cosmetics.

PubMed

Nizioł-Łukaszewska, Zofia; Osika, Paweł; Wasilewski, Tomasz; Bujak, Tomasz

2017-02-19

A significant problem related to the use of surfactants in body wash cosmetics is their propensity to trigger skin irritations. Only scarce literature exists on the effect of plant extracts on the skin irritation potential. The present study is an attempt to determine the effect of hydrophilic dogwood extracts on the irritant potential of body wash gels. Extractants used in the study were water and mixtures of water with glycerine, water with trimethylglycine (betaine), and water with plant-derived glycol (propanediol). The basic biochemical properties, i.e., the ability to neutralize free radicals, and the content of polyphenols, anthocyanins and flavonoids, were determined. An attempt was undertaken to analyze the impact of the extract added to natural body wash gel formulations on product properties. The skin irritation potential was assessed by determining the zein number and the increase in the pH level of the bovine serum albumin (BSA) solution. The viscosity and foaming ability of the resulting products were evaluated. The studies revealed that an addition of dogwood extract contributes to an improvement in the properties of body wash gels and significantly increases the safety of product use through reducing the skin irritation effect.

Correlations between female breast density and biochemical markers.

PubMed

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

2015-07-01

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

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.

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.

Combining phytoextraction and biochar addition improves soil biochemical properties in a soil contaminated with Cd.

PubMed

Lu, Huanping; Li, Zhian; Fu, Shenglei; Méndez, Ana; Gascó, Gabriel; Paz-Ferreiro, Jorge

2015-01-01

The main goal of phytoremediation is to improve ecosystem functioning. Soil biochemical properties are considered as effective indicators of soil quality and are sensitive to various environmental stresses, including heavy metal contamination. The biochemical response in a soil contaminated with cadmium was tested after several treatments aimed to reduce heavy metal availability including liming, biochar addition and phytoextraction using Amaranthus tricolor L. Two biochars were added to the soil: eucalyptus pyrolysed at 600 °C (EB) and poultry litter at 400 °C (PLB). Two liming treatments were chosen with the aim of bringing soil pH to the same values as in the treatments EB and PLB. The properties studied included soil microbial biomass C, soil respiration and the activities of invertase, β-glucosidase, β-glucosaminidase, urease and phosphomonoesterase. Both phytoremediation and biochar addition improved soil biochemical properties, although results were enzyme specific. For biochar addition these changes were partly, but not exclusively, mediated by alterations in soil pH. A careful choice of biochar must be undertaken to optimize the remediation process from the point of view of metal phytoextraction and soil biological activity. Copyright © 2014 Elsevier Ltd. All rights reserved.

Determination of the floral origin of some Romanian honeys on the basis of physical and biochemical properties.

PubMed

Cimpoiu, Claudia; Hosu, Anamaria; Miclaus, Vasile; Puscas, Anitta

2013-01-01

The aim of this study was to determine the physical and biochemical properties of some Romanian honeys in order to discriminate between their floral origins. The evaluated properties were total phenolic content, total protein content, total free amino acids content, color intensity (ABS(450)), pH, ash content, antioxidant activity. Twenty-six commercial honeys from six types of flowers (acacia, sunflower, forest, polyfloral, lime and Sea Buckthorn) were investigated. All samples showed considerable variations with reference to their properties. The properties values were in the range of approved limits (according to EU legislation). The total phenolic, total protein and total free amino acids contents and color intensity varied considerably. Similarly, forest honey had the highest antioxidant activity while the lowest was found in acacia honey. Correlation between the floral origin of honeys and the physical and biochemical properties, respectively, was observed. Moreover, this study demonstrates remarkable variation in DPPH scavenging activity and content of total phenols in honey, depending on its botanic source. Copyright © 2012 Elsevier B.V. All rights reserved.

Hericium erinaceus (Yamabushitake): a unique resource for developing functional foods and medicines.

PubMed

Wang, Mingxing; Gao, Yang; Xu, Duoduo; Konishi, Tetsuya; Gao, Qipin

2014-12-01

Hericium erinaceus (HE) is a fungus inhabiting the mountainous areas of the northeast territories in Asia. HE has been used in traditional folk medicine and medicinal cuisine in China, Korea and Japan. Evidence has been adduced for a variety of physiological effects, including anti-aging, anti-cancer, anti-gastritis, and anti-metabolic disease properties. Hence, HE is an attractive target resource for developing not only medicines, but also functional foods. Basic studies on the physiological functions of HE and on the chemical identification of its active ingredients have progressed in recent decades. In this article, we provide an overview of the biochemical and pharmacological studies on HE, especially of its antitumor and neuroprotective functions, together with a survey of recent developments in the chemical analysis of its polysaccharides, which comprise its major active components.

The biology and polymer physics underlying large‐scale chromosome organization

PubMed Central

2017-01-01

Chromosome large‐scale organization is a beautiful example of the interplay between physics and biology. DNA molecules are polymers and thus belong to the class of molecules for which physicists have developed models and formulated testable hypotheses to understand their arrangement and dynamic properties in solution, based on the principles of polymer physics. Biologists documented and discovered the biochemical basis for the structure, function and dynamic spatial organization of chromosomes in cells. The underlying principles of chromosome organization have recently been revealed in unprecedented detail using high‐resolution chromosome capture technology that can simultaneously detect chromosome contact sites throughout the genome. These independent lines of investigation have now converged on a model in which DNA loops, generated by the loop extrusion mechanism, are the basic organizational and functional units of the chromosome. PMID:29105235

Biochemical and biomechanical characterisation of equine cervical facet joint cartilage.

PubMed

O'Leary, S A; White, J L; Hu, J C; Athanasiou, K A

2018-04-15

The equine cervical facet joint is a site of significant pathology. Located bilaterally on the dorsal spine, these diarthrodial joints work in conjunction with the intervertebral disc to facilitate appropriate spinal motion. Despite the high prevalence of pathology in this joint, the facet joint is understudied and thus lacking in viable treatment options. The goal of this study was to characterise equine facet joint cartilage and provide a comprehensive database describing the morphological, histological, biochemical and biomechanical properties of this tissue. Descriptive cadaver studies. A total of 132 facet joint surfaces were harvested from the cervical spines of six skeletally mature horses (11 surfaces per animal) for compiling biomechanical and biochemical properties of hyaline cartilage of the equine cervical facet joints. Gross morphometric measurements and histological staining were performed on facet joint cartilage. Creep indentation and uniaxial strain-to-failure testing were used to determine the biomechanical compressive and tensile properties. Biochemical assays included quantification of total collagen, sulfated glycosaminoglycan and DNA content. The facet joint surfaces were ovoid in shape with a flat articular surface. Histological analyses highlighted structures akin to articular cartilage of other synovial joints. In general, biomechanical and biochemical properties did not differ significantly between the inferior and superior joint surfaces as well as among spinal levels. Interestingly, compressive and tensile properties of cervical facet articular cartilage were lower than those of articular cartilage from other previously characterised equine joints. Removal of the superficial zone reduced the tissue's tensile strength, suggesting that this zone is important for the tensile integrity of the tissue. Facet surfaces were sampled at a single, central location and do not capture the potential topographic variation in cartilage properties. This is the first study to report the properties of equine cervical facet joint cartilage and may serve as the foundation for the development of future tissue-engineered replacements as well as other treatment strategies. © 2018 EVJ Ltd.

Textural and biochemical properties of cobia (Rachycentron canadum) sashimi tenderised with the ultrasonic water bath.

PubMed

Chang, Hung-Chia; Wong, Ren-Xian

2012-06-01

The present study investigated the tenderisation effects ultrasound processing (UT) on farmed cobia sashimi. Age-treated cobia trunk muscles (AT) were used as the control. The pH, total volatile base nitrogen, trimethylamine nitrogen, thiobarbituric acid reactive substances, ATP catabolism components, K 1 value, and texture were evaluated. The texture of AT sashimi reached the optimal firmness range with 8.53N at day 7. However, AT samples could not be served raw after day 7 because of their poor freshness indexes, including a TVBN value of 18.53g/100g, a TMAN value of 3.25mg/100g, and a TBARS value 0.983MDAmg/100g. Moreover, the K 1 value of AT sashimi was 20.21% at day 5. UT was employed to efficiently tenderise cobia sashimi with an initial firmness of 9.70-7.82N after 90min of treatment. The results of this study indicate that UT accelerates the biochemical reaction rate, as evidenced by the increases in the TVBN, TMAN, and TBARS contents; however, these values were very low. The results of this study could provide basic information for the development of a novel ultrasonic tenderisation technique in raw seafood designed for restaurants and consumers. Copyright © 2011 Elsevier Ltd. All rights reserved.

Bacterial and Fungal Proteolytic Enzymes: Production, Catalysis and Potential Applications.

PubMed

da Silva, Ronivaldo Rodrigues

2017-09-01

Submerged and solid-state bioprocesses have been extensively explored worldwide and employed in a number of important studies dealing with microbial cultivation for the production of enzymes. The development of these production technologies has facilitated the generation of new enzyme-based products with applications in pharmaceuticals, food, bioactive peptides, and basic research studies, among others. The applicability of microorganisms in biotechnology is potentiated because of their various advantages, including large-scale production, short time of cultivation, and ease of handling. Currently, several studies are being conducted to search for new microbial peptidases with peculiar biochemical properties for industrial applications. Bioprospecting, being an important prerequisite for research and biotechnological development, is based on exploring the microbial diversity for enzyme production. Limited information is available on the production of specific proteolytic enzymes from bacterial and fungal species, especially on the subgroups threonine and glutamic peptidases, and the seventh catalytic type, nonhydrolytic asparagine peptide lyase. This gap in information motivated the present study about these unique biocatalysts. In this study, the biochemical and biotechnological aspects of the seven catalytic types of proteolytic enzymes, namely aspartyl, cysteine, serine, metallo, glutamic, and threonine peptidase, and asparagine peptide lyase, are summarized, with an emphasis on new studies, production, catalysis, and application of these enzymes.

Effect of tea polyphenols on microbiological and biochemical quality of Collichthys fish ball.

PubMed

Yi, Shumin; Li, Jianrong; Zhu, Junli; Lin, Yi; Fu, Linglin; Chen, Wei; Li, Xuepeng

2011-07-01

Tea polyphenols (TP), as the most active constituents of tea, are considered natural food additives. This study examined the preservative properties of TP for Collichthys fish ball in well storage. Vacuum-packed Collichthys fish balls were treated with 0, 0.1, 0.15, 0.20, 0.25, and 0.30 g kg(-1) TP and stored at 0 °C for 17 days. Microbiological results were obtained using a biochemical test, API system kit, and 16S rDNA sequence analysis. Results confirmed that the dominant bacteria in Collichthys fish balls are the genera Serratia and Pseudomonas. Total viable counts dropped two orders of magnitude in Collichthys fish balls with 0.25 g kg(-1) TP compared with the control. The advantages of total volatile basic nitrogen value, 2-thiobarbituric acid value and texture value were clearly observed, whereas pH and whiteness value exhibited no significant decrease for the group treated with 0.25 g kg(-1) TP. More than 0.25 g kg(-1) TP added could retain excellent fish ball characteristics in terms of sensory assessment after 17 days. The shelf life of Collichthys fish balls supplemented with tea polyphenols can be prolonged for an additional 6 days in good condition at 0 °C storage. Copyright © 2011 Society of Chemical Industry.

The human gene SLC25A29, of solute carrier family 25, encodes a mitochondrial transporter of basic amino acids.

PubMed

Porcelli, Vito; Fiermonte, Giuseppe; Longo, Antonella; Palmieri, Ferdinando

2014-05-09

The human genome encodes 53 members of the solute carrier family 25 (SLC25), also called the mitochondrial carrier family, many of which have been shown to transport carboxylates, amino acids, nucleotides, and cofactors across the inner mitochondrial membrane, thereby connecting cytosolic and matrix functions. In this work, a member of this family, SLC25A29, previously reported to be a mitochondrial carnitine/acylcarnitine- or ornithine-like carrier, has been thoroughly characterized biochemically. The SLC25A29 gene was overexpressed in Escherichia coli, and the gene product was purified and reconstituted in phospholipid vesicles. Its transport properties and kinetic parameters demonstrate that SLC25A29 transports arginine, lysine, homoarginine, methylarginine and, to a much lesser extent, ornithine and histidine. Carnitine and acylcarnitines were not transported by SLC25A29. This carrier catalyzed substantial uniport besides a counter-exchange transport, exhibited a high transport affinity for arginine and lysine, and was saturable and inhibited by mercurial compounds and other inhibitors of mitochondrial carriers to various degrees. The main physiological role of SLC25A29 is to import basic amino acids into mitochondria for mitochondrial protein synthesis and amino acid degradation.

An introduction to the molecular basics of aryl hydrocarbon receptor biology.

PubMed

Abel, Josef; Haarmann-Stemmann, Thomas

2010-11-01

Depending on their chemical structure and properties, environmental chemicals and other xenobiotics that enter the cell can affect cellular function by either nonselective binding to cellular macromolecules or by interference with cellular receptors, which would initiate a more defined cell biological response. One of these intracellular chemosensor molecules is the aryl hydrocarbon receptor (AhR), a transcription factor of the bHLH/PAS family that is known to mediate the biochemical and toxic effects of dioxins, polyaromatic hydrocarbons and related compounds. Numerous investigations have revealed that the AhR is not only a master regulator of drug metabolism activated by anthropogenic chemicals, but is also triggered by natural and endogenous ligands and can influence cell biological endpoints such as growth and differentiation. Cutting-edge research has identified new intriguing functions of the AhR, such as during proteasomal degradation of steroid hormone receptors, the cellular UVB stress response and the differentiation of certain T-cell subsets. In this review we provide both a survey of the fundamental basics of AhR biology and an insight into new functional aspects of AhR signaling to further stimulate research on this intriguing transcription factor at the interface between toxicology, cell biology and immunology.

Evolution-Based Functional Decomposition of Proteins

PubMed Central

Rivoire, Olivier; Reynolds, Kimberly A.; Ranganathan, Rama

2016-01-01

The essential biological properties of proteins—folding, biochemical activities, and the capacity to adapt—arise from the global pattern of interactions between amino acid residues. The statistical coupling analysis (SCA) is an approach to defining this pattern that involves the study of amino acid coevolution in an ensemble of sequences comprising a protein family. This approach indicates a functional architecture within proteins in which the basic units are coupled networks of amino acids termed sectors. This evolution-based decomposition has potential for new understandings of the structural basis for protein function. To facilitate its usage, we present here the principles and practice of the SCA and introduce new methods for sector analysis in a python-based software package (pySCA). We show that the pattern of amino acid interactions within sectors is linked to the divergence of functional lineages in a multiple sequence alignment—a model for how sector properties might be differentially tuned in members of a protein family. This work provides new tools for studying proteins and for generally testing the concept of sectors as the principal units of function and adaptive variation. PMID:27254668

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Biochemical Regulatory Features of Activation-Induced Cytidine Deaminase Remain Conserved from Lampreys to Humans

PubMed Central

King, Justin J.; Amemiya, Chris T.; Hsu, Ellen

2017-01-01

ABSTRACT Activation-induced cytidine deaminase (AID) is a genome-mutating enzyme that initiates class switch recombination and somatic hypermutation of antibodies in jawed vertebrates. We previously described the biochemical properties of human AID and found that it is an unusual enzyme in that it exhibits binding affinities for its substrate DNA and catalytic rates several orders of magnitude higher and lower, respectively, than a typical enzyme. Recently, we solved the functional structure of AID and demonstrated that these properties are due to nonspecific DNA binding on its surface, along with a catalytic pocket that predominantly assumes a closed conformation. Here we investigated the biochemical properties of AID from a sea lamprey, nurse shark, tetraodon, and coelacanth: representative species chosen because their lineages diverged at the earliest critical junctures in evolution of adaptive immunity. We found that these earliest-diverged AID orthologs are active cytidine deaminases that exhibit unique substrate specificities and thermosensitivities. Significant amino acid sequence divergence among these AID orthologs is predicted to manifest as notable structural differences. However, despite major differences in sequence specificities, thermosensitivities, and structural features, all orthologs share the unusually high DNA binding affinities and low catalytic rates. This absolute conservation is evidence for biological significance of these unique biochemical properties. PMID:28716949

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

DTIC Science & Technology

2010-09-01

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

A biochemical protocol for the isolation and identification of current species of Vibrio in seafood.

PubMed

Ottaviani, D; Masini, L; Bacchiocchi, S

2003-01-01

We report a biochemical method for the isolation and identification of the current species of vibrios using just one operative protocol. The method involves an enrichment phase with incubation at 30 degrees C for 8-24 h in alkaline peptone water and an isolation phase on thiosulphate-citrate-salt sucrose agar plates incubating at 30 degrees C for 24 h. Four biochemical tests and Alsina's scheme were performed for genus and species identification, respectively. All biochemical tests were optimized as regards conditions of temperature, time of incubation and media composition. The whole standardized protocol was always able to give a correct identification when applied to 25 reference strains of Vibrio and 134 field isolates. The data demonstrated that the assay method allows an efficient recovery, isolation and identification of current species of Vibrio in seafood obtaining results within 2-7 days. This method based on biochemical tests could be applicable even in basic microbiology laboratories, and can be used simultaneously to isolate and discriminate all clinically relevant species of Vibrio.

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.

Formation of peptides from amino acids by single or multiple additions of ATP to suspensions of nucleoproteinoid microparticles

NASA Technical Reports Server (NTRS)

Nakashima, T.; Fox, S. W.

1981-01-01

The synthesis of peptides from individual amino acids or pairs of amino acids and ATP in the presence of catalysis by nucleoproteinoid microparticles is investigated. Experiments were performed with suspensions formed from the condensation of lysine-rich and acidic proteinoids with polyadenylic acid, to which were added glycine, phenylalanine, proline, lysine or glycine-phenylalanine mixtures, and ATP either at once or serially. Peptide yields are found to be greatest for equal amounts of acidic and basic proteinoids. The addition of imidazole is found to alter the preference of glycine-phenylalanine mixtures to form mixed heteropeptides rather than homopeptides. A rapid ATP decay in the peptide synthesis reaction is observed, and a greater yield is obtained for repeated small additions than for a single addition of ATP. The experimental system has properties similar to modern cells, and represents an organizational unit ready for the evolution of associated biochemical pathways.

Kallikreins - The melting pot of activity and function.

PubMed

Kalinska, Magdalena; Meyer-Hoffert, Ulf; Kantyka, Tomasz; Potempa, Jan

2016-03-01

The human tissue kallikrein and kallikrein-related peptidases (KLKs), encoded by the largest contiguous cluster of protease genes in the human genome, are secreted serine proteases with diverse expression patterns and physiological roles. Because of the broad spectrum of processes that are modulated by kallikreins, these proteases are the subject of extensive investigations. This review brings together basic information about the biochemical properties affecting enzymatic activity, with highlights on post-translational modifications, especially glycosylation. Additionally, we present the current state of knowledge regarding the physiological functions of KLKs in major human organs and outline recent discoveries pertinent to the involvement of kallikreins in cell signaling and in viral infections. Despite the current depth of knowledge of these enzymes, many questions regarding the roles of kallikreins in health and disease remain unanswered. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Laccases: Production, Expression Regulation, and Applications in Pharmaceutical Biodegradation

PubMed Central

Yang, Jie; Li, Wenjuan; Ng, Tzi Bun; Deng, Xiangzhen; Lin, Juan; Ye, Xiuyun

2017-01-01

Laccases are a family of copper-containing oxidases with important applications in bioremediation and other various industrial and biotechnological areas. There have been over two dozen reviews on laccases since 2010 covering various aspects of this group of versatile enzymes, from their occurrence, biochemical properties, and expression to immobilization and applications. This review is not intended to be all-encompassing; instead, we highlighted some of the latest developments in basic and applied laccase research with an emphasis on laccase-mediated bioremediation of pharmaceuticals, especially antibiotics. Pharmaceuticals are a broad class of emerging organic contaminants that are recalcitrant and prevalent. The recent surge in the relevant literature justifies a short review on the topic. Since low laccase yields in natural and genetically modified hosts constitute a bottleneck to industrial-scale applications, we also accentuated a genus of laccase-producing white-rot fungi, Cerrena, and included a discussion with regards to regulation of laccase expression. PMID:28559880

The biology and polymer physics underlying large-scale chromosome organization.

PubMed

Sazer, Shelley; Schiessel, Helmut

2018-02-01

Chromosome large-scale organization is a beautiful example of the interplay between physics and biology. DNA molecules are polymers and thus belong to the class of molecules for which physicists have developed models and formulated testable hypotheses to understand their arrangement and dynamic properties in solution, based on the principles of polymer physics. Biologists documented and discovered the biochemical basis for the structure, function and dynamic spatial organization of chromosomes in cells. The underlying principles of chromosome organization have recently been revealed in unprecedented detail using high-resolution chromosome capture technology that can simultaneously detect chromosome contact sites throughout the genome. These independent lines of investigation have now converged on a model in which DNA loops, generated by the loop extrusion mechanism, are the basic organizational and functional units of the chromosome. © 2017 The Authors. Traffic published by John Wiley & Sons Ltd.

The Roles of Primary Cilia in Cardiovascular System

DTIC Science & Technology

2016-10-01

mitochondrial generation of hydrogen peroxide. General properties and effect of hyperbaric oxygen . Biochem J 134:707–716. Boveris A, Oshino N, Chance B. 1972...The mitochondrial generation of hydrogen peroxide. General properties and effect of hyperbaric oxygen . Biochem J 134:707–716. Boveris A, Oshino N...Aim 1.2 (months 13-30): We will examine signaling mechanisms of cilia & their effects on blood pressure. Aim 2 (months 7-36). We will study

Randomizing Genome-Scale Metabolic Networks

PubMed Central

Samal, Areejit; Martin, Olivier C.

2011-01-01

Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have “unusual” properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the network is not statistically different from expected in a motivated ensemble. However, when dealing with metabolic networks, the randomization of the network using edge exchange generates fictitious reactions that are biochemically meaningless. Here we provide several natural ensembles of randomized metabolic networks. A first constraint is to use valid biochemical reactions. Further constraints correspond to imposing appropriate functional constraints. We explain how to perform these randomizations with the help of Markov Chain Monte Carlo (MCMC) and show that they allow one to approach the properties of biological metabolic networks. The implication of the present work is that the observed global structural properties of real metabolic networks are likely to be the consequence of simple biochemical and functional constraints. PMID:21779409

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.

Positron Emission Tomography: Human Brain Function and Biochemistry.

ERIC Educational Resources Information Center

Phelps, Michael E.; Mazziotta, John C.

1985-01-01

Describes the method, present status, and application of positron emission tomography (PET), an analytical imaging technique for "in vivo" measurements of the anatomical distribution and rates of specific biochemical reactions. Measurements and image dynamic biochemistry link basic and clinical neurosciences with clinical findings…

Rational Design of Thermally Stable Novel Biocatalytic Nanomaterials: Enzyme Stability in Restricted Spatial Dimensions

NASA Astrophysics Data System (ADS)

Mudhivarthi, Vamsi K.

Enzyme stability is of intense interest in bio-materials science as biocatalysts, and as sensing platforms. This is essentially because the unique properties of DNA, RNA, PAA can be coupled with the interesting and novel properties of proteins to produce systems with unprecedented control over their properties. In this article, the very first examples of enzyme/NA/inorganic hybrid nanomaterials and enzyme-Polyacrylic acid conjugates will be presented. The basic principles of design, synthesis and control of properties of these hybrid materials will be presented first, and this will be followed by a discussion of selected examples from our recent research findings. Data show that key properties of biological catalysts are improved by the inorganic framework especially when the catalyst is co-embedded with DNA. Several examples of such studies with various enzymes and proteins, including horseradish peroxidase (HRP), glucose oxidase (GO), cytochrome c (Cyt c), met-hemoglobin (Hb) and met-myoglobin (Mb) will be discussed. Additionally, key insights obtained by the standard methods of materials science including XRD, SEM and TEM as well as biochemical, calorimetric and spectroscopic methods will be discussed. Furthermore, improved structure and enhanced activities of the biocatalysts in specific cases will be demonstrated along with the potential stabilization mechanisms. Our hypothesis is that nucleic acids provide an excellent control over the enzyme-solid interactions as well as rational assembly of nanomaterials. These novel nanobiohybrid materials may aid in engineering more effective synthetic materials for gene-delivery, RNA-delivery and drug delivery applications.

Clinical Metabolomics: The New Metabolic Window for Inborn Errors of Metabolism Investigations in the Post-Genomic Era

PubMed Central

Tebani, Abdellah; Abily-Donval, Lenaig; Afonso, Carlos; Marret, Stéphane; Bekri, Soumeya

2016-01-01

Inborn errors of metabolism (IEM) represent a group of about 500 rare genetic diseases with an overall estimated incidence of 1/2500. The diversity of metabolic pathways involved explains the difficulties in establishing their diagnosis. However, early diagnosis is usually mandatory for successful treatment. Given the considerable clinical overlap between some inborn errors, biochemical and molecular tests are crucial in making a diagnosis. Conventional biological diagnosis procedures are based on a time-consuming series of sequential and segmented biochemical tests. The rise of “omic” technologies offers holistic views of the basic molecules that build a biological system at different levels. Metabolomics is the most recent “omic” technology based on biochemical characterization of metabolites and their changes related to genetic and environmental factors. This review addresses the principles underlying metabolomics technologies that allow them to comprehensively assess an individual biochemical profile and their reported applications for IEM investigations in the precision medicine era. PMID:27447622

T1ρ MR Imaging of Human Musculoskeletal System

PubMed Central

Wang, Ligong; Regatte, Ravinder R.

2014-01-01

Magnetic resonance imaging (MRI) offers the direct visualization of human musculoskeletal (MSK) system, especially all diarthrodial tissues including cartilage, bone, menisci, ligaments, tendon, hip, synovium etc. Conventional MR imaging techniques based on T1- and T2-weighted, proton density (PD) contrast are inconclusive in quantifying early biochemically degenerative changes in MSK system in general and articular cartilage in particular. In recent years, quantitative MR parameter mapping techniques have been used to quantify the biochemical changes in articular cartilage with a special emphasis on evaluating joint injury, cartilage degeneration, and soft tissue repair. In this article, we will focus on cartilage biochemical composition, basic principles of T1ρ MR imaging, implementation of T1ρ pulse sequences, biochemical validation, and summarize the potential applications of T1ρ MR imaging technique in MSK diseases including osteoarthritis (OA), anterior cruciate ligament (ACL) injury, and knee joint repair. Finally, we will also review the potential advantages, challenges, and future prospects of T1ρ MR imaging for widespread clinical translation. PMID:24935818

T₁ρ MRI of human musculoskeletal system.

PubMed

Wang, Ligong; Regatte, Ravinder R

2015-03-01

Magnetic resonance imaging (MRI) offers the direct visualization of the human musculoskeletal (MSK) system, especially all diarthrodial tissues including cartilage, bone, menisci, ligaments, tendon, hip, synovium, etc. Conventional MRI techniques based on T1 - and T2 -weighted, proton density (PD) contrast are inconclusive in quantifying early biochemically degenerative changes in MSK system in general and articular cartilage in particular. In recent years, quantitative MR parameter mapping techniques have been used to quantify the biochemical changes in articular cartilage, with a special emphasis on evaluating joint injury, cartilage degeneration, and soft tissue repair. In this article we focus on cartilage biochemical composition, basic principles of T1ρ MRI, implementation of T1ρ pulse sequences, biochemical validation, and summarize the potential applications of the T1ρ MRI technique in MSK diseases including osteoarthritis (OA), anterior cruciate ligament (ACL) injury, and knee joint repair. Finally, we also review the potential advantages, challenges, and future prospects of T1ρ MRI for widespread clinical translation. © 2014 Wiley Periodicals, Inc.

[Morphological and biochemical adaptations to feeding in some herbivorous gastropods].

PubMed

Aliakrinskaia, O I

2005-01-01

Diet and feeding modes as well as morphological and biochemical adaptations to feeding are analyzed in herbivorous mollusks. The content of hemoglobin in radular tissues and weight properties of the radula are evaluated for different modes of feeding.

Comparison of biochemical properties of liver arginase from streptozocin-induced diabetic and control mice.

PubMed

Spolarics, Z; Bond, J S

1989-11-01

Arginase activity is elevated in livers of diabetic animals compared to controls and there is evidence that this is due in part to increased specific activity (activity/mg arginase protein). To investigate the molecular basis of this increased activity, the physicochemical and kinetic properties of hepatic arginase from diabetic and control mice were compared. Two types of arginase subunits with molecular weights of 35,000 and 38,000 were found in both the diabetic and control animals and the subunits in these animals had similar, multiple ionic forms. Kinetic parameters of purified preparations of arginase for arginine (apparent Km and Vmax values) and the thermal stability of these preparations from diabetics and controls were also similar. Furthermore, no difference was found in the distribution of arginase activity among different subcellular liver fractions. Separation of basic and acidic oligomeric forms of arginase by fast-protein liquid chromatography resulted in a slightly different distribution of activity among the forms in the normal and diabetic group. The apparent Km values for Mn2+ of the basic form of the enzyme were 25 and 33 microM for the enzyme from normal and diabetic animals, respectively; for acidic forms, for which two apparent Km values were measured, the values were 8 and 197 microM for arginase from controls and 35 and 537 microM from diabetics. These results indicate that in diabetes, while no marked changes in the physicochemical characteristics of arginase are obvious, some changes are found in the interaction of arginase with its cofactor Mn.

The art and design of genetic screens: maize

USDA-ARS?s Scientific Manuscript database

Maize (Zea mays) is an excellent model for basic research. Genetic screens have informed our understanding of developmental processes, meiosis, epigenetics and biochemical pathways--not only in maize but also in other cereal crops. We discuss the forward and reverse genetic screens that are possible...

Investigations Into Life Science.

ERIC Educational Resources Information Center

Mentzer, Dean Samuel

This laboratory manual, containing 44 exercises, is intended to be used as part of an audio-tutorial approach to laboratory work in a life-science course for student nurses. Exercises include basic techniques of miscroscopy, microbiology, electrophysiology, routine biochemical analyses of blood and urine, and microscopic examination of prepared…

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…

Seeking Optimal Nutrition for Healthy Body Mass Reduction among Former Athletes

PubMed Central

Maciejewska, Dominika; Michalczyk, Małgorzata; Czerwińska-Rogowska, Maja; Banaszczak, Marcin; Ryterska, Karina; Jakubczyk, Karolina; Piotrwski, Jakub; Hołowko, Joanna; Drozd, Arleta; Wysokińki, Paweł; Ficek, Krzysztof; Wilk, Krzysztof; Lubkowska, Anna; Cięszczyk, Paweł; Bertrand, Jerzy

2017-01-01

Abstract The aim of the study was to investigate the efficacy of 6 week Mediterranean diet or 30% calorie restriction on the fatty acid profile and eicosanoids (hydroxyoctadecadienoi acids and hydroxyeicosatetraenoic acids) concentration. Furthermore, basic biochemical variables such as insulin, glucose, HOMA-IR, and a lipid profile were estimated. The study enrolled 94 Caucasian former athletes aged 20-42, with body height of 179 ± 16.00 cm and body mass of 89.26 ± 13.25 kg who had not been active for at least 5 years. The subjects were randomly assigned to one of the three intervention groups: CR group – the 30% calorie restriction (n = 32), MD group - the Mediterranean diet (n = 34), and C group - a control group (n = 28). The pattern of nutrition was analysed before and after the experiment using the 72 h food diaries. In order to evaluate the effect of diet intervention, the following variables were measured: anthropometrics, basic biochemical variables (insulin, fasting glucose, HOMA-IR, lipid profile), fatty acids and their blood derivatives profiles. The CR group showed significantly lower levels of several biochemical variables, i.e., BMI, total cholesterol LDL, TG, total lipids, insulin and HOMA – IR (p < 0.05). Subjects consuming the MD diet significantly decreased their BMI and reduced the level of total lipids (p < 0.05). We did not find any significant changes in the C group. The analysis of the fatty acid profile revealed that the CR group had a significantly decreased EPA level (p < 0.05). The MD group showed a significantly increased level of the DHA (p < 0.05) and improvement in the omega - 3 index (p < 0.05). Subjects following the MD also showed significantly lower concentrations of 15 - hydroxyicosatetraenoic acid (15-HETE). We did not observe any significant differences between the CR and C groups. Within short time, calorie restriction helps to improve lipid variables and insulin resistance. The MD diet seems to be more advantageous in the decrease of inflammation, but does not improve basic biochemical variables. We can conclude that calorie restriction can be a good choice for former athletes, although EPA and DHA supplementation is needed. PMID:29339986

Examining Myddosome Formation by Luminescence-Based Mammalian Interactome Mapping (LUMIER).

PubMed

Wolz, Olaf-Oliver; Koegl, Manfred; Weber, Alexander N R

2018-01-01

Recent structural, biochemical, and functional studies have led to the notion that many of the post-receptor signaling complexes in innate immunity have a multimeric, multi-protein architecture whose hierarchical assembly is vital for function. The Myddosome is a post-receptor complex in the cytoplasmic signaling of Toll-like receptors (TLR) and the Interleukin-1 receptor (IL-1R), involving the proteins MyD88, IL-1R-associated kinase 4 (IRAK4), and IRAK2. Its importance is strikingly illustrated by the fact that rare germline mutations in MYD88 causing high susceptibility to infections are characterized by failure to assemble Myddosomes; conversely, gain-of-function MYD88 mutations leading to oncogenic hyperactivation of NF-κB show increased Myddosome formation. Reliable methods to probe Myddosome formation experimentally are therefore vital to further study the properties of this important post-receptor complex and its role in innate immunity, such as its regulation by posttranslational modification. Compared to structural and biochemical analyses, luminescence-based mammalian interactome mapping (LUMIER) is a straightforward, automatable, quantifiable, and versatile technique to study protein-protein interactions in a physiologically relevant context. We adapted LUMIER for Myddosome analysis and provide here a basic background of this technique, suitable experimental protocols, and its potential for medium-throughput screening. The principles presented herein can be adapted to other signaling pathways.

Changes in photosynthesis and leaf characteristics with tree height in five dipterocarp species in a tropical rain forest.

PubMed

Kenzo, Tanaka; Ichie, Tomoaki; Watanabe, Yoko; Yoneda, Reiji; Ninomiya, Ikuo; Koike, Takayoshi

2006-07-01

Variations in leaf photosynthetic, morphological and biochemical properties with increasing plant height from seedlings to emergent trees were investigated in five dipterocarp species in a Malaysian tropical rain forest. Canopy openness increased significantly with tree height. Photosynthetic properties, such as photosynthetic capacity at light saturation, light compensation point, maximum rate of carboxylation and maximum rate of photosynthetic electron transport, all increased significantly with tree height. Leaf morphological and biochemical traits, such as leaf mass per area, palisade layer thickness, nitrogen concentration per unit area, chlorophyll concentration per unit dry mass and chlorophyll to nitrogen ratio, also changed significantly with tree height. Leaf properties had simple and significant relationships with tree height, with few intra- and interspecies differences. Our results therefore suggest that the photosynthetic capacity of dipterocarp trees depends on tree height, and that the trees adapt to the light environment by adjusting their leaf morphological and biochemical properties. These results should aid in developing models that can accurately estimate carbon dioxide flux and biomass production in tropical rain forests.

Physiologically based microenvironment for in vitro neural differentiation of adipose-derived stem cells.

PubMed

Graziano, Adriana Carol Eleonora; Avola, Rosanna; Perciavalle, Vincenzo; Nicoletti, Ferdinando; Cicala, Gianluca; Coco, Marinella; Cardile, Venera

2018-03-26

The limited capacity of nervous system to promote a spontaneous regeneration and the high rate of neurodegenerative diseases appearance are keys factors that stimulate researches both for defining the molecular mechanisms of pathophysiology and for evaluating putative strategies to induce neural tissue regeneration. In this latter aspect, the application of stem cells seems to be a promising approach, even if the control of their differentiation and the maintaining of a safe state of proliferation should be troubled. Here, we focus on adipose tissue-derived stem cells and we seek out the recent advances on the promotion of their neural differentiation, performing a critical integration of the basic biology and physiology of adipose tissue-derived stem cells with the functional modifications that the biophysical, biomechanical and biochemical microenvironment induces to cell phenotype. The pre-clinical studies showed that the neural differentiation by cell stimulation with growth factors benefits from the integration with biomaterials and biophysical interaction like microgravity. All these elements have been reported as furnisher of microenvironments with desirable biological, physical and mechanical properties. A critical review of current knowledge is here proposed, underscoring that a real advance toward a stable, safe and controllable adipose stem cells clinical application will derive from a synergic multidisciplinary approach that involves material engineer, basic cell biology, cell and tissue physiology.

The Human Gene SLC25A29, of Solute Carrier Family 25, Encodes a Mitochondrial Transporter of Basic Amino Acids*

PubMed Central

Porcelli, Vito; Fiermonte, Giuseppe; Longo, Antonella; Palmieri, Ferdinando

2014-01-01

The human genome encodes 53 members of the solute carrier family 25 (SLC25), also called the mitochondrial carrier family, many of which have been shown to transport carboxylates, amino acids, nucleotides, and cofactors across the inner mitochondrial membrane, thereby connecting cytosolic and matrix functions. In this work, a member of this family, SLC25A29, previously reported to be a mitochondrial carnitine/acylcarnitine- or ornithine-like carrier, has been thoroughly characterized biochemically. The SLC25A29 gene was overexpressed in Escherichia coli, and the gene product was purified and reconstituted in phospholipid vesicles. Its transport properties and kinetic parameters demonstrate that SLC25A29 transports arginine, lysine, homoarginine, methylarginine and, to a much lesser extent, ornithine and histidine. Carnitine and acylcarnitines were not transported by SLC25A29. This carrier catalyzed substantial uniport besides a counter-exchange transport, exhibited a high transport affinity for arginine and lysine, and was saturable and inhibited by mercurial compounds and other inhibitors of mitochondrial carriers to various degrees. The main physiological role of SLC25A29 is to import basic amino acids into mitochondria for mitochondrial protein synthesis and amino acid degradation. PMID:24652292

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

PubMed

Papagianni, Maria

2007-01-01

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

41 CFR 102-80.10 - What are the basic safety and environmental management policies for real property?

Code of Federal Regulations, 2010 CFR

2010-07-01

... safety and environmental management policies for real property? 102-80.10 Section 102-80.10 Public... MANAGEMENT REGULATION REAL PROPERTY 80-SAFETY AND ENVIRONMENTAL MANAGEMENT General Provisions § 102-80.10 What are the basic safety and environmental management policies for real property? The basic safety and...

Survey of Biochemical Separation Techniques

ERIC Educational Resources Information Center

Nilsson, Melanie R.

2007-01-01

A simple laboratory exercise is illustrated that exposes students to wide range of separation techniques in one laboratory program and provides a nice complement to a project-oriented program. Students have learned the basic principles of syringe filtration, centricon, dialysis, gel filtration and solid-phase extraction methodologies and have got…

Biochemical Thermodynamics under near Physiological Conditions

ERIC Educational Resources Information Center

Mendez, Eduardo

2008-01-01

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

Atomic force microscopy as an advanced tool in neuroscience

PubMed Central

Jembrek, Maja Jazvinšćak; Šimić, Goran; Hof, Patrick R.; Šegota, Suzana

2015-01-01

This review highlights relevant issues about applications and improvements of atomic force microscopy (AFM) toward a better understanding of neurodegenerative changes at the molecular level with the hope of contributing to the development of effective therapeutic strategies for neurodegenerative illnesses. The basic principles of AFM are briefly discussed in terms of evaluation of experimental data, including the newest PeakForce Quantitative Nanomechanical Mapping (QNM) and the evaluation of Young’s modulus as the crucial elasticity parameter. AFM topography, revealed in imaging mode, can be used to monitor changes in live neurons over time, representing a valuable tool for high-resolution detection and monitoring of neuronal morphology. The mechanical properties of living cells can be quantified by force spectroscopy as well as by new AFM. A variety of applications are described, and their relevance for specific research areas discussed. In addition, imaging as well as non-imaging modes can provide specific information, not only about the structural and mechanical properties of neuronal membranes, but also on the cytoplasm, cell nucleus, and particularly cytoskeletal components. Moreover, new AFM is able to provide detailed insight into physical structure and biochemical interactions in both physiological and pathophysiological conditions. PMID:28123795

[Some adaptations of Monodonta turbinata (born, 1780) (Gastropoda, Prosobranchia, Trochidae) to feeding and habitation in the littoral zone].

PubMed

Aliakrinskaia, I O

2010-01-01

The basic morphological, ethological, and physiological-biochemical adaptations of Monodonta turbinata to survival in the littoral zone were investigated in this work. Quantitative estimation of myoglobin content in radular tissues of mollusks inhabiting the Mediterranean Sea Basin has been carried out.

Nutritional Assessment: Its Significance in Medical Education.

ERIC Educational Resources Information Center

Ozerol, Nail H.

1982-01-01

Medical educators must make every effort to achieve an adequate level of nutrition education for all health professionals. Medical schools should adopt a basic, required curriculum including biochemical and physiological aspects of nutrients, a clinical nutrition program for prevention of health hazards, and a course in nutritional assessment.…

78 FR 49547 - Manufacturer of Controlled Substances; Notice of Registration; American Radiolabeled Chemicals, Inc.

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-14

... manufacture small quantities of the listed controlled substances as radiolabeled compounds for biochemical... the listed basic classes of controlled substances is consistent with the public interest at this time... is consistent with the public interest. The investigation has included inspection and testing of the...

Maximizing the Biochemical Resolving Power of Fluorescence Microscopy

PubMed Central

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

2013-01-01

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

Soya bean Gα proteins with distinct biochemical properties exhibit differential ability to complement Saccharomyces cerevisiae gpa1 mutant.

PubMed

Roy Choudhury, Swarup; Wang, Yuqi; Pandey, Sona

2014-07-01

Signalling pathways mediated by heterotrimeric G-proteins are common to all eukaryotes. Plants have a limited number of each of the G-protein subunits, with the most elaborate G-protein network discovered so far in soya bean (Glycine max, also known as soybean) which has four Gα, four Gβ and ten Gγ proteins. Biochemical characterization of Gα proteins from plants suggests significant variation in their properties compared with the well-characterized non-plant proteins. Furthermore, the four soya bean Gα (GmGα) proteins exhibit distinct biochemical activities among themselves, but the extent to which such biochemical differences contribute to their in vivo function is also not known. We used the yeast gpa1 mutant which displays constitutive signalling and growth arrest in the pheromone-response pathway as an in vivo model to evaluate the effect of distinct biochemical activities of GmGα proteins. We showed that specific GmGα proteins can be activated during pheromone-dependent receptor-mediated signalling in yeast and they display different strengths towards complementation of yeast gpa1 phenotypes. We also identified amino acids that are responsible for differential complementation abilities of specific Gα proteins. These data establish that specific plant Gα proteins are functional in the receptor-mediated pheromone-response pathway in yeast and that the subtle biochemical differences in their activity are physiologically relevant.

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.

Acetylcholinesterase of the sand fly, Phlebotomus papatasi (Scopoli): construction, expression and biochemical properties of the G119S orthologous mutant

USDA-ARS?s Scientific Manuscript database

Phlebotomus papatasi vectors zoonotic cutaneous leishmaniasis, widespread in intertropical and temperate regions of the world. Previous cloning, expression, and biochemical characterization of recombinant P. papatasi acetylcholinesterase 1 (PpAChE1) revealed 85% amino acid sequence identity to mosq...

Acetylcholinesterases of Rhipicephalus (Boophilus) microplus and Phlebotomus papatasi: Gene identification, expression and biochemical properties of recombinant proteins

USDA-ARS?s Scientific Manuscript database

Rhipicephalus (Boophilus) microplus (Bm) is a vector of bovine babesiosis and anaplasmosis. Tick resistance to organophosphate (OP) acaricide involves acetylcholinesterase (AChE) insensitivity to OP and metabolic detoxification. In vitro expression of Bm genes encoding AChE allowed biochemical chara...

Pathophysiology of chronic pancreatitis.

PubMed

Behrman, Stephen W; Fowler, Eric S

2007-12-01

Although the most common causes of chronic pancreatitis have not changed, it has become clear that a host of modifying biochemical, inflammatory, neural, and genetic deviations allows the disease to progress. Alterations in biochemical composition allow calcific stone formation, whereas various toxins, cytokines, and neuropeptides contribute to the progression of fibrosis and pain production. The basic cellular structure contributing to fibrosis of the pancreas has been elucidated and factors responsible for its activation delineated. Of most importance is the recent recognition of a set of genetic mutations that results in several aberrations of normal pancreatic physiology, which, in conjunction with other inciting insults or by themselves, allow the disease to begin and progress.

Stoichiometric network theory for nonequilibrium biochemical systems.

PubMed

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

2003-02-01

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

Predictive value of plasma β2-microglobulin on human body function and senescence.

PubMed

Dong, X-M; Cai, R; Yang, F; Zhang, Y-Y; Wang, X-G; Fu, S-L; Zhang, J-R

2016-06-01

To explore the correlation between plasma β2-microglobulin (β2-MG) as senescence factor with age, heart, liver and kidney function as well as the predictive value of β2-MG in human metabolism function and senescence. 387 cases of healthy people of different ages were selected and the automatic biochemical analyzer was used to test β2-MG in plasma based on immunoturbidimetry and also all biochemical indexes. The correlation between β2-MG and age, gender and all biochemical indexes was analyzed. β2-MG was positively correlated to age, r = 0.373; and the difference was of statistical significance (p < 0.010). It was significantly negative correlated to HDL-C but positively correlated to LP (a), BUN, CREA, UA, CYS-C, LDH, CK-MB, HBDH, AST, GLB and HCY. β2-MG was closely correlated to age, heart, kidney and liver biochemical indexes, which can be taken as an important biomarker for human body function and anti-senescence and have significant basic research and clinical guidance values.

Minimal models of electric potential oscillations in non-excitable membranes.

PubMed

Perdomo, Guillermo; Hernández, Julio A

2010-01-01

Sustained oscillations in the membrane potential have been observed in a variety of cellular and subcellular systems, including several types of non-excitable cells and mitochondria. For the plasma membrane, these electrical oscillations have frequently been related to oscillations in intracellular calcium. For the inner mitochondrial membrane, in several cases the electrical oscillations have been attributed to modifications in calcium dynamics. As an alternative, some authors have suggested that the sustained oscillations in the mitochondrial membrane potential induced by some metabolic intermediates depends on the direct effect of internal protons on proton conductance. Most theoretical models developed to interpret oscillations in the membrane potential integrate several transport and biochemical processes. Here we evaluate whether three simple dynamic models may constitute plausible representations of electric oscillations in non-excitable membranes. The basic mechanism considered in the derivation of the models is based upon evidence obtained by Hattori et al. for mitochondria and assumes that an ionic species (i.e., the proton) is transported via passive and active transport systems between an external and an internal compartment and that the ion affects the kinetic properties of transport by feedback regulation. The membrane potential is incorporated via its effects on kinetic properties. The dynamic properties of two of the models enable us to conclude that they may represent alternatives enabling description of the generation of electrical oscillations in membranes that depend on the transport of a single ionic species.

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

PubMed Central

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

2009-01-01

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

41 CFR 102-77.10 - What basic Art-in-Architecture policy governs Federal agencies?

Code of Federal Regulations, 2012 CFR

2012-01-01

... 41 Public Contracts and Property Management 3 2012-01-01 2012-01-01 false What basic Art-in-Architecture policy governs Federal agencies? 102-77.10 Section 102-77.10 Public Contracts and Property... PROPERTY 77-ART-IN-ARCHITECTURE General Provisions § 102-77.10 What basic Art-in-Architecture policy...

41 CFR 102-77.10 - What basic Art-in-Architecture policy governs Federal agencies?

Code of Federal Regulations, 2014 CFR

2014-01-01

... 41 Public Contracts and Property Management 3 2014-01-01 2014-01-01 false What basic Art-in-Architecture policy governs Federal agencies? 102-77.10 Section 102-77.10 Public Contracts and Property... PROPERTY 77-ART-IN-ARCHITECTURE General Provisions § 102-77.10 What basic Art-in-Architecture policy...

41 CFR 102-77.10 - What basic Art-in-Architecture policy governs Federal agencies?

Code of Federal Regulations, 2013 CFR

2013-07-01

... 41 Public Contracts and Property Management 3 2013-07-01 2013-07-01 false What basic Art-in-Architecture policy governs Federal agencies? 102-77.10 Section 102-77.10 Public Contracts and Property... PROPERTY 77-ART-IN-ARCHITECTURE General Provisions § 102-77.10 What basic Art-in-Architecture policy...

Physical Models Have Gender-Specific Effects on Student Understanding of Protein Structure-Function Relationships

ERIC Educational Resources Information Center

Forbes-Lorman, Robin M.; Harris, Michelle A.; Chang, Wesley S.; Dent, Erik W.; Nordheim, Erik V.; Franzen, Margaret A.

2016-01-01

Understanding how basic structural units influence function is identified as a foundational/core concept for undergraduate biological and biochemical literacy. It is essential for students to understand this concept at all size scales, but it is often more difficult for students to understand structure-function relationships at the molecular…

Transient hypothyroidism after withdrawal of thyroxin therapy

PubMed Central

Distiller, L. A.; Joffe, B. I.

1975-01-01

Continued administration of large doses of thyroid may not produce hyperthyroidism in euthyroid individuals. Cessation of prolonged high-dosage thyroid replacement can cause transient clinical and biochemical hypothyroidism owing to pituitary suppression. A case is recorded in which both these phenomena are well demonstrated. This case highlights these basic endocrinological principles. PMID:1197170

Exploring the evolution of protein function in Archaea.

PubMed

Goncearenco, Alexander; Berezovsky, Igor N

2012-05-30

Despite recent progress in studies of the evolution of protein function, the questions what were the first functional protein domains and what were their basic building blocks remain unresolved. Previously, we introduced the concept of elementary functional loops (EFLs), which are the functional units of enzymes that provide elementary reactions in biochemical transformations. They are presumably descendants of primordial catalytic peptides. We analyzed distant evolutionary connections between protein functions in Archaea based on the EFLs comprising them. We show examples of the involvement of EFLs in new functional domains, as well as reutilization of EFLs and functional domains in building multidomain structures and protein complexes. Our analysis of the archaeal superkingdom yields the dominating mechanisms in different periods of protein evolution, which resulted in several levels of the organization of biochemical function. First, functional domains emerged as combinations of prebiotic peptides with the very basic functions, such as nucleotide/phosphate and metal cofactor binding. Second, domain recombination brought to the evolutionary scene the multidomain proteins and complexes. Later, reutilization and de novo design of functional domains and elementary functional loops complemented evolution of protein function.

The effects of Zebra Chip disease development and bacterial titer on biochemical properties in relation to the time of infection

USDA-ARS?s Scientific Manuscript database

Potato tuber biochemical responses to ‘Candidatus’ Liberibacter solanacearum (Lso), the causal agent of Zebra chip disease, were evaluated both within infected tubers and across different infection dates. Tuber biochemistry also was related to symptom severity and bacterial titer. Symptom severity w...

Reduced linear noise approximation for biochemical reaction networks with time-scale separation: The stochastic tQSSA+

NASA Astrophysics Data System (ADS)

Herath, Narmada; Del Vecchio, Domitilla

2018-03-01

Biochemical reaction networks often involve reactions that take place on different time scales, giving rise to "slow" and "fast" system variables. This property is widely used in the analysis of systems to obtain dynamical models with reduced dimensions. In this paper, we consider stochastic dynamics of biochemical reaction networks modeled using the Linear Noise Approximation (LNA). Under time-scale separation conditions, we obtain a reduced-order LNA that approximates both the slow and fast variables in the system. We mathematically prove that the first and second moments of this reduced-order model converge to those of the full system as the time-scale separation becomes large. These mathematical results, in particular, provide a rigorous justification to the accuracy of LNA models derived using the stochastic total quasi-steady state approximation (tQSSA). Since, in contrast to the stochastic tQSSA, our reduced-order model also provides approximations for the fast variable stochastic properties, we term our method the "stochastic tQSSA+". Finally, we demonstrate the application of our approach on two biochemical network motifs found in gene-regulatory and signal transduction networks.

Near infrared spectroscopy for determination of various physical, chemical and biochemical properties in Mediterranean soils.

PubMed

Zornoza, R; Guerrero, C; Mataix-Solera, J; Scow, K M; Arcenegui, V; Mataix-Beneyto, J

2008-07-01

The potential of near infrared (NIR) reflectance spectroscopy to predict various physical, chemical and biochemical properties in Mediterranean soils from SE Spain was evaluated. Soil samples (n=393) were obtained by sampling thirteen locations during three years (2003-2005 period). These samples had a wide range of soil characteristics due to variations in land use, vegetation cover and specific climatic conditions. Biochemical properties also included microbial biomarkers based on phospholipid fatty acids (PLFA). Partial least squares (PLS) regression with cross validation was used to establish relationships between the NIR spectra and the reference data from physical, chemical and biochemical analyses. Based on the values of coefficient of determination (r(2)) and the ratio of standard deviation of validation set to root mean square error of cross validation (RPD), predicted results were evaluated as excellent (r(2)>0.90 and RPD>3) for soil organic carbon, Kjeldahl nitrogen, soil moisture, cation exchange capacity, microbial biomass carbon, basal soil respiration, acid phosphatase activity, β-glucosidase activity and PLFA biomarkers for total bacteria, Gram positive bacteria, actinomycetes, vesicular-arbuscular mycorrhizal fungi and total PLFA biomass. Good predictions (0.81

Optical Biopsy: A New Frontier in Endoscopic Detection and Diagnosis

PubMed Central

WANG, THOMAS D.; VAN DAM, JACQUES

2007-01-01

Endoscopic diagnosis currently relies on the ability of the operator to visualize abnormal patterns in the image created by light reflected from the mucosal surface of the gastrointestinal tract. Advances in fiber optics, light sources, detectors, and molecular biology have led to the development of several novel methods for tissue evaluation in situ. The term “optical biopsy” refers to methods that use the properties of light to enable the operator to make an instant diagnosis at endoscopy, previously possible only by using histological or cytological analysis. Promising imaging techniques include fluorescence endoscopy, optical coherence tomography, confocal microendoscopy, and molecular imaging. Point detection schemes under development include light scattering and Raman spectroscopy. Such advanced diagnostic methods go beyond standard endoscopic techniques by offering improved image resolution, contrast, and tissue penetration and providing biochemical and molecular information about mucosal disease. This review describes the basic biophysics of light-tissue interactions, assesses the strengths and weaknesses of each method, and examines clinical and preclinical evidence for each approach. PMID:15354274

Oxygen regulates molecular mechanisms of cancer progression and metastasis.

PubMed

Gupta, Kartik; Madan, Esha; Sayyid, Muzzammil; Arias-Pulido, Hugo; Moreno, Eduardo; Kuppusamy, Periannan; Gogna, Rajan

2014-03-01

Oxygen is the basic molecule which supports life and it truly is "god's gift to life." Despite its immense importance, research on "oxygen biology" has never received the light of the day and has been limited to physiological and biochemical studies. It seems that in modern day biology, oxygen research is summarized in one word "hypoxia." Scientists have focused on hypoxia-induced transcriptomics and molecular-cellular alterations exclusively in disease models. Interestingly, the potential of oxygen to control the basic principles of biology like homeostatic maintenance, transcription, replication, and protein folding among many others, at the molecular level, has been completely ignored. Here, we present a perspective on the crucial role played by oxygen in regulation of basic biological phenomena. Our conclusion highlights the importance of establishing novel research areas like oxygen biology, as there is great potential in this field for basic science discoveries and clinical benefits to the society.

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.

Exploring, tuning, and exploiting the basicity of hydrotalcites for applications in heterogeneous catalysis.

PubMed

Debecker, Damien P; Gaigneaux, Eric M; Busca, Guido

2009-01-01

Basic catalysis! The basic properties of hydrotalcites (see picture) make them attractive for numerous catalytic applications. Probing the basicity of the catalysts is crucial to understand the base-catalysed processes and to optimise the catalyst preparation. Various parameters can be employed to tune the basic properties of hydrotalcite-based catalysts towards the basicity demanded by each target chemical reaction.Hydrotalcites offer unique basic properties that make them very attractive for catalytic applications. It is of primary interest to make use of accurate tools for probing the basicity of hydrotalcite-based catalysts for the purpose of 1) fundamental understanding of base-catalysed processes with hydrotalcites and 2) optimisation of the catalytic performance achieved in reactions of industrial interest. Techniques based on probe molecules, titration techniques and test reactions along with physicochemical characterisation are overviewed in the first part of this review. The aim is to provide the tools for understanding how series of parameters involved in the preparation of hydrotalcite-based catalytic materials can be employed to control and adapt the basic properties of the catalyst towards the basicity demanded by each target chemical reaction. An overview of recent and significant achievements in that perspective is presented in the second part of the paper.

Long-term administration of Greek Royal Jelly decreases GABA concentration in the striatum and hypothalamus of naturally aged Wistar male rats.

PubMed

Pyrzanowska, Justyna; Wawer, Adriana; Joniec-Maciejak, Ilona; Piechal, Agnieszka; Blecharz-Klin, Kamilla; Graikou, Konstantia; Chinou, Ioanna; Widy-Tyszkiewicz, Ewa

2018-05-14

Royal Jelly (RJ) is a unique substance obtained from bees that has been used widely in European and Asian traditional medicine for its potential to prevent signs of aging through its antioxidative, anti-inflammatory, anti-hyperglycemic and anti-hypercholesterolemic properties. We recently reported an enhancement in spatial memory along with changes in monoaminergic transmission in aged rats after chronic RJ administration. Here, we aim to further explore the action of RJ on central nervous system activity by examining levels of amino acids in selected brain structures of aged male Wistar rats following 2-months of Greek RJ administration. RJ powder was previously chemically characterized and given orally (50 or 100 mg of powder/kg b.w./day) by gastric gavage. The concentrations of amino acids (alanine, aspartic acid, gamma-aminobutyric acid, glutamic acid, histidine and taurine) in the brain regions examined (prefrontal cortex, hippocampus, striatum and hypothalamus) were quantified using HPLC. We also examined basic biochemical parameters of renal and hepatic activity, as damage of these organs could potentially explain the changes in brain function and behavior. Upon biochemical examination, a decrease in the concentration of gamma-aminobutyric acid was observed in both the striatum and hypothalamus. Liver and kidney functions were not changed by chronic RJ-administration. Our results provide insight toward understanding the mechanism of action of RJ and its effects on neurotransmission in the central nervous system. Copyright © 2018 Elsevier B.V. All rights reserved.

Simulating carbon dioxide exchange rates of deciduous tree species: evidence for a general pattern in biochemical changes and water stress response.

PubMed

Reynolds, Robert F; Bauerle, William L; Wang, Ying

2009-09-01

Deciduous trees have a seasonal carbon dioxide exchange pattern that is attributed to changes in leaf biochemical properties. However, it is not known if the pattern in leaf biochemical properties - maximum Rubisco carboxylation (V(cmax)) and electron transport (J(max)) - differ between species. This study explored whether a general pattern of changes in V(cmax), J(max), and a standardized soil moisture response accounted for carbon dioxide exchange of deciduous trees throughout the growing season. The model MAESTRA was used to examine V(cmax) and J(max) of leaves of five deciduous trees, Acer rubrum 'Summer Red', Betula nigra, Quercus nuttallii, Quercus phellos and Paulownia elongata, and their response to soil moisture. MAESTRA was parameterized using data from in situ measurements on organs. Linking the changes in biochemical properties of leaves to the whole tree, MAESTRA integrated the general pattern in V(cmax) and J(max) from gas exchange parameters of leaves with a standardized soil moisture response to describe carbon dioxide exchange throughout the growing season. The model estimates were tested against measurements made on the five species under both irrigated and water-stressed conditions. Measurements and modelling demonstrate that the seasonal pattern of biochemical activity in leaves and soil moisture response can be parameterized with straightforward general relationships. Over the course of the season, differences in carbon exchange between measured and modelled values were within 6-12 % under well-watered conditions and 2-25 % under water stress conditions. Hence, a generalized seasonal pattern in the leaf-level physiological change of V(cmax) and J(max), and a standardized response to soil moisture was sufficient to parameterize carbon dioxide exchange for large-scale evaluations. Simplification in parameterization of the seasonal pattern of leaf biochemical activity and soil moisture response of deciduous forest species is demonstrated. This allows reliable modelling of carbon exchange for deciduous trees, thus circumventing the need for extensive gas exchange experiments on different species.

[Investigation of the accurate measurement of the basic imaging properties for the digital radiographic system based on flat panel detector].

PubMed

Katayama, R; Sakai, S; Sakaguchi, T; Maeda, T; Takada, K; Hayabuchi, N; Morishita, J

2008-07-20

PURPOSE/AIM OF THE EXHIBIT: The purpose of this exhibit is: 1. To explain "resampling", an image data processing, performed by the digital radiographic system based on flat panel detector (FPD). 2. To show the influence of "resampling" on the basic imaging properties. 3. To present accurate measurement methods of the basic imaging properties of the FPD system. 1. The relationship between the matrix sizes of the output image and the image data acquired on FPD that automatically changes depending on a selected image size (FOV). 2. The explanation of the image data processing of "resampling". 3. The evaluation results of the basic imaging properties of the FPD system using two types of DICOM image to which "resampling" was performed: characteristic curves, presampled MTFs, noise power spectra, detective quantum efficiencies. CONCLUSION/SUMMARY: The major points of the exhibit are as follows: 1. The influence of "resampling" should not be disregarded in the evaluation of the basic imaging properties of the flat panel detector system. 2. It is necessary for the basic imaging properties to be measured by using DICOM image to which no "resampling" is performed.

Tendon and ligament as novel cell sources for engineering the knee meniscus.

PubMed

Hadidi, P; Paschos, N K; Huang, B J; Aryaei, A; Hu, J C; Athanasiou, K A

2016-12-01

The application of cell-based therapies in regenerative medicine is hindered by the difficulty of acquiring adequate numbers of competent cells. For the knee meniscus in particular, this may be solved by harvesting tissue from neighboring tendons and ligaments. In this study, we have investigated the potential of cells from tendon and ligament, as compared to meniscus cells, to engineer scaffold-free self-assembling fibrocartilage. Self-assembling meniscus-shaped constructs engineered from a co-culture of articular chondrocytes and either meniscus, tendon, or ligament cells were cultured for 4 weeks with TGF-β1 in serum-free media. After culture, constructs were assessed for their mechanical properties, histological staining, gross appearance, and biochemical composition including cross-link content. Correlations were performed to evaluate relationships between biochemical content and mechanical properties. In terms of mechanical properties as well as biochemical content, constructs engineered using tenocytes and ligament fibrocytes were found to be equivalent or superior to constructs engineered using meniscus cells. Furthermore, cross-link content was found to be correlated with engineered tissue tensile properties. Tenocytes and ligament fibrocytes represent viable cell sources for engineering meniscus fibrocartilage using the self-assembling process. Due to greater cross-link content, fibrocartilage engineered with tenocytes and ligament fibrocytes may maintain greater tensile properties than fibrocartilage engineered with meniscus cells. Copyright © 2016 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Tendon and ligament as novel cell sources for engineering the knee meniscus

PubMed Central

Hadidi, Pasha; Paschos, Nikolaos K.; Huang, Brian J.; Aryaei, Ashkan; Hu, Jerry C.; Athanasiou, Kyriacos A.

2016-01-01

Objective The application of cell-based therapies in regenerative medicine is hindered by the difficulty of acquiring adequate numbers of competent cells. For the knee meniscus in particular, this may be solved by harvesting tissue from neighboring tendons and ligaments. In this study, we have investigated the potential of cells from tendon and ligament, as compared to meniscus cells, to engineer scaffold-free self-assembling fibrocartilage. Method Self-assembling meniscus-shaped constructs engineered from a co-culture of articular chondrocytes and either meniscus, tendon, or ligament cells were cultured for 4 weeks with TGF-β1 in serum-free media. After culture, constructs were assessed for their mechanical properties, histological staining, gross appearance, and biochemical composition including cross-link content. Correlations were performed to evaluate relationships between biochemical content and mechanical properties. Results In terms of mechanical properties as well as biochemical content, constructs engineered using tenocytes and ligament fibrocytes were found to be equivalent or superior to constructs engineered using meniscus cells. Furthermore, cross-link content was found to be correlated with engineered tissue tensile properties. Conclusion Tenocytes and ligament fibrocytes represent viable cell sources for engineering meniscus fibrocartilage using the self-assembling process. Due to greater cross-link content, fibrocartilage engineered with tenocytes and ligament fibrocytes may maintain greater tensile properties than fibrocartilage engineered with meniscus cells. PMID:27473559

In vitro three-dimensional cancer metastasis modeling: Past, present, and future

NASA Astrophysics Data System (ADS)

Wei-jing, Han; Wei, Yuan; Jiang-rui, Zhu; Qihui, Fan; Junle, Qu; Li-yu, Liu

2016-01-01

Metastasis is the leading cause of most cancer deaths, as opposed to dysregulated cell growth of the primary tumor. Molecular mechanisms of metastasis have been studied for decades and the findings have evolved our understanding of the progression of malignancy. However, most of the molecular mechanisms fail to address the causes of cancer and its evolutionary origin, demonstrating an inability to find a solution for complete cure of cancer. After being a neglected area of tumor biology for quite some time, recently several studies have focused on the impact of the tumor microenvironment on cancer growth. The importance of the tumor microenvironment is gradually gaining attention, particularly from the perspective of biophysics. In vitro three-dimensional (3-D) metastatic models are an indispensable platform for investigating the tumor microenvironment, as they mimic the in vivo tumor tissue. In 3-D metastatic in vitro models, static factors such as the mechanical properties, biochemical factors, as well as dynamic factors such as cell-cell, cell-ECM interactions, and fluid shear stress can be studied quantitatively. With increasing focus on basic cancer research and drug development, the in vitro 3-D models offer unique advantages in fundamental and clinical biomedical studies. Project supported by the National Basic Research Program of China (Grant No. 2013CB837200), the National Natural Science Foundation of China (Grant No. 11474345), and the Beijing Natural Science Foundation, China (Grant No. 7154221).

Physiologically based microenvironment for in vitro neural differentiation of adipose-derived stem cells

PubMed Central

Graziano, Adriana Carol Eleonora; Avola, Rosanna; Perciavalle, Vincenzo; Nicoletti, Ferdinando; Cicala, Gianluca; Coco, Marinella; Cardile, Venera

2018-01-01

The limited capacity of nervous system to promote a spontaneous regeneration and the high rate of neurodegenerative diseases appearance are keys factors that stimulate researches both for defining the molecular mechanisms of pathophysiology and for evaluating putative strategies to induce neural tissue regeneration. In this latter aspect, the application of stem cells seems to be a promising approach, even if the control of their differentiation and the maintaining of a safe state of proliferation should be troubled. Here, we focus on adipose tissue-derived stem cells and we seek out the recent advances on the promotion of their neural differentiation, performing a critical integration of the basic biology and physiology of adipose tissue-derived stem cells with the functional modifications that the biophysical, biomechanical and biochemical microenvironment induces to cell phenotype. The pre-clinical studies showed that the neural differentiation by cell stimulation with growth factors benefits from the integration with biomaterials and biophysical interaction like microgravity. All these elements have been reported as furnisher of microenvironments with desirable biological, physical and mechanical properties. A critical review of current knowledge is here proposed, underscoring that a real advance toward a stable, safe and controllable adipose stem cells clinical application will derive from a synergic multidisciplinary approach that involves material engineer, basic cell biology, cell and tissue physiology. PMID:29588808

Insights from the Shell Proteome: Biomineralization to Adaptation

PubMed Central

Arivalagan, Jaison; Yarra, Tejaswi; Marie, Benjamin; Sleight, Victoria A.; Duvernois-Berthet, Evelyne; Clark, Melody S.; Marie, Arul; Berland, Sophie

2017-01-01

Bivalves have evolved a range of complex shell forming mechanisms that are reflected by their incredible diversity in shell mineralogy and microstructures. A suite of proteins exported to the shell matrix space plays a significant role in controlling these features, in addition to underpinning some of the physical properties of the shell itself. Although, there is a general consensus that a minimum basic protein tool kit is required for shell construction, to date, this remains undefined. In this study, the shell matrix proteins (SMPs) of four highly divergent bivalves (The Pacific oyster, Crassostrea gigas; the blue mussel, Mytilus edulis; the clam, Mya truncata, and the king scallop, Pecten maximus) were analyzed in an identical fashion using proteomics pipeline. This enabled us to identify the critical elements of a “basic tool kit” for calcification processes, which were conserved across the taxa irrespective of the shell morphology and arrangement of the crystal surfaces. In addition, protein domains controlling the crystal layers specific to aragonite and calcite were also identified. Intriguingly, a significant number of the identified SMPs contained domains related to immune functions. These were often are unique to each species implying their involvement not only in immunity, but also environmental adaptation. This suggests that the SMPs are selectively exported in a complex mix to endow the shell with both mechanical protection and biochemical defense. PMID:27744410

How to turn industrial biotechnology into reality.

PubMed

Kircher, Manfred

2012-01-15

The emerging bioeconomy is pulled by consumers asking for sustainable products and processes, governments enforcing climate protection and industries demanding feedstock flexibility and last but not least it is pushed by progress in basic and applied science. It will use renewable carbon sources not only from agri- and silviculture, but potentially also from industrial flue gases - for example, from power generation and steel production. Connecting such industries with the future bio-chemical industry results in a challenging new value chain which connects thus far separated industries. Realising this value chain needs disruptive technologies in providing sustainable carbon sources and transforming them into precursors for biochemical production up to consumer products. Copyright © 2011 Elsevier B.V. All rights reserved.

41 CFR 102-80.10 - What are the basic safety and environmental management policies for real property?

Code of Federal Regulations, 2014 CFR

2014-01-01

... 41 Public Contracts and Property Management 3 2014-01-01 2014-01-01 false What are the basic safety and environmental management policies for real property? 102-80.10 Section 102-80.10 Public Contracts and Property Management Federal Property Management Regulations System (Continued) FEDERAL...

Biochemical characterization of a recombinant Lactobacillus acidophilus strain expressing exogenous FomA protein.

PubMed

Ma, Li; Li, Fei; Zhang, Xiangyu; Feng, Xiping

2018-04-30

In previous research, to combine the immunogenicity of Fusobacterium nucleatum (F. nucleatum) and the probiotic properties of Lactobacillus acidophilus (L. acidophilus), we constructed a FomA-expressing L. acidophilus strain and assessed its immunogenicity. Our findings indicated that oral administration of the recombinant L. acidophilus strain reduced the risk of periodontal infection by Porphyromonas gingivalis (P. gingivalis) and F. nucleatum. However, because the exogenous FomA is an heterologous protein for the original bacterium, in this study, we assessed whether the biochemical characteristics of the recombinant L. acidophilus strain change due to the expression of the exogenous FomA protein. To test the biochemical characteristics of a recombinant L. acidophilus strain expressing exogenous FomA and assess its antibiotic sensitivity. We assessed the colony morphology, growth, acid production, and carbohydrate fermentation abilities of the recombinant L. acidophilus strain. In addition, we tested the adhesive ability and antimicrobial activity of the recombinant and assessed its antibiotic sensitivity through a drug susceptibility test. The experimental results showed that the colony and microscopic morphology of the recombinant L. acidophilus strain was consistent with the original strain, and the recombinant strain grew well when cultured under aerobic or anaerobic conditions, exhibiting a growth rate that was identical to that of the standard strain. Similarly, the supernatants of the recombinant L. acidophilus can inhibit the growth of E. coli and P. gingivalis at different concentrations, and the recombinant strain displayed essentially the same drug sensitivity profile as the original L. acidophilus. However, to our surprise, the recombinant strains exhibited a greater adhesion ability than the reference strain. Our study demonstrated that, in addition to an increased adhesion ability, the recombinant L. acidophilus strain maintained the basic characteristics of the standard strain ATCC 4356, including antibiotic sensitivity. Thus, the recombinant strains have great potential to be utilized as a safe and effective periodontitis vaccine in the future. Copyright © 2018 Elsevier Ltd. All rights reserved.

From Purines to Basic Biochemical Concepts: Experiments for High School Students

ERIC Educational Resources Information Center

Marini, Isabella; Ipata, Piero Luigi

2007-01-01

Many high school biology courses address mainly the molecular and cellular basis of life. The complexity that underlies the most essential processes is often difficult for the students to understand; possibly, in part, because of the inability to see and explore them. Six simple practical experiments on purine catabolism as a part of a…

Teaching Protein Purification and Characterization Techniques: A Student-Initiated, Project-Oriented Biochemistry Laboratory Course

ERIC Educational Resources Information Center

MacDonald, Gina

2008-01-01

This report describes a biochemistry laboratory that is completely project-oriented. Upper-level biology and chemistry majors work in teams to purify a protein of their choice. After the student groups have completed literature searches, ordered reagents, and made buffers they continue to learn basic protein purification and biochemical techniques…

Topographic variations in biomechanical and biochemical properties in the ankle joint: an in vitro bovine study evaluating native and engineered cartilage.

PubMed

Paschos, Nikolaos K; Makris, Eleftherios A; Hu, Jerry C; Athanasiou, Kyriacos A

2014-10-01

The purposes of this study were to identify differences in the biomechanical and biochemical properties among the articulating surfaces of the ankle joint and to evaluate the functional and biological properties of engineered neocartilage generated using chondrocytes from different locations in the ankle joint. The properties of the different topographies within the ankle joint (tibial plafond, talar dome, and distal fibula) were evaluated in 28 specimens using 7 bovine ankles; the femoral condyle was used as a control. Chondrocytes from the same locations were used to form 28 neocartilage constructs by tissue engineering using an additional 7 bovine ankles. The functional properties of neocartilage were compared with native tissue values. Articular cartilage from the tibial plafond, distal fibula, talar dome, and femoral condyle exhibited Young modulus values of 4.8 ± 0.5 MPa, 3.9 ± 0.1 MPa, 1.7 ± 0.2 MPa, and 4.0 ± 0.5 MPa, respectively. The compressive properties of the corresponding tissues were 370 ± 22 kPa, 242 ± 18 kPa, 255 ± 26 kPa, and 274 ± 18 kPa, respectively. The tibial plafond exhibited 3-fold higher tensile properties and 2-fold higher compressive and shear moduli compared with its articulating talar dome; the same disparity was observed in neocartilage. Similar trends were detected in biochemical data for both native and engineered tissues. The cartilage properties of the various topographic locations within the ankle are significantly different. In particular, the opposing articulating surfaces of the ankle have significantly different biomechanical and biochemical properties. The disparity between tibial plafond and talar dome cartilage and chondrocytes warrants further evaluation in clinical studies to evaluate their exact role in the pathogenesis of ankle lesions. Therapeutic modalities for cartilage lesions need to consider the exact topographic source of the cells or cartilage grafts used. Furthermore, the capacity of generating neocartilage implants from location-specific chondrocytes of the ankle joint may be used in the future as a tool for the treatment of chondral lesions. Copyright © 2014 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

A review of digital microfluidics as portable platforms for lab-on a-chip applications.

PubMed

Samiei, Ehsan; Tabrizian, Maryam; Hoorfar, Mina

2016-07-07

Following the development of microfluidic systems, there has been a high tendency towards developing lab-on-a-chip devices for biochemical applications. A great deal of effort has been devoted to improve and advance these devices with the goal of performing complete sets of biochemical assays on the device and possibly developing portable platforms for point of care applications. Among the different microfluidic systems used for such a purpose, digital microfluidics (DMF) shows high flexibility and capability of performing multiplex and parallel biochemical operations, and hence, has been considered as a suitable candidate for lab-on-a-chip applications. In this review, we discuss the most recent advances in the DMF platforms, and evaluate the feasibility of developing multifunctional packages for performing complete sets of processes of biochemical assays, particularly for point-of-care applications. The progress in the development of DMF systems is reviewed from eight different aspects, including device fabrication, basic fluidic operations, automation, manipulation of biological samples, advanced operations, detection, biological applications, and finally, packaging and portability of the DMF devices. Success in developing the lab-on-a-chip DMF devices will be concluded based on the advances achieved in each of these aspects.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

41 CFR 102-74.10 - What is the basic facility management policy?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What is the basic facility management policy? 102-74.10 Section 102-74.10 Public Contracts and Property Management Federal Property Management Regulations System (Continued) FEDERAL MANAGEMENT REGULATION REAL PROPERTY 74-FACILITY...

Biochemical properties of thyroid peroxidase (TPO) expressed in human breast and mammary-derived cell lines

PubMed Central

Godlewska, Marlena; Krasuska, Wanda

2018-01-01

Thyroid peroxidase (TPO) is an enzyme and autoantigen expressed in thyroid and breast tissues. Thyroid TPO undergoes a complex maturation process however, nothing is known about post-translational modifications of breast-expressed TPO. In this study, we have investigated the biochemical properties of TPO expressed in normal and cancerous human breast tissues, and the maturation process and antigenicity of TPO present in a panel of human breast tissue-derived cell lines. We found that the molecular weight of breast TPO was slightly lower than that of thyroid TPO due to decreased glycosylation and as suggest results of Western blot also shorter amino acid chain. Breast TPO exhibit enzymatic activity and isoelectric point comparable to that of thyroid TPO. The biochemical properties of TPO expressed in mammary cell lines and normal thyrocytes are similar regarding glycan content, molecular weight and isoelectric point. However, no peroxidase activity and dimer formation was detected in any of these cell lines since the majority of TPO protein was localized in the cytoplasmic compartment, and the TPO expression at the cell surface was too low to detect its enzymatic activity. Lactoperoxidase, a protein highly homologous to TPO expressed also in breast tissues, does not influence the obtained data. TPO expressed in the cell lines was recognized by a broad panel of TPO-specific antibodies. Although some differences in biochemical properties between thyroid and breast TPO were observed, they do not seem to be critical for the overall three-dimensional structure. This conclusion is supported by the fact that TPO expressed in breast tissues and cell lines reacts well with conformation-sensitive antibodies. Taking into account a close resemblance between both proteins, especially high antigenicity, future studies should investigate the potential immunotherapies directed against breast-expressed TPO and its specific epitopes. PMID:29513734

Biochemical properties of thyroid peroxidase (TPO) expressed in human breast and mammary-derived cell lines.

PubMed

Godlewska, Marlena; Krasuska, Wanda; Czarnocka, Barbara

2018-01-01

Thyroid peroxidase (TPO) is an enzyme and autoantigen expressed in thyroid and breast tissues. Thyroid TPO undergoes a complex maturation process however, nothing is known about post-translational modifications of breast-expressed TPO. In this study, we have investigated the biochemical properties of TPO expressed in normal and cancerous human breast tissues, and the maturation process and antigenicity of TPO present in a panel of human breast tissue-derived cell lines. We found that the molecular weight of breast TPO was slightly lower than that of thyroid TPO due to decreased glycosylation and as suggest results of Western blot also shorter amino acid chain. Breast TPO exhibit enzymatic activity and isoelectric point comparable to that of thyroid TPO. The biochemical properties of TPO expressed in mammary cell lines and normal thyrocytes are similar regarding glycan content, molecular weight and isoelectric point. However, no peroxidase activity and dimer formation was detected in any of these cell lines since the majority of TPO protein was localized in the cytoplasmic compartment, and the TPO expression at the cell surface was too low to detect its enzymatic activity. Lactoperoxidase, a protein highly homologous to TPO expressed also in breast tissues, does not influence the obtained data. TPO expressed in the cell lines was recognized by a broad panel of TPO-specific antibodies. Although some differences in biochemical properties between thyroid and breast TPO were observed, they do not seem to be critical for the overall three-dimensional structure. This conclusion is supported by the fact that TPO expressed in breast tissues and cell lines reacts well with conformation-sensitive antibodies. Taking into account a close resemblance between both proteins, especially high antigenicity, future studies should investigate the potential immunotherapies directed against breast-expressed TPO and its specific epitopes.

Identification of a highly active tannase enzyme from the oral pathogen Fusobacterium nucleatum subsp. polymorphum.

PubMed

Tomás-Cortázar, Julen; Plaza-Vinuesa, Laura; de Las Rivas, Blanca; Lavín, José Luis; Barriales, Diego; Abecia, Leticia; Mancheño, José Miguel; Aransay, Ana M; Muñoz, Rosario; Anguita, Juan; Rodríguez, Héctor

2018-02-26

Tannases are tannin-degrading enzymes that have been described in fungi and bacteria as an adaptative mechanism to overcome the stress conditions associated with the presence of these phenolic compounds. We have identified and expressed in E. coli a tannase from the oral microbiota member Fusobacterium nucleatum subs. polymorphum (TanB Fnp ). TanB Fnp is the first tannase identified in an oral pathogen. Sequence analyses revealed that it is closely related to other bacterial tannases. The enzyme exhibits biochemical properties that make it an interesting target for industrial use. TanB Fnp has one of the highest specific activities of all bacterial tannases described to date and shows optimal biochemical properties such as a high thermal stability: the enzyme keeps 100% of its activity after prolonged incubations at different temperatures up to 45 °C. TanB Fnp also shows a wide temperature range of activity, maintaining above 80% of its maximum activity between 22 and 55 °C. The use of a panel of 27 esters of phenolic acids demonstrated activity of TanB Fnp only against esters of gallic and protocatechuic acid, including tannic acid, gallocatechin gallate and epigallocatechin gallate. Overall, TanB Fnp possesses biochemical properties that make the enzyme potentially useful in biotechnological applications. We have identified and characterized a metabolic enzyme from the oral pathogen Fusobacterium nucleatum subsp. polymorphum. The biochemical properties of TanB Fnp suggest that it has a major role in the breakdown of complex food tannins during oral processing. Our results also provide some clues regarding its possible participation on bacterial survival in the oral cavity. Furthermore, the characteristics of this enzyme make it of potential interest for industrial use.

Cartilage matrix formation by bovine mesenchymal stem cells in three-dimensional culture is age-dependent.

PubMed

Erickson, Isaac E; van Veen, Steven C; Sengupta, Swarnali; Kestle, Sydney R; Mauck, Robert L

2011-10-01

Cartilage degeneration is common in the aged, and aged chondrocytes are inferior to juvenile chondrocytes in producing cartilage-specific extracellular matrix. Mesenchymal stem cells (MSCs) are an alternative cell type that can differentiate toward the chondrocyte phenotype. Aging may influence MSC chondrogenesis but remains less well studied, particularly in the bovine system. The objectives of this study were (1) to confirm age-related changes in bovine articular cartilage, establish how age affects chondrogenesis in cultured pellets for (2) chondrocytes and (3) MSCs, and (4) determine age-related changes in the biochemical and biomechanical development of clinically relevant MSC-seeded hydrogels. Native bovine articular cartilage from fetal (n = 3 donors), juvenile (n = 3 donors), and adult (n = 3 donors) animals was analyzed for mechanical and biochemical properties (n = 3-5 per donor). Chondrocyte and MSC pellets (n = 3 donors per age) were cultured for 6 weeks before analysis of biochemical content (n = 3 per donor). Bone marrow-derived MSCs of each age were also cultured within hyaluronic acid hydrogels for 3 weeks and analyzed for matrix deposition and mechanical properties (n = 4 per age). Articular cartilage mechanical properties and collagen content increased with age. We observed robust matrix accumulation in three-dimensional pellet culture by fetal chondrocytes with diminished collagen-forming capacity in adult chondrocytes. Chondrogenic induction of MSCs was greater in fetal and juvenile cell pellets. Likewise, fetal and juvenile MSCs in hydrogels imparted greater matrix and mechanical properties. Donor age and biochemical microenvironment were major determinants of both bovine chondrocyte and MSC functional capacity. In vitro model systems should be evaluated in the context of age-related changes and should be benchmarked against human MSC data.

Fibrin Formation, Structure and Properties

PubMed Central

Weisel, John W.; Litvinov, Rustem I.

2017-01-01

Fibrinogen and fibrin are essential for hemostasis and are major factors in thrombosis, wound healing, and several other biological functions and pathological conditions. The X-ray crystallographic structure of major parts of fibrin(ogen), together with computational reconstructions of missing portions and numerous biochemical and biophysical studies, have provided a wealth of data to interpret molecular mechanisms of fibrin formation, its organization, and properties. On cleavage of fibrinopeptides by thrombin, fibrinogen is converted to fibrin monomers, which interact via knobs exposed by fibrinopeptide removal in the central region, with holes always exposed at the ends of the molecules. The resulting half-staggered, double-stranded oligomers lengthen into protofibrils, which aggregate laterally to make fibers, which then branch to yield a three-dimensional network. Much is now known about the structural origins of clot mechanical properties, including changes in fiber orientation, stretching and buckling, and forced unfolding of molecular domains. Studies of congenital fibrinogen variants and post-translational modifications have increased our understanding of the structure and functions of fibrin(ogen). The fibrinolytic system, with the zymogen plasminogen binding to fibrin together with tissue-type plasminogen activator to promote activation to the active proteolytic enzyme, plasmin, results in digestion of fibrin at specific lysine residues. In spite of a great increase in our knowledge of all these interconnected processes, much about the molecular mechanisms of the biological functions of fibrin(ogen) remains unknown, including some basic aspects of clotting, fibrinolysis, and molecular origins of fibrin mechanical properties. Even less is known concerning more complex (patho)physiological implications of fibrinogen and fibrin. PMID:28101869

Recommendations for terminology and databases for biochemical thermodynamics.

PubMed

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

2011-05-01

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

Changes in Biochemical Properties of the Blood in Winter Swimmers.

PubMed

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

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

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.

Synergizing 13C Metabolic Flux Analysis and Metabolic Engineering for Biochemical Production.

PubMed

Guo, Weihua; Sheng, Jiayuan; Feng, Xueyang

Metabolic engineering of industrial microorganisms to produce chemicals, fuels, and drugs has attracted increasing interest as it provides an environment-friendly and renewable route that does not depend on depleting petroleum sources. However, the microbial metabolism is so complex that metabolic engineering efforts often have difficulty in achieving a satisfactory yield, titer, or productivity of the target chemical. To overcome this challenge, 13 C Metabolic Flux Analysis ( 13 C-MFA) has been developed to investigate rigorously the cell metabolism and quantify the carbon flux distribution in central metabolic pathways. In the past decade, 13 C-MFA has been widely used in academic labs and the biotechnology industry to pinpoint the key issues related to microbial-based chemical production and to guide the development of the appropriate metabolic engineering strategies for improving the biochemical production. In this chapter we introduce the basics of 13 C-MFA and illustrate how 13 C-MFA has been applied to synergize with metabolic engineering to identify and tackle the rate-limiting steps in biochemical production.

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.

Biochemical analysis of secretory proteins synthesized by normal rat pancreas and by pancreatic acinar tumor cells

PubMed Central

1982-01-01

We have examined the secretogogue responsiveness and the pattern of secretory proteins produced by a transplantable rat pancreatic acinar cell tumor. Dispersed tumor cells were found to discharge secretory proteins in vitro when incubated with hormones that act on four different classes of receptors: carbamylcholine, caerulein, secretin- vasoactive intestinal peptide, and bombesin. With all hormones tested, maximal discharge from tumor cells was only about one-half that of control pancreatic lobules, but occurred at the same dose optima except for secretin, whose dose optimum was 10-fold higher. Biochemical analysis of secretory proteins discharged by the tumor cells was carried out by crossed immunoelectrophoresis and by two-dimensional isoelectric focusing-SDS polyacrylamide gel electrophoresis. To establish a baseline for comparison, secretory proteins from normal rat pancreas were identified according to enzymatic activity and correlated with migration position on two-dimensional gels. Our results indicate that a group of basic polypeptides including proelastase, basic trypsinogen, basic chymotrypsinogen, and ribonuclease, two out of three forms of procarboxypeptidase B, and the major lipase species were greatly reduced or absent in tumor cell secretion. In contrast, the amount of acidic chymotrypsinogen was notably increased compared with normal acinar cells. Although the acinar tumor cells are highly differentiated cytologically and express functional receptors for several classes of pancreatic secretagogues, they show quantitative and qualitative differences when compared with normal pancreas with regard to their production of secretory proteins. PMID:6185502

Distinct structural and mechanical properties of the nuclear lamina in Hutchinson-Gilford progeria syndrome.

PubMed

Dahl, Kris Noel; Scaffidi, Paola; Islam, Mohammad F; Yodh, Arjun G; Wilson, Katherine L; Misteli, Tom

2006-07-05

The nuclear lamina is a network of structural filaments, the A and B type lamins, located at the nuclear envelope and throughout the nucleus. Lamin filaments provide the nucleus with mechanical stability and support many basic activities, including gene regulation. Mutations in LMNA, the gene encoding A type lamins, cause numerous human diseases, including the segmental premature aging disease Hutchinson-Gilford progeria syndrome (HGPS). Here we show that structural and mechanical properties of the lamina are altered in HGPS cells. We demonstrate by live-cell imaging and biochemical analysis that lamins A and C become trapped at the nuclear periphery in HGPS patient cells. Using micropipette aspiration, we show that the lamina in HGPS cells has a significantly reduced ability to rearrange under mechanical stress. Based on polarization microscopy results, we suggest that the lamins are disordered in the healthy nuclei, whereas the lamins in HGPS nuclei form orientationally ordered microdomains. The reduced deformability of the HGPS nuclear lamina possibly could be due to the inability of these orientationally ordered microdomains to dissipate mechanical stress. Surprisingly, intact HGPS cells exhibited a degree of resistance to acute mechanical stress similar to that of cells from healthy individuals. Thus, in contrast to the nuclear fragility seen in lmna null cells, the lamina network in HGPS cells has unique mechanical properties that might contribute to disease phenotypes by affecting responses to mechanical force and misregulation of mechanosensitive gene expression.

Comparisons of Auricular Cartilage Tissues from Different Species.

PubMed

Chiu, Loraine L Y; Giardini-Rosa, Renata; Weber, Joanna F; Cushing, Sharon L; Waldman, Stephen D

2017-12-01

Tissue engineering of auricular cartilage has great potential in providing readily available materials for reconstructive surgeries. As the field of tissue engineering moves forward to developing human tissues, there needs to be an interspecies comparison of the native auricular cartilage in order to determine a suitable animal model to assess the performance of engineered auricular cartilage in vivo. Here, we performed interspecies comparisons of auricular cartilage by comparing tissue microstructure, protein localization, biochemical composition, and mechanical properties of auricular cartilage tissues from rat, rabbit, pig, cow, and human. Human, pig, and cow auricular cartilage have smaller lacunae compared to rat and rabbit cartilage ( P < .05). Despite differences in tissue microstructure, human auricular cartilage has similar biochemical composition to both rat and rabbit. Auricular cartilage from pig and cow, alternatively, display significantly higher glycosaminoglycan and collagen contents compared to human, rat, and rabbit ( P < .05). The mechanical properties of human auricular cartilage were comparable to that of all 4 animal species. This is the first study that compares the microstructural, biochemical, and mechanical properties of auricular cartilage from different species. This study showed that different experimental animal models of human auricular cartilage may be suitable in different cases.

Red Blood Cell Susceptibility to Pneumolysin

PubMed Central

Bokori-Brown, Monika; Petrov, Peter G.; Khafaji, Mawya A.; Mughal, Muhammad K.; Naylor, Claire E.; Shore, Angela C.; Gooding, Kim M.; Casanova, Francesco; Mitchell, Tim J.; Titball, Richard W.; Winlove, C. Peter

2016-01-01

This study investigated the effect of the biochemical and biophysical properties of the plasma membrane as well as membrane morphology on the susceptibility of human red blood cells to the cholesterol-dependent cytolysin pneumolysin, a key virulence factor of Streptococcus pneumoniae, using single cell studies. We show a correlation between the physical properties of the membrane (bending rigidity and surface and dipole electrostatic potentials) and the susceptibility of red blood cells to pneumolysin-induced hemolysis. We demonstrate that biochemical modifications of the membrane induced by oxidative stress, lipid scrambling, and artificial cell aging modulate the cell response to the toxin. We provide evidence that the diversity of response to pneumolysin in diabetic red blood cells correlates with levels of glycated hemoglobin and that the mechanical properties of the red blood cell plasma membrane are altered in diabetes. Finally, we show that diabetic red blood cells are more resistant to pneumolysin and the related toxin perfringolysin O relative to healthy red blood cells. Taken together, these studies indicate that the diversity of cell response to pneumolysin within a population of human red blood cells is influenced by the biophysical and biochemical status of the plasma membrane and the chemical and/or oxidative stress pre-history of the cell. PMID:26984406

Multivariate analysis of fatty acid and biochemical constitutes of seaweeds to characterize their potential as bioresource for biofuel and fine chemicals.

PubMed

Verma, Priyanka; Kumar, Manoj; Mishra, Girish; Sahoo, Dinabandhu

2017-02-01

In the present study bio prospecting of thirty seaweeds from Indian coasts was analyzed for their biochemical components including pigments, fatty acid and ash content. Multivariate analysis of biochemical components and fatty acids was done using Principal Component Analysis (PCA) and Agglomerative hierarchical clustering (AHC) to manifest chemotaxonomic relationship among various seaweeds. The overall analysis suggests that these seaweeds have multi-functional properties and can be utilized as promising bioresource for proteins, lipids, pigments and carbohydrates for the food/feed and biofuel industry. Copyright © 2016. Published by Elsevier Ltd.

Diagnosis of sarcoidosis

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

Sharma, O.P.

1983-07-01

During the last decade, many biochemical and immunologic advances have been made in the treatment and understanding of sarcoidosis. These studies have helped us to understand the basic mechanisms involved in granuloma formation, and many clinicians have used the information to diagnose and assess the activity of sarcoidosis. Further studies are needed to clearly establish the role of these advances in the everyday management of patients with sarcoidosis.

TAF1, From a General Transcription Factor to Modulator of Androgen Receptor in Prostate Cancer

DTIC Science & Technology

2010-02-01

kinase CK2. Mol Cell Biochem 316:99-106 21. Lively TN, Ferguson HA, Galasinski SK, Seto AG, Goodrich JA 2001 c-Jun binds the N terminus of human TAF(II...Nguyen TN, Galasinski SK, Goodrich JA 2004 The basic leucine zipper domain of c-Jun functions in transcriptional activation through interaction with

European spruce bark beetle (Ips typographus, L.) green attack affects foliar reflectance and biochemical properties

NASA Astrophysics Data System (ADS)

Abdullah, Haidi; Darvishzadeh, Roshanak; Skidmore, Andrew K.; Groen, Thomas A.; Heurich, Marco

2018-02-01

The European spruce bark beetle Ips typographus, L. (hereafter bark beetle), causes major economic loss to the forest industry in Europe, especially in Norway Spruce (Picea abies). To minimise economic loss and preclude a mass outbreak, early detection of bark beetle infestation (so-called ;green attack; stage - a period at which trees are yet to show visual signs of infestation stress) is, therefore, a crucial step in the management of Norway spruce stands. It is expected that a bark beetle infestation at the green attack stage affects a tree's physiological and chemical status. However, the concurrent effect on key foliar biochemical such as foliar nitrogen and chlorophyll as well as spectral responses are not well documented in the literature. Therefore, in this study, the early detection of bark beetle green attacks is investigated by examining foliar biochemical and spectral properties (400-2000 nm). We also assessed whether bark beetle infestation affects the estimation accuracy of foliar biochemicals. An extensive field survey was conducted in the Bavarian Forest National Park (BFNP), Germany, in the early summer of 2015 to collect leaf samples from 120 healthy and green attacked trees. The spectra of the leaf samples were measured using an ASD FieldSpec3 equipped with an integrating sphere. Significant differences (p < 0.05) between healthy and infested needle samples were found in the mean reflectance spectra, with the most pronounced differences being observed in the NIR and SWIR regions between 730 and 1370 nm. Furthermore, significant differences (p < 0.05) were found in the biochemical compositions (chlorophyll and nitrogen concentration) of healthy versus green attacked samples. Our results further demonstrate that the estimation accuracy of foliar chlorophyll and nitrogen concentrations, utilising partial least square regression model, was lower for the infested compared to the healthy trees. We show that early stage of infestation reduces not only foliar biochemical content but also their retrieval accuracy. Our results further indicate that remote sensing measurements can be successfully used for the early detection of the bark beetle infestation. We demonstrated that bark beetle infestation at the green attack stage effects leaf spectral response as well as leaf biochemical properties and their retrievals from hyperspectral measurements.

Guiding Neuronal Growth in Tissues with Light

DTIC Science & Technology

2010-02-27

and structural properties of their surroundings in addition to the biochemical properties. Furthermore, three-dimensional biopolymer matrices provide...Properties of Biopolymer Networks Biopolymer networks exhibit unique nonlinear rheological behavior that differs dramatically from most synthetic...and presumably other biopolymers , is not well defined in variable gap geometries. These findings have broad implications for the interpretation of

Amino acid sequence of the smaller basic protein from rat brain myelin

PubMed Central

Dunkley, Peter R.; Carnegie, Patrick R.

1974-01-01

1. The complete amino acid sequence of the smaller basic protein from rat brain myelin was determined. This protein differs from myelin basic proteins of other species in having a deletion of a polypeptide of 40 amino acid residues from the centre of the molecule. 2. A detailed comparison is made of the constant and variable regions in a group of myelin basic proteins from six species. 3. An arginine residue in the rat protein was found to be partially methylated. The ratio of methylated to unmethylated arginine at this position differed from that found for the human basic protein. 4. Three tryptic peptides were isolated in more than one form. The differences between the two forms of each peptide are discussed in relation to the electrophoretic heterogeneity of myelin basic proteins, which is known to occur at alkaline pH values. 5. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50029 at the British Library (Lending Division) (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1973) 131, 5. PMID:4141893

Molecular design, synthesis and physical properties of novel Cytisine-derivatives - Experimental and theoretical study

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka; Spiteller, Michael

2013-02-01

The paper presented a comprehensive theoretical and experimental study on the molecular drugs-design, synthesis, isolation, physical spectroscopic and mass spectrometric elucidation of novel functionalization derivatives of Cytisine (Cyt), using nucleosidic residues. Since these alkaloids have established biochemical profile, related the binding affinity of the nicotinic acetylcholine receptors (nAChRs), particularly α7 sub-type, the presented correlation between the molecular structure and properties allowed to evaluated the highlights of the biochemical hypothesises related the Schizophrenia. The anticancer activity of α7 subtype agonists and the crucial role of the nucleoside-based medications in the cancer therapy provided opportunity for further study on the biochemical relationship between Schizophrenia and few kinds of cancers, which has been hypothesized recently. The physical electronic absorptions (EAs), circular dichroic (CD) and Raman spectroscopic (RS) properties as well as mass spectrometric (MS) data, obtained using electrospray ionization (ESI) and atmospheric-pressure chemical ionization (APCI) methods under the positive single (MS) and tandem (MS/MS) modes of operation are discussed. Taking into account reports on a fatal intoxication of Cyt, the presented data would be of interest in the field of forensic chemistry, through development of highly selective and sensitive analytical protocols. Quantum chemical method is used to predict the physical properties of the isolated alkaloids, their affinity to the receptor loop and gas-phase stabilized species, observed mass spectrometrically.

Effective constitutive relations for large repetitive frame-like structures

NASA Technical Reports Server (NTRS)

Nayfeh, A. H.; Hefzy, M. S.

1981-01-01

Effective mechanical properties for large repetitive framelike structures are derived using combinations of strength of material and orthogonal transformation techniques. Symmetry considerations are used in order to identify independent property constants. The actual values of these constants are constructed according to a building block format which is carried out in the three consecutive steps: (1) all basic planar lattices are identified; (2) effective continuum properties are derived for each of these planar basic grids using matrix structural analysis methods; and (3) orthogonal transformations are used to determine the contribution of each basic set to the overall effective continuum properties of the structure.

Interannual Variations in Ecosystem Oxidative Ratio in Croplands, Deciduous Forest, Coniferous Forest, and Early Successional Forest Ecosystems

NASA Astrophysics Data System (ADS)

Masiello, C. A.; Hockaday, W. C.; Gallagher, M. E.; Calligan, L.

2009-12-01

Ecosystem net primary productivity (NPP) can vary significantly with annual variations in precipitation and temperature. These climate variations can also drive changes in plant carbon allocation patterns. Shifting allocation patterns can lead to variation in net ecosystem biochemical stocks (e.g. kg cellulose, lignin, protein, and lipid/ha), which can in turn lead to shifts in ecosystem oxidative ratio (OR). OR is the molar ratio of O2 released : CO2 fixed during biosynthesis. Major plant biochemicals vary substantially in oxidative ratio, ranging from average organic acid OR values of 0.75 to average lipid OR values of 1.37 (Masiello et al., 2008). OR is a basic property of ecosystem biochemistry, and is also an essential variable needed to constrain the size of the terrestrial biospheric carbon sink (Keeling et al., 1996). OR is commonly assumed to be 1.10 (e.g. Prentice et al., 2001), but small variations in net ecosystem OR can drive large errors in estimates of the size of the terrestrial carbon sink (Randerson et al., 2006). We hypothesized that interannual changes in climate may drive interannual variation in ecosystem OR values. Working at Kellogg Biological Station NSF LTER, we measured the annual average OR of coniferous and deciduous forests, an early successional forest, and croplands under both corn and soy. There are clear distinctions between individual ecosystems (e.g., the soy crops have a higher OR than the corn crops, and the coniferous forests have a higher OR than the deciduous forests), but the ecosystems themselves retained remarkably constant annual OR values between 1998 and 2008.

The X-Ray Crystal Structure of the Keratin 1-Keratin 10 Helix 2B Heterodimer Reveals Molecular Surface Properties and Biochemical Insights into Human Skin Disease

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

Bunick, Christopher G.; Milstone, Leonard M.

Keratins 1 (K1) and 10 (K10) are the primary keratins expressed in differentiated epidermis. Mutations in K1/K10 are associated with human skin diseases. We determined the crystal structure of the complex between the distal (2B) helices of K1 and K10 to better understand how human keratin structure correlates with function. The 3.3 Å resolution structure confirms many features inferred by previous biochemical analyses, but adds unexpected insights. It demonstrates a parallel, coiled-coil heterodimer with a predominantly hydrophobic intermolecular interface; this heterodimer formed a higher order complex with a second K1-K10-2B heterodimer via a Cys401K10 disulfide link, although the bond anglemore » is unanticipated. The molecular surface analysis of K1-K10-2B identified several pockets, one adjacent to the disulfide linkage and conserved in K5-K14. The solvent accessible surface area of the K1-K10 structure is 20–25% hydrophobic. The 2B region contains mixed acidic and basic patches proximally (N-terminal), whereas it is largely acidic distally (C-terminal). Mapping of conserved and nonconserved residues between K1-K10 and K5-K14 onto the structure demonstrated the majority of unique residues align along the outer helical ridge. Finally, the structure permitted a fresh analysis of the deleterious effects caused by K1/K10 missense mutations found in patients with phenotypic skin disease.« less

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

PubMed

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

2015-06-01

To analyze chondral flaps debrided during hip arthroscopy to determine their biochemical and cellular composition. Thirty-one full-thickness acetabular chondral flaps were collected during hip arthroscopy. Biochemical analysis was undertaken in 21 flaps from 20 patients, and cellular viability was determined in 10 flaps from 10 patients. Biochemical analysis included concentrations of (1) DNA (an indicator of chondrocyte content), (2) hydroxyproline (an indicator of collagen content), and (3) glycosaminoglycan (an indicator of chondrocyte biosynthesis). Higher values for these parameters indicated more healthy tissue. The flaps were examined to determine the percentage of viable chondrocytes. The percentage of acetabular chondral flap specimens that had concentrations within 1 SD of the mean values reported in previous normal cartilage studies was 38% for DNA, 0% for glycosaminoglycan, and 43% for hydroxyproline. The average cellular viability of our acetabular chondral flap specimens was 39% (SD, 14%). Only 2 of the 10 specimens had more than half the cells still viable. There was no correlation between (1) the gross examination of the joint or knowledge of the patient's demographic characteristics and symptoms and (2) biochemical properties and cell viability of the flap, with one exception: a degenerative appearance of the surrounding cartilage correlated with a higher hydroxyproline concentration. Although full-thickness acetabular chondral flaps can appear normal grossly, the biochemical properties and percentage of live chondrocytes in full-thickness chondral flaps encountered in hip arthroscopy show that this tissue is not normal. There has been recent interest in repairing chondral flaps encountered during hip arthroscopy. These data suggest that acetabular chondral flaps are not biochemically and cellularly normal. Although these flaps may still be valuable mechanically and/or as a scaffold in some conductive or inductive capacity, further study is required to assess the clinical benefit of repair. Copyright © 2015 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Conditions for duality between fluxes and concentrations in biochemical networks

PubMed Central

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

2016-01-01

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

Conditions for duality between fluxes and concentrations in biochemical networks

DOE PAGES

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

2016-06-23

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

Conditions for duality between fluxes and concentrations in biochemical networks

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

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

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

41 CFR 102-77.10 - What basic Art-in-Architecture policy governs Federal agencies?

Code of Federal Regulations, 2011 CFR

2011-01-01

... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 false What basic Art-in... PROPERTY 77-ART-IN-ARCHITECTURE General Provisions § 102-77.10 What basic Art-in-Architecture policy governs Federal agencies? Federal agencies must incorporate fine arts as an integral part of the total...

41 CFR 102-77.10 - What basic Art-in-Architecture policy governs Federal agencies?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What basic Art-in... PROPERTY 77-ART-IN-ARCHITECTURE General Provisions § 102-77.10 What basic Art-in-Architecture policy governs Federal agencies? Federal agencies must incorporate fine arts as an integral part of the total...

41 CFR 102-76.10 - What basic design and construction policy governs Federal agencies?

Code of Federal Regulations, 2011 CFR

2011-01-01

... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 false What basic design and construction policy governs Federal agencies? 102-76.10 Section 102-76.10 Public Contracts and Property Management Federal Property Management Regulations System (Continued) FEDERAL MANAGEMENT REGULATION REAL...

Prospect redux

NASA Technical Reports Server (NTRS)

Jacquemoud, S.; Ustin, S. L.; Verdebout, J.; Schmuck, G.; Andreoli, G.; Hosgood, B.

1995-01-01

The remote estimation of leaf biochemical content from spaceborne platforms has been the subject of many studies aimed at better understanding of terrestrial ecosystem functioning. The major ecological processes involved in exchange of matter and energy, like photosynthesis, primary production, evaportranspiration, respiration, and decomposition can be related to plant properties e.g., chlorophyll, water, protein, cellulose and lignin contents. As leaves represent the most important plant surfaces interacting with solar energy, a top priority has been to relate optical properties to biochemical constituents. Two different approaches have been considered: first, statistical correlations between the leaf reflectance (or transmittance) and biochemical content, and second, physically based models of leaf scattering and absorption developed using the laws of optics. Recently reviewed by Verdebout et al., the development of models of leaf optical properties has resulted in better understanding of the interaction of light with plant leaves. Present radiative transfer models mainly use chlorophyll and/or water contents as input parameters to calculate leaf reflectance. Inversion of these models allows to retrieve these constituents from spectrophotometric measurements. Conel et al. recently proposed a two-stream Kubelka-Munk model to analyze the influence of protein, cellulose, lignin, and starch on leaf reflectance, but in fact, the estimation of leaf biochemistry from remote sensing is still an open question. In order to clarify it, a laboratory experiment associating visible/infrared spectra of plan leaves both with physical measurements and biochemical analyses was conducted at the Joint Research Center during the summer of 1993. This unique data set has been used to upgrade the PROSPECT model, by including leaf biochemistry.

Biochemical Characterization of Prions.

PubMed

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

2017-01-01

Prion disease or transmissible spongiform encephalopathies are characterized by the presence of the abnormal form of the prion protein (PrP Sc ). The pathological and transmissible properties of PrP Sc are enciphered in its secondary and tertiary structures. Since it's well established that different strains of prions are linked to different conformations of PrP Sc , biochemical characterization of prions seems a preliminary but reliable approach to detect, analyze, and compare prion strains. Experimental biochemical procedures might be helpful in distinguishing PrP Sc physicochemical properties and include resistance to proteinase K (PK) digestion, insolubility in nonionic detergents, PK-resistance under denaturing conditions and sedimentation properties in sucrose gradients. This biochemical approach has been extensively applied in human prion disorders and subsequently expanded for PrP Sc characterization in animals. In particular, in sporadic Creutzfedlt-Jakob disease (sCJD) PrP Sc is characterized by two main glycotypes conventionally named Type 1 and Type 2, based on the apparent gel migration at 21 and 19kDa of the PrP Sc PK-resistant fragment. An additional PrP Sc type was identified in sCJD characterized by an unglycosylated dominant glycoform pattern and in 2010 a variably protease-sensitive prionopathy (VPSPr) was reported showing a PrP Sc with an electrophoretic ladder like pattern. Additionally, the presence of PrP Sc truncated fragments completes the electrophoretic characterization of different prion strains. By two-dimensional (2D) electrophoretic analysis additional PrP Sc pattern was identified, since this procedure provides information about the isoelectric point and the different peptides length related to PK cleavage, as well as to glycosylation extent or GPI anchor presence. We here provide and extensive review on PrP Sc biochemical analysis in human and animal prion disorders. Further, we show that PrP Sc glycotypes observed in CJD share similarities with PrP Sc in bovine spongiform encephalopathy forms (BSE). © 2017 Elsevier Inc. All rights reserved.

Procurement specifications report. IMBLS phase B-4

NASA Technical Reports Server (NTRS)

1970-01-01

Procurement specifications to provide vendors of space systems with supporting information to accurately price the selected major buy items are illustrated. In performing this task, rigid constraints on specifications and drawing details are avoided beyond those necessary to define basic requirements. Described are digital processing equipment, mass spectrometer, body mass measuring device, sensors, bio-belt power source, vision tester and instrumentation for a biochemical station.

Enzymes: principles and biotechnological applications

PubMed Central

Robinson, Peter K.

2015-01-01

Enzymes are biological catalysts (also known as biocatalysts) that speed up biochemical reactions in living organisms, and which can be extracted from cells and then used to catalyse a wide range of commercially important processes. This chapter covers the basic principles of enzymology, such as classification, structure, kinetics and inhibition, and also provides an overview of industrial applications. In addition, techniques for the purification of enzymes are discussed. PMID:26504249

Fundamentals of microfluidic cell culture in controlled microenvironments†

PubMed Central

Young, Edmond W. K.; Beebe, David J.

2010-01-01

Microfluidics has the potential to revolutionize the way we approach cell biology research. The dimensions of microfluidic channels are well suited to the physical scale of biological cells, and the many advantages of microfluidics make it an attractive platform for new techniques in biology. One of the key benefits of microfluidics for basic biology is the ability to control parameters of the cell microenvironment at relevant length and time scales. Considerable progress has been made in the design and use of novel microfluidic devices for culturing cells and for subsequent treatment and analysis. With the recent pace of scientific discovery, it is becoming increasingly important to evaluate existing tools and techniques, and to synthesize fundamental concepts that would further improve the efficiency of biological research at the microscale. This tutorial review integrates fundamental principles from cell biology and local microenvironments with cell culture techniques and concepts in microfluidics. Culturing cells in microscale environments requires knowledge of multiple disciplines including physics, biochemistry, and engineering. We discuss basic concepts related to the physical and biochemical microenvironments of the cell, physicochemical properties of that microenvironment, cell culture techniques, and practical knowledge of microfluidic device design and operation. We also discuss the most recent advances in microfluidic cell culture and their implications on the future of the field. The goal is to guide new and interested researchers to the important areas and challenges facing the scientific community as we strive toward full integration of microfluidics with biology. PMID:20179823

Expanding pH screening space using multiple droplets with secondary buffers for protein crystallization

NASA Astrophysics Data System (ADS)

Zhang, Chen-Yan; Dong, Chen; Lu, Xiao-Li; Wang, Bei; He, Tian-Yuan; Yang, Rui-Zeng; Lin, Hua-Long; Yang, Xue-Zhou; Yin, Da-Chuan

2017-04-01

We have proposed a rational strategy for selecting a suitable pH of protein solution based on protein biochemical properties. However, it is difficult to use this strategy for biochemical properties unknown proteins. In this paper, a simpler and faster pH buffer strategy was proposed. An additional pH-controlling buffer was added to crystallization droplet mixed with protein solution and commercial crystallization reagents to adjust its pH. The results revealed that protein crystallization success rates were enhanced by this strategy due to expansion of the pH screening space, which was closely related with protein solubility. Thus, the possibility of reaching supersaturation was increased by using this strategy.

The structure and function of the pericellular matrix of articular cartilage.

PubMed

Wilusz, Rebecca E; Sanchez-Adams, Johannah; Guilak, Farshid

2014-10-01

Chondrocytes in articular cartilage are surrounded by a narrow pericellular matrix (PCM) that is both biochemically and biomechanically distinct from the extracellular matrix (ECM) of the tissue. While the PCM was first observed nearly a century ago, its role is still under investigation. In support of early hypotheses regarding its function, increasing evidence indicates that the PCM serves as a transducer of biochemical and biomechanical signals to the chondrocyte. Work over the past two decades has established that the PCM in adult tissue is defined biochemically by several molecular components, including type VI collagen and perlecan. On the other hand, the biomechanical properties of this structure have only recently been measured. Techniques such as micropipette aspiration, in situ imaging, computational modeling, and atomic force microscopy have determined that the PCM exhibits distinct mechanical properties as compared to the ECM, and that these properties are influenced by specific PCM components as well as disease state. Importantly, the unique relationships among the mechanical properties of the chondrocyte, PCM, and ECM in different zones of cartilage suggest that this region significantly influences the stress-strain environment of the chondrocyte. In this review, we discuss recent advances in the measurement of PCM mechanical properties and structure that further increase our understanding of PCM function. Taken together, these studies suggest that the PCM plays a critical role in controlling the mechanical environment and mechanobiology of cells in cartilage and other cartilaginous tissues, such as the meniscus or intervertebral disc. Copyright © 2014 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties

PubMed Central

2011-01-01

Background Existing methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical properties and determination of their corresponding feature vectors rely mainly on known properties of binding mechanism and experience of designers. However, there exists a troublesome problem for designers that some different physicochemical properties have similar vectors of representing 20 amino acids and some closely related physicochemical properties have dissimilar vectors. Results This study proposes a systematic approach (named Auto-IDPCPs) to automatically identify a set of physicochemical and biochemical properties in the AAindex database to design SVM-based classifiers for predicting and analyzing DNA-binding domains/proteins. Auto-IDPCPs consists of 1) clustering 531 amino acid indices in AAindex into 20 clusters using a fuzzy c-means algorithm, 2) utilizing an efficient genetic algorithm based optimization method IBCGA to select an informative feature set of size m to represent sequences, and 3) analyzing the selected features to identify related physicochemical properties which may affect the binding mechanism of DNA-binding domains/proteins. The proposed Auto-IDPCPs identified m=22 features of properties belonging to five clusters for predicting DNA-binding domains with a five-fold cross-validation accuracy of 87.12%, which is promising compared with the accuracy of 86.62% of the existing method PSSM-400. For predicting DNA-binding sequences, the accuracy of 75.50% was obtained using m=28 features, where PSSM-400 has an accuracy of 74.22%. Auto-IDPCPs and PSSM-400 have accuracies of 80.73% and 82.81%, respectively, applied to an independent test data set of DNA-binding domains. Some typical physicochemical properties discovered are hydrophobicity, secondary structure, charge, solvent accessibility, polarity, flexibility, normalized Van Der Waals volume, pK (pK-C, pK-N, pK-COOH and pK-a(RCOOH)), etc. Conclusions The proposed approach Auto-IDPCPs would help designers to investigate informative physicochemical and biochemical properties by considering both prediction accuracy and analysis of binding mechanism simultaneously. The approach Auto-IDPCPs can be also applicable to predict and analyze other protein functions from sequences. PMID:21342579

Biochemical and functional characterization of an albumin protein belonging to the hemopexin superfamily from Lens culinaris seeds.

PubMed

Scarafoni, Alessio; Gualtieri, Elisa; Barbiroli, Alberto; Carpen, Aristodemo; Negri, Armando; Duranti, Marcello

2011-09-14

The present paper reports the purification and biochemical characterization of an albumin identified in mature lentil seeds with high sequence similarity to pea PA2. These proteins are found in many edible seeds and are considered potentially detrimental for human health due to the potential allergenicity and lectin-like activity. Thus, the description of their possible presence in food and the assessment of the molecular properties are relevant. The M(r), pI, and N-terminal sequence of this protein have been determined. The work included the study of (i) the binding properties to hemine to assess the presence of hemopexin structural domains and (ii) the binding properties of the protein to thiamin. In addition, the structural changes induced by heating have been evaluated by means of spectroscopic techniques. Denaturation temperature has also been determined. The present work provides new insights about the structural molecular features and the ligand-binding properties and dynamics of this kind of seed albumin.

Estimation of nutrients and organic matter in Korean swine slurry using multiple regression analysis of physical and chemical properties.

PubMed

Suresh, Arumuganainar; Choi, Hong Lim

2011-10-01

Swine waste land application has increased due to organic fertilization, but excess application in an arable system can cause environmental risk. Therefore, in situ characterizations of such resources are important prior to application. To explore this, 41 swine slurry samples were collected from Korea, and wide differences were observed in the physico-biochemical properties. However, significant (P<0.001) multiple property correlations (R²) were obtained between nutrients with specific gravity (SG), electrical conductivity (EC), total solids (TS) and pH. The different combinations of hydrometer, EC meter, drying oven and pH meter were found useful to estimate Mn, Fe, Ca, K, Al, Na, N and 5-day biochemical oxygen demands (BOD₅) at improved R² values of 0.83, 0.82, 0.77, 0.75, 0.67, 0.47, 0.88 and 0.70, respectively. The results from this study suggest that multiple property regressions can facilitate the prediction of micronutrients and organic matter much better than a single property regression for livestock waste. Copyright © 2011 Elsevier Ltd. All rights reserved.

QM/MM Molecular Dynamics Studies of Metal Binding Proteins

PubMed Central

Vidossich, Pietro; Magistrato, Alessandra

2014-01-01

Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu) and main group (Mg) metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions. PMID:25006697

Conformational Switching of a Foldamer in a Multicomponent System by pH-Filtered Selection between Competing Noncovalent Interactions

PubMed Central

2015-01-01

Biomolecular systems are able to respond to their chemical environment through reversible, selective, noncovalent intermolecular interactions. Typically, these interactions induce conformational changes that initiate a signaling cascade, allowing the regulation of biochemical pathways. In this work, we describe an artificial molecular system that mimics this ability to translate selective noncovalent interactions into reversible conformational changes. An achiral but helical foldamer carrying a basic binding site interacts selectively with the most acidic member of a suite of chiral ligands. As a consequence of this noncovalent interaction, a global absolute screw sense preference, detectable by 13C NMR, is induced in the foldamer. Addition of base, or acid, to the mixture of ligands competitively modulates their interaction with the binding site, and reversibly switches the foldamer chain between its left and right-handed conformations. As a result, the foldamer–ligand mixture behaves as a biomimetic chemical system with emergent properties, functioning as a “proton-counting” molecular device capable of providing a tunable, pH-dependent conformational response to its environment. PMID:25915163

Structural basis for membrane targeting by the MVB12-associated [beta]-prism domain of the human ESCRT-I MVB12 subunit

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

Boura, Evzen; Hurley, James H.

2012-03-15

MVB12-associated {beta}-prism (MABP) domains are predicted to occur in a diverse set of membrane-associated bacterial and eukaryotic proteins, but their existence, structure, and biochemical properties have not been characterized experimentally. Here, we find that the MABP domains of the MVB12A and B subunits of ESCRT-I are functional modules that bind in vitro to liposomes containing acidic lipids depending on negative charge density. The MABP domain is capable of autonomously localizing to subcellular puncta and to the plasma membrane. The 1.3-{angstrom} atomic resolution crystal structure of the MVB12B MABP domain reveals a {beta}-prism fold, a hydrophobic membrane-anchoring loop, and an electropositivemore » phosphoinositide-binding patch. The basic patch is open, which explains how it senses negative charge density but lacks stereoselectivity. These observations show how ESCRT-I could act as a coincidence detector for acidic phospholipids and protein ligands, enabling it to function both in protein transport at endosomes and in cytokinesis and viral budding at the plasma membrane.« less

Biochemical Engineering Approaches for Increasing Viability and Functionality of Probiotic Bacteria

PubMed Central

Nguyen, Huu-Thanh; Truong, Dieu-Hien; Kouhoundé, Sonagnon; Ly, Sokny; Razafindralambo, Hary; Delvigne, Frank

2016-01-01

The literature presents a growing body of evidence demonstrating the positive effect of probiotics on health. Probiotic consumption levels are rising quickly in the world despite the fluctuation of their viability and functionality. Technological methods aiming at improving probiotic characteristics are thus highly wanted. However, microbial metabolic engineering toolbox is not available for this kind of application. On the other hand, basic microbiology teaches us that bacteria are able to exhibit adaptation to external stresses. It is known that adequately applied sub-lethal stress, i.e., controlled in amplitude and frequency at a given stage of the culture, is able to enhance microbial robustness. This property could be potentially used to improve the viability of probiotic bacteria, but some technical challenges still need to be overcome before any industrial implementation. This review paper investigates the different technical tools that can be used in order to define the proper condition for improving viability of probiotic bacteria and their implementation at the industrial scale. Based on the example of Bifidobacterium bifidum, potentialities for simultaneously improving viability, but also functionality of probiotics will be described. PMID:27271598

Multifunctional roles of leader protein of foot-and-mouth disease viruses in suppressing host antiviral responses.

PubMed

Liu, Yingqi; Zhu, Zixiang; Zhang, Miaotao; Zheng, Haixue

2015-10-28

Foot-and-mouth disease virus (FMDV) leader protein (L(pro)) is a papain-like proteinase, which plays an important role in FMDV pathogenesis. L(pro) exists as two forms, Lab and Lb, due to translation being initiated from two different start codons separated by 84 nucleotides. L(pro) self-cleaves from the nascent viral polyprotein precursor as the first mature viral protein. In addition to its role as a viral proteinase, L(pro) also has the ability to antagonize host antiviral effects. To promote FMDV replication, L(pro) can suppress host antiviral responses by three different mechanisms: (1) cleavage of eukaryotic translation initiation factor 4 γ (eIF4G) to shut off host protein synthesis; (2) inhibition of host innate immune responses through restriction of interferon-α/β production; and (3) L(pro) can also act as a deubiquitinase and catalyze deubiquitination of innate immune signaling molecules. In the light of recent functional and biochemical findings regarding L(pro), this review introduces the basic properties of L(pro) and the mechanisms by which it antagonizes host antiviral responses.

Epigenetic Biomarkers and Cardiovascular Disease: Circulating MicroRNAs.

PubMed

de Gonzalo-Calvo, David; Iglesias-Gutiérrez, Eduardo; Llorente-Cortés, Vicenta

2017-09-01

MicroRNAs (miRNAs) are a class of small noncoding RNA (20-25 nucleotides) involved in gene regulation. In recent years, miRNAs have emerged as a key epigenetic mechanism in the development and physiology of the cardiovascular system. These molecular species regulate basic functions in virtually all cell types, and are therefore directly associated with the pathophysiology of a large number of cardiovascular diseases. Since their relatively recent discovery in extracellular fluids, miRNAs have been studied as potential biomarkers of disease. A wide array of studies have proposed miRNAs as circulating biomarkers of different cardiovascular pathologies (eg, myocardial infarction, coronary heart disease, and heart failure, among others), which may have superior physicochemical and biochemical properties than the conventional protein indicators currently used in clinical practice. In the present review, we provide a brief introduction to the field of miRNAs, paying special attention to their potential clinical application. This includes their possible role as new diagnostic or prognostic biomarkers in cardiovascular disease. Copyright © 2017 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

A PP2A-B55 recognition signal controls substrate dephosphorylation kinetics during mitotic exit

PubMed Central

Cundell, Michael J.; Holder, James

2016-01-01

PP2A-B55 is one of the major phosphatases regulating cell division. Despite its importance for temporal control during mitotic exit, how B55 substrates are recognized and differentially dephosphorylated is unclear. Using phosphoproteomics combined with kinetic modeling to extract B55-dependent rate constants, we have systematically identified B55 substrates and assigned their temporal order in mitotic exit. These substrates share a bipartite polybasic recognition determinant (BPR) flanking a Cdk1 phosphorylation site. Experiments and modeling show that dephosphorylation rate is encoded into B55 substrates, including its inhibitor ENSA, by cooperative action of basic residues within the BPR. A complementary acidic surface on B55 decodes this signal, supporting a cooperative electrostatic mechanism for substrate selection. A further level of specificity is encoded into B55 substrates because B55 displays selectivity for phosphothreonine. These simple biochemical properties, combined with feedback control of B55 activity by the phosphoserine-containing substrate/inhibitor ENSA, can help explain the temporal sequence of events during exit from mitosis. PMID:27551054

Adaptation in Living Systems

NASA Astrophysics Data System (ADS)

Tu, Yuhai; Rappel, Wouter-Jan

2018-03-01

Adaptation refers to the biological phenomenon where living systems change their internal states in response to changes in their environments in order to maintain certain key functions critical for their survival and fitness. Adaptation is one of the most ubiquitous and arguably one of the most fundamental properties of living systems. It occurs throughout all biological scales, from adaptation of populations of species over evolutionary time to adaptation of a single cell to different environmental stresses during its life span. In this article, we review some of the recent progress made in understanding molecular mechanisms of cellular-level adaptation. We take the minimalist (or the physicist) approach and study the simplest systems that exhibit generic adaptive behaviors, namely chemotaxis in bacterium cells (Escherichia coli) and eukaryotic cells (Dictyostelium). We focus on understanding the basic biochemical interaction networks that are responsible for adaptation dynamics. By combining theoretical modeling with quantitative experimentation, we demonstrate universal features in adaptation as well as important differences in different cellular systems. Future work in extending the modeling framework to study adaptation in more complex systems such as sensory neurons is also discussed.

Marine actinobacteria as a drug treasure house.

PubMed

Hassan, Syed Shams Ul; Shaikh, Abdul Lateef

2017-03-01

Marine actinobacteria have been considered as a gold mine with respect to great potential regarding their secondary metabolites. Most of the researches have been conducted on actinobacteria's derived secondary metabolites to examine its pharmacological properties. Actinobacteria have a potential to provide future drugs against crucial diseases, such as drug-resistance bacteria, cancer, a range of viral illnesses, malaria, several infections and inflammations. Although, the mode of action of many bio molecules are still untapped, for a tangible number of compounds by which they interfere with human pathogenesis are reported here with detailed diagrammed illustrations. This knowledge is one of the basic vehicles to be known especially for transforming bio medicinal molecules to medicines. Actinobacteria produce a different kind of biochemical substances with numerous carbon skeletons, which have been found to be the main component interfering with human pathogenesis at different sites. Different diseases have the capability to fight at different sites inside the body can lead to a new wave of increasing the chances to produce targeted medicines. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Basic Soils. Revision.

ERIC Educational Resources Information Center

Montana State Univ., Bozeman. Dept. of Agricultural and Industrial Education.

This curriculum guide is designed for use in teaching a course in basic soils that is intended for college freshmen. Addressed in the individual lessons of the unit are the following topics: the way in which soil is formed, the physical properties of soil, the chemical properties of soil, the biotic properties of soil, plant-soil-water…

41 CFR 102-78.10 - What basic historic preservation policy governs Federal agencies?

Code of Federal Regulations, 2014 CFR

2014-01-01

... governs Federal agencies? To protect, enhance and preserve historic and cultural property under their... 41 Public Contracts and Property Management 3 2014-01-01 2014-01-01 false What basic historic preservation policy governs Federal agencies? 102-78.10 Section 102-78.10 Public Contracts and Property...

Microendophenotypes of psychiatric disorders: phenotypes of psychiatric disorders at the level of molecular dynamics, synapses, neurons, and neural circuits.

PubMed

Kida, S; Kato, T

2015-01-01

Psychiatric disorders are caused not only by genetic factors but also by complicated factors such as environmental ones. Moreover, environmental factors are rarely quantitated as biological and biochemical indicators, making it extremely difficult to understand the pathological conditions of psychiatric disorders as well as their underlying pathogenic mechanisms. Additionally, we have actually no other option but to perform biological studies on postmortem human brains that display features of psychiatric disorders, thereby resulting in a lack of experimental materials to characterize the basic biology of these disorders. From these backgrounds, animal, tissue, or cell models that can be used in basic research are indispensable to understand biologically the pathogenic mechanisms of psychiatric disorders. In this review, we discuss the importance of microendophenotypes of psychiatric disorders, i.e., phenotypes at the level of molecular dynamics, neurons, synapses, and neural circuits, as targets of basic research on these disorders.

Physical Chemistry of Bile: Detailed Pathogenesis of Cholelithiasis.

PubMed

Itani, Malak; Dubinsky, Theodore J

2017-09-01

Despite the overwhelming prevalence of cholelithiasis, many health care professionals are not familiar with the basic pathophysiology of gallstone formation. This article provides an overview of the biochemical pathways related to bile, with a focus on the physical chemistry of bile. We describe the important factors in bile synthesis and secretion that affect the composition of bile and consequently its liquid state. Within this biochemical background lies the foundation for understanding the clinical and sonographic manifestation of cholelithiasis, including the pathophysiology of cholesterol crystallization, gallbladder sludge, and gallstones. There is a brief discussion of the clinical manifestations of inflammatory and obstructive cholestasis and the impact on bile metabolism and subsequently on liver function tests. Despite being the key modality in diagnosing cholelithiasis, ultrasound has a limited role in the characterization of stone composition.

A study of the competency of third year medical students to interpret biochemically based clinical scenarios using knowledge and skills gained in year 1 and 2.

PubMed

Gowda, Veena Bhaskar S; Nagaiah, Bhaskar Hebbani; Sengodan, Bharathi

2016-01-01

Medical students build clinical knowledge on the grounds of previously obtained basic knowledge. The study aimed to evaluate the competency of third year medical students to interpret biochemically based clinical scenarios using knowledge and skills gained during year 1 and 2 of undergraduate medical training. Study was conducted on year 3 MBBS students at AIMST University, Malaysia. Clinical scenarios (25) were constructed and administered to student volunteers, making sure at least one question from each system of year 2 was represented. Feedback was obtained on a five-point Likert scale regarding perception of learning biochemistry in MBBS year 1 versus 2. Mean score of test was 18 (72.11%). Performance was comparatively better in questions related to topics learnt in year 1 and reinforced in year 2 compared to those learnt for first time in year 2. In the feedback obtained, 31% strongly agreed and 56% agreed understanding the subject was helped more by learning biochemistry in year 2 than in year 1. Likewise, 36% strongly agreed and 56% agreed appreciating the importance of biochemistry in patient diagnosis was helped more by learning biochemistry in year 2 than year 1. Thirty one percent strongly agreed and 54% agreed that year 1 biochemistry would have been more relevant if case discussions were done simultaneously. Students retain basic science subjects better and appreciate the importance of basic sciences in patient diagnosis if they are reinforced in the context of clinical situations. © 2016 The International Union of Biochemistry and Molecular Biology.

Characterization of Degenerative Changes in the Temporomandibular Joint of the Bengal Tiger (Panthera tigris tigris) and Siberian Tiger (Panthera tigris altaica)

PubMed Central

Murphy, M. K.; Arzi, B.; Vapniarsky-Arzi, N.; Athanasiou, K. A.

2013-01-01

Summary The articulation of the temporomandibular joint (TMJ) is composed of the temporal bone dorsally, the mandibular condyle ventrally and a fibrous articular disc. The TMJ disc plays an essential role in distributing load between the two articular surfaces. Degeneration of the disc in the presence of joint pathology has been shown in man; however, TMJ pathology has not been documented previously in tigers (Panthera tigris). The mandibular condyle and TMJ disc of a Bengal tiger (P. tigris tigris) and a Siberian tiger (P. tigris altaica) were evaluated grossly and the TMJ disc was characterized biochemically and mechanically. Characterization of the TMJ disc verified region- and direction-dependent biochemical and mechanical properties, reflective of the functional demands on the joint. Degenerative joint disease was observed in both cases and this was more severe in the Siberian tiger. Simultaneous evaluation of joint pathology, biochemical composition and mechanical properties of the TMJ disc revealed a loss in functional properties (tensile anisotropy) of the disc as joint pathology advanced from moderate to severe. TMJ degeneration may compromise the ability of the animal to eat and thrive and may be a factor contributing to the endangered status of these species. PMID:23809909

Towards Understanding Plant Calcium Signaling through Calmodulin-Like Proteins: A Biochemical and Structural Perspective.

PubMed

La Verde, Valentina; Dominici, Paola; Astegno, Alessandra

2018-04-30

Ca 2+ ions play a key role in a wide variety of environmental responses and developmental processes in plants, and several protein families with Ca 2+ -binding domains have evolved to meet these needs, including calmodulin (CaM) and calmodulin-like proteins (CMLs). These proteins have no catalytic activity, but rather act as sensor relays that regulate downstream targets. While CaM is well-studied, CMLs remain poorly characterized at both the structural and functional levels, even if they are the largest class of Ca 2+ sensors in plants. The major structural theme in CMLs consists of EF-hands, and variations in these domains are predicted to significantly contribute to the functional versatility of CMLs. Herein, we focus on recent advances in understanding the features of CMLs from biochemical and structural points of view. The analysis of the metal binding and structural properties of CMLs can provide valuable insight into how such a vast array of CML proteins can coexist, with no apparent functional redundancy, and how these proteins contribute to cellular signaling while maintaining properties that are distinct from CaM and other Ca 2+ sensors. An overview of the principal techniques used to study the biochemical properties of these interesting Ca 2+ sensors is also presented.

Characterization of degenerative changes in the temporomandibular joint of the bengal tiger (Panthera tigris tigris) and siberian tiger (Panthera tigris altaica).

PubMed

Murphy, M K; Arzi, B; Vapniarsky-Arzi, N; Athanasiou, K A

2013-11-01

The articulation of the temporomandibular joint (TMJ) is composed of the temporal bone dorsally, the mandibular condyle ventrally and a fibrous articular disc. The TMJ disc plays an essential role in distributing load between the two articular surfaces. Degeneration of the disc in the presence of joint pathology has been shown in man; however, TMJ pathology has not been documented previously in tigers (Panthera tigris). The mandibular condyle and TMJ disc of a Bengal tiger (P. tigris tigris) and a Siberian tiger (P. tigris altaica) were evaluated grossly and the TMJ disc was characterized biochemically and mechanically. Characterization of the TMJ disc verified region- and direction-dependent biochemical and mechanical properties, reflective of the functional demands on the joint. Degenerative joint disease was observed in both cases and this was more severe in the Siberian tiger. Simultaneous evaluation of joint pathology, biochemical composition and mechanical properties of the TMJ disc revealed a loss in functional properties (tensile anisotropy) of the disc as joint pathology advanced from moderate to severe. TMJ degeneration may compromise the ability of the animal to eat and thrive and may be a factor contributing to the endangered status of these species. Copyright © 2013 Elsevier Ltd. All rights reserved.

Requirement for serum in medium supplemented with insulin-transferrin-selenium for hydrodynamic cultivation of engineered cartilage.

PubMed

Yang, Yueh-Hsun; Barabino, Gilda A

2011-08-01

Achievement of viable engineered tissues through in vitro cultivation in bioreactor systems requires a thorough understanding of the complex interplay between hydrodynamic forces and biochemical cues such as serum. To this end, chondrocyte-seeded constructs were cultured under continuous fluid-induced shear forces with reduced serum content (0%-2%, v/v), which was partially or completely replaced by a potential substitute, insulin-transferrin-selenium, to minimize deleterious effects associated with the use of culture media containing high levels of serum (10%-20%). Low-serum cultures yielded constructs with similar biochemical properties to those cultivated with high-serum supplements, whereas the serum-free constructs exhibited poor cell proliferation, insufficient extracellular matrix production, and rapid degradation of and/or shear-induced damage to polyglycolic acid scaffolds. A fibrous outer capsule typically observed in hydrodynamic cultures and characterized by increased cell density and decreased (virtually none) glycosaminoglycan deposition was eliminated when serum concentration was equal to or <0.2% in the presence of hydrodynamic stimuli. Our findings suggest that serum is a requirement in insulin-transferrin-selenium-supplemented cultures in order for constructs to exhibit improved properties in response to hydrodynamic forces, and that mechanical and biochemical stimuli may synergistically modulate tissue properties and morphology through shear-responsive signals.

Actin dynamics, architecture, and mechanics in cell motility.

PubMed

Blanchoin, Laurent; Boujemaa-Paterski, Rajaa; Sykes, Cécile; Plastino, Julie

2014-01-01

Tight coupling between biochemical and mechanical properties of the actin cytoskeleton drives a large range of cellular processes including polarity establishment, morphogenesis, and motility. This is possible because actin filaments are semi-flexible polymers that, in conjunction with the molecular motor myosin, can act as biological active springs or "dashpots" (in laymen's terms, shock absorbers or fluidizers) able to exert or resist against force in a cellular environment. To modulate their mechanical properties, actin filaments can organize into a variety of architectures generating a diversity of cellular organizations including branched or crosslinked networks in the lamellipodium, parallel bundles in filopodia, and antiparallel structures in contractile fibers. In this review we describe the feedback loop between biochemical and mechanical properties of actin organization at the molecular level in vitro, then we integrate this knowledge into our current understanding of cellular actin organization and its physiological roles.

Archetypal tryptophan-rich antimicrobial peptides: properties and applications.

PubMed

Shagaghi, Nadin; Palombo, Enzo A; Clayton, Andrew H A; Bhave, Mrinal

2016-02-01

Drug-resistant microorganisms ('superbugs') present a serious challenge to the success of antimicrobial treatments. Subsequently, there is a crucial need for novel bio-control agents. Many antimicrobial peptides (AMPs) show a broad-spectrum activity against bacteria, fungi or viruses and are strong candidates to complement or substitute current antimicrobial agents. Some AMPs are also effective against protozoa or cancer cells. The tryptophan (Trp)-rich peptides (TRPs) are a subset of AMPs that display potent antimicrobial activity, credited to the unique biochemical properties of tryptophan that allow it to insert into biological membranes. Further, many Trp-rich AMPs cross bacterial membranes without compromising their integrity and act intracellularly, suggesting interactions with nucleic acids and enzymes. In this work, we overview some archetypal TRPs derived from natural sources, i.e., indolicidin, tritrpticin and lactoferricin, summarising their biochemical properties, structures, antimicrobial activities, mechanistic studies and potential applications.

Soil biochemical properties and microbial resilience in agroforestry systems: effects on wheat growth under controlled drought and flooding conditions.

PubMed

Rivest, David; Lorente, Miren; Olivier, Alain; Messier, Christian

2013-10-01

Agroforestry is increasingly viewed as an effective means of maintaining or even increasing crop and tree productivity under climate change while promoting other ecosystem functions and services. This study focused on soil biochemical properties and resilience following disturbance within agroforestry and conventional agricultural systems and aimed to determine whether soil differences in terms of these biochemical properties and resilience would subsequently affect crop productivity under extreme soil water conditions. Two research sites that had been established on agricultural land were selected for this study. The first site included an 18-year-old windbreak, while the second site consisted in an 8-year-old tree-based intercropping system. In each site, soil samples were used for the determination of soil nutrient availability, microbial dynamics and microbial resilience to different wetting-drying perturbations and for a greenhouse pot experiment with wheat. Drying and flooding were selected as water stress treatments and compared to a control. These treatments were initiated at the beginning of the wheat anthesis period and maintained over 10 days. Trees contributed to increase soil nutrient pools, as evidenced by the higher extractable-P (both sites), and the higher total N and mineralizable N (tree-based intercropping site) found in the agroforestry compared to the conventional agricultural system. Metabolic quotient (qCO2) was lower in the agroforestry than in the conventional agricultural system, suggesting higher microbial substrate use efficiency in agroforestry systems. Microbial resilience was higher in the agroforestry soils compared to soils from the conventional agricultural system (windbreak site only). At the windbreak site, wheat growing in soils from agroforestry system exhibited higher aboveground biomass and number of grains per spike than in conventional agricultural system soils in the three water stress treatments. At the tree-based intercropping site, higher wheat biomass, grain yield and number of grains per spike were observed in agroforestry than in conventional agricultural system soils, but in the drought treatment only. Drought (windbreak site) and flooding (both sites) treatments significantly reduced wheat yield and 1000-grain weight in both types of system. Relationships between soil biochemical properties and soil microbial resilience or wheat productivity were strongly dependent on site. This study suggests that agroforestry systems may have a positive effect on soil biochemical properties and microbial resilience, which could operate positively on crop productivity and tolerance to severe water stress. Copyright © 2013 Elsevier B.V. All rights reserved.

Helicases as molecular motors: An insight

NASA Astrophysics Data System (ADS)

Tuteja, Narendra; Tuteja, Renu

2006-12-01

Helicases are one of the smallest motors of biological system, which harness the chemical free energy of ATP hydrolysis to catalyze the opening of energetically stable duplex nucleic acids and thereby are involved in almost all aspect of nucleic acid metabolism including replication, repair, recombination, transcription, translation, and ribosome biogenesis. Basically, they break the hydrogen bonding between the duplex helix and translocate unidirectionally along the bound strand. Mostly all the helicases contain some conserved signature motifs, which act as an engine to power the unwinding. After the discovery of the first prokaryotic DNA helicase from Escherichia coli bacteria in 1976 and the first eukaryotic one from the lily plant in 1978, many more (>100) have been isolated. All the helicases share some common properties, including nucleic acid binding, NTP hydrolysis and unwinding of the duplex. Many helicases have been crystallized and their structures have revealed an underlying common structural fold for their function. The defects in helicases gene have also been reported to be responsible for variety of human genetic disorders, which can lead to cancer, premature aging or mental retardation. Recently, a new role of a helicase in abiotic stress signaling in plant has been discovered. Overall, helicases act as essential molecular tools for cellular machinery and help in maintaining the integrity of genome. Here an overview of helicases has been covered which includes history, biochemical assay, properties, classification, role in human disease and mechanism of unwinding and translocation.

Photoluminescence Architectures for Disease Diagnosis: From Graphene to Thin-Layer Transition Metal Dichalcogenides and Oxides.

PubMed

He, Xiao-Peng; Tian, He

2016-01-13

Ever since the discovery of graphene, increasing efforts have been devoted to the use of this stellar material as well as the development of other graphene-like materials such as thin-layer transition metal dichalcogenides and oxides (TMD/Os) for a variety of applications. Because of their large surface area and unique optical properties, these two-dimensional materials with a size ranging from the micro- to the nanoscale have been employed as the substrate to construct photoluminescence architectures for disease diagnosis as well as theranostics. These architectures are built through the simple self-assembly of labeled biomolecular probes with the substrate material, leading to signal quenching. Upon the specific interaction of the architecture with a target biomarker, the signal can be spontaneously restored in a reversible manner. Meanwhile, by co-loading therapeutic agents and employing the inherent photo-thermal properties of the material substrates, a combined disease imaging and therapy (theranostics) can be achieved. This review highlights the latest advances in the construction and application of graphene and TMD/O based thin-layer material composites for single-target and multiplexed detection of a variety of biomarkers and theranostics. These versatile material architectures, owing to their ease in preparation, low cost and flexibility in functionalization, provide promising tools for both basic biochemical research and clinical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biotechnology Research Requirements for Aeronautical Systems through the Year 2000. Volume 1

DTIC Science & Technology

1982-07-30

signature. Reducing the aero contain radic.?z,:"ve fallout. vehicle’s detectibility by reducing the optical, electro, acoustic, and infrared 0 Pulsed...arsenal devoted to agent doses. At this time, basic biochemical and chemical agents, reported use of mycotoxins and pharmacological data are minimal and...mass spectroscopy , quartz chemical agents must be developed. This research microbalances, Industrial hygiene dosimetry, damp should quantify human

Teaching the Role of Mitochondrial Transport in Energy Metabolism

ERIC Educational Resources Information Center

Passarella, Salvatore; Atlante, Anna

2007-01-01

Studies from our laboratories over recent years have uncovered the existence, and established the properties of a variety of mitochondrial transporters. The properties of these transporters throw light on a variety of biochemical phenomena that were previously poorly understood. In particular the role of mitochondrial transport in energy…

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.

[The influence of N-, S-containing chinasolone derivatives (NC-224) on the biochemical and physicochemical parameters of membrane endoplasmatic reticulum and nuclear chromatine fractions of rats liver cells in conditions of its injury by tetrachloromethane].

PubMed

Gubs'kyî, Iu I; Goriushko, G G; Belenichev, I F; Kovalenko, S I; Litvinova, N V; Marchenko, O M; Kurapova, T M; Babenko, L P; Velychko, O M

2010-01-01

Using biochemical and physicochemical methods of investigation in vivo, the effect of the substance NC-224, N-, S-chinasolone-derivative, on the lipoperoxidation activity in rat liver endoplasmatic reticulum membranes and nuclear chromatin fractions under tetrachloromethane intoxication have been studied. It was shown that NC-224 has pronounced antioxidant activity which is the biochemical basis of the substance membrane- and genome-protective effects and its ability to restore physicochemical properties of the surface and hydrophobic zones of hepatocyte membranes and structural parameter nuclear chromatin fractions in the conditions of chemical liver injury.

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

Isolation of Clostridium absonum and its cultural and biochemical properties.

PubMed

Hayase, M; Mitsui, N; Tamai, K; Nakamura, S; Nishida, S

1974-01-01

A new procedure for isolation of Clostridium absonum was devised. Sixtyseven strains of C. absonum were isolated from 135 soil samples, but no strain of C. absonum could be found from human fecal samples. The lecithinase, hemolysin, and lethal toxin in the culture filtrates of this species exhibited low avidity for C. perfringens type A antitoxin. The three activities were inseparable by the present method of purification. A reinvestigation of biochemical properties revealed that incomplete suppression of lecithinase reaction by C. perfringens type A antitoxin and no fermentation of raffinose, melibiose, and starch are useful criteria to differentiate C. absonum from C. perfringens, and that positive, although weak, gelatin liquefaction and fermentation of trehalose are useful to differentiate it from C. paraperfringens.

eQuilibrator--the biochemical thermodynamics calculator.

PubMed

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

2012-01-01

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

eQuilibrator—the biochemical thermodynamics calculator

PubMed Central

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

2012-01-01

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

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.

Intracellular Physiology of the Rat Suprachiasmatic Nucleus: Electrical Properties, Neurotransmission, and Effects of Neuromodulators.

DTIC Science & Technology

1992-08-24

Rat Suprachiasmatic Nucleus: Electrical Properties, Neurotransmission, and Effects of Neuromodulators 12. PERSONAL AUTHOR(S) F. Edward Dudek 13a...intrinsic electrical properties, synaptic and non-synaptic transmission, and neuromodulation . We have studied the role of excitatory and inhibitory amino... Neuromodulation : Smithson. K.G.. MacVicar. B.A. and Hatton. G.I. (1983) The Biochemical Control of Neuronal Excitability. Oxford Polyethylene glycol

NS3 from Hepatitis C Virus Strain JFH-1 Is an Unusually Robust Helicase That Is Primed To Bind and Unwind Viral RNA

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

Zhou, Ting; Ren, Xiaoming; Adams, Rebecca L.

Hepatitis C viruses (HCV) encode a helicase enzyme that is essential for viral replication and assembly (nonstructural protein 3 [NS3]). This helicase has become the focus of extensive basic research on the general helicase mechanism, and it is also of interest as a novel drug target. Despite the importance of this protein, mechanistic work on NS3 has been conducted almost exclusively on variants from HCV genotype 1. Our understanding of NS3 from the highly active HCV strains that are used to study HCV genetics and mechanism in cell culture (such as JFH-1) is lacking. We therefore set out to determinemore » whether NS3 from the replicatively efficient genotype 2a strain JFH-1 displays novel functional or structural properties. Using biochemical assays for RNA binding and duplex unwinding, we show that JFH-1 NS3 binds RNA much more rapidly than the previously studied NS3 variants from genotype 1b. Unlike NS3 variants from other genotypes, JFH-1 NS3 binds RNA with high affinity in a functionally active form that is capable of immediately unwinding RNA duplexes without undergoing rate-limiting conformational changes that precede activation. Unlike other superfamily 2 (SF2) helicases, JFH-1 NS3 does not require long 3' overhangs, and it unwinds duplexes that are flanked by only a few nucleotides, as in the folded HCV genome. To understand the physical basis for this, we solved the crystal structure of JFH-1 NS3, revealing a novel conformation that contains an open, positively charged RNA binding cleft that is primed for productive interaction with RNA targets, potentially explaining robust replication by HCV JFH-1. IMPORTANCEGenotypes of HCV are as divergent as different types of flavivirus, and yet mechanistic features of HCV variants are presumed to be held in common. One of the most well-studied components of the HCV replication complex is a helicase known as nonstructural protein 3 (NS3). We set out to determine whether this important mechanical component possesses biochemical and structural properties that differ between common strains such as those of genotype 1b and a strain of HCV that replicates with exceptional efficiency (JFH-1, classified as genotype 2a). Indeed, unlike the inefficient genotype 1b NS3, which has been well studied, JFH-1 NS3 is a superhelicase with strong RNA affinity and high unwinding efficiency on a broad range of targets. Crystallographic analysis reveals architectural features that promote enhanced biochemical activity of JFH-1 NS3. These findings show that even within a single family of viruses, drift in sequence can result in the acquisition of radically new functional properties that enhance viral fitness.« less

Acetylcholinesterase of Rhipicephalus (Boophilus) microplus and Phlebotomus papatasi: Gene Identification, Expression, and Biochemical Properties of Recombinant Proteins

DTIC Science & Technology

2013-01-01

predicted amino acid sequences of the three encoded BmAChEs were no more closely related to one another than AChEs from different organisms and their...solely on nucleotide and amino acid sequence similarity; however, the cholinesterase gene family contains a number of related enzymes and structural...acetylcholinesterase of P. papatasi was cloned, sequenced , and expressed in the baculo- virus system to generate a recombinant enzyme for biochemical

Optical Fiber Sensing Using Quantum Dots

PubMed Central

Jorge, Pedro; Martins, Manuel António; Trindade, Tito; Santos, José Luís; Farahi, Faramarz

2007-01-01

Recent advances in the application of semiconductor nanocrystals, or quantum dots, as biochemical sensors are reviewed. Quantum dots have unique optical properties that make them promising alternatives to traditional dyes in many luminescence based bioanalytical techniques. An overview of the more relevant progresses in the application of quantum dots as biochemical probes is addressed. Special focus will be given to configurations where the sensing dots are incorporated in solid membranes and immobilized in optical fibers or planar waveguide platforms. PMID:28903308

Experiment K-6-02. Biomedical, biochemical and morphological alterations of muscle and dense, fibrous connective tissues during 14 days of spaceflight

NASA Technical Reports Server (NTRS)

Vailas, A.; Zernicke, R.; Grindeland, R.; Kaplanski, A.

1990-01-01

Findings on the connective tissue response to short-term space flight (12 days) are discussed. Specifically, data regarding the biochemical, biomechanical and morphological characteristics of selected connective tissues (humerus, vertebral body, tendon and skeletal muscle) of growing rats is given. Results are given concerning the humerus cortical bone, the vertebral bone, nutritional effects on bone biomechanical properties, and soft tense fiber connective tissue response.

Transparent Conducting Oxides: Status and Opportunities in Basic Research

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

Coutts, T. J.; Perkins, J. D.; Ginley, D.S.

1999-08-01

In this paper, we begin by discussing the historical background of transparent conducting oxides and then make some general remarks about their typical properties. This is followed by a short discussion of the desired properties for future applications (particularly photovoltaic devices). These are ambitious objectives but they provide targets for future basic research and development. Although it may be possible to obtain these properties in the laboratory, it is vital to ensure that account is taken of industrial perceptions to the development of the next generation of materials. Hence, we spend some time discussing industrial criteria. Next, we discuss keymore » physical properties that determine the macroscopic physical properties that, in turn, affect the performance of devices. Finally, we select several key topics that ought to be included in future basic research programs.« less

Characterization of basic physical properties of Sb 2Se 3 and its relevance for photovoltaics

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

Chen, Chao; Bobela, David C.; Yang, Ye

Antimony selenide (Sb 2Se 3) is a promising absorber material for thin film photovoltaics because of its attractive material, optical and electrical properties. In recent years, the power conversion efficiency (PCE) of Sb 2Se 3 thin film solar cells has gradually enhanced to 5.6%. In this article, we systematically studied the basic physical properties of Sb 2Se 3 such as dielectric constant, anisotropic mobility, carrier lifetime, diffusion length, defect depth, defect density and optical band tail states. Here, we believe such a comprehensive characterization of the basic physical properties of Sb 2Se 3 lays a solid foundation for further optimizationmore » of solar device performance.« less

Characterization of basic physical properties of Sb 2Se 3 and its relevance for photovoltaics

DOE PAGES

Chen, Chao; Bobela, David C.; Yang, Ye; ...

2017-03-17

Antimony selenide (Sb 2Se 3) is a promising absorber material for thin film photovoltaics because of its attractive material, optical and electrical properties. In recent years, the power conversion efficiency (PCE) of Sb 2Se 3 thin film solar cells has gradually enhanced to 5.6%. In this article, we systematically studied the basic physical properties of Sb 2Se 3 such as dielectric constant, anisotropic mobility, carrier lifetime, diffusion length, defect depth, defect density and optical band tail states. Here, we believe such a comprehensive characterization of the basic physical properties of Sb 2Se 3 lays a solid foundation for further optimizationmore » of solar device performance.« less

Biological actions of curcumin on articular chondrocytes.

PubMed

Henrotin, Y; Clutterbuck, A L; Allaway, D; Lodwig, E M; Harris, P; Mathy-Hartert, M; Shakibaei, M; Mobasheri, A

2010-02-01

Curcumin (diferuloylmethane) is the principal biochemical component of the spice turmeric and has been shown to possess potent anti-catabolic, anti-inflammatory and antioxidant, properties. This article aims to provide a summary of the actions of curcumin on articular chondrocytes from the available literature with the use of a text-mining tool. We highlight both the potential benefits and drawbacks of using this chemopreventive agent for treating osteoarthritis (OA). We also explore the recent literature on the molecular mechanisms of curcumin mediated alterations in gene expression mediated via activator protein 1 (AP-1)/nuclear factor-kappa B (NF-kappaB) signalling in chondrocytes, osteoblasts and synovial fibroblasts. A computer-aided search of the PubMed/Medline database aided by a text-mining tool to interrogate the ResNet Mammalian database 6.0. Recent work has shown that curcumin protects human chondrocytes from the catabolic actions of interleukin-1 beta (IL-1beta) including matrix metalloproteinase (MMP)-3 up-regulation, inhibition of collagen type II and down-regulation of beta1-integrin expression. Curcumin blocks IL-1beta-induced proteoglycan degradation, AP-1/NF-kappaB signalling, chondrocyte apoptosis and activation of caspase-3. The available data from published in vitro and in vivo studies suggest that curcumin may be a beneficial complementary treatment for OA in humans and companion animals. Nevertheless, before initiating extensive clinical trials, more basic research is required to improve its solubility, absorption and bioavailability and gain additional information about its safety and efficacy in different species. Once these obstacles have been overcome, curcumin and structurally related biochemicals may become safer and more suitable nutraceutical alternatives to the non-steroidal anti-inflammatory drugs that are currently used for the treatment of OA. Copyright 2009 Osteoarthritis Research Society International. All rights reserved.

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.

Water-quality and ancillary data collected from the Arroyo Colorado near Rio Hondo, Texas, 2006

USGS Publications Warehouse

Roussel, Meghan C.; Canova, Michael G.; Asquith, William H.; Kiesling, Richard L.

2007-01-01

The Arroyo Colorado is in the lower Rio Grande Valley of southern Texas and extends from near Mission, Texas, eastward to the Laguna Madre estuarine and coastal marine system, which separates Padre Island from the Texas mainland. Streamflow in the Arroyo Colorado primarily is sustained by effluent from municipal wastewater-treatment plants along the stream banks. Since 1986, the tidal segment of the Arroyo Colorado from the port of Harlingen to the Laguna Madre has been designated by the State of Texas as an impaired water body because of low dissolved oxygen concentrations. Efforts to develop predictive water-quality models for the tidal segment of the Arroyo Colorado have been hampered by a lack of physical, biological, and biochemical data. Specifically, data on primary algal productivity, nutrient cycling, sediment deposition rates, and the relations between these processes and dissolved oxygen dynamics in the stream have been inadequate to support water-quality modeling efforts. The U.S. Geological Survey, in cooperation with the Texas Commission on Environmental Quality, did a study in 2006 to collect data associated with primary algal productivity, nutrient cycling, and dissolved oxygen dynamics in the tidal segment (2201) of the Arroyo Colorado near Rio Hondo. Specific objectives of the study were to (1) characterize water quality by measuring basic properties; (2) characterize the concentrations of carbon and nutrients, biochemical oxygen demand, total organic carbon, total suspended solids, and volatile suspended solids; (3) measure the seasonal differences of nutrient-dependent algal growth and algal production in the water column; (4) measure oxygen respiration or production rates; and (5) measure rates of sediment deposition.

Analysis of DNA interactions using single-molecule force spectroscopy.

PubMed

Ritzefeld, Markus; Walhorn, Volker; Anselmetti, Dario; Sewald, Norbert

2013-06-01

Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.

Two-Dimensional Photonic Crystals for Sensitive Microscale Chemical and Biochemical Sensing

PubMed Central

Miller, Benjamin L.

2015-01-01

Photonic crystals – optical devices able to respond to changes in the refractive index of a small volume of space – are an emerging class of label-free chemical-and bio-sensors. This review focuses on one class of photonic crystal, in which light is confined to a patterned planar material layer of sub-wavelength thickness. These devices are small (on the order of tens to 100s of microns square), suitable for incorporation into lab-on-a-chip systems, and in theory can provide exceptional sensitivity. We introduce the defining characteristics and basic operation of two-dimensional photonic crystal sensors, describe variations of their basic design geometry, and summarize reported detection results from chemical and biological sensing experiments. PMID:25563402

Tuning the acid/base properties of nanocarbons by functionalization via amination.

PubMed

Arrigo, Rosa; Hävecker, Michael; Wrabetz, Sabine; Blume, Raoul; Lerch, Martin; McGregor, James; Parrott, Edward P J; Zeitler, J Axel; Gladden, Lynn F; Knop-Gericke, Axel; Schlögl, Robert; Su, Dang Sheng

2010-07-21

The surface chemical properties and the electronic properties of vapor grown carbon nanofibers (VGCNFs) have been modified by treatment of the oxidized CNFs with NH(3). The effect of treatment temperature on the types of nitrogen functionalities introduced was evaluated by synchrotron based X-ray photoelectron spectroscopy (XPS), while the impact of the preparation methods on the surface acid-base properties was investigated by potentiometric titration, microcalorimetry, and zeta potential measurements. The impact of the N-functionalization on the electronic properties was measured by THz-Time Domain spectroscopy. The samples functionalized via amination are characterized by the coexistence of acidic and basic O and N sites. The population of O and N species is temperature dependent. In particular, at 873 K nitrogen is stabilized in substitutional positions within the graphitic structure, as heterocyclic-like moieties. The surface presents heterogeneously distributed and energetically different basic sites. A small amount of strong basic sites gives rise to a differential heat of CO(2) adsorption of 150 kJ mol(-1). However, when functionalization is carried out at 473 K, nitrogen moieties with basic character are introduced and the maximum heat of adsorption is significantly lower, at approximately 90 kJ mol(-1). In the latter sample, energetically different basic sites coexist with acidic oxygen groups introduced during the oxidative step. Under these conditions, a bifunctional acidic and basic surface is obtained with high hydrophilic character. N-functionalization carried out at higher temperature changes the electronic properties of the CNFs as evaluated by THz-TDS. The functionalization procedure presented in this work allows high versatility and flexibility in tailoring the surface chemistry of nanocarbon material to specific needs. This work shows the potential of the N-containing nanocarbon materials obtained via amination in catalysis as well as electronic device materials.

From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes.

PubMed

Singh, Raushan Kumar; Tiwari, Manish Kumar; Singh, Ranjitha; Lee, Jung-Kul

2013-01-10

Enzymes found in nature have been exploited in industry due to their inherent catalytic properties in complex chemical processes under mild experimental and environmental conditions. The desired industrial goal is often difficult to achieve using the native form of the enzyme. Recent developments in protein engineering have revolutionized the development of commercially available enzymes into better industrial catalysts. Protein engineering aims at modifying the sequence of a protein, and hence its structure, to create enzymes with improved functional properties such as stability, specific activity, inhibition by reaction products, and selectivity towards non-natural substrates. Soluble enzymes are often immobilized onto solid insoluble supports to be reused in continuous processes and to facilitate the economical recovery of the enzyme after the reaction without any significant loss to its biochemical properties. Immobilization confers considerable stability towards temperature variations and organic solvents. Multipoint and multisubunit covalent attachments of enzymes on appropriately functionalized supports via linkers provide rigidity to the immobilized enzyme structure, ultimately resulting in improved enzyme stability. Protein engineering and immobilization techniques are sequential and compatible approaches for the improvement of enzyme properties. The present review highlights and summarizes various studies that have aimed to improve the biochemical properties of industrially significant enzymes.

Design and basic properties of ternary gypsum-based mortars

NASA Astrophysics Data System (ADS)

Doleželová, M.; Vimmrová, A.

2017-10-01

Ternary mortars, prepared from gypsum, hydrated lime and three types of pozzolan were designed and tested. As a pozzolan admixture crushed ceramic, silica fume and granulated blast slag were used. The amount of pozzolans in the mixtures was determined according to molar weight of amorphous SiO2 in the material. The samples were stored under the water. The basic physical properties and mechanical properties were measured. The properties were compared with the properties of material without pozzolan. The best results in the water environment were achieved by the samples with silica fume.

Spatial distribution analysis of chemical and biochemical properties across Koiliaris CZO

NASA Astrophysics Data System (ADS)

Tsiknia, Myrto; Varouchakis, Emmanouil A.; Paranychianakis, Nikolaos V.; Nikolaidis, Nikolaos P.

2015-04-01

Arid and semi-arid ecosystems cover approximately 47% of the Earth's surface. Soils in these climatic zones are often severely degraded and poor in organic carbon and nutrients. Anthropogenic activities like overgrazing and intensive agricultural practices further exacerbate the quality of the soils making them more vulnerable to erosion and accelerating losses of nutrients which might end up to surface waterways degrading their quality. Data of the geospatial distribution of nutrient availability as well as on the involved processes at watershed level might help us to identify areas which will potentially act as sources of nutrients and probably will allow us to adopt appropriate management practices to mitigate environmental impacts. In the present study we have performed an extensive sampling campaign (50 points) across a typical Mediterranean watershed, the Koiliaris Critical Zone Observatory (CZO), organized in such a way to effectively capture the complex variability (climatic, soil properties, hydrology, land use) of the watershed. Analyses of soil physico-chemical properties (texture, pH, EC, TOC, TN, NO3--N, and NH4+-N) and biochemical assays (potential nitrification rate, nitrogen mineralization rate, enzymes activities) were carried out. Geostatistical analysis and more specifically the kriging interpolation method was employed to generate distribution maps of the distribution of nitrogen forms and of the related biochemical assays. Such maps could provide an important tool for effective ecosystem management and monitoring decisions.

Predicting autism at birth.

PubMed

Steinman, Gary

2013-07-01

The amounts of at least three biochemical factors are more often abnormal in autistic people than neurologically normal ones. They include insulin-like growth factor, anti-myelin basic protein, and serotonin. This may explain why processes initiated in utero which hinder normal neurogenesis, especially myelination, continue after delivery. Quantitation of these parameters may make possible the calculation of an autism index, anticipating at birth which children will ultimately develop overt autism. Copyright © 2013 Elsevier Ltd. All rights reserved.

Results of medical studies during long-term manned flights on the orbital Salyut-6 and Soyuz complex

NASA Technical Reports Server (NTRS)

Yegorov, A. D. (Compiler)

1979-01-01

Results of tests made on the crews of the Salyut-6 and Soyuz complex are presented. The basic results of studies made before, during and after 96-day and 140-day flights are presented in 5 sections: characteristics of flight conditions in the orbital complex; the cardiovascular system; the motor sphere and vestibular analyzer; biochemical, hematologic and immunologic studies; and recovery measures in the readaptation period.

The contribution of collagen fibers to the mechanical compressive properties of the temporomandibular joint disc.

PubMed

Fazaeli, S; Ghazanfari, S; Everts, V; Smit, T H; Koolstra, J H

2016-07-01

The Temporomandibular Joint (TMJ) disc is a fibrocartilaginous structure located between the mandibular condyle and the temporal bone, facilitating smooth movements of the jaw. The load-bearing properties of its anisotropic collagenous network have been well characterized under tensile loading conditions. However, recently it has also been speculated that the collagen fibers may contribute dominantly in reinforcing the disc under compression. Therefore, in this study, the structural-functional role of collagen fibers in mechanical compressive properties of TMJ disc was investigated. Intact porcine TMJ discs were enzymatically digested with collagenase to disrupt the collagenous network of the cartilage. The digested and non-digested articular discs were analyzed mechanically, biochemically and histologically in five various regions. These tests included: (1) cyclic compression tests, (2) biochemical quantification of collagen and glycosaminoglycan (GAG) content and (3) visualization of collagen fibers' alignment by polarized light microscopy (PLM). The instantaneous compressive moduli of the articular discs were reduced by as much as 50-90% depending on the region after the collagenase treatment. The energy dissipation properties of the digested discs showed a similar tendency. Biochemical analysis of the digested samples demonstrated an average of 14% and 35% loss in collagen and GAG, respectively. Despite the low reduction of collagen content the PLM images showed considerable perturbation of the collagenous network of the TMJ disc. The results indicated that even mild disruption of collagen fibers can lead to substantial mechanical softening of TMJ disc undermining its reinforcement and mechanical stability under compression. Copyright © 2016 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Beyond leaf color: Comparing camera-based phenological metrics with leaf biochemical, biophysical, and spectral properties throughout the growing season of a temperate deciduous forest

NASA Astrophysics Data System (ADS)

Yang, Xi; Tang, Jianwu; Mustard, John F.

2014-03-01

Plant phenology, a sensitive indicator of climate change, influences vegetation-atmosphere interactions by changing the carbon and water cycles from local to global scales. Camera-based phenological observations of the color changes of the vegetation canopy throughout the growing season have become popular in recent years. However, the linkages between camera phenological metrics and leaf biochemical, biophysical, and spectral properties are elusive. We measured key leaf properties including chlorophyll concentration and leaf reflectance on a weekly basis from June to November 2011 in a white oak forest on the island of Martha's Vineyard, Massachusetts, USA. Concurrently, we used a digital camera to automatically acquire daily pictures of the tree canopies. We found that there was a mismatch between the camera-based phenological metric for the canopy greenness (green chromatic coordinate, gcc) and the total chlorophyll and carotenoids concentration and leaf mass per area during late spring/early summer. The seasonal peak of gcc is approximately 20 days earlier than the peak of the total chlorophyll concentration. During the fall, both canopy and leaf redness were significantly correlated with the vegetation index for anthocyanin concentration, opening a new window to quantify vegetation senescence remotely. Satellite- and camera-based vegetation indices agreed well, suggesting that camera-based observations can be used as the ground validation for satellites. Using the high-temporal resolution dataset of leaf biochemical, biophysical, and spectral properties, our results show the strengths and potential uncertainties to use canopy color as the proxy of ecosystem functioning.

Bioactive glass 13-93 as a subchondral substrate for tissue-engineered osteochondral constructs: a pilot study.

PubMed

Jayabalan, Prakash; Tan, Andrea R; Rahaman, Mohammed N; Bal, B Sonny; Hung, Clark T; Cook, James L

2011-10-01

Replacement of diseased areas of the joint with tissue-engineered osteochondral grafts has shown potential in the treatment of osteoarthritis. Bioactive glasses are candidates for the osseous analog of these grafts. (1) Does Bioactive Glass 13-93 (BG 13-93) as a subchondral substrate improve collagen and glycosaminoglycan production in a tissue-engineered cartilage layer? (2) Does BG 13-93 as a culture medium supplement increase the collagen and glycosaminoglycan production and improve the mechanical properties in a tissue-engineered cartilage layer? In Study 1, bioactive glass samples (n = 4) were attached to a chondrocyte-seeded agarose layer to form an osteochondral construct, cultured for 6 weeks, and compared to controls. In Study 2, bioactive glass samples (n = 5) were cocultured with cell-seeded agarose for 6 weeks. The cell-seeded agarose layer was exposed to BG 13-93 either continuously or for the first or last 2 weeks in culture or had no exposure. Osteochondral constructs with a BG 13-93 base had improved glycosaminoglycan deposition but less collagen II content. Agarose scaffolds that had a temporal exposure to BG 13-93 within the culture medium had improved mechanical and biochemical properties compared to continuous or no exposure. When used as a subchondral substrate, BG 13-93 did not improve biochemical properties compared to controls. However, as a culture medium supplement, BG 13-93 improved the biochemical and mechanical properties of a tissue-engineered cartilage layer. BG 13-93 may not be suitable in osteochondral constructs but could have potential as a medium supplement for neocartilage formation.

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.

Obtaining edaphic biostimulants/biofertilizers from sewage sludge using fermentative processes. Short-time effects on soil biochemical properties.

PubMed

Rodríguez-Morgado, Bruno; Caballero, Pablo; Paneque, Patricia; Gómez, Isidoro; Parrado, Juan; Tejada, Manuel

2017-10-28

In this manuscript, we study the manufacture and effect on soils of different edaphic biostimulants/biofertilizers (BS) obtained from sewage sludge using Bacillus licheniformis as biological tool. These BS consist of different combinations of organic matter, bacteria and enzymes that were subjected to several treatments. These BS were applied in soil in order to observe their influence on the biochemical properties (enzymatic activities and ergosterol content). Dehydrogenase, urease, β-glucosidase, phosphatase activities and ergosterol content were measured at different incubation days. Only dehydrogenase activity and ergosterol content were significantly stimulated after the application of BS1 and BS4. Rest of the extracellular activities were not stimulated probably because B. licheniformis practically has digested all organic substrates during fermentation process.

Biomacromolecules as carriers in drug delivery and tissue engineering.

PubMed

Zhang, Yujie; Sun, Tao; Jiang, Chen

2018-01-01

Natural biomacromolecules have attracted increased attention as carriers in biomedicine in recent years because of their inherent biochemical and biophysical properties including renewability, nontoxicity, biocompatibility, biodegradability, long blood circulation time and targeting ability. Recent advances in our understanding of the biological functions of natural-origin biomacromolecules and the progress in the study of biological drug carriers indicate that such carriers may have advantages over synthetic material-based carriers in terms of half-life, stability, safety and ease of manufacture. In this review, we give a brief introduction to the biochemical properties of the widely used biomacromolecule-based carriers such as albumin, lipoproteins and polysaccharides. Then examples from the clinic and in recent laboratory development are summarized. Finally the current challenges and future prospects of present biological carriers are discussed.

γ-Glutamyltranspeptidases: sequence, structure, biochemical properties, and biotechnological applications.

PubMed

Castellano, Immacolata; Merlino, Antonello

2012-10-01

γ-Glutamyltranspeptidases (γ-GTs) are ubiquitous enzymes that catalyze the hydrolysis of γ-glutamyl bonds in glutathione and glutamine and the transfer of the released γ-glutamyl group to amino acids or short peptides. These enzymes are involved in glutathione metabolism and play critical roles in antioxidant defense, detoxification, and inflammation processes. Moreover, γ-GTs have been recently found to be involved in many physiological disorders, such as Parkinson's disease and diabetes. In this review, the main biochemical and structural properties of γ-GTs isolated from different sources, as well as their conformational stability and mechanism of catalysis, are described and examined with the aim of contributing to the discussion on their structure-function relationships. Possible applications of γ-glutamyltranspeptidases in different fields of biotechnology and medicine are also discussed.

The diverse biological properties of the chemically inert noble gases.

PubMed

Winkler, David A; Thornton, Aaron; Farjot, Géraldine; Katz, Ira

2016-04-01

The noble gases represent an intriguing scientific paradox. They are extremely inert chemically but display a remarkable spectrum of clinically useful biological properties. Despite a relative paucity of knowledge of their mechanisms of action, some of the noble gases have been used successfully in the clinic. Studies with xenon have suggested that the noble gases as a class may exhibit valuable biological properties such as anaesthesia; amelioration of ischemic damage; tissue protection prior to transplantation; analgesic properties; and a potentially wide range of other clinically useful effects. Xenon has been shown to be safe in humans, and has useful pharmacokinetic properties such as rapid onset, fast wash out etc. The main limitations in wider use are that: many of the fundamental biochemical studies are still lacking; the lighter noble gases are likely to manifest their properties only under hyperbaric conditions, impractical in surgery; and administration of xenon using convectional gaseous anaesthesia equipment is inefficient, making its use very expensive. There is nonetheless a significant body of published literature on the biochemical, pharmacological, and clinical properties of noble gases but no comprehensive reviews exist that summarize their properties and the existing knowledge of their models of action at the molecular (atomic) level. This review provides such an up-to-date summary of the extensive, useful biological properties of noble gases as drugs and prospects for wider application of these atoms. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

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

PubMed Central

Ge, Hao; Qian, Hong

2011-01-01

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

Assessing the use of treated waste water for irrigation agricultural lands by using soil quality indices

NASA Astrophysics Data System (ADS)

Arcenegui, V.; Morugán, A.; García-Orenes, F.; Zornoza, R.; Mataix-Solera, J.; Navarro, M. A.; Guerrero, C.; Mataix-Beneyto, J.

2009-04-01

The use of treated wastewater for the irrigation of agricultural soils is an alternative to utilizing better-quality water, especially in semiarid regions where water shortage is a very serious problem. However, this practise can modify the soil equilibrium and affect its quality. In this work two soil quality indices (models) are used to evaluate the effects of long-term irrigation with treated wastewater in soil. The models were developed studying different soil properties in undisturbed forest soils in SE Spain, and the relationships between soil parameters were established using multiple linear regressions. Model 1, that explained 92% of the variance in soil organic carbon (SOC) showed that the SOC can be calculated by the linear combination of 6 physical, chemical and biochemical properties (acid phosphatase, water holding capacity (WHC), electrical conductivity (EC), available phosphorus (P), cation exchange capacity (CEC) and aggregate stability (AS)). Model 2 explains 89% of the SOC variance, which can be calculated by means of 7 chemical and biochemical properties (urease, phosphatase, and

Preservation of kombucha tea-effect of temperature on tea components and free radical scavenging properties.

PubMed

Jayabalan, Rasu; Marimuthu, Subbaiya; Thangaraj, Periyasamy; Sathishkumar, Muthuswamy; Binupriya, Arthur Raj; Swaminathan, Krishnaswami; Yun, Sei Eok

2008-10-08

Kombucha tea is sugared black tea fermented with a consortium of acetic acid bacteria and yeasts (tea fungus) for 14 days. The tea tastes slightly sweet and acidic. The formation of tea fungal biofilms during storage is a big problem when kombucha tea is being stored and commercialized. Various thermal treatments have been tried for long-term storage of kombucha tea. The present study revealed the influence of heat on the biochemical constituents and the free radical scavenging properties of kombucha tea. Heat treatment at 60, 65, and 68 degrees C for 1 min controlled biofilm formation in kombucha tea without changing its clarity, taste, and flavor. However, tea polyphenols and black tea quality parameters showed varying stability during the storage period. A decrease in free radical scavenging properties was also found during the storage period. Because the biological activities of kombucha tea depended on the biochemical constituents, it was concluded that heat treatment was not a suitable method for kombucha tea preservation.

Changes in the functional properties and antinutritional factors of extruded hard-to-cook common beans (Phaseolus vulgaris, L.).

PubMed

Batista, Karla A; Prudêncio, Sandra H; Fernandes, Kátia F

2010-04-01

The biochemical and functional properties of 2 hard-to-cook common bean cultivars (Phaseolus vulgaris, L.) were investigated after the extrusion process. Beans of BRS pontal and BRS grafite cultivars were milled and extruded at 150 degrees C, with a compression ratio screw of 3 : 1, 5-mm die, and screw speed of 150 rpm. Extrudate flours were evaluated for water solubility (WS), water absorption index (WAI), oil absorption capacity (OAC), foaming capacity (FC), emulsifying activity (EA), antinutritional factors, and in vitro protein and starch digestibility. Results indicated that the extrusion significantly decreased antinutrients such as phytic acid, lectin, alpha-amylase, and trypsin inhibitors, reduced the emulsifying capacity and eliminated the FC in both BRS pontal and BRS grafite cultivars. In addition, the WS, WAI, and in vitro protein and starch digestibility were improved by the extrusion process. These results indicate that it is possible to produce new extruded products with good functional and biochemical properties from these common bean cultivars.

Fcγ1 fragment of IgG1 as a powerful affinity tag in recombinant Fc-fusion proteins: immunological, biochemical and therapeutic properties.

PubMed

Soleimanpour, Saman; Hassannia, Tahereh; Motiee, Mahdieh; Amini, Abbas Ali; Rezaee, S A R

2017-05-01

Affinity tags are vital tools for the production of high-throughput recombinant proteins. Several affinity tags, such as the hexahistidine tag, maltose-binding protein, streptavidin-binding peptide tag, calmodulin-binding peptide, c-Myc tag, glutathione S-transferase and FLAG tag, have been introduced for recombinant protein production. The fragment crystallizable (Fc) domain of the IgG1 antibody is one of the useful affinity tags that can facilitate detection, purification and localization of proteins and can improve the immunogenicity, modulatory effects, physicochemical and pharmaceutical properties of proteins. Fcγ recombinant forms a group of recombinant proteins called Fc-fusion proteins (FFPs). FFPs are widely used in drug discovery, drug delivery, vaccine design and experimental research on receptor-ligand interactions. These fusion proteins have become successful alternatives to monoclonal antibodies for drug developments. In this review, the physicochemical, biochemical, immunological, pharmaceutical and therapeutic properties of recombinant FFPs were discussed as a new generation of bioengineering strategies.

41 CFR 102-76.10 - What basic design and construction policy governs Federal agencies?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What basic design and... Management Federal Property Management Regulations System (Continued) FEDERAL MANAGEMENT REGULATION REAL... must be timely, efficient, and cost effective. (b) Use a distinguished architectural style and form in...

Selenium uptake, translocation, assimilation and metabolic fate in plants.

PubMed

Sors, T G; Ellis, D R; Salt, D E

2005-12-01

The chemical and physical resemblance between selenium (Se) and sulfur (S) establishes that both these elements share common metabolic pathways in plants. The presence of isologous Se and S compounds indicates that these elements compete in biochemical processes that affect uptake, translocation and assimilation throughout plant development. Yet, minor but crucial differences in reactivity and other metabolic interactions infer that some biochemical processes involving Se may be excluded from those relating to S. This review examines the current understanding of physiological and biochemical relationships between S and Se metabolism by highlighting their similarities and differences in relation to uptake, transport and assimilation pathways as observed in Se hyperaccumulator and non-accumulator plant species. The exploitation of genetic resources used in bioengineering strategies of plants is illuminating the function of sulfate transporters and key enzymes of the S assimilatory pathway in relation to Se accumulation and final metabolic fate. These strategies are providing the basic framework by which to resolve questions relating to the essentiality of Se in plants and the mechanisms utilized by Se hyperaccumulators to circumvent toxicity. In addition, such approaches may assist in the future application of genetically engineered Se accumulating plants for environmental renewal and human health objectives.

[The influence of C-taurine antioxidant complex on biochemical blood parameters in the process of treatment of patients with diabetes mellitus of type II with nonproliferative diabetic retinopathy].

PubMed

Lekishvili, S E

2014-02-01

The purpose of this investigation is to study the effect of C- taurine complex of antioxidants on blood biochemical parameters in the process of treatment of patients with diabetes mellitus of type II with NPDR. 68 patients (136 eyes) were enrolled in the study. The monitoring of the patient lasted for 3 months. The character of changes of the basic visual functions has been examined. The patients were divided into 2 groups (main and control). Treatment of patients with main group conducted antioxidant complex Taurine + Vitamin C for 42 days. namely. Thus, we have revealed antioxidant activity of the combination of taurine and vitamin C with positive effect on the indexes of carbohydrate, lipid metabolism and hepatoprotective characteristics in patients with diabetes mellitus type II with NPDR. Taking into consideration the peculiarities of correlation relationships between functional, clinical and biochemical parameters and the results of experimental studies on animal it is acceptable to use Taurine complex + Vitamin C as part of conservative treatment of patients with diabetes mellitus type II with NPDR.

Cellular Signaling Networks Function as Generalized Wiener-Kolmogorov Filters to Suppress Noise

NASA Astrophysics Data System (ADS)

Hinczewski, Michael; Thirumalai, D.

2014-10-01

Cellular signaling involves the transmission of environmental information through cascades of stochastic biochemical reactions, inevitably introducing noise that compromises signal fidelity. Each stage of the cascade often takes the form of a kinase-phosphatase push-pull network, a basic unit of signaling pathways whose malfunction is linked with a host of cancers. We show that this ubiquitous enzymatic network motif effectively behaves as a Wiener-Kolmogorov optimal noise filter. Using concepts from umbral calculus, we generalize the linear Wiener-Kolmogorov theory, originally introduced in the context of communication and control engineering, to take nonlinear signal transduction and discrete molecule populations into account. This allows us to derive rigorous constraints for efficient noise reduction in this biochemical system. Our mathematical formalism yields bounds on filter performance in cases important to cellular function—such as ultrasensitive response to stimuli. We highlight features of the system relevant for optimizing filter efficiency, encoded in a single, measurable, dimensionless parameter. Our theory, which describes noise control in a large class of signal transduction networks, is also useful both for the design of synthetic biochemical signaling pathways and the manipulation of pathways through experimental probes such as oscillatory input.

13C-Metabolic Flux Analysis: An Accurate Approach to Demystify Microbial Metabolism for Biochemical Production

PubMed Central

Guo, Weihua; Sheng, Jiayuan; Feng, Xueyang

2015-01-01

Metabolic engineering of various industrial microorganisms to produce chemicals, fuels, and drugs has raised interest since it is environmentally friendly, sustainable, and independent of nonrenewable resources. However, microbial metabolism is so complex that only a few metabolic engineering efforts have been able to achieve a satisfactory yield, titer or productivity of the target chemicals for industrial commercialization. In order to overcome this challenge, 13C Metabolic Flux Analysis (13C-MFA) has been continuously developed and widely applied to rigorously investigate cell metabolism and quantify the carbon flux distribution in central metabolic pathways. In the past decade, many 13C-MFA studies have been performed in academic labs and biotechnology industries to pinpoint key issues related to microbe-based chemical production. Insightful information about the metabolic rewiring has been provided to guide the development of the appropriate metabolic engineering strategies for improving the biochemical production. In this review, we will introduce the basics of 13C-MFA and illustrate how 13C-MFA has been applied via integration with metabolic engineering to identify and tackle the rate-limiting steps in biochemical production for various host microorganisms PMID:28952565

[A study of biomechanical method for urine test based on color difference estimation].

PubMed

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

2008-02-01

The biochemical analysis of urine is an important inspection and diagnosis method in hospitals. The conventional method of urine analysis covers mainly colorimetric visual appraisement and automation detection, in which the colorimetric visual appraisement technique has been superseded basically, and the automation detection method is adopted in hospital; moreover, the price of urine biochemical analyzer on market is around twenty thousand RMB yuan (Y), which is hard to enter into ordinary families. It is known that computer vision system is not subject to the physiological and psychological influence of person, its appraisement standard is objective and steady. Therefore, according to the color theory, we have established a computer vision system, which can carry through collection, management, display, and appraisement of color difference between the color of standard threshold value and the color of urine test paper after reaction with urine liquid, and then the level of an illness can be judged accurately. In this paper, we introduce the Urine Test Biochemical Analysis method, which is new and can be popularized in families. Experimental result shows that this test method is easy-to-use and cost-effective. It can realize the monitoring of a whole course and can find extensive applications.

Molecular sled sequences are common in mammalian proteins.

PubMed

Xiong, Kan; Blainey, Paul C

2016-03-18

Recent work revealed a new class of molecular machines called molecular sleds, which are small basic molecules that bind and slide along DNA with the ability to carry cargo along DNA. Here, we performed biochemical and single-molecule flow stretching assays to investigate the basis of sliding activity in molecular sleds. In particular, we identified the functional core of pVIc, the first molecular sled characterized; peptide functional groups that control sliding activity; and propose a model for the sliding activity of molecular sleds. We also observed widespread DNA binding and sliding activity among basic polypeptide sequences that implicate mammalian nuclear localization sequences and many cell penetrating peptides as molecular sleds. These basic protein motifs exhibit weak but physiologically relevant sequence-nonspecific DNA affinity. Our findings indicate that many mammalian proteins contain molecular sled sequences and suggest the possibility that substantial undiscovered sliding activity exists among nuclear mammalian proteins. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Microbial and chemical properties of log ponds along the Oregon Coast.

Treesearch

Iwan Ho; Ching Yan Li

1987-01-01

The microbial and chemical properties of log ponds along the Oregon coast were investigated. The log ponds were highly eutrophic, containing high concentrations of ammonium and nitrate nitrogen, phosphate, and organic compounds. Because of large microbial populations, the biochemical oxygen demand was high and dissolved oxygen was low. Bacterial species in log ponds...

Interactions of Soil Order and Land Use Management on Soil Properties in the Kukart Watershed, Kyrgyzstan

USDA-ARS?s Scientific Manuscript database

Surveys of soil properties related to soil functioning for many regions of Kyrgyzstan are limited. This study established ranges of selected chemical [soil organic matter (SOM), pH and total N (TN)], physical (soil texture), and biochemical (six enzyme activities of C, N, P and S cycling) character...

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.

The Contribution of Buckwheat Genetic Resources to Health and Dietary Diversity

PubMed Central

Sytar, Oksana; Brestic, Marian; Zivcak, Marek; Tran, Lam-Son Phan

2016-01-01

Despite several reports on the beneficial effects of buckwheat in prevention of human diseases, little attention has been devoted to the variability of biochemical and physiological traits in different buckwheat genetic resources. This review describes the biochemical evaluation of buckwheat genetic resources and the identification of elite genotypes for plant breeding and exploitation. The various types of bioactive compounds present in different varieties provide basic background information needed for the efficient production of buckwheat foods with added value. In this review, we will provide an integrated view of the biochemistry of bioactive compounds of buckwheat plants of different origin, especially of fagopyrin, proteins and amino acids, as well as of other phenolic compounds including rutin and chlorogenic acid. In addition to the genetic background, the effect of different growth conditions is discussed. The health effects of fagopyrin, phenolic acids, specific proteins and rutin are also presented. PMID:27252586

Characterizing the Diversity and Biological Relevance of the MLPCN Assay Manifold and Screening Set

PubMed Central

Zhang, Jintao; Lushington, Gerald H.; Huan, Jun

2011-01-01

The NIH Molecular Libraries Initiative (MLI), launched in 2004 with initial goals of identifying chemical probes for characterizing gene function and druggability, has produced PubChem, a chemical genomics knowledgebase for fostering translation of basic research into new therapeutic strategies. This paper assesses progress toward these goals by evaluating MLI target novelty and propensity for undergoing biochemically or therapeutically relevant modulations and the degree of chemical diversity and biogenic bias inherent in the MLI screening set. Our analyses suggest that while MLI target selection has not yet been fully optimized for biochemical diversity, it covers biologically interesting pathway space that complements established drug targets. We find the MLI screening set to be chemically diverse and to have greater biogenic bias than comparable collections of commercially available compounds. Biogenic enhancements such as incorporation of more metabolite-like chemotypes are suggested. PMID:21568288

Resilience of biochemical activity in protein domains in the face of structural divergence.

PubMed

Zhang, Dapeng; Iyer, Lakshminarayan M; Burroughs, A Maxwell; Aravind, L

2014-06-01

Recent studies point to the prevalence of the evolutionary phenomenon of drastic structural transformation of protein domains while continuing to preserve their basic biochemical function. These transformations span a wide spectrum, including simple domains incorporated into larger structural scaffolds, changes in the structural core, major active site shifts, topological rewiring and extensive structural transmogrifications. Proteins from biological conflict systems, such as toxin-antitoxin, restriction-modification, CRISPR/Cas, polymorphic toxin and secondary metabolism systems commonly display such transformations. These include endoDNases, metal-independent RNases, deaminases, ADP ribosyltransferases, immunity proteins, kinases and E1-like enzymes. In eukaryotes such transformations are seen in domains involved in chromatin-related peptide recognition and protein/DNA-modification. Intense selective pressures from 'arms-race'-like situations in conflict and macromolecular modification systems could favor drastic structural divergence while preserving function. Published by Elsevier Ltd.

Imaging trace element distributions in single organelles and subcellular features

NASA Astrophysics Data System (ADS)

Kashiv, Yoav; Austin, Jotham R.; Lai, Barry; Rose, Volker; Vogt, Stefan; El-Muayed, Malek

2016-02-01

The distributions of chemical elements within cells are of prime importance in a wide range of basic and applied biochemical research. An example is the role of the subcellular Zn distribution in Zn homeostasis in insulin producing pancreatic beta cells and the development of type 2 diabetes mellitus. We combined transmission electron microscopy with micro- and nano-synchrotron X-ray fluorescence to image unequivocally for the first time, to the best of our knowledge, the natural elemental distributions, including those of trace elements, in single organelles and other subcellular features. Detected elements include Cl, K, Ca, Co, Ni, Cu, Zn and Cd (which some cells were supplemented with). Cell samples were prepared by a technique that minimally affects the natural elemental concentrations and distributions, and without using fluorescent indicators. It could likely be applied to all cell types and provide new biochemical insights at the single organelle level not available from organelle population level studies.

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

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

Marx, D.H.

1990-12-01

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

Dispersion relation in oscillatory reaction-diffusion systems with self-consistent flow in true slime mold.

PubMed

Yamada, H; Nakagaki, T; Baker, R E; Maini, P K

2007-06-01

In the large amoeboid organism Physarum, biochemical oscillators are spatially distributed throughout the organism and their collective motion exhibits phase waves, which carry physiological signals. The basic nature of this wave behaviour is not well-understood because, to date, an important effect has been neglected, namely, the shuttle streaming of protoplasm which accompanies the biochemical rhythms. Here we study the effects of self-consistent flow on the wave behaviour of oscillatory reaction-diffusion models proposed for the Physarum plasmodium, by means of numerical simulation for the dispersion relation and weakly nonlinear analysis for derivation of the phase equation. We conclude that the flow term is able to increase the speed of phase waves (similar to elongation of wave length). We compare the theoretical consequences with real waves observed in the organism and also point out the physiological roles of these effects on control mechanisms of intracellular communication.

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.

Lessons from (patho)physiological tissue stiffness and their implications for drug screening, drug delivery and regenerative medicine.

PubMed

Chen, Wen Li Kelly; Simmons, Craig A

2011-04-30

Diseased tissues are noted for their compromised mechanical properties, which contribute to organ failure; regeneration entails restoration of tissue structure and thereby functions. Thus, the physical signature of a tissue is closely associated with its biological function. In this review, we consider a mechanics-centric view of disease and regeneration by drawing parallels between in vivo tissue-level observations and corroborative cellular evidence in vitro to demonstrate the importance of the mechanical stiffness of the extracellular matrix in these processes. This is not intended to devalue the importance of biochemical signaling; in fact, as we discuss, many mechanical stiffness-driven processes not only require cooperation with biochemical cues, but they ultimately converge at common signaling cascades to influence cell and tissue function in an integrative manner. The study of how physical and biochemical signals collectively modulate cell function not only brings forth a more holistic understanding of cell (patho)biology, but it also creates opportunities to control material properties to improve culture platforms for research and drug screening and aid in the rationale design of biomaterials for molecular therapy and tissue engineering applications. Copyright © 2011 Elsevier B.V. All rights reserved.

Hereditary sensory and autonomic neuropathy type 1 (HSANI) caused by a novel mutation in SPTLC2

PubMed Central

Murphy, Sinéad M.; Ernst, Daniela; Wei, Yu; Laurà, Matilde; Liu, Yo-Tsen; Polke, James; Blake, Julian; Winer, John; Houlden, Henry; Hornemann, Thorsten

2013-01-01

Objective: To describe the clinical and neurophysiologic phenotype of a family with hereditary sensory and autonomic neuropathy type 1 (HSANI) due to a novel mutation in SPTLC2 and to characterize the biochemical properties of this mutation. Methods: We screened 107 patients with HSAN who were negative for other genetic causes for mutations in SPTLC2. The biochemical properties of a new mutation were characterized in cell-free and cell-based activity assays. Results: A novel mutation (A182P) was found in 2 subjects of a single family. The phenotype of the 2 subjects was an ulcero-mutilating sensory-predominant neuropathy as described previously for patients with HSANI, but with prominent motor involvement and earlier disease onset in the first decade of life. Affected patients had elevated levels of plasma 1-deoxysphingolipids (1-deoxySLs). Biochemically, the A182P mutation was associated with a reduced canonical activity but an increased alternative activity with alanine, which results in largely increased 1-deoxySL levels, supporting their pathogenicity. Conclusion: This study confirms that mutations in SPTLC2 are associated with increased deoxySL formation causing HSANI. PMID:23658386

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

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.

Phytoremediation of Polycyclic Aromatic Hydrocarbons in Soils Artificially Polluted Using Plant-Associated-Endophytic Bacteria and Dactylis glomerata as the Bioremediation Plant.

PubMed

Gałązka, Ann; Gałązka, Rafał

2015-01-01

The reaction of soil microorganisms to the contamination of soil artificially polluted with polycyclic aromatic hydrocarbons (PAHs) was evaluated in pot experiments. The plant used in the tests was cock's foot (Dactylis glomerata). Three different soils artificially contaminated with PAHs were applied in the studies. Three selected PAHs (anthracene, phenanthrene, and pyrene) were used at the doses of 100, 500, and 1000 mg/kg d.m. of soil and diesel fuel at the doses of 100, 500, and 1000 mg/kg d.m. of soil. For evaluation of the synergistic effect of nitrogen fixing bacteria, the following strains were selected: associative Azospirillum spp. and Pseudomonas stutzerii. Additionally, in the bioremediation process, the inoculation of plants with a mixture of the bacterial strains in the amount of 1 ml suspension per 500 g of soil was used. Chamber pot-tests were carried out in controlled conditions during four weeks of plant growth period. The basic physical, microbiological and biochemical properties in contaminated soils were determined. The obtained results showed a statistically important increase in the physical properties of soils polluted with PAHs and diesel fuel compared with the control and also an important decrease in the content of PAHs and heavy metals in soils inoculated with Azospirillum spp. and P. stutzeri after cock's foot grass growth. The bioremediation processes were especially intensive in calcareous rendzina soil artificially polluted with PAHs.

Electro fluido dynamic techniques to design instructive biomaterials for tissue engineering and drug delivery

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

Guarino, Vincenzo, E-mail: vguarino@unina.it; Altobelli, Rosaria; Cirillo, Valentina

A large variety of processes and tools is continuously investigated to discover new solutions to design instructive materials with controlled chemical, physical and biological properties for tissue engineering and drug delivery. Among them, electro fluido dynamic techniques (EFDTs) are emerging as an interesting strategy, based on highly flexible and low-cost processes, to revisit old biomaterial’s manufacturing approach by utilizing electrostatic forces as the driving force for the fabrication of 3D architectures with controlled physical and chemical functionalities to guide in vitro and in vivo cell activities. By a rational selection of polymer solution properties and process conditions, EFDTs allow tomore » produce fibres and/or particles at micro and/or nanometric size scale which may be variously assembled by tailored experimental setups, thus giving the chance to generate a plethora of different 3D devices able to incorporate biopolymers (i.e., proteins, polysaccharides) or active molecules (e.g., drugs) for different applications. Here, we focus on the optimization of basic EFDTs - namely electrospinning, electrospraying and electrodynamic atomization - to develop active platforms (i.e., monocomponent, protein and drug loaded scaffolds and µ-scaffolds) made of synthetic (PCL, PLGA) or natural (chitosan, alginate) polymers. In particular, we investigate how to set materials and process parameters to impart specific morphological, biochemical or physical cues to trigger all the fundamental cell–biomaterial and cell– cell cross-talking elicited during regenerative processes, in order to reproduce the complex microenvironment of native or pathological tissues.« less

Electro fluido dynamic techniques to design instructive biomaterials for tissue engineering and drug delivery

NASA Astrophysics Data System (ADS)

Guarino, Vincenzo; Altobelli, Rosaria; Cirillo, Valentina; Ambrosio, Luigi

2015-12-01

A large variety of processes and tools is continuously investigated to discover new solutions to design instructive materials with controlled chemical, physical and biological properties for tissue engineering and drug delivery. Among them, electro fluido dynamic techniques (EFDTs) are emerging as an interesting strategy, based on highly flexible and low-cost processes, to revisit old biomaterial's manufacturing approach by utilizing electrostatic forces as the driving force for the fabrication of 3D architectures with controlled physical and chemical functionalities to guide in vitro and in vivo cell activities. By a rational selection of polymer solution properties and process conditions, EFDTs allow to produce fibres and/or particles at micro and/or nanometric size scale which may be variously assembled by tailored experimental setups, thus giving the chance to generate a plethora of different 3D devices able to incorporate biopolymers (i.e., proteins, polysaccharides) or active molecules (e.g., drugs) for different applications. Here, we focus on the optimization of basic EFDTs - namely electrospinning, electrospraying and electrodynamic atomization - to develop active platforms (i.e., monocomponent, protein and drug loaded scaffolds and µ-scaffolds) made of synthetic (PCL, PLGA) or natural (chitosan, alginate) polymers. In particular, we investigate how to set materials and process parameters to impart specific morphological, biochemical or physical cues to trigger all the fundamental cell-biomaterial and cell- cell cross-talking elicited during regenerative processes, in order to reproduce the complex microenvironment of native or pathological tissues.

The Interaction of Water with Solid Surfaces: Fundamental Aspects Revisited

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

Henderson, Michael A.

2002-05-01

Water is perhaps the most important and most pervasive chemical on our planet. The influence of water permeates virtually all areas of biochemical, chemical and physical importance, and is especially evident in phenomena occurring at the interfaces of solid surfaces. Since 1987, when Thiel and Madey (TM) published their review titled "The Interaction of Water with Solid Surfaces: Fundamental Aspects" in Surface Science Reports, there has been considerable progress made in further understanding the fundamental interactions of water with solid surfaces. In the decade and a half, the increased capability of surface scientists to probe at the molecular-level has resultedmore » in more detailed information of the properties of water on progressively more complicated materials and under more stringent conditions. This progress in understanding the properties of water on solid surfaces is evident both in areas for which surface science methodology has traditionally been strong (catalysis and electronic materials) and also in new areas not traditionally studied by surface scientists, such as electrochemistry, photoconversion, mineralogy, adhesion, sensors, atmospheric chemistry, and tribology. Researchers in all these fields grapple with very basic questions regarding the interactions of water with solid surfaces, such as how is water adsorbed, what are the chemical and electrostatic forces that constitute the adsorbed layer, how is water thermally or non-thermally activated, and how do coadsorbates influence these properties of water. The attention paid to these and other fundamental questions in the past decade and a half has been immense. In this review, experimental studies published since the TM review are assimilated with those covered by TM to provide a current picture of the fundamental interactions of water with solid surfaces.« less

Boron-containing organic pigments from a Jurassic red alga

PubMed Central

Wolkenstein, Klaus; Gross, Jürgen H.; Falk, Heinz

2010-01-01

Organic biomolecules that have retained their basic chemical structures over geological periods (molecular fossils) occur in a wide range of geological samples and provide valuable paleobiological, paleoenvironmental, and geochemical information not attainable from other sources. In rare cases, such compounds are even preserved with their specific functional groups and still occur within the organisms that produced them, providing direct information on the biochemical inventory of extinct organisms and their possible evolutionary relationships. Here we report the discovery of an exceptional group of boron-containing compounds, the borolithochromes, causing the distinct pink coloration of well-preserved specimens of the Jurassic red alga Solenopora jurassica. The borolithochromes are characterized as complicated spiroborates (boric acid esters) with two phenolic moieties as boron ligands, representing a unique class of fossil organic pigments. The chiroptical properties of the pigments unequivocally demonstrate a biogenic origin, at least of their ligands. However, although the borolithochromes originated from a fossil red alga, no analogy with hitherto known present-day red algal pigments was found. The occurrence of the borolithochromes or their possible diagenetic products in the fossil record may provide additional information on the classification and phylogeny of fossil calcareous algae. PMID:20974956

Boron-containing organic pigments from a Jurassic red alga.

PubMed

Wolkenstein, Klaus; Gross, Jürgen H; Falk, Heinz

2010-11-09

Organic biomolecules that have retained their basic chemical structures over geological periods (molecular fossils) occur in a wide range of geological samples and provide valuable paleobiological, paleoenvironmental, and geochemical information not attainable from other sources. In rare cases, such compounds are even preserved with their specific functional groups and still occur within the organisms that produced them, providing direct information on the biochemical inventory of extinct organisms and their possible evolutionary relationships. Here we report the discovery of an exceptional group of boron-containing compounds, the borolithochromes, causing the distinct pink coloration of well-preserved specimens of the Jurassic red alga Solenopora jurassica. The borolithochromes are characterized as complicated spiroborates (boric acid esters) with two phenolic moieties as boron ligands, representing a unique class of fossil organic pigments. The chiroptical properties of the pigments unequivocally demonstrate a biogenic origin, at least of their ligands. However, although the borolithochromes originated from a fossil red alga, no analogy with hitherto known present-day red algal pigments was found. The occurrence of the borolithochromes or their possible diagenetic products in the fossil record may provide additional information on the classification and phylogeny of fossil calcareous algae.

Elements Required for an Efficient NADP-Malic Enzyme Type C4 Photosynthesis1[C][W][OPEN

PubMed Central

Wang, Yu; Long, Stephen P.; Zhu, Xin-Guang

2014-01-01

C4 photosynthesis has higher light, nitrogen, and water use efficiencies than C3 photosynthesis. Although the basic anatomical, cellular, and biochemical features of C4 photosynthesis are well understood, the quantitative significance of each element of C4 photosynthesis to the high photosynthetic efficiency are not well defined. Here, we addressed this question by developing and using a systems model of C4 photosynthesis, which includes not only the Calvin-Benson cycle, starch synthesis, sucrose synthesis, C4 shuttle, and CO2 leakage, but also photorespiration and metabolite transport between the bundle sheath cells and mesophyll cells. The model effectively simulated the CO2 uptake rates, and the changes of metabolite concentrations under varied CO2 and light levels. Analyses show that triose phosphate transport and CO2 leakage can help maintain a high photosynthetic rate by balancing ATP and NADPH amounts in bundle sheath cells and mesophyll cells. Finally, we used the model to define the optimal enzyme properties and a blueprint for C4 engineering. As such, this model provides a theoretical framework for guiding C4 engineering and studying C4 photosynthesis in general. PMID:24521879

Resistive switching characteristic of electrolyte-oxide-semiconductor structures

NASA Astrophysics Data System (ADS)

Chen, Xiaoyu; Wang, Hao; Sun, Gongchen; Ma, Xiaoyu; Gao, Jianguang; Wu, Wengang

2017-08-01

The resistive switching characteristic of SiO2 thin film in electrolyte-oxide-semiconductor (EOS) structures under certain bias voltage is reported. To analyze the mechanism of the resistive switching characteristic, a batch of EOS structures were fabricated under various conditions and their electrical properties were measured with a set of three-electrode systems. A theoretical model based on the formation and rupture of conductive filaments in the oxide layer is proposed to reveal the mechanism of the resistive switching characteristic, followed by an experimental investigation of Auger electron spectroscopy (AES) and secondary ion mass spectroscopy (SIMS) to verify the proposed theoretical model. It is found that different threshold voltage, reverse leakage current and slope value features of the switching I-V characteristic can be observed in different EOS structures with different electrolyte solutions as well as different SiO2 layers made by different fabrication processes or in different thicknesses. With a simple fabrication process and significant resistive switching characteristic, the EOS structures show great potential for chemical/biochemical applications. Project supported by the National Natural Science Foundation of China (No. 61274116) and the National Basic Research Program of China (No. 2015CB352100).

Fluorescence lifetime based bioassays

NASA Astrophysics Data System (ADS)

Meyer-Almes, Franz-Josef

2017-12-01

Fluorescence lifetime (FLT) is a robust intrinsic property and material constant of fluorescent matter. Measuring this important physical indicator has evolved from a laboratory curiosity to a powerful and established technique for a variety of applications in drug discovery, medical diagnostics and basic biological research. This distinct trend was mainly driven by improved and meanwhile affordable laser and detection instrumentation on the one hand, and the development of suitable FLT probes and biological assays on the other. In this process two essential working approaches emerged. The first one is primarily focused on high throughput applications employing biochemical in vitro assays with no requirement for high spatial resolution. The second even more dynamic trend is the significant expansion of assay methods combining highly time and spatially resolved fluorescence data by fluorescence lifetime imaging. The latter approach is currently pursued to enable not only the investigation of immortal tumor cell lines, but also specific tissues or even organs in living animals. This review tries to give an actual overview about the current status of FLT based bioassays and the wide range of application opportunities in biomedical and life science areas. In addition, future trends of FLT technologies will be discussed.

Identification of the gene encoding the major NAD(P)H-flavin oxidoreductase of the bioluminescent bacterium Vibrio fischeri ATCC 7744.

PubMed Central

Zenno, S; Saigo, K; Kanoh, H; Inouye, S

1994-01-01

The gene encoding the major NAD(P)H-flavin oxidoreductase (flavin reductase) of the luminous bacterium Vibrio fischeri ATCC 7744 was isolated by using synthetic oligonucleotide probes corresponding to the N-terminal amino acid sequence of the enzyme. Nucleotide sequence analysis suggested that the major flavin reductase of V. fischeri consisted of 218 amino acids and had a calculated molecular weight of 24,562. Cloned flavin reductase expressed in Escherichia coli was purified virtually to homogeneity, and its basic biochemical properties were examined. As in the major flavin reductase in crude extracts of V. fischeri, cloned flavin reductase showed broad substrate specificity and served well as a catalyst to supply reduced flavin mononucleotide (FMNH2) to the bioluminescence reaction. The major flavin reductase of V. fischeri not only showed significant similarity in amino acid sequence to oxygen-insensitive NAD(P)H nitroreductases of Salmonella typhimurium, Enterobacter cloacae, and E. coli but also was associated with a low level of nitroreductase activity. The major flavin reductase of V. fischeri and the nitroreductases of members of the family Enterobacteriaceae would thus appear closely related in evolution and form a novel protein family. Images PMID:8206830

Microburger Biochemistry: Extraction and Spectral Characterization of Myoglyobin from Hamburger

NASA Astrophysics Data System (ADS)

Bylkas, Sheri A.; Andersson, Laura A.

1997-04-01

This experiment provides a demonstration of useful biochemical methods at a Basic or Advanced Level, depending upon the available spectrophotometric equipment. The protocol combines protein extraction, ox-i-dation and reduction, and simple spectroscopic analysis, as well as gel filtration chromatography and generation/analysis of spectral scans. Mammalian myoglobin (Mb) is a monomeric O2-binding protein that functions in muscle to store oxygen. The single iron protoporphyrin IX (heme) group is bound to protein by the amino acid Histidine93. The common, stable forms, Met-Mb and Oxy-Mb are studied because in a non-living system, red Oxy-Mb is converted to brown Met-Mb as bound O2 molecule is released. Mb is easily extracted from steak, to illustrate and address why fresh meat is red and aged meat is brown; the protein has unique spectral properties that are diagnostic for characterization of sample identity. After application of heme redox chemical methods, the MetMb or OxyMb samples can be studied spectroscopically. The color change between Oxy-Mb and Met-Mb is dramatic (illustrating bright red fresh meat vs. brown older meat), and method(s) used in this laboratory are simple, inexpensive, and non-harmful to the student.

Evaluation of the catalytic specificity, biochemical properties, and milk clotting abilities of an aspartic peptidase from Rhizomucor miehei.

PubMed

da Silva, Ronivaldo Rodrigues; Souto, Tatiane Beltramini; de Oliveira, Tássio Brito; de Oliveira, Lilian Caroline Gonçalves; Karcher, Daniel; Juliano, Maria Aparecida; Juliano, Luiz; de Oliveira, Arthur H C; Rodrigues, André; Rosa, Jose C; Cabral, Hamilton

2016-08-01

In this study, we detail the specificity of an aspartic peptidase from Rhizomucor miehei and evaluate the effects of this peptidase on clotting milk using the peptide sequence of k-casein (Abz-LSFMAIQ-EDDnp) and milk powder. Molecular mass of the peptidase was estimated at 37 kDa, and optimum activity was achieved at pH 5.5 and 55 °C. The peptidase was stable at pH values ranging from 3 to 5 and temperatures of up 45 °C for 60 min. Dramatic reductions in proteolytic activity were observed with exposure to sodium dodecyl sulfate, and aluminum and copper (II) chloride. Peptidase was inhibited by pepstatin A, and mass spectrometry analysis identified four peptide fragments (TWSISYGDGSSASGILAK, ASNGGGGEYIFGGYDSTK, GSLTTVPIDNSR, and GWWGITVDRA), similar to rhizopuspepsin. The analysis of catalytic specificity showed that the coagulant activity of the peptidase was higher than the proteolytic activity and that there was a preference for aromatic, basic, and nonpolar amino acids, particularly methionine, with specific cleavage of the peptide bond between phenylalanine and methionine. Thus, this peptidase may function as an important alternative enzyme in milk clotting during the preparation of cheese.

Effects of ammonia and hydrogen sulfide on physical and biochemical properties of the claw horn of Holstein cows

PubMed Central

Higuchi, Hidetoshi; Kurumado, Hisatoshi; Mori, Maya; Degawa, Aiko; Fujisawa, Hideyo; Kuwano, Atsutoshi; Nagahata, Hajime

2009-01-01

The effects of ammonia and hydrogen sulfide on the physical and biochemical properties of the claw horn of Holstein cows were evaluated. Significant (P < 0.05, 0.01) decreases in hardness and elasticity were found in claw horns soaked in ammonia (NH3) and hydrogen sulfide (H2S) solutions compared with those that were soaked in water for 12, 24, and 48 h. Water absorption rate, as a indicator of permeability barrier function, increased significantly (P < 0.05) over time during the soaking period and was found to be dependent on the concentrations of NH3 and H2S in the solutions. The contents of ceramide, the main lipid component for the permeability barrier system of the stratum corneum, were significantly decreased in claw horns soaked in NH3 and H2S solutions compared with the values before soaking. Quantities of eluted protein released from claw horns treated with NH3 and H2S solutions were approximately 20 times and 30 to 40 times greater than those released from claw horns treated with water alone. Interestingly, the quantities of cytokeratin 10, the main cytoskeletal protein of the stratum corneum, eluted from claw horns treated with NH3 and H2S solutions were markedly greater than the quantity released from horns soaked in water. Our results suggest that abnormal changes in the physical property of claw horn caused by NH3 and H2S treatment are due to disruption of the biochemical property of the claw horn induced by these chemical agents derived from slurry. PMID:19337390

Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties.

PubMed

Hobbs, Joanne K; Prentice, Erica J; Groussin, Mathieu; Arcus, Vickery L

2015-10-01

Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported--high thermostability and high catalytic activity--compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered "superior" to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a ΔleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network.

Racial differences in cortical bone and their relationship to biochemical variables in black and white children in the early stages of puberty

PubMed Central

Warden, Stuart J.; Hill, Kathleen M.; Ferira, Ashley J.; Laing, Emma M.; Martin, Berdine R.; Hausman, Dorothy B.; Weaver, Connie M.; Peacock, Munro; Lewis, Richard D.

2014-01-01

Introduction Racial differences in bone structure likely have roots in childhood as bone size develops predominantly during growth. This study aimed to compare cortical bone health within the tibial diaphysis of black and white children in the early stages of puberty, and explore the contributions of biochemical variables in explaining racial variation in cortical bone properties. Methods A cross-sectional study was performed comparing peripheral quantitative computed tomography-derived cortical bone measures of the tibial diaphysis and biochemical variables in 314 participants (n=155 males; n=164 blacks) in the early stages of puberty. Results Blacks had greater cortical volumetric bone mineral density, mass and size compared to whites (all p<0.01), contributing to blacks having 17.0% greater tibial strength (polar strength-strain index [SSIP]) (p<0.001). Turnover markers indicated blacks had higher bone formation (osteocalcin [OC] and bone specific alkaline phosphatase) and lower bone resorption (N-terminal telopeptide) than whites (all p<0.01). Blacks also had lower 25-hydroxyvitamin D [25(OH)D], and higher 1,25-dihydroxyvitamin D [1,25(OH)2D] and parathyroid hormone (PTH) (all p<0.05). There were no correlations between tibial bone properties, and 25(OH)D and PTH in whites (all p≥0.10); however, SSIP was negatively and positively correlated with 25(OH)D and PTH in blacks, respectively (all p≤0.02). Variation in bone cross-sectional area and SSIP attributable to race was partially explained by tibial length, 25(OH)D/PTH and OC. Conclusions Divergence in tibial cortical bone properties between blacks and whites is established by the early stages of puberty with the enhanced cortical bone properties in black children possibly being explained by higher PTH and OC. PMID:23093348

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.

Litchi chinensis as a Functional Food and a Source of Antitumor Compounds: An Overview and a Description of Biochemical Pathways.

PubMed

Emanuele, Sonia; Lauricella, Marianna; Calvaruso, Giuseppe; D'Anneo, Antonella; Giuliano, Michela

2017-09-08

Litchi is a tasty fruit that is commercially grown for food consumption and nutritional benefits in various parts of the world. Due to its biological activities, the fruit is becoming increasingly known and deserves attention not only for its edible part, the pulp, but also for its peel and seed that contain beneficial substances with antioxidant, cancer preventive, antimicrobial, and anti-inflammatory functions. Although literature demonstrates the biological activity of Litchi components in reducing tumor cell viability in in vitro or in vivo models, data about the biochemical mechanisms responsible for these effects are quite fragmentary. This review specifically describes, in a comprehensive analysis, the antitumor properties of the different parts of Litchi and highlights the main biochemical mechanisms involved.

Haematological and biochemical effects of polyphenolics in animal models.

PubMed

Gnanamani, Arumugam; Sudha, Munusamy; Deepa, G; Sudha, M; Deivanai, K; Sadulla, S

2008-07-01

Polyphenols of natural and synthetic origin are exploited in tanning sector to convert putrescible skin/hide to non-putrescible leather. However, only 30-40% of the inputs have been taken up for processing, the remaining is released as unspent. The existing conventional wastewater treatment systems are inefficient in removing or degrading these unspent polyphenols and thus detrimental to ecosystem. The present study demonstrates the evaluation of impact of both synthetic and natural polyphenols on biochemical and haematological properties of blood and serum in animal models. The results reveal that concentrations of polyphenols play a major role. At higher concentrations, irrespective of their nature, there was a marked change in the lipid profile (81% reduction), followed by insignificant change in glucose levels, RBC and WBC counts and other haematological parameters. At lower concentrations, no significant changes in the above said properties were observed.

Fauna-associated changes in chemical and biochemical properties of soil.

PubMed

Tripathi, G; Sharma, B M

2006-12-01

To study the impacts of abundance of woodlice, termites, and mites on some functional aspects of soil in order to elucidate the specific role of soil fauna in improving soil fertility in desert. Fauna-rich sites were selected as experimental sites and adjacent areas were taken as control. Soil samples were collected from both sites. Soil respiration was measured at both sites. The soil samples were sent to laboratory, their chemical and biochemical properties were analyzed. Woodlice showed 25% decrease in organic carbon and organic matter as compared to control site. Whereas termites and mites showed 58% and 16% decrease in organic carbon and organic matter. In contrast, available nitrogen (nitrate and ammonical both) and phosphorus exhibited 2-fold and 1.2-fold increase, respectively. Soil respiration and dehydrogenase activity at the sites rich in woodlice, termites and mites produced 2.5-, 3.5- and 2-fold increases, respectively as compared to their control values. Fauna-associated increase in these biological parameters clearly reflected fauna-induced microbial activity in soil. Maximum decrease in organic carbon and increase in nitrate-nitrogen and ammonical-nitrogen, available phosphorus, soil respiration and dehydrogenase activity were produced by termites and minimum by mites reflecting termite as an efficient soil improver in desert environment. The soil fauna-associated changes in chemical (organic carbon, nitrate-nitrogen, ammonical-nitrogen, phosphorus) and biochemical (soil respiration, dehydrogenase activity) properties of soil improve soil health and help in conservation of desert pedoecosystem.

From Protein Engineering to Immobilization: Promising Strategies for the Upgrade of Industrial Enzymes

PubMed Central

Singh, Raushan Kumar; Tiwari, Manish Kumar; Singh, Ranjitha; Lee, Jung-Kul

2013-01-01

Enzymes found in nature have been exploited in industry due to their inherent catalytic properties in complex chemical processes under mild experimental and environmental conditions. The desired industrial goal is often difficult to achieve using the native form of the enzyme. Recent developments in protein engineering have revolutionized the development of commercially available enzymes into better industrial catalysts. Protein engineering aims at modifying the sequence of a protein, and hence its structure, to create enzymes with improved functional properties such as stability, specific activity, inhibition by reaction products, and selectivity towards non-natural substrates. Soluble enzymes are often immobilized onto solid insoluble supports to be reused in continuous processes and to facilitate the economical recovery of the enzyme after the reaction without any significant loss to its biochemical properties. Immobilization confers considerable stability towards temperature variations and organic solvents. Multipoint and multisubunit covalent attachments of enzymes on appropriately functionalized supports via linkers provide rigidity to the immobilized enzyme structure, ultimately resulting in improved enzyme stability. Protein engineering and immobilization techniques are sequential and compatible approaches for the improvement of enzyme properties. The present review highlights and summarizes various studies that have aimed to improve the biochemical properties of industrially significant enzymes. PMID:23306150

Simple route for nano-hydroxyapatite properties expansion.

PubMed

Rojas, L; Olmedo, H; García-Piñeres, A J; Silveira, C; Tasic, L; Fraga, F; Montero, M L

2015-10-20

Simple surface modification of nano-hydroxyapatite, through acid-basic reactions, allows expanding the properties of this material. Introduction of organic groups such as hydrophobic alkyl chains, carboxylic acid, and amide or amine basic groups on the hydroxyapatite surface systematically change the polarity, surface area, and reactivity of hydroxyapatite without modifying its phase. Physical and chemical properties of the new derivative particles were analyzed. The biocompatibility of modified Nano-Hap on Raw 264.7 cells was also assessed.

Organic Food: A Comparative Study of the Effect of Tomato Cultivars and Cultivation Conditions on the Physico-Chemical Properties

PubMed Central

Araujo, Jacqueline C.; Telhado, Samuel F. P.

2015-01-01

The objective of this review was to present an update of the currently managed studies on the characterization physical, chemical, and sensory analysis of several tomato cultivars. This review has indicated the importance of farming system and genotype on sensory and biochemical characteristics. It is necessary to use selected genotypes responding positively to organic farming in terms of sensory, biochemical characteristics and productivity aspects and to evaluate systems over more than one year of sampling. PMID:28231203

Histochemical identification of malignant and premalignant lesions

NASA Astrophysics Data System (ADS)

Liebow, Charles; Maloney, M. J.

1991-06-01

Malignant and transforming cells can be identified by biochemical parameters which can be used to localize lesions in situ for laser surgery. These cells express unique proteins, proteins in unusual quantities, or other biochemical alterations which can be utilized to image lesions of such cells. Several methods have been identified, both in vitro and in vivo, to identify such lesions. Several antibodies were examined for their properties of tissue identification, including CEA, F36/22, and AE1/AE3. F36/22, an antibody developed by M. T. Chu against human breast cancer cells, associated with two lines of oral cancer (KB and HCPC), and against two naturally occurring human oral squamous cell cancers. CEA, an antibody developed against human colon cancer, also reacted against both cell lines and both pathological samples. AE1/AE3, developed against normal fibrous components, also reacted against the samples, but in a much less regular manner. F36/22 associated with the histologically identifiably most dedifferentiated cells at the leading edge of the invading cancer. CEA, on the other hand, associated with more quiescent, older, established cancer cells. This demonstrates that antibodies developed against cancers of different organs can be used to identify a wide variety of cancers, and may have prognostic value. F36/22 coupled to fluorescein was used to identify oral cancer cells. Other properties of cancers and developing cancers can also be exploited to identify cancers, including their over-expression of tyrosine kinase and tyrosine kinase stimulating hormones such as Epidermal Growth Factor (EGF). A model of premalignant lesion produced in the hamster buccal cheek pouch with 6 week application of DMBA over-expresses constitutive tyrosine kinase which can be demonstrated biochemically. This initiated lesion can be promoted to frank cancer by growth factors released in response to laser surgery. Preliminary results suggest that these lesions can be identified by Photofrin II uptake. This work suggests that biochemical properties of cancers can be used to identify premalignant cells.

Molecular Cloning, Biochemical Characterization, and Antitumor Properties of a Novel L-Asparaginase from Synechococcus elongatus PCC6803.

PubMed

Kebeish, R; El-Sayed, A; Fahmy, H; Abdel-Ghany, A

2016-10-01

L-asparaginase (EC 3.5.1.1), which catalyzes the deamidation of L-asparagine to L-aspartic acid and ammonia, has been widely used as a key therapeutic tool in the treatment of tumors. The current commercially available L-asparaginases, produced from bacteria, have signs of toxicity and hypersensitivity reactions during the course of tumor therapy. Therefore, searching for L-asparaginases with unique biochemical properties and fewer adverse effects was the objective of this work. In this study, cyanobacterial strain Synechococcus elongatus PCC6803 was found as a novel source of L-asparaginase. The L-asparaginase gene coding sequence (gi:939195038) was cloned and expressed in E. coli BL21(DE3), and the recombinant protein (Se.ASPII) was purified by affinity chromatography. The enzyme has high affinity towards L-asparagine and shows very weak affinity towards L-glutamine. The enzymatic properties of the recombinant enzyme were investigated, and the kinetic parameters (K m , V max ) were measured. The pH and temperature dependence profiles of the novel enzyme were analyzed. The work was extended to measure the antitumor properties of the novel enzyme against different human tumor cell lines.

Alternative Fuels Characterization | Transportation Research | NREL

Science.gov Websites

. Research at NREL focuses on the basic properties of these fuels and what levels of oxygen can be tolerated conventional cars and on understanding the performance of flex-fuel vehicles that can operate on ethanol levels basic properties of these fuels, as well as determining what levels of oxygen can be tolerated in drop

41 CFR 102-83.10 - What basic location of space policy governs an Executive agency?

Code of Federal Regulations, 2014 CFR

2014-01-01

... space policy governs an Executive agency? 102-83.10 Section 102-83.10 Public Contracts and Property... PROPERTY 83-LOCATION OF SPACE General Provisions § 102-83.10 What basic location of space policy governs an... delineated area within which it wishes to locate specific activities, consistent with its mission and program...

41 CFR 102-83.10 - What basic location of space policy governs an Executive agency?

Code of Federal Regulations, 2012 CFR

2012-01-01

... space policy governs an Executive agency? 102-83.10 Section 102-83.10 Public Contracts and Property... PROPERTY 83-LOCATION OF SPACE General Provisions § 102-83.10 What basic location of space policy governs an... delineated area within which it wishes to locate specific activities, consistent with its mission and program...

41 CFR 102-83.10 - What basic location of space policy governs an Executive agency?

Code of Federal Regulations, 2013 CFR

2013-07-01

... space policy governs an Executive agency? 102-83.10 Section 102-83.10 Public Contracts and Property... PROPERTY 83-LOCATION OF SPACE General Provisions § 102-83.10 What basic location of space policy governs an... delineated area within which it wishes to locate specific activities, consistent with its mission and program...

41 CFR 102-83.10 - What basic location of space policy governs an Executive agency?

Code of Federal Regulations, 2011 CFR

2011-01-01

... space policy governs an Executive agency? 102-83.10 Section 102-83.10 Public Contracts and Property... PROPERTY 83-LOCATION OF SPACE General Provisions § 102-83.10 What basic location of space policy governs an... delineated area within which it wishes to locate specific activities, consistent with its mission and program...

41 CFR 102-83.10 - What basic location of space policy governs an Executive agency?

Code of Federal Regulations, 2010 CFR

2010-07-01

... space policy governs an Executive agency? 102-83.10 Section 102-83.10 Public Contracts and Property... PROPERTY 83-LOCATION OF SPACE General Provisions § 102-83.10 What basic location of space policy governs an... delineated area within which it wishes to locate specific activities, consistent with its mission and program...

Know your fibers : process and properties, or, a material science approach to designing pulp molded products

Treesearch

John F. Hunt

1998-01-01

The following results are preliminary, but show some basic information that will be used in an attempt to model pulp molded structures so that by measuring several basic fundamental properties of a fiber furnish and specifying process conditions, a molded structure could be designed for a particular performance need.

Revisiting Preschoolers' Living Things Concept: A Microgenetic Analysis of Conceptual Change in Basic Biology

ERIC Educational Resources Information Center

Opfer, John E.; Siegler, Robert S.

2004-01-01

Many preschoolers know that plants and animals share basic biological properties, but this knowledge does not usually lead them to conclude that plants, like animals, are living things. To resolve this seeming paradox, we hypothesized that preschoolers largely base their judgments of life status on a biological property, capacity for teleological…

Biochemical properties and subcellular localization of tyrosine aminotransferases in Arabidopsis thaliana.

PubMed

Wang, Minmin; Toda, Kyoko; Maeda, Hiroshi A

2016-12-01

Plants produce various L-tyrosine (Tyr)-derived compounds that are of pharmaceutical or nutritional importance to humans. Tyr aminotransferase (TAT) catalyzes the reversible transamination between Tyr and 4-hydroxyphenylpyruvate (HPP), the initial step in the biosynthesis of many Tyr-derived plant natural products. Herein reported is the biochemical characterization and subcellular localization of TAT enzymes from the model plant Arabidopsis thaliana. Phylogenetic analysis showed that Arabidopsis has at least two homologous TAT genes, At5g53970 (AtTAT1) and At5g36160 (AtTAT2). Their recombinant enzymes showed distinct biochemical properties: AtTAT1 had the highest activity towards Tyr, while AtTAT2 exhibited a broad substrate specificity for both amino and keto acid substrates. Also, AtTAT1 favored the direction of Tyr deamination to HPP, whereas AtTAT2 preferred transamination of HPP to Tyr. Subcellular localization analysis using GFP-fusion proteins and confocal microscopy showed that AtTAT1, AtTAT2, and HPP dioxygenase (HPPD), which catalyzes the subsequent step of TAT, are localized in the cytosol, unlike plastid-localized Tyr and tocopherol biosynthetic enzymes. Furthermore, subcellular fractionation indicated that, while HPPD activity is restricted to the cytosol, TAT activity is detected in both cytosolic and plastidic fractions of Arabidopsis leaf tissue, suggesting that an unknown aminotransferase(s) having TAT activity is also present in the plastids. Biochemical and cellular analyses of Arabidopsis TATs provide a fundamental basis for future in vivo studies and metabolic engineering for enhanced production of Tyr-derived phytochemicals in plants. Copyright © 2016 Elsevier Ltd. All rights reserved.

Correlation Between Monoamine Oxidase Inhibitors and Anticonvulsants

PubMed Central

Dwivedi, Chandradhar; Misra, Radhey S.; Chaudhari, Anshumali; Parmar, Surendra S.

1980-01-01

Monoamine oxidase inhibitory and anticonvulsant properties of 2-substituted styryl-6-bromo-3-(4-ethylbenzoate/4 benzhydrazide)-4-quinazoles are studied. All styryl quinazolone esters except compound number 9 exhibited monoamine oxidase inhibitory properties during oxidative deamination of kynuramine. Corresponding hydrazides were found to have relatively higher activity. All these quinazolones were able to protect against pentylenetetrazol induced seizures. These observations in general do not prove that monoamine oxidase inhibitory properties represent the biochemical basis for the anticonvulsant activity of these compounds. PMID:7420438

Sphingobium sp. SYK-6 LigG involved in lignin degradation is structurally and biochemically related to the glutathione transferase ω class.

PubMed

Meux, Edgar; Prosper, Pascalita; Masai, Eiji; Mulliert, Guillermo; Dumarçay, Stéphane; Morel, Mélanie; Didierjean, Claude; Gelhaye, Eric; Favier, Frédérique

2012-11-16

SpLigG is one of the three glutathione transferases (GSTs) involved in the process of lignin breakdown in the soil bacterium Sphingobium sp. SYK-6. Sequence comparisons showed that SpLigG and several proteobacteria homologues form an independent cluster within cysteine-containing GSTs. The relationship between SpLigG and other GSTs was investigated. The X-ray structure and biochemical properties of SpLigG indicate that this enzyme belongs to the omega class of glutathione transferases. However, the hydrophilic substrate binding site of SpLigG, together with its known ability to stereoselectively deglutathionylate the physiological substrate α-glutathionyl-β-hydroxypropiovanillone, argues for broadening the definition of the omega class. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Nutritional Evaluation of Australian Microalgae as Potential Human Health Supplements

PubMed Central

Kent, Megan; Welladsen, Heather M.; Mangott, Arnold; Li, Yan

2015-01-01

This study investigated the biochemical suitability of Australian native microalgal species Scenedesmus sp., Nannochloropsis sp., Dunaliella sp., and a chlorophytic polyculture as nutritional supplements for human health. The four microalgal cultures were harvested during exponential growth, lyophilized, and analysed for proximate composition (moisture, ash, lipid, carbohydrates, and protein), pigments, and amino acid and fatty acid profiles. The resulting nutritional value, based on biochemical composition, was compared to commercial Spirulina and Chlorella products. The Australian native microalgae exhibited similar, and in several cases superior, organic nutritional properties relative to the assessed commercial products, with biochemical profiles rich in high-quality protein, nutritious polyunsaturated fats (such as α-linolenic acid, arachidonic acid, and eicosapentaenoic acid), and antioxidant pigments. These findings indicate that the microalgae assessed have great potential as multi-nutrient human health supplements. PMID:25723496

Dependence of the basic properties of meso-nitro-substituted derivatives of β-octaethylporphyrin on the nature of substituents

NASA Astrophysics Data System (ADS)

Pukhovskaya, S. G.; Ivanova, Yu. B.; Nam, Dao The; Vashurin, A. S.

2014-10-01

Spectrophotometric titration is used to study the basic properties of a series of porphyrins with a continuously increasing degree of macrocycle deformation resulting from the introduction of strong electron-withdrawing substituents: 2,3,7,8,12,13,17,18-octaethylporphyrin ( I), 5-nitro-2,3,7,8,12,13,17,18-octaethylporphyrin ( II), 5,15-dinitro-2,3,7,8,12,13,17,18-octaethylporphyrin ( III), 5,10,15-trinitro-2,3,7,8,12,13,17,18-octaethylporphyrin ( IV), and 5,10,15,20-tetranitro-2,3,7,8,12,13,17,18-octaethylporphyrin ( V). It is found that the values of log K b (total basicity constants) obtained for the investigated compounds consistently diminish with an increase in the number of meso-substituents: 11.85 ( I) > 10.45 ( II) > 10.31 ( III) > 10.23 ( IV) > 9.56 ( V). It is shown that two opposing factors, the steric and electronic effects of the substituents, change the basic properties of the above series of compounds.

Posttranslational nitro-glycative modifications of albumin in Alzheimer's disease: implications in cytotoxicity and amyloid-β peptide aggregation.

PubMed

Ramos-Fernández, Eva; Tajes, Marta; Palomer, Ernest; Ill-Raga, Gerard; Bosch-Morató, Mònica; Guivernau, Biuse; Román-Dégano, Irene; Eraso-Pichot, Abel; Alcolea, Daniel; Fortea, Juan; Nuñez, Laura; Paez, Antonio; Alameda, Francesc; Fernández-Busquets, Xavier; Lleó, Alberto; Elosúa, Roberto; Boada, Mercé; Valverde, Miguel A; Muñoz, Francisco J

2014-01-01

Glycation and nitrotyrosination are pathological posttranslational modifications that make proteins prone to losing their physiological properties. Since both modifications are increased in Alzheimer's disease (AD) due to amyloid-β peptide (Aβ) accumulation, we have studied their effect on albumin, the most abundant protein in cerebrospinal fluid and blood. Brain and plasmatic levels of glycated and nitrated albumin were significantly higher in AD patients than in controls. In vitro turbidometry and electron microscopy analyses demonstrated that glycation and nitrotyrosination promote changes in albumin structure and biochemical properties. Glycated albumin was more resistant to proteolysis and less uptake by hepatoma cells occurred. Glycated albumin also reduced the osmolarity expected for a solution containing native albumin. Both glycation and nitrotyrosination turned albumin cytotoxic in a cell type-dependent manner for cerebral and vascular cells. Finally, of particular relevance to AD, these modified albumins were significantly less effective in avoiding Aβ aggregation than native albumin. In summary, nitrotyrosination and especially glycation alter albumin structural and biochemical properties, and these modifications might contribute for the progression of AD.

Radionuclides, radiotracers and radiopharmaceuticals for in vivo diagnosis

NASA Astrophysics Data System (ADS)

Wiebe, Leonard I.

Radioactive tracers for in vivo clinical diagnosis fall within a narrow, strictly-defined set of specifications in respect of their physical properties, chemical and biochemical characteristics, and (approved) medical applications. The type of radioactive decay and physical half-life of the radionuclide are immutable properties which, along with the demands of production and supply, limit the choice of radionuclides used in medicine to only a small fraction of those known to exist. In use, the biochemical and physiological properties of a radiotracer are dictated by the chemical form of the radionuclide. This chemical form may range from elemental, molecular or ionic, to complex compounds formed by coordinate or covalent bonding of the radionuclide to either simple organic or inorganic molecules, or complex macromolecules. Few of the radiotracers which are tested in model systems ever become radiopharmaceuticals in the strictest sense. Radionuclides, radiotracers and radiopharmaceuticals in use are reviewed. Drug legislation and regulations concerning drug manufacture, as well as hospital ethical constraints and legislation concerning unsealed sources of radiation must all be satisfied in order to translate a radiopharmaceutical from the laboratory to clinical use.

Influence of biochemical composition during hydrothermal liquefaction of algae on product yields and fuel properties.

PubMed

Shakya, Rajdeep; Adhikari, Sushil; Mahadevan, Ravishankar; Shanmugam, Saravanan R; Nam, Hyungseok; Hassan, El Barbary; Dempster, Thomas A

2017-11-01

Hydrothermal liquefaction (HTL) of nine algae species were performed at two reaction temperatures (280 and 320°C) to compare the effect of their biomass composition on product yields and properties. Results obtained after HTL indicate large variations in terms of bio-oil yields and its properties. The maximum bio-oil yield (66wt%) was obtained at 320°C with a high lipid containing algae Nannochloropsis. The higher heating value of bio-oils ranged from 31 to 36MJ/kg and around 50% of the bio-oils was in the vacuum gas oil range while high lipid containing algae Nannochloropsis contained a significant portion (33-42%) in the diesel range. A predictive relationship between bio-oil yields and biochemical compositions was developed and showed a broad agreement between predictive and experimental yields. The aqueous phases obtained had high amount of TOC (12-43g/L), COD (35-160g/L), TN (1-18g/L), ammonium (0.34-12g/L) and phosphate (0.7-12g/L). Copyright © 2017 Elsevier Ltd. All rights reserved.

In situ self-assembly of polarizing chromogen nanofibers catalyzed with hybrid films of gold nanoparticles and cellulose

NASA Astrophysics Data System (ADS)

Liu, Zhiming; Wu, Wenjian

2017-09-01

Hybrid materials of metal nanoparticles and biopolymers with catalytic properties are very promising to be used as detectors in biochemical reactions. In this work, the catalytic properties and relevant in situ self-assembly abilities of hybrid films of gold nanoparticles (GNPs) and cellulose for the oxidation of benign chromogen 3,3‧,5,5‧-tetramethylbenzidine (TMB) with hydrogen peroxide (H2O2) are revealed for the first time. The peroxidase-like properties of hybrid films are inherited from those of colloidal GNPs and increase with their contents of GNPs. It is discovered that the oxidized products of TMB grow in situ and assemble into rod-like and tumbleweed-like nanofiber assemblies on hybrid films. The rod-like nanofibers show a magnificent polarizing phenomenon under polarized light because of polycrystalline globular nanoparticles inside. The in situ self-assembly of polarizing nanofibers of chromogen catalyzed with hybrid films creates an opportunity for the synthesis of novel organic nanomaterials and the enhanced detection of biochemical products under polarized light.

Developing Meaning for Algebraic Procedures: An Exploration of the Connections Undergraduate Students Make between Algebraic Rational Expressions and Basic Number Properties

ERIC Educational Resources Information Center

Yantz, Jennifer

2013-01-01

The attainment and retention of later algebra skills in high school has been identified as a factor significantly impacting the postsecondary success of students majoring in STEM fields. Researchers maintain that learners develop meaning for algebraic procedures by forming connections to the basic number system properties. The present study…

Technetium-99m: basic nuclear physics and chemical properties.

PubMed

Castronovo, F P

1975-05-01

The nuclear physics and chemical properties of technetium-99m are reviewed. The review of basic nuclear physics includes: classification of nuclides, nuclear stability, production of radionuclides, artificial production of molybdenum-99, production of technetium 99m and -99Mo-99mTc generators. The discussion of the chemistry of technetium includes a profile of several -99mCc-labeled radiopharmaceuticals.

Spearhead Nanometric Field-Effect Transistor Sensors for Single-Cell Analysis.

PubMed

Zhang, Yanjun; Clausmeyer, Jan; Babakinejad, Babak; Córdoba, Ainara López; Ali, Tayyibah; Shevchuk, Andrew; Takahashi, Yasufumi; Novak, Pavel; Edwards, Christopher; Lab, Max; Gopal, Sahana; Chiappini, Ciro; Anand, Uma; Magnani, Luca; Coombes, R Charles; Gorelik, Julia; Matsue, Tomokazu; Schuhmann, Wolfgang; Klenerman, David; Sviderskaya, Elena V; Korchev, Yuri

2016-03-22

Nanometric field-effect-transistor (FET) sensors are made on the tip of spear-shaped dual carbon nanoelectrodes derived from carbon deposition inside double-barrel nanopipettes. The easy fabrication route allows deposition of semiconductors or conducting polymers to comprise the transistor channel. A channel from electrodeposited poly pyrrole (PPy) exhibits high sensitivity toward pH changes. This property is exploited by immobilizing hexokinase on PPy nano-FETs to give rise to a selective ATP biosensor. Extracellular pH and ATP gradients are key biochemical constituents in the microenvironment of living cells; we monitor their real-time changes in relation to cancer cells and cardiomyocytes. The highly localized detection is possible because of the high aspect ratio and the spear-like design of the nano-FET probes. The accurately positioned nano-FET sensors can detect concentration gradients in three-dimensional space, identify biochemical properties of a single living cell, and after cell membrane penetration perform intracellular measurements.

Spearhead Nanometric Field-Effect Transistor Sensors for Single-Cell Analysis

PubMed Central

Córdoba, Ainara López; Ali, Tayyibah; Shevchuk, Andrew; Takahashi, Yasufumi; Novak, Pavel; Edwards, Christopher; Lab, Max; Gopal, Sahana; Chiappini, Ciro; Anand, Uma; Magnani, Luca; Coombes, R. Charles; Gorelik, Julia; Matsue, Tomokazu; Schuhmann, Wolfgang; Klenerman, David; Sviderskaya, Elena V.; Korchev, Yuri

2016-01-01

Nanometric field-effect-transistor (FET) sensors are made on the tip of spear-shaped dual carbon nanoelectrodes derived from carbon deposition inside double-barrel nanopipettes. The easy fabrication route allows deposition of semiconductors or conducting polymers to comprise the transistor channel. A channel from electrodeposited poly pyrrole (PPy) exhibits high sensitivity toward pH changes. This property is exploited by immobilizing hexokinase on PPy nano-FETs to give rise to a selective ATP biosensor. Extracellular pH and ATP gradients are key biochemical constituents in the microenvironment of living cells; we monitor their real-time changes in relation to cancer cells and cardiomyocytes. The highly localized detection is possible because of the high aspect ratio and the spear-like design of the nano-FET probes. The accurately positioned nano-FET sensors can detect concentration gradients in three-dimensional space, identify biochemical properties of a single living cell, and after cell membrane penetration perform intracellular measurements. PMID:26816294

Characteristics of opportunistic species of the Corynebacterium and related coryneforms isolated from different clinical materials.

PubMed

Chudnicka, Alina; Kozioł-Montewka, Maria

2003-01-01

Taking into account the increasing contribution of species, which enter into the composition of purely physiological flora of the organism, of the Corynebacterium type and related coryneforms in opportunistic infections in people, the analysis of strains was made from different clinical materials from patients. Their identification was made on the basis of biochemical properties and their antibiotic sensitivity was characterized. It was found that strains with similar biochemical properties (C.striatum, C.amycolatum ) should be identified by means of genetic methods, all the more that they were isolated from clinically important materials. Out of the examined strains the biggest number of infections were caused by C.pseudodiphtheriticum, next C. striatum/C. amycolatum, Brevibacterium sp., C.propinquum, one: C.afermentans, C.jeikeium, C.group G, C.group F1, C.accolens, C.macqinleyi. The highest sensitivity of isolated strains was to Vancomycin, Teicoplanin and Imipenem.

Taxonomic composition and physiological and biochemical properties of bacteria in the digestive tracts of earthworms

NASA Astrophysics Data System (ADS)

Byzov, B. A.; Tikhonov, V. V.; Nechitailo, T. Yu.; Demin, V. V.; Zvyagintsev, D. G.

2015-03-01

Several hundred bacterial strains belonging to different taxa were isolated and identified from the digestive tracts of soil and compost earthworms. Some physiological and biochemical properties of the bacteria were characterized. The majority of intestinal bacteria in the earthworms were found to be facultative anaerobes. The intestinal isolates as compared to the soil ones had elevated activity of proteases and dehydrogenases. In addition, bacteria associated with earthworms' intestines are capable of growth on humic acids as a sole carbon source. Humic acid stimulated the growth of the intestinal bacteria to a greater extent than those of the soil ones. In the digestive tracts, polyphenol oxidase activity was found. Along with the data on the taxonomic separation of the intestinal bacteria, the features described testified to the presence of a group of bacteria in the earthworms intestines that is functionally characteristic and is different from the soil bacteria.

Roles for Msx and Dlx homeoproteins in vertebrate development.

PubMed

Bendall, A J; Abate-Shen, C

2000-04-18

This review provides a comparative analysis of the expression patterns, functions, and biochemical properties of Msx and Dlx homeobox genes. These comprise multi-gene families that are closely related with respect to sequence features as well as expression patterns during vertebrate development. Thus, members of the Msx and Dlx families are expressed in overlapping, but distinct, patterns and display complementary or antagonistic functions, depending upon the context. A common theme shared among Msx and Dlx genes is that they are required during early, middle, and late phases of development where their differential expression mediates patterning, morphogenesis, and histogenesis of tissues in which they are expressed. With respect to their biochemical properties, Msx proteins function as transcriptional repressors, while Dlx proteins are transcriptional activators. Moreover, their ability to oppose each other's transcriptional actions implies a mechanism underlying their complementary or antagonistic functions during development.

Physiological-biochemical properties and the ability to synthesize polyhydroxyalkanoates of the glucose-utilizing strain of the hydrogen bacterium Ralstonia eutropha B8562.

PubMed

Volova, T G; Trusova, M Y; Kalacheva, G S; Kozhevnicov, I V

2006-11-01

Physiological-biochemical, genetic, and cultural properties of the glucose-utilizing mutant strain Ralstonia eutropha B8562 have been compared with those of its parent strain R. eutropha B5786. It has been shown that growth characteristics of the strain cultured on glucose as the sole carbon and energy source are comparable with those of the parent strain. Strain B8562 is characterized by high polyhydroxyalkanoate (PHA) yields on different carbon sources (CO(2), fructose, and glucose). PHA accumulation in the strain batch cultured on glucose under nitrogen deficiency reaches 90 %. The major monomer in the PHA is beta-hydroxybutyric acid (more than 99 mol %); the identified minor components are beta-hydroxyvaleric acid (0.25-0.72 mol %) and beta-hydroxyhexanoic acid (0.08-1.5 mol %). The strain is a promising PHA producer on available sugar-containing media with glucose.

Physical, Chemical and Biochemical Modifications of Protein-Based Films and Coatings: An Extensive Review

PubMed Central

Zink, Joël; Wyrobnik, Tom; Prinz, Tobias; Schmid, Markus

2016-01-01

Protein-based films and coatings are an interesting alternative to traditional petroleum-based materials. However, their mechanical and barrier properties need to be enhanced in order to match those of the latter. Physical, chemical, and biochemical methods can be used for this purpose. The aim of this article is to provide an overview of the effects of various treatments on whey, soy, and wheat gluten protein-based films and coatings. These three protein sources have been chosen since they are among the most abundantly used and are well described in the literature. Similar behavior might be expected for other protein sources. Most of the modifications are still not fully understood at a fundamental level, but all the methods discussed change the properties of the proteins and resulting products. Mastering these modifications is an important step towards the industrial implementation of protein-based films. PMID:27563881

Order-of-magnitude physics of neutron stars. Estimating their properties from first principles

NASA Astrophysics Data System (ADS)

Reisenegger, Andreas; Zepeda, Felipe S.

2016-03-01

We use basic physics and simple mathematics accessible to advanced undergraduate students to estimate the main properties of neutron stars. We set the stage and introduce relevant concepts by discussing the properties of "everyday" matter on Earth, degenerate Fermi gases, white dwarfs, and scaling relations of stellar properties with polytropic equations of state. Then, we discuss various physical ingredients relevant for neutron stars and how they can be combined in order to obtain a couple of different simple estimates of their maximum mass, beyond which they would collapse, turning into black holes. Finally, we use the basic structural parameters of neutron stars to briefly discuss their rotational and electromagnetic properties.

Prediction of pH-Dependent Hydrophobic Profiles of Small Molecules from Miertus-Scrocco-Tomasi Continuum Solvation Calculations.

PubMed

Zamora, William J; Curutchet, Carles; Campanera, Josep M; Luque, F Javier

2017-10-26

Hydrophobicity is a key physicochemical descriptor used to understand the biological profile of (bio)organic compounds as well as a broad variety of biochemical, pharmacological, and toxicological processes. This property is estimated from the partition coefficient between aqueous and nonaqueous environments for neutral compounds (P N ) and corrected for the pH-dependence of ionizable compounds as the distribution coefficient (D). Here, we have extended the parametrization of the Miertus-Scrocco-Tomasi continuum solvation model in n-octanol to nitrogen-containing heterocyclic compounds, as they are present in many biologically relevant molecules (e.g., purines and pyrimidines bases, amino acids, and drugs), to obtain accurate log P N values for these molecules. This refinement also includes solvation calculations for ionic species in n-octanol with the aim of reproducing the experimental partition of ionic compounds (P I ). Finally, the suitability of different formalisms to estimate the distribution coefficient for a wide range of pH values has been examined for a set of small acidic and basic compounds. The results indicate that in general the simple pH-dependence model of the ionizable compound in water suffices to predict the partitioning at or around physiological pH. However, at extreme pH values, where ionic species are predominant, more elaborate models provide a better prediction of the n-octanol/water distribution coefficient, especially for amino acid analogues. Finally, the results also show that these formalisms are better suited to reproduce the experimental pH-dependent distribution curves of log D for both acidic and basic compounds as well as for amino acid analogues.

Structural analysis and unique molecular recognition properties of a Bauhinia forficata lectin that inhibits cancer cell growth.

PubMed

Lubkowski, Jacek; Durbin, Sarah V; Silva, Mariana C C; Farnsworth, David; Gildersleeve, Jeffrey C; Oliva, Maria Luiza V; Wlodawer, Alexander

2017-02-01

Lectins have been used at length for basic research and clinical applications. New insights into the molecular recognition properties enhance our basic understanding of carbohydrate-protein interactions and aid in the design/development of new lectins. In this study, we used a combination of cell-based assays, glycan microarrays, and X-ray crystallography to evaluate the structure and function of the recombinant Bauhinia forficata lectin (BfL). The lectin was shown to be cytostatic for several cancer cell lines included in the NCI-60 panel; in particular, it inhibited growth of melanoma cancer cells (LOX IMVI) by over 95%. BfL is dimeric in solution and highly specific for binding of oligosaccharides and glycopeptides with terminal N-acetylgalactosamine (GalNAc). BfL was found to have especially strong binding (apparent K d  = 0.5-1.0 nm) to the tumor-associated Tn antigen. High-resolution crystal structures were determined for the ligand-free lectin, as well as for its complexes with three Tn glycopeptides, globotetraose, and the blood group A antigen. Extensive analysis of the eight crystal structures and comparison to structures of related lectins revealed several unique features of GalNAc recognition. Of special note, the carboxylate group of Glu126, lining the glycan-binding pocket, forms H-bonds with both the N-acetyl of GalNAc and the peptide amido group of Tn antigens. Stabilization provided by Glu126 is described here for the first time for any GalNAc-specific lectin. Taken together, the results provide new insights into the molecular recognition of carbohydrates and provide a structural understanding that will enable rational engineering of BfL for a variety of applications. Structural data are available in the PDB under the accession numbers 5T50, 5T52, 5T55, 5T54, 5T5L, 5T5J, 5T5P, and 5T5O. © 2016 Federation of European Biochemical Societies.

Intestinal Alterations, Basal Hematology, and Biochemical Parameters in Adolescent Rats Fed Different Sources of Dietary Copper.

PubMed

Tomaszewska, Ewa; Dobrowolski, Piotr; Kwiecień, Małgorzata

2016-05-01

Copper (Cu) is required for basically all biochemical and physiological processes in the body. The aim was to evaluate the effects of different sources of dietary copper on jejunal epithelium histomorphometry in adolescent rats. Male rats at the age of 5 weeks were used in the 12-week experiment. The control group was fed with standard diet providing the required Cu level (5 mg/kg body weight (bw) per day) in an inorganic form (sulfate) covered 100 % of daily demand, and the other three groups were supplemented with Cu-glycine complex covered 50, 75, and 100 % daily demand. Basal hematological and plasma biochemical analyses as well as histomorphometric examinations of the jejunal epithelium and liver were performed. Cu given in the organic form in 100 % of daily demand depressed the muscular and submucosa layer and the crypt depth (P < 0.05) without an influence of the innervation of the jejunum. In turn, organic Cu given in 75 % of daily demand did not influence the intestinal morphology in adult rats. Dietary organic Cu given to rats covering the daily demand in 50 or 75 % appears to be less harmful with regard to the intestinal epithelium than when administered in 100 % of daily demand.

[Etiological and molecular characteristics of diarrhea caused Proteus mirabilis].

PubMed

Shi, Xiaolu; Hu, Qinghua; Lin, Yiman; Qiu, Yaqun; Li, Yinghui; Jiang, Min; Chen, Qiongcheng

2014-06-01

To analyze the etiological characteristics, virulence genes and plasmids that carrying diarrhea-causing Proteus mirabilis and to assess their relationship with drug resistance and pathogenicity. Proteus mirabilis coming from six different sources (food poisoning, external environment and healthy people) were analyzed biochemically, on related susceptibility and pulsed-field gel electrophoresis (PFGE). Virulence genes were detected by PCR. Plasmids were extracted and sequenced after gel electrophoresis purification. The biochemical characteristics of Proteus mirabilis from different sources seemed basically the same, and each of them showed having common virulence genes, as ureC, rsmA, hpmA and zapA. However, the PFGE patterns and susceptibility of these strains were different, so as the plasmids that they carried. Plasmid that presented in the sequenced strain showed that the 2 683 bp length plasmid encodes qnrD gene was associated with the quinolone resistance. Etiological characteristics and molecular characteristics of Proteus mirabilis gathered from different sources, were analyzed. Results indicated that traditional biochemical analysis and common virulence gene identification might be able to distinguish the strains with different sources. However, PFGE and plasmids analysis could distinguish the sources of strains and to identify those plasmids that commonly carried by the drug-resistant strains. These findings also provided theoretical basis for further study on the nature of resistance and pathogenicity in Proteus mirabilis.

The Differences between NAD-ME and NADP-ME Subtypes of C4 Photosynthesis: More than Decarboxylating Enzymes.

PubMed

Rao, Xiaolan; Dixon, Richard A

2016-01-01

As an adaptation to changing climatic conditions that caused high rates of photorespiration, C 4 plants have evolved to display higher photosynthetic efficiency than C 3 plants under elevated temperature, high light intensities, and drought. The C 4 plants independently evolved more than 60 times in 19 families of angiosperms to establish similar but not uniform C 4 mechanisms to concentrate CO 2 around the carboxylating enzyme Rubisco (ribulose bisphosphate carboxylase oxygenase). C 4 photosynthesis is divided into at least two basic biochemical subtypes based on the primary decarboxylating enzymes, NAD-dependent malic enzyme (NAD-ME) and NADP-dependent malic enzyme (NADP-ME). The multiple polygenetic origins of these subtypes raise questions about the association of C 4 variation between biochemical subtypes and diverse lineages. This review addresses the differences in evolutionary scenario, leaf anatomy, and especially C 4 metabolic flow, C 4 transporters, and cell-specific function deduced from recently reported cell-specific transcriptomic, proteomic, and metabolic analyses of NAD-ME and NADP-ME subtypes. Current omic analysis has revealed the extent to which component abundances differ between the two biochemical subtypes, leading to a better understanding of C 4 photosynthetic mechanisms in NAD-ME and NADP-ME subtypes.

The Differences between NAD-ME and NADP-ME Subtypes of C4 Photosynthesis: More than Decarboxylating Enzymes

PubMed Central

Rao, Xiaolan; Dixon, Richard A.

2016-01-01

As an adaptation to changing climatic conditions that caused high rates of photorespiration, C4 plants have evolved to display higher photosynthetic efficiency than C3 plants under elevated temperature, high light intensities, and drought. The C4 plants independently evolved more than 60 times in 19 families of angiosperms to establish similar but not uniform C4 mechanisms to concentrate CO2 around the carboxylating enzyme Rubisco (ribulose bisphosphate carboxylase oxygenase). C4 photosynthesis is divided into at least two basic biochemical subtypes based on the primary decarboxylating enzymes, NAD-dependent malic enzyme (NAD-ME) and NADP-dependent malic enzyme (NADP-ME). The multiple polygenetic origins of these subtypes raise questions about the association of C4 variation between biochemical subtypes and diverse lineages. This review addresses the differences in evolutionary scenario, leaf anatomy, and especially C4 metabolic flow, C4 transporters, and cell-specific function deduced from recently reported cell-specific transcriptomic, proteomic, and metabolic analyses of NAD-ME and NADP-ME subtypes. Current omic analysis has revealed the extent to which component abundances differ between the two biochemical subtypes, leading to a better understanding of C4 photosynthetic mechanisms in NAD-ME and NADP-ME subtypes. PMID:27790235

[Fundamentals of quality control systems in medical-biochemical laboratories--the role of marketing].

PubMed

Topić, E; Turek, S

2000-01-01

The basic criterion for the overall quality system in medical biochemistry laboratories concerning equipment, premises and laboratory staff in primary health care (PHC) (Regulations on quality systems and good laboratory practice of the Croatian Medical Biochemists Chamber, 1995, Regulations on categorization of medical biochemistry laboratories of the Croatian Medical Biochemists Chamber, 1996, EC4: Essential criteria for quality systems in medical laboratories. Eur J Clin Chem Clin Biochem 1997 in medical biochemical laboratories included in the First Croatia health project, Primary health care subproject, has been met by the marketing approach to the project. The equipment ensuring implementation of the complete laboratory program (NN/96), more accurate and precise analytical procedures, and higher reliability of laboratory test results compared with previous equipment, has been purchased by an international tender. Uniform technology and methods of analysis have ensured high standards of good laboratory services, yielding test results than can be transferred from primary to secondary health care level. The new equipment has improved organization between central and detached medical biochemistry laboratory units, while the high quality requirement has led to improvement in the staff structure, e.g., medical biochemists have been employed in laboratories that had previously worked without such a professional. Equipment renewal has been accompanied by proper education for all levels of PHC professionals.

Designing degradable hydrogels for orthogonal control of cell microenvironments

PubMed Central

Kharkar, Prathamesh M.

2013-01-01

Degradable and cell-compatible hydrogels can be designed to mimic the physical and biochemical characteristics of native extracellular matrices and provide tunability of degradation rates and related properties under physiological conditions. Hence, such hydrogels are finding widespread application in many bioengineering fields, including controlled bioactive molecule delivery, cell encapsulation for controlled three-dimensional culture, and tissue engineering. Cellular processes, such as adhesion, proliferation, spreading, migration, and differentiation, can be controlled within degradable, cell-compatible hydrogels with temporal tuning of biochemical or biophysical cues, such as growth factor presentation or hydrogel stiffness. However, thoughtful selection of hydrogel base materials, formation chemistries, and degradable moieties is necessary to achieve the appropriate level of property control and desired cellular response. In this review, hydrogel design considerations and materials for hydrogel preparation, ranging from natural polymers to synthetic polymers, are overviewed. Recent advances in chemical and physical methods to crosslink hydrogels are highlighted, as well as recent developments in controlling hydrogel degradation rates and modes of degradation. Special attention is given to spatial or temporal presentation of various biochemical and biophysical cues to modulate cell response in static (i.e., non-degradable) or dynamic (i.e., degradable) microenvironments. This review provides insight into the design of new cell-compatible, degradable hydrogels to understand and modulate cellular processes for various biomedical applications. PMID:23609001

EFFECT OF $gamma$-RAYS ON THE BIOCHEMICAL PROPERTIES OF WHEAT

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

Sosedov, N.I.; Vakar, A.B.

1963-01-01

Progress in the Soviet Union on radiation effects on biochemical and baking properties of wheat is reported. biochemical analysis of the various forms of nitrogenous substances in wheat with moisture contents of 13.4 and 25.8 percent after irradiation with gamma rays shows that the radiation effects on giuten are dependent upon moisture content. Gluten in dry grain exposed to gamma rays became weak, inelastic, and too extensile while that in moist grain became excessively stiff with consequent loss of extensibility and cohesion. In dry irradiated grain increases were found in protein substance solubility and protein splitting, whereas in irradiated grainmore » with a higher moisture content, there was less protein splitting and solubility of protein substances was reduced. When the moisture content was 16.4-percent, radintion damage was least, the two opposite sets of deleterious effects being somewhat (not completely) balanced. The different effects of the same radiation doses on moist and dry grain was corfirmed by spectrophotometric examination. Large gamma doses increase the quantity of reducing sugars and decrease the starch content. These carbohydrate changes are more pronounced with dry than with moist grain. It is concluded that with present knowledge and techniques the method of radiational treatment of grain cannot be recommended for practical use. (H.M.G.)« less

Lysyl hydroxylase 2 induces a collagen cross-link switch in tumor stroma

PubMed Central

Chen, Yulong; Terajima, Masahiko; Yang, Yanan; Sun, Li; Ahn, Young-Ho; Pankova, Daniela; Puperi, Daniel S.; Watanabe, Takeshi; Kim, Min P.; Blackmon, Shanda H.; Rodriguez, Jaime; Liu, Hui; Behrens, Carmen; Wistuba, Ignacio I.; Minelli, Rosalba; Scott, Kenneth L.; Sanchez-Adams, Johannah; Guilak, Farshid; Pati, Debananda; Thilaganathan, Nishan; Burns, Alan R.; Creighton, Chad J.; Martinez, Elisabeth D.; Zal, Tomasz; Grande-Allen, K. Jane; Yamauchi, Mitsuo; Kurie, Jonathan M.

2015-01-01

Epithelial tumor metastasis is preceded by an accumulation of collagen cross-links that heighten stromal stiffness and stimulate the invasive properties of tumor cells. However, the biochemical nature of collagen cross-links in cancer is still unclear. Here, we postulated that epithelial tumorigenesis is accompanied by changes in the biochemical type of collagen cross-links. Utilizing resected human lung cancer tissues and a p21CIP1/WAF1-deficient, K-rasG12D-expressing murine metastatic lung cancer model, we showed that, relative to normal lung tissues, tumor stroma contains higher levels of hydroxylysine aldehyde–derived collagen cross-links (HLCCs) and lower levels of lysine aldehyde–derived cross-links (LCCs), which are the predominant types of collagen cross-links in skeletal tissues and soft tissues, respectively. Gain- and loss-of-function studies in tumor cells showed that lysyl hydroxylase 2 (LH2), which hydroxylates telopeptidyl lysine residues on collagen, shifted the tumor stroma toward a high-HLCC, low-LCC state, increased tumor stiffness, and enhanced tumor cell invasion and metastasis. Together, our data indicate that LH2 enhances the metastatic properties of tumor cells and functions as a regulatory switch that controls the relative abundance of biochemically distinct types of collagen cross-links in the tumor stroma. PMID:25664850

An Unprecedented NADPH Domain Conformation in Lysine Monooxygenase NbtG Provides Insights into Uncoupling of Oxygen Consumption from Substrate Hydroxylation

DOE PAGES

Binda, Claudia; Robinson, Reeder M.; Martin del Campo, Julia S.; ...

2015-03-23

N-hydroxylating monooxygenases (NMOs) are involved in the biosynthesis of iron-chelating hydroxamate-containing siderophores that play a role in microbial virulence. These flavoenzymes catalyze the NADPH- and oxygen-dependent hydroxylation of amines, such as those found on the side chains of lysine and ornithine. In this work we report the biochemical and structural characterization of Nocardia farcinica Lys monooxygenase (NbtG), which has similar biochemical properties to mycobacterial homologs. NbtG is also active on D-Lys although it binds L-Lys with a higher affinity. Differently from the ornithine monooxygenases PvdA, SidA and KtzI, NbtG can use both NADH and NADPH and is highly uncoupled, producingmore » more superoxide and hydrogen peroxide than hydroxylated Lys. The crystal structure of NbtG solved at 2.4 Å resolution revealed an unexpected protein conformation with a 30° rotation of the NAD(P)H domain with respect to the FAD domain that precludes binding of the nicotinamide cofactor. This “occluded” structure may explain the biochemical properties of NbtG, specifically with regard to the substantial uncoupling and limited stabilization of the C4a-hydroperoxyflavin intermediate. We discuss the biological implications of these findings.« less

Beneficial effects of mangiferin isolated from Salacia chinensis on biochemical and hematological parameters in rats with streptozotocin-induced diabetes.

PubMed

Sellamuthu, Periyar Selvam; Arulselvan, Palanisamy; Fakurazi, Sharida; Kandasamy, Murugesan

2014-01-01

Salacia chinensis L. is a traditional Southeast Asian herbal medicine and used in the treatment of diabetes. To investigate the antidiabetic properties of mangiferin from Salacia chinensis and its beneficial effect on toxicological and hematological parameters in streptozotocin induced diabetic rats. Mangiferin was orally treated with the dose of 40 mg/kg body weight/day for 30 days to diabetic rats. Biochemical (blood glucose, uric acid, urea and creatinine), toxicological (AST, ALT and ALP) and hematological parameters (red and white blood cells) and their functional indices were evaluated in diabetic treated groups with mangiferin and glibenclamide. Mangiferin treated diabetic rats significantly (p<0.05) lowered the level of blood glucose, in addition, altered the levels of biochemical parameters including urea, uric acid, and creatinine. Toxicological parameters including AST, ALT and ALP were also significantly reduced after treatment with mangiferin in diabetic rats. Similarly, the levels of red blood, white blood cells and their functional indices were significantly improved through the administration of mangiferin. Thus, our results indicate that mangiferin present in S. chinensis possesses antidiabetic properties and nontoxic nature against chemically induced diabetic rats. Further experimental investigations are warrant to make use of its relevant therapeutic effect to substantiate its ethno-medicinal usage.

Investigation of biochemical property changes in activation-induced CD 8 + T cell apoptosis using Raman spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Young Ju; Ahn, Hyung Joon; Lee, Gi-Ja; Jung, Gyeong Bok; Lee, Gihyun; Kim, Dohyun; Shin, Jae-Ho; Jin, Kyung-Hyun; Park, Hun-Kuk

2015-07-01

The study was to investigate the changes in biochemical properties of activated mature CD8+ T cells related to apoptosis at a molecular level. We confirmed the activation and apoptosis of CD8+ T cells by fluorescence-activated cell sorting and atomic force microscopy and then performed Raman spectral measurements on activated mature CD8+ T cells and cellular deoxyribose nucleic acid (DNA). In the activated mature CD8+ T cells, there were increases in protein spectra at 1002 and 1234 cm-1. In particular, to assess the apoptosis-related DNA spectral signatures, we investigated the spectra of the cellular DNA isolated from resting and activated mature CD8+ T cells. Raman spectra at 765 to 786 cm-1 and 1053 to 1087 cm-1 were decreased in activated mature DNA. In addition, we analyzed Raman spectrum using the multivariate statistical method including principal component analysis. Raman spectra of activated mature DNA are especially well-discriminated from those of resting DNA. Our findings regarding the biochemical and structural changes associated with apoptosis in activated mature T cells and cellular DNA according to Raman spectroscopy provide important insights into allospecific immune responses generated after organ transplantation, and may be useful for therapeutic manipulation of the immune response.

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil

PubMed Central

Wang, Lei; Yang, Fang; E, Yaoyao; Yuan, Jun; Raza, Waseem; Huang, Qiwei; Shen, Qirong

2016-01-01

Soil biochemical properties and microbial communities are usually considered as important indicators of soil health because of their association with plant nutrition. In this study, we investigated the impact of long-term application of bioorganic fertilizer (BOF) on soil biochemical properties and microbial communities in the apple orchard soil of the Loess Plateau. The experiment included three treatments: (1) control without fertilization (CK); (2) chemical fertilizer application (CF); and (3) bioorganic fertilizer application (BOF). The high throughput sequencing was used to examine the bacterial and fungal communities in apple orchard soil. The results showed that the BOF treatment significantly increased the apple yield during the experimental time (2009–2015). The application of BOF significantly increased the activities of catalase and invertase compared to those in CK and CF treatments. The high throughput sequencing data showed that the application of BOF changed the microbial community composition of all soil depths considered (0–20 cm, 20–40 cm, and 40–60 cm), e.g., the relative abundance of bio-control bacteria (Xanthomonadales, Lysobacter, Pseudomonas, and Bacillus), Proteobacteria, Bacteroidetes, Ohtaekwangia, Ilyonectria, and Lecanicillium was increased while that of Acidobacteria, Chloroflexi, Gp4, Gp6 and Sphaerobacter was decreased. The increase in apple yield after the application of BOF might be due to increase in organic matter, total nitrogen and catalase and invertase activities of soil and change in the bacterial community composition by enriching Bacillus, Pseudomonas, Lysobacter, and Ohtaekwangia. These results further enhance the understanding on how BOFs alter soil microbial community composition to stimulate soil productivity. PMID:27965631

Laterally confined growth of cells induces nuclear reprogramming in the absence of exogenous biochemical factors.

PubMed

Roy, Bibhas; Venkatachalapathy, Saradha; Ratna, Prasuna; Wang, Yejun; Jokhun, Doorgesh Sharma; Nagarajan, Mallika; Shivashankar, G V

2018-05-22

Cells in tissues undergo transdifferentiation programs when stimulated by specific mechanical and biochemical signals. While seminal studies have demonstrated that exogenous biochemical factors can reprogram somatic cells into pluripotent stem cells, the critical roles played by mechanical signals in such reprogramming process have not been well documented. In this paper, we show that laterally confined growth of fibroblasts on micropatterned substrates induces nuclear reprogramming with high efficiency in the absence of any exogenous reprogramming factors. We provide compelling evidence on the induction of stem cell-like properties using alkaline phosphatase assays and expression of pluripotent markers. Early onset of reprogramming was accompanied with enhanced nuclear dynamics and changes in chromosome intermingling degrees, potentially facilitating rewiring of the genome. Time-lapse analysis of promoter occupancy by immunoprecipitation of H3K9Ac chromatin fragments revealed that epithelial, proliferative, and reprogramming gene promoters were progressively acetylated, while mesenchymal promoters were deacetylated by 10 days. Consistently, RNA sequencing analysis showed a systematic progression from mesenchymal to stem cell transcriptome, highlighting pathways involving mechanisms underlying nuclear reprogramming. We then demonstrated that these mechanically reprogrammed cells could be maintained as stem cells and can be redifferentiated into multiple lineages with high efficiency. Importantly, we also demonstrate the induction of cancer stemness properties in MCF7 cells grown in such laterally confined conditions. Collectively, our results highlight an important generic property of somatic cells that, when grown in laterally confined conditions, acquire stemness. Such mechanical reprogramming of somatic cells demonstrated here has important implications in tissue regeneration and disease models. Copyright © 2018 the Author(s). Published by PNAS.

Yeast mitochondrial HMG proteins: DNA-binding properties of the most evolutionarily divergent component of mitochondrial nucleoids.

PubMed

Bakkaiova, Jana; Marini, Victoria; Willcox, Smaranda; Nosek, Jozef; Griffith, Jack D; Krejci, Lumir; Tomaska, Lubomir

2015-12-08

Yeast mtDNA is compacted into nucleoprotein structures called mitochondrial nucleoids (mt-nucleoids). The principal mediators of nucleoid formation are mitochondrial high-mobility group (HMG)-box containing (mtHMG) proteins. Although these proteins are some of the fastest evolving components of mt-nucleoids, it is not known whether the divergence of mtHMG proteins on the level of their amino acid sequences is accompanied by diversification of their biochemical properties. In the present study we performed a comparative biochemical analysis of yeast mtHMG proteins from Saccharomyces cerevisiae (ScAbf2p), Yarrowia lipolytica (YlMhb1p) and Candida parapsilosis (CpGcf1p). We found that all three proteins exhibit relatively weak binding to intact dsDNA. In fact, ScAbf2p and YlMhb1p bind quantitatively to this substrate only at very high protein to DNA ratios and CpGcf1p shows only negligible binding to dsDNA. In contrast, the proteins exhibit much higher preference for recombination intermediates such as Holliday junctions (HJ) and replication forks (RF). Therefore, we hypothesize that the roles of the yeast mtHMG proteins in maintenance and compaction of mtDNA in vivo are in large part mediated by their binding to recombination/replication intermediates. We also speculate that the distinct biochemical properties of CpGcf1p may represent one of the prerequisites for frequent evolutionary tinkering with the form of the mitochondrial genome in the CTG-clade of hemiascomycetous yeast species. © 2016 Authors.

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil.

PubMed

Wang, Lei; Yang, Fang; E, Yaoyao; Yuan, Jun; Raza, Waseem; Huang, Qiwei; Shen, Qirong

2016-01-01

Soil biochemical properties and microbial communities are usually considered as important indicators of soil health because of their association with plant nutrition. In this study, we investigated the impact of long-term application of bioorganic fertilizer (BOF) on soil biochemical properties and microbial communities in the apple orchard soil of the Loess Plateau. The experiment included three treatments: (1) control without fertilization (CK); (2) chemical fertilizer application (CF); and (3) bioorganic fertilizer application (BOF). The high throughput sequencing was used to examine the bacterial and fungal communities in apple orchard soil. The results showed that the BOF treatment significantly increased the apple yield during the experimental time (2009-2015). The application of BOF significantly increased the activities of catalase and invertase compared to those in CK and CF treatments. The high throughput sequencing data showed that the application of BOF changed the microbial community composition of all soil depths considered (0-20 cm, 20-40 cm, and 40-60 cm), e.g., the relative abundance of bio-control bacteria ( Xanthomonadales, Lysobacter, Pseudomonas , and Bacillus ), Proteobacteria, Bacteroidetes, Ohtaekwangia, Ilyonectria , and Lecanicillium was increased while that of Acidobacteria, Chloroflexi, Gp4, Gp6 and Sphaerobacter was decreased. The increase in apple yield after the application of BOF might be due to increase in organic matter, total nitrogen and catalase and invertase activities of soil and change in the bacterial community composition by enriching Bacillus, Pseudomonas, Lysobacter , and Ohtaekwangia . These results further enhance the understanding on how BOFs alter soil microbial community composition to stimulate soil productivity.

Simulation of flow and water quality of the Arroyo Colorado, Texas, 1989-99

USGS Publications Warehouse

Raines, Timothy H.; Miranda, Roger M.

2002-01-01

A model parameter set for use with the Hydrological Simulation Program—FORTRAN watershed model was developed to simulate flow and water quality for selected properties and constituents for the Arroyo Colorado from the city of Mission to the Laguna Madre, Texas. The model simulates flow, selected water-quality properties, and constituent concentrations. The model can be used to estimate a total maximum daily load for selected properties and constituents in the Arroyo Colorado. The model was calibrated and tested for flow with data measured during 1989–99 at three streamflow-gaging stations. The errors for total flow volume ranged from -0.1 to 29.0 percent, and the errors for total storm volume ranged from -15.6 to 8.4 percent. The model was calibrated and tested for water quality for seven properties and constituents with 1989–99 data. The model was calibrated sequentially for suspended sediment, water temperature, biochemical oxygen demand, dissolved oxygen, nitrate nitrogen, ammonia nitrogen, and orthophosphate. The simulated concentrations of the selected properties and constituents generally matched the measured concentrations available for the calibration and testing periods. The model was used to simulate total point- and nonpoint-source loads for selected properties and constituents for 1989–99 for urban, natural, and agricultural land-use types. About one-third to one-half of the biochemical oxygen demand and nutrient loads are from urban point and nonpoint sources, although only 13 percent of the total land use in the basin is urban.

Biochemical processes in sagebrush ecosystems: Interactions with terrain

NASA Technical Reports Server (NTRS)

Matson, P. (Principal Investigator); Reiners, W.; Strong, L.

1985-01-01

The objectives of a biogeochemical study of sagebrush ecosystems in Wyoming and their interactions with terrain are as follows: to describe the vegetational pattern on the landscape and elucidate controlling variables, to measure the soil properties and chemical cycling properties associated with the vegetation units, to associate soil properties with vegetation properties as measured on the ground, to develop remote sensing capabilities for vegetation and surface characteristics of the sagebrush landscape, to develop a system of sensing snow cover and indexing seasonal soil to moisture; and to develop relationships between temporal Thematic Mapper (TM) data and vegetation phenological state.

Near infrared spectra are more sensitive to land use changes than physical, chemical and biological soil properties

NASA Astrophysics Data System (ADS)

Guerrero, C.; Zornoza, R.; Mataix-Solera, J.; Mataix-Beneyto, J.; Scow, K.

2009-04-01

We studied the sensibility of the near infrared spectra (NIR) of soils to the changes caused by land use, and we compared with the sensibility of different sets of physical, chemical and biological soil properties. For this purpose, we selected three land uses, constituted by forest, almond trees orchards, and orchards abandoned between 10 and 15 years previously to sampling. Sampling was carried out in four different locations from the province of Alicante (SE Spain). We used discriminant analysis (DA) using different sets of soil properties. The different sets tested in this study using DA were: (1) physical and chemical properties (organic carbon, total nitrogen, available phosphorus, pH, electrical conductivity, cation exchange capacity, aggregate stability, water holding capacity, and available Ca, Mg, K and Na), (2) biochemical properties (microbial biomass carbon, basal respiration and urease, phosphatase and β-glucosidase activities), (3) phospholipids fatty acids (PLFAs), (4) physical, chemical and biochemical properties (all properties of the previous sets), and (5) the NIR spectra of soils (scores of the principal components). In general, all sets of properties were sensible to land use. This was observed in the DAs by the separation (more or less clear) of samples in groups defined by land use (irrespective of site). The worst results were obtained using soil physical and chemical properties. The combination of physical, chemical and biological properties enhanced the separation of samples in groups, indicating higher sensibility. It is accepted than combination of properties of different nature is more effective to evaluate the soil quality. The microbial community structure (PLFAs) was highly sensible to the land use, grouping correctly the 100% of the samples according with the land use. The NIR spectra were also sensitive to land use. The scores of the first 5 components, which explained 99.97% of the variance, grouped correctly the 85% of the soil samples by land use, but were unable to group correctly the 100% of the samples. Surprisingly, when the scarce variance presents in components 5 to 40 was also used, the 100% of the samples were grouped by land use, as it was observed with PLFAs. But PLFAs analysis is expensive and time-consuming (some weeks). In contrast, only some minutes are needed for the obtainment of the NIR spectra. Additionally, no chemicals are need, decreasing the costs. The NIR spectrum of a soil contains relevant information about physical, chemical and biochemical properties. NIR spectrum could be considered as an integrated vision of soil quality, and as consequence offers an integrated vision of perturbations. Thus, NIR spectroscopy could be used as tool to monitoring soil quality in large areas. Acknowledgements: Authors acknowledge to "Bancaja-UMH" for the financial support of the project "NIRPRO"

Effect of fire severity on physical and biochemical soil properties in Zagros oak (Quercus brantii Lindl.) forests in Iran

Treesearch

M. Heydari; A. Rostamy; F. Najafi; D. C. Dey

2017-01-01

Fire affects the physical and chemical properties and soil biological activity of natural ecosystems. This study was conducted in the Miyan Tang region, Ilam Province in western Iran. The study site was 110 hectares, where we sampled soils in areas that were classified by fire severity: low (LS), high (HS) and medium severity (MS), and unburned (UB), which served as...

Fish trypsins: potential applications in biomedicine and prospects for production.

PubMed

Jesús-de la Cruz, Kristal; Álvarez-González, Carlos Alfonso; Peña, Emyr; Morales-Contreras, José Antonio; Ávila-Fernández, Ángela

2018-04-01

In fishes, trypsins are adapted to different environmental conditions, and the biochemical and kinetic properties of a broad variety of native isoforms have been studied. Proteolytic enzymes remain in high demand in the detergent, food, and feed industries; however, our analysis of the literature showed that, in the last decade, some fish trypsins have been studied for the synthesis of industrial peptides and for specific biomedical uses as antipathogenic agents against viruses and bacteria, which have been recently patented. In addition, innovative strategies of trypsin administration have been studied to ensure that trypsins retain their properties until they exert their action. Biomedical uses require the production of high-quality enzymes. In this context, the production of recombinant trypsins is an alternative. For this purpose, E. coli -based systems have been tested for the production of fish trypsins; however, P. pastoris -based systems also seem to show great potential in the production of fish trypsins with higher production quality. On the other hand, there is a lack of information regarding the specific structures, biochemical and kinetic properties, and characteristics of trypsins produced using heterologous systems. This review describes the potential uses of fish trypsins in biomedicine and the enzymatic and structural properties of native and recombinant fish trypsins obtained to date, outlining some prospects for their study.

Production, purification and biochemical characterization of two laccase isoforms produced by Trametes versicolor grown on oak sawdust.

PubMed

Martínez-Morales, Fernando; Bertrand, Brandt; Pasión Nava, Angélica A; Tinoco, Raunel; Acosta-Urdapilleta, Lourdes; Trejo-Hernández, María R

2015-02-01

Two laccase isoforms (lcc1 and lcc2) produced by Trametes versicolor, grown on oak sawdust under solid-state fermentation conditions, were purified and characterized. The two isoforms showed significant biochemical differences. Lcc1 and lcc2 had MWs of 60 and 100 kDa, respectively. Both isoforms had maximal activity at pH 3 with ABTS and 2,6-dimethyloxyphenol (DMP). Lcc1 was the most attractive isoform due to its greater affinity towards all the laccase substrates used. Lcc1 had Km values of 12, 10, 15 and 17 mM towards ABTS, DMP, guaiacol and syringaldazine, respectively. Lcc2 had equivalent values of 45, 47, 15 and 39 mM. The biochemical properties of lcc1 substantiate the potential of this enzyme for application in the treatment of contaminated water with low pH values and high phenolic content.

Simple modification of basic dyes with bulky &symmetric WCAs for improving their solubilities in organic solvents without color change.

PubMed

Kim, Jeong Yun; Hwang, Tae Gyu; Woo, Sung Wun; Lee, Jae Moon; Namgoong, Jin Woong; Yuk, Sim Bum; Chung, Sei-Won; Kim, Jae Pil

2017-04-06

A simple and easy solubility enhancement of basic dyes was performed with bulky and symmetric weakly coordinating anions (WCAs). The WCAs decreased the ionic character of the dyes by broadening the partial charge distribution and causing a screening effect on the ionic bonding. This new modification with WCAs has advantages in that it has no influence on the optical properties of the dyes. The solubilities of unmodified and modified dyes were tested in several organic solvents. X-ray powder diffraction patterns of the dyes were measured. Color films were prepared with the dyes and their color loci were analyzed to evaluate the optical properties. By the modification with WCAs, commercial basic dyes showed sufficient solubilities for be applied to various applications while preserving their superior optical properties.

A Computational Approach to Investigate Properties of Estimators

ERIC Educational Resources Information Center

Caudle, Kyle A.; Ruth, David M.

2013-01-01

Teaching undergraduates the basic properties of an estimator can be difficult. Most definitions are easy enough to comprehend, but difficulties often lie in gaining a "good feel" for these properties and why one property might be more desired as compared to another property. Simulations which involve visualization of these properties can…

Short-term regulation of the alpha-ketoglutarate dehydrogenase complex by energy-linked and some other effectors.

PubMed

Strumilo, S

2005-07-01

The question of regulation of alpha-ketoglutarate dehydrogenase complex (KGDHC) has been considered in the biochemical literature very rarely. Moreover, such information is not usually accurate, especially in biochemical textbooks. From the mini-review of research works published during the last 25 years, the following basic view is clear: a) animal KGDHC is very sensitive to ADP, P(i), and Ca2+; b) these positive effectors increase manifold the affinity of KGDHC to alpha-ketoglutarate; c) KGDHC is inhibited by ATP, NADH, and succinyl-CoA; d) the ATP effect is realized in several ways, probably mainly via opposition versus ADP activation; e) NADH, besides inhibiting dihydrolipoamide dehydrogenase component competitively versus NAD+, decreases the affinity of alpha-ketoglutarate dehydrogenase to substrate and inactivates it; f) thioredoxin protects KGDHC from self-inactivation during catalysis; g) bacterial and plant KGDHC is activated by AMP instead of ADP. These main effects form the basis of short-term regulation of KGDHC.

Water quality in the Sugar Creek basin, Bloomington and Normal, Illinois

USGS Publications Warehouse

Prugh, Byron J.

1978-01-01

Urban runoff and overflows from combined sewers affect water quantity and quality in Sugar Creek within the twin cities of Bloomington and Normal, Illinois. Water-quality data from five primary and eight secondary locations showed three basic types of responses to climatic and hydrologic stresses. Stream temperatures and concentrations of dissolved oxygen, ammonia nitrogen, total phosphorus, biochemical oxygen demand, and fecal bacteria showed seasonal variations. Specific conductivity, pH, chloride, and suspended solids concentrations varied more closely with stream discharges. Total organic carbon, total nitrogen, total phosphorus, biochemical oxygen demand, and fecal coliform and fecal streptococcal bacteria concentrations exhibited variations indicative of intial flushing action during storm runoff. Selected analyses for herbicides, insecticides, and other complex organic compounds in solution and in bed material showed that these constituents were coming from sources other than the municipal sanitary treatment plant effluent. Analyses for 10 common metals: arsenic, cadmium, chromium, copper, iron, lead, manganese, mercury, nickel, and zinc showed changes in concentrations below the municipal sanitary plant outfall. (Woodard-USGS)

Fungal biology and agriculture: revisiting the field

USGS Publications Warehouse

Yarden, O.; Ebbole, D.J.; Freeman, S.; Rodriguez, R.J.; Dickman, M. B.

2003-01-01

Plant pathology has made significant progress over the years, a process that involved overcoming a variety of conceptual and technological hurdles. Descriptive mycology and the advent of chemical plant-disease management have been followed by biochemical and physiological studies of fungi and their hosts. The later establishment of biochemical genetics along with the introduction of DNA-mediated transformation have set the stage for dissection of gene function and advances in our understanding of fungal cell biology and plant-fungus interactions. Currently, with the advent of high-throughput technologies, we have the capacity to acquire vast data sets that have direct relevance to the numerous subdisciplines within fungal biology and pathology. These data provide unique opportunities for basic research and for engineering solutions to important agricultural problems. However, we also are faced with the challenge of data organization and mining to analyze the relationships between fungal and plant genomes and to elucidate the physiological function of pertinent DNA sequences. We present our perspective of fungal biology and agriculture, including administrative and political challenges to plant protection research.

Imaging trace element distributions in single organelles and subcellular features

DOE PAGES

Kashiv, Yoav; Austin, Jotham R.; Lai, Barry; ...

2016-02-25

The distributions of chemical elements within cells are of prime importance in a wide range of basic and applied biochemical research. An example is the role of the subcellular Zn distribution in Zn homeostasis in insulin producing pancreatic beta cells and the development of type 2 diabetes mellitus. We combined transmission electron microscopy with micro-and nano-synchrotron X-ray fluorescence to image unequivocally for the first time, to the best of our knowledge, the natural elemental distributions, including those of trace elements, in single organelles and other subcellular features. Detected elements include Cl, K, Ca, Co, Ni, Cu, Zn and Cd (whichmore » some cells were supplemented with). Cell samples were prepared by a technique that minimally affects the natural elemental concentrations and distributions, and without using fluorescent indicators. In conclusion, it could likely be applied to all cell types and provide new biochemical insights at the single organelle level not available from organelle population level studies.« less

The ONIOM molecular dynamics method for biochemical applications: cytidine deaminase

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

Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako

2007-03-22

Abstract We derived and implemented the ONIOM-molecular dynamics (MD) method for biochemical applications. The implementation allows the characterization of the functions of the real enzymes taking account of their thermal motion. In this method, the direct MD is performed by calculating the ONIOM energy and gradients of the system on the fly. We describe the first application of this ONOM-MD method to cytidine deaminase. The environmental effects on the substrate in the active site are examined. The ONIOM-MD simulations show that the product uridine is strongly perturbed by the thermal motion of the environment and dissociates easily from the activemore » site. TM and MA were supported in part by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan. MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE.« less

Climbing plants: attachment adaptations and bioinspired innovations.

PubMed

Burris, Jason N; Lenaghan, Scott C; Stewart, C Neal

2018-04-01

Climbing plants have unique adaptations to enable them to compete for sunlight, for which they invest minimal resources for vertical growth. Indeed, their stems bear relatively little weight, as they traverse their host substrates skyward. Climbers possess high tensile strength and flexibility, which allows them to utilize natural and manmade structures for support and growth. The climbing strategies of plants have intrigued scientists for centuries, yet our understanding about biochemical adaptations and their molecular undergirding is still in the early stages of research. Nonetheless, recent discoveries are promising, not only from a basic knowledge perspective, but also for bioinspired product development. Several adaptations, including nanoparticle and adhesive production will be reviewed, as well as practical translation of these adaptations to commercial applications. We will review the botanical literature on the modes of adaptation to climb, as well as specialized organs-and cellular innovations. Finally, recent molecular and biochemical data will be reviewed to assess the future needs and new directions for potential practical products that may be bioinspired by climbing plants.

Tryptophan as key biomarker to detect gastrointestinal tract cancer using non-negative biochemical analysis of native fluorescence and Stokes Shift spectroscopy

NASA Astrophysics Data System (ADS)

Wang, Leana; Zhou, Yan; Liu, Cheng-hui; Zhou, Lixin; He, Yong; Pu, Yang; Nguyen, Thien An; Alfano, Robert R.

2015-03-01

The objective of this study was to find out the emission spectral fingerprints for discrimination of human colorectal and gastric cancer from normal tissue in vitro by applying native fluorescence. The native fluorescence (NFL) and Stokes shift spectra of seventy-two human cancerous and normal colorectal (colon, rectum) and gastric tissues were analyzed using three selected excitation wavelengths (e.g. 300 nm, 320 nm and 340 nm). Three distinct biomarkers, tryptophan, collagen and reduced nicotinamide adenine dinucleotide hydrate (NADH), were found in the samples of cancerous and normal tissues from eighteen subjects. The spectral profiles of tryptophan exhibited a sharp peak in cancerous colon tissues under a 300 nm excitation when compared with normal tissues. The changes in compositions of tryptophan, collagen, and NADH were found between colon cancer and normal tissues under an excitation of 300 nm by the non-negative basic biochemical component analysis (BBCA) model.

Future Threats or Clear and Present Dangers?

ERIC Educational Resources Information Center

Eisenberg, Leon

1976-01-01

Addresses the questions of the social and medical uses and limitations of stimulant drugs. Reviews the biochemical models of learning and concludes that the temptation to ascribe magical or science fiction-like properties to chemical agents must be resisted. (Editor/RK)

Bacterial dye-decolorizing peroxidases: biochemical properties and biotechnological opportunities

EPA Science Inventory

In biorefineries, processing biomass begins with separating lignin from cellulose and hemicellulose. The latter two are depolymerized to give monosaccharides (e.g. glucose and xylose), which can be converted to fuels or chemicals. In contrast, lignin presents a challenging target...

Electrical properties of epoxies used in hybrid microelectronics

NASA Technical Reports Server (NTRS)

Stout, C. W.

1976-01-01

The electrical properties and basic characteristics of the structure of conductive epoxies were studied. The results of the experimental work performed to measure the electrical properties of epoxies are presented.

Evaluation of Autogenous Engineered Septal Cartilage Grafts in Rabbits- A Minimally Invasive Preclinical Model.

PubMed

Kushnaryov, Anton; Yamaguchi, Tomonoro; Briggs, Kristen K; Wong, Van W; Reuther, Marsha; Neuman, Monica; Lin, Victor; Sah, Robert L; Masuda, Koichi; Watson, Deborah

2014-07-23

Evaluate safety of autogenous engineered septal neocartilage grafts.Compare properties of implanted grafts versus in vitro controls. Prospective, basic science. Research laboratory. Constructs were fabricated from septal cartilage and serum harvested from adult rabbits and then cultured in vitro or implanted on the nasal dorsum as autogenous grafts for 30 or 60 days. Rabbits were monitored for local and systemic complications. Histological, biochemical and biomechanical properties of implanted and in vitro constructs were evaluated and compared. No systemic or serious local complications were observed. After 30 and 60 days, implanted constructs contained more DNA (p<0.01) and less sGAG per DNA (p<0.05) when compared with in vitro controls. Confined compressive aggregate moduli were also higher in implanted constructs when compared with in vitro controls (p<0.05) and increased with longer in vivo incubation time (p<0.01). Implanted constructs displayed resorption rates of 20-45 percent. Calcium deposition in implanted constructs was observed using alizarin red histochemistry and microtomographic analyses. Autogenous engineered septal cartilage grafts were well tolerated. As seen in experiments with athymic mice, implanted constructs accumulated more DNA and less sGAG when compared with in vitro controls. Confined compressive aggregate moduli were also higher in implanted constructs. Implanted constructs displayed resorption rates similar to previously published studies using autogenous implants of native cartilage. The basis for observed calcification in implanted constructs and its effect on long-term graft efficacy is unknown at this time and will be a focus of future studies.

Intellectual Property.

ERIC Educational Resources Information Center

Swinson, John V.

2000-01-01

Intellectual property is a term that covers a number of different rights. Considers issues such as what are the basic forms of intellectual property; who owns the intellectual property created by a teacher; who owns intellectual property created by students; and use of downloaded materials from the internet. (Author/LM)

Biochemical, structural and functional diversity between two digestive α-amylases from Helicoverpa armigera.

PubMed

Bhide, Amey J; Channale, Sonal M; Patil, Sucheta S; Gupta, Vidya S; Ramasamy, Sureshkumar; Giri, Ashok P

2015-09-01

Helicoverpa armigera (Lepidoptera) feeds on various plants using diverse digestive enzymes as one of the survival tool-kit. The aim of the present study was to understand biochemical properties of recombinant α-amylases of H. armigera viz., HaAmy1 and HaAmy2. The open reading frames of HaAmy1 and HaAmy2 were cloned in Pichia pastoris and expressed heterologously. Purified recombinant enzymes were characterized for their biochemical and biophysical attributes using established methods. Sequence alignment and homology modeling showed that HaAmy1 and HaAmy2 were conserved in their amino acid sequences and structures. HaAmy1 and HaAmy2 showed optimum activity at 60°C; however, they differed in their optimum pH. Furthermore, HaAmy2 showed higher affinity for starch and amylopectin whereas HaAmy1 had higher catalytic efficiency. HaAmy1 and HaAmy2 were inhibited to the same magnitude by a synthetic amylase inhibitor (acarbose) while wheat amylase inhibitor showed about 2-fold higher inhibition of HaAmy1 than HaAmy2 at pH7 while 6-fold difference at pH11. Interactions of HaAmy1 and HaAmy2 with wheat amylase inhibitor revealed 2:1 stoichiometric ratio and much more complex interaction with HaAmy1. The diversity of amylases in perspective of their biochemical and biophysical properties, and their differential interactions with amylase inhibitors signify the potential role of these enzymes in adaptation of H. armigera on diverse plant diets. Characterization of digestive enzymes of H. armigera provides the molecular basis for the polyphagous nature and thus could assist in designing future strategies for the insect control. Copyright © 2015 Elsevier B.V. All rights reserved.

Biochemical, histologic, and biomechanical characterization of native and decellularized flexor tendon specimens harvested from the pelvic limbs of orthopedically normal dogs.

PubMed

Balogh, Daniel G; Biskup, Jeffery J; O'Sullivan, M Gerard; Scott, Ruth M; Groschen, Donna; Evans, Richard B; Conzemius, Michael G

2016-04-01

To evaluate the biochemical and biomechanical properties of native and decellularized superficial digital flexor tendons (SDFTs) and deep digital flexor tendons (DDFTs) harvested from the pelvic limbs of orthopedically normal dogs. 22 commercially supplied tendon specimens (10 SDFT and 12 DDFT) harvested from the pelvic limbs of 13 canine cadavers. DNA, glycosaminoglycan, collagen, and protein content were measured to biochemically compare native and decellularized SDFT and DDFT specimens. Mechanical testing was performed on 4 groups consisting of native tendons (5 SDFTs and 6 DDFTs) and decellularized tendons (5 SDFTs and 6 DDFTs). All tendons were preconditioned, and tension was applied to failure at 0.5 mm/s. Failure mode was video recorded for each tendon. Load-deformation and stress-strain curves were generated; calculations were performed to determine the Young modulus and stiffness. Biochemical and biomechanical data were statistically compared by use of the Wilcoxon rank sum test. Decellularized SDFT and DDFT specimens had significantly less DNA content than did native tendons. No significant differences were identified between native and decellularized specimens with respect to glycosaminoglycan, collagen, or protein content. Biomechanical comparison yielded no significant intra- or intergroup differences. All DDFT constructs failed at the tendon-clamp interface, whereas nearly half (4/10) of the SDFT constructs failed at midsubstance. Decellularized commercial canine SDFT and DDFT specimens had similar biomechanical properties, compared with each other and with native tendons. The decellularization process significantly decreased DNA content while minimizing loss of extracellular matrix components. Decellularized canine flexor tendons may provide suitable, biocompatible graft scaffolds for bioengineering applications such as tendon or ligament repair.

Behavioral epigenetics

PubMed Central

Lester, Barry M.; Tronick, Edward; Nestler, Eric; Abel, Ted; Kosofsky, Barry; Kuzawa, Christopher W.; Marsit, Carmen J.; Maze, Ian; Meaney, Michael J.; Monteggia, Lisa M.; Reul, Johannes M. H. M.; Skuse, David H.; Sweatt, J. David; Wood, Marcelo A.

2013-01-01

Sponsored by the New York Academy of Sciences, the Warren Alpert Medical School of Brown University and the University of Massachusetts Boston, “Behavioral Epigenetics” was held on October 29–30, 2010 at the University of Massachusetts Boston Campus Center, Boston, Massachusetts. This meeting featured speakers and panel discussions exploring the emerging field of behavioral epigenetics, from basic biochemical and cellular mechanisms to the epigenetic modulation of normative development, developmental disorders, and psychopathology. This report provides an overview of the research presented by leading scientists and lively discussion about the future of investigation at the behavioral epigenetic level. PMID:21615751

41 CFR 301-73.106 - What are the basic services that should be covered by a TMS?

Code of Federal Regulations, 2010 CFR

2010-07-01

..., confirmation of reservations, etc.). (b) Provide basic management information, such as— (1) Number of... 41 Public Contracts and Property Management 4 2010-07-01 2010-07-01 false What are the basic... Management Federal Travel Regulation System TEMPORARY DUTY (TDY) TRAVEL ALLOWANCES AGENCY RESPONSIBILITIES 73...

41 CFR 102-73.10 - What is the basic real estate acquisition policy?

Code of Federal Regulations, 2013 CFR

2013-07-01

... ESTATE ACQUISITION General Provisions § 102-73.10 What is the basic real estate acquisition policy? When... real estate and related services in an efficient and cost effective manner. ... 41 Public Contracts and Property Management 3 2013-07-01 2013-07-01 false What is the basic real...

41 CFR 102-73.10 - What is the basic real estate acquisition policy?

Code of Federal Regulations, 2012 CFR

2012-01-01

... ESTATE ACQUISITION General Provisions § 102-73.10 What is the basic real estate acquisition policy? When... real estate and related services in an efficient and cost effective manner. ... 41 Public Contracts and Property Management 3 2012-01-01 2012-01-01 false What is the basic real...

41 CFR 102-73.10 - What is the basic real estate acquisition policy?

Code of Federal Regulations, 2014 CFR

2014-01-01

... ESTATE ACQUISITION General Provisions § 102-73.10 What is the basic real estate acquisition policy? When... real estate and related services in an efficient and cost effective manner. ... 41 Public Contracts and Property Management 3 2014-01-01 2014-01-01 false What is the basic real...

41 CFR 102-73.10 - What is the basic real estate acquisition policy?

Code of Federal Regulations, 2010 CFR

2010-07-01

... ESTATE ACQUISITION General Provisions § 102-73.10 What is the basic real estate acquisition policy? When... real estate and related services in an efficient and cost effective manner. ... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What is the basic real...

41 CFR 102-73.10 - What is the basic real estate acquisition policy?

Code of Federal Regulations, 2011 CFR

2011-01-01

... ESTATE ACQUISITION General Provisions § 102-73.10 What is the basic real estate acquisition policy? When... real estate and related services in an efficient and cost effective manner. ... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 false What is the basic real...

An Independent Evaluation of the Technical Features of the Basic Reading Inventory

ERIC Educational Resources Information Center

Bieber, Gregg; Hulac, David M.; Schweinle, William

2015-01-01

The present study investigated some psychometric properties of the Basic Reading Inventory (BRI), a widely used informal reading inventory. The BRI and Dynamic Indicators of Basic Early Literacy Skills (DIBELS) probes were administered to 149 third, fourth, and fifth graders. Test--retest and alternate forms reliability analyses indicated adequate…

Biochemical Characterization, Action on Macrophages, and Superoxide Anion Production of Four Basic Phospholipases A2 from Panamanian Bothrops asper Snake Venom

PubMed Central

Rueda, Aristides Quintero; Rodríguez, Isela González; Arantes, Eliane C.; Setúbal, Sulamita S.; Calderon, Leonardo de A.; Zuliani, Juliana P.; Stábeli, Rodrigo G.; Soares, Andreimar M.

2013-01-01

Bothrops asper (Squamata: Viperidae) is the most important venomous snake in Central America, being responsible for the majority of snakebite accidents. Four basic PLA2s (pMTX-I to -IV) were purified from crude venom by a single-step chromatography using a CM-Sepharose ion-exchange column (1.5 × 15 cm). Analysis of the N-terminal sequence demonstrated that pMTX-I and III belong to the catalytically active Asp49 phospholipase A2 subclass, whereas pMTX-II and IV belong to the enzymatically inactive Lys49 PLA2s-like subclass. The PLA2s isolated from Panama Bothrops asper venom (pMTX-I, II, III, and IV) are able to induce myotoxic activity, inflammatory reaction mainly leukocyte migration to the muscle, and induce J774A.1 macrophages activation to start phagocytic activity and superoxide production. PMID:23509779

Virulence and extended-spectrum β-lactamase encoding genes in Escherichia coli recovered from chicken meat intended for hospitalized human consumption.

PubMed

Younis, Gamal A; Elkenany, Rasha M; Fouda, Mohamed A; Mostafa, Noura F

2017-10-01

This study describes the prevalence of Escherichia coli in frozen chicken meat intended for human consumption with emphasis on their virulence determinants through detection of the virulence genes and recognition of the extended-spectrum β-lactamase (ESBL) encoding genes ( bla OXA and bla TEM genes). A total of 120 frozen chicken meat samples were investigated for isolation of E. coli . All isolates were subjected to biochemical and serological tests. Eight serotypes isolated from samples were analyzed for the presence of various virulence genes ( stx1, stx2 , and eae A genes) using multiplex polymerase chain reaction (PCR) technique. Moreover, the strains were evaluated for the ESBL encoding genes ( bla TEM and bla OXA ). Overall, 11.66% (14/120) chicken meat samples carried E. coli according to cultural and biochemical properties. The most predominant serotypes were O78 and O128: H2 (21.5%, each), followed by O121: H7 and O44: H18. Molecular method detected that 2 strains (25%) harbored stx1 , 3 strains (37.5%) stx2 , and 3 strains (37.5%) both stx1 and stx2 , while 1 (12.5%) strain carried eae A gene. Particularly, only O26 serotype had all tested virulence genes ( stx1, stx2, and eae A ). The results revealed that all examined 8 serotypes were Shiga toxin-producing E. coli (STEC). The ESBL encoding genes ( bla TEM and bla OXA ) of STEC were detected in 4 (50%) isolates by multiplex PCR. The overall incidence of bla TEM and bla OXA genes was 3 (37.5%) and 2 (25%) isolates. The present study indicates the prevalence of virulent and ESBL-producing E. coli in frozen chicken meat intended for hospitalized human consumption due to poor hygienic measures and irregular use of antibiotics. Therefore, the basic instructions regarding good hygienic measures should be adapted to limit public health hazard.

Tradeoffs between hydraulic and mechanical stress responses of mature Norway spruce trunk wood.

PubMed

Rosner, Sabine; Klein, Andrea; Müller, Ulrich; Karlsson, Bo

2008-08-01

We tested the effects of growth characteristics and basic density on hydraulic and mechanical properties of mature Norway spruce (Picea abies (L.) Karst.) wood from six 24-year-old clones, grown on two sites in southern Sweden differing in water availability. Hydraulic parameters assessed were specific hydraulic conductivity at full saturation (ks100) and vulnerability to cavitation (Psi50), mechanical parameters included bending strength (sigma b), modulus of elasticity (MOE), compression strength (sigma a) and Young's modulus (E). Basic density, diameter at breast height, tree height, and hydraulic and mechanical parameters varied considerably among clones. Clonal means of hydraulic and mechanical properties were strongly related to basic density and to growth parameters across sites, especially to diameter at breast height. Compared with stem wood of slower growing clones, stem wood of rapidly growing clones had significantly lower basic density, lower sigma b, MOE, sigma a and E, was more vulnerable to cavitation, but had higher ks100. Basic density was negatively correlated to Psi50 and ks100. We therefore found a tradeoff between Psi50 and ks100. Clones with high basic density had significantly lower hydraulic vulnerability, but also lower hydraulic conductivity at full saturation and thus less rapid growth than clones with low basic density. This tradeoff involved a negative relationship between Psi50 and sigma b as well as MOE, and between ks100 and sigma b, MOE and sigma a. Basic density and Psi50 showed no site-specific differences, but tree height, diameter at breast height, ks100 and mechanical strength and stiffness were significantly lower at the drier site. Basic density had no influence on the site-dependent differences in hydraulic and mechanical properties, but was strongly negatively related to diameter at breast height. Selecting for growth may thus lead not only to a reduction in mechanical strength and stiffness but also to a reduction in hydraulic safety.

Composition and Molecular Weight Distribution of Carob Germ Proteins Fractions

USDA-ARS?s Scientific Manuscript database

Biochemical properties of carob germ proteins were analyzed using a combination of selective extraction, reversed-phase high performance liquid chromatography (RP-HPLC), size exclusion chromatography coupled with multi-angle laser light scattering (SEC-MALS) and electrophoretic analysis. Using a mo...

Denervation and reinnervation of skeletal muscle

NASA Technical Reports Server (NTRS)

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

1983-01-01

A review is presented of the physiological and biochemical changes that occur in mammalian skeletal muscle after denervation and reinnervation. These changes are compared with those observed after altered motor function. Also considered is the nature of the trophic influence by which nerves control muscle properties. Topics examined include the membrane and contractile properties of denervated and reinnervated muscle; the cholinergic proteins, such as choline acetyltransferase, acetylcholinesterase, and the acetylcholine receptor; and glucose-6-phosphate dehydrogenase.

The influence of leaf anatomy on the internal light environment and photosynthetic electron transport rate: exploration with a new leaf ray tracing model

PubMed Central

Xiao, Yi; Tholen, Danny; Zhu, Xin-Guang

2016-01-01

Leaf photosynthesis is determined by biochemical properties and anatomical features. Here we developed a three-dimensional leaf model that can be used to evaluate the internal light environment of a leaf and its implications for whole-leaf electron transport rates (J). This model includes (i) the basic components of a leaf, such as the epidermis, palisade and spongy tissues, as well as the physical dimensions and arrangements of cell walls, vacuoles and chloroplasts; and (ii) an efficient forward ray-tracing algorithm, predicting the internal light environment for light of wavelengths between 400 and 2500nm. We studied the influence of leaf anatomy and ambient light on internal light conditions and J. The results show that (i) different chloroplasts can experience drastically different light conditions, even when they are located at the same distance from the leaf surface; (ii) bundle sheath extensions, which are strips of parenchyma, collenchyma or sclerenchyma cells connecting the vascular bundles with the epidermis, can influence photosynthetic light-use efficiency of leaves; and (iii) chloroplast positioning can also influence the light-use efficiency of leaves. Mechanisms underlying leaf internal light heterogeneity and implications of the heterogeneity for photoprotection and for the convexity of the light response curves are discussed. PMID:27702991

Identification of Specific DNA Binding Residues in the TCP Family of Transcription Factors in Arabidopsis[W

PubMed Central

Aggarwal, Pooja; Das Gupta, Mainak; Joseph, Agnel Praveen; Chatterjee, Nirmalya; Srinivasan, N.; Nath, Utpal

2010-01-01

The TCP transcription factors control multiple developmental traits in diverse plant species. Members of this family share an ∼60-residue-long TCP domain that binds to DNA. The TCP domain is predicted to form a basic helix-loop-helix (bHLH) structure but shares little sequence similarity with canonical bHLH domain. This classifies the TCP domain as a novel class of DNA binding domain specific to the plant kingdom. Little is known about how the TCP domain interacts with its target DNA. We report biochemical characterization and DNA binding properties of a TCP member in Arabidopsis thaliana, TCP4. We have shown that the 58-residue domain of TCP4 is essential and sufficient for binding to DNA and possesses DNA binding parameters comparable to canonical bHLH proteins. Using a yeast-based random mutagenesis screen and site-directed mutants, we identified the residues important for DNA binding and dimer formation. Mutants defective in binding and dimerization failed to rescue the phenotype of an Arabidopsis line lacking the endogenous TCP4 activity. By combining structure prediction, functional characterization of the mutants, and molecular modeling, we suggest a possible DNA binding mechanism for this class of transcription factors. PMID:20363772

Effects of L-arginine on solubilization and purification of plant membrane proteins.

PubMed

Arakawa, Junji; Uegaki, Masamichi; Ishimizu, Takeshi

2011-11-01

Biochemical analysis of membrane proteins is problematic at the level of solubilization and/or purification because of their hydrophobic nature. Here, we developed methods for efficient solubilization and purification of membrane proteins using L-arginine. The addition of 100 mM of basic amino acids (L-arginine, L-lysine, and L-ornithine) to a detergent-containing solubilization buffer enhanced solubilization (by 2.6-4.3 fold) of a model membrane protein-polygalacturonic acid synthase. Of all the amino acids, arginine was the most effective additive for solubilization of this membrane protein. Arginine addition also resulted in the best solubilization of other plant membrane proteins. Next, we examined the effects of arginine on purification of a model membrane protein. In anion-exchange chromatography, the addition of arginine to the loading and elution buffers resulted in a greater recovery of a membrane protein. In ultrafiltration, the addition of arginine to a protein solution significantly improved the recovery of a membrane protein. These results were thought to be due to the properties of arginine that prevent aggregation of hydrophobic proteins. Taken together, the results of our study showed that arginine is useful for solubilization and purification of aggregate-prone membrane proteins. Copyright © 2011 Elsevier Inc. All rights reserved.

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

Jeffries, H P

As a test of the hypothesis that fatty acid patterns of entire planktonic communities should be less variable and more predictable in offshore waters than estuarine habitats, monthly samples have been taken in Block Island Sound, Narragansett Bay, and Green Hill Pond (a brackish lagoon), R.I. Observations include physical environmental properties, standing crop estimates, and fatty acid distribution in two size fractions - phytoplankton-microzooplankton and zooplankton. A second hypothesis states that the annual sample trajectory of a zooplankton community displayed in biochemical(fatty acid) phase space is related to production, but only under certain circumstances. Samples were also taken along themore » major axes of Ria de Arosa and Ria de Muros y Noya, two deep embayments on the Atlantic coast of northern Spain. Results on the first hypothesis show that each system in the gradient of environmental severity behaves individually during the autumnal cooling period, when plankton production declines to annual minima. Spatial distribution of zooplankton in the two adjacent Spanish rias differ completely, both qualitatively and quantitatively. A comparison between the Spanish rias and the three US estuaries should reveal the basic nature of chemically defined stable domain in community structure. From these relations, the fate of communities subjected to either natural stressors or anthrogenic perturbation may be predicted with economy, speed, and objectivity.« less

Bioinspired smart asymmetric nanochannel membranes.

PubMed

Zhang, Zhen; Wen, Liping; Jiang, Lei

2018-01-22

Bioinspired smart asymmetric nanochannel membranes (BSANM) have been explored extensively to achieve the delicate ionic transport functions comparable to those of living organisms. The abiotic system exhibits superior stability and robustness, allowing for promising applications in many fields. In view of the abundance of research concerning BSANM in the past decade, herein, we present a systematic overview of the development of the state-of-the-art BSANM system. The discussion is focused on the construction methodologies based on raw materials with diverse dimensions (i.e. 0D, 1D, 2D, and bulk). A generic strategy for the design and construction of the BSANM system is proposed first and put into context with recent developments from homogeneous to heterogeneous nanochannel membranes. Then, the basic properties of the BSANM are introduced including selectivity, gating, and rectification, which are associated with the particular chemical and physical structures. Moreover, we summarized the practical applications of BSANM in energy conversion, biochemical sensing and other areas. In the end, some personal opinions on the future development of the BSANM are briefly illustrated. This review covers most of the related literature reported since 2010 and is intended to build up a broad and deep knowledge base that can provide a solid information source for the scientific community.

Biochemistry of the tale transcription factors PREP, MEIS, and PBX in vertebrates.

PubMed

Longobardi, E; Penkov, D; Mateos, D; De Florian, G; Torres, M; Blasi, Francesco

2014-01-01

TALE (three amino acids loop extension) homeodomain transcription factors are required in various steps of embryo development, in many adult physiological functions, and are involved in important pathologies. This review focuses on the PREP, MEIS, and PBX sub-families of TALE factors and aims at giving information on their biochemical properties, i.e., structure, interactors, and interaction surfaces. Members of the three sets of protein form dimers in which the common partner is PBX but they can also directly interact with other proteins forming higher-order complexes, in particular HOX. Finally, recent advances in determining the genome-wide DNA-binding sites of PREP1, MEIS1, and PBX1, and their partial correspondence with the binding sites of some HOX proteins, are reviewed. These studies have generated a few general rules that can be applied to all members of the three gene families. PREP and MEIS recognize slightly different consensus sequences: PREP prefers to bind to promoters and to have PBX as a DNA-binding partner; MEIS prefers HOX as partner, and both PREP and MEIS drive PBX to their own binding sites. This outlines the clear individuality of the PREP and MEIS proteins, the former mostly devoted to basic cellular functions, the latter more to developmental functions. Copyright © 2013 Wiley Periodicals, Inc.

Setters and samoyeds: the emergence of subordinate level categories as a basis for inductive inference in preschool-age children.

PubMed

Waxman, S R; Lynch, E B; Casey, K L; Baer, L

1997-11-01

Basic level categories are a rich source of inductive inference for children and adults. These 3 experiments examine how preschool-age children partition their inductively rich basic level categories to form subordinate level categories and whether these have inductive potential. Children were taught a novel property about an individual member of a familiar basic level category (e.g., a collie). Then, children's extensions of that property to other objects from the same subordinate (e.g., other collies), basic (e.g., other dogs), and superordinate (e.g., other animals) level categories were examined. The results suggest (a) that contrastive information promotes the emergence of subordinate categories as a basis of inductive inference and (b) that newly established subordinate categories can retain their inductive potential in subsequent reasoning over a week's time.

[Research on basic questions of intellectual property rights of acupuncture and moxibustion].

PubMed

Dong, Guo-Feng; Wu, Xiao-Dong; Han, Yan-Jing; Meng, Hong; Wang, Xin

2011-12-01

Along with the modernization and internationalization of acupuncture-moxibustion (acu-moxibustion), the issue of intellectual property rights has been becoming prominent and remarkable increasingly. In the present paper, the authors explain the basic issues of acu-moxibustion learning from the concept, scope, subject, object, contents and acquisition way of intellectual property rights. To make clear these questions will help us inherit and carry forward the existing civilization achievements of acu-moxibustion, and unceasingly bring forth new ideas and further improvement in clinical application, so as to serve the people's health in a better way.

The Cryogenic Properties of Several Aluminum-Beryllium Alloys and a Beryllium Oxide Material

NASA Technical Reports Server (NTRS)

Gamwell, Wayne R.; McGill, Preston B.

2003-01-01

Performance related mechanical properties for two aluminum-beryllium (Al-Be) alloys and one beryllium-oxide (BeO) material were developed at cryogenic temperatures. Basic mechanical properties (Le., ultimate tensile strength, yield strength, percent elongation, and elastic modulus were obtained for the aluminum-beryllium alloy, AlBeMetl62 at cryogenic [-195.5"C (-320 F) and -252.8"C (-423"F)I temperatures. Basic mechanical properties for the Be0 material were obtained at cyrogenic [- 252.8"C (-423"F)] temperatures. Fracture properties were obtained for the investment cast alloy Beralcast 363 at cryogenic [-252.8"C (-423"F)] temperatures. The AlBeMetl62 material was extruded, the Be0 material was hot isostatic pressing (HIP) consolidated, and the Beralcast 363 material was investment cast.

Biochemical composition and antioxidant properties of Lavandula angustifolia Miller essential oil are shielded by propolis against UV radiations.

PubMed

Gismondi, Angelo; Angelo, Gismondi; Canuti, Lorena; Lorena, Canuti; Grispo, Marta; Marta, Grispo; Canini, Antonella; Antonella, Canini

2014-01-01

UV radiations are principal causes of skin cancer and aging. Suntan creams were developed to protect epidermis and derma layers against photodegradation and photooxidation. The addition of antioxidant plant extracts (i.e. essential oil) to sunscreens is habitually performed, to increase their UV protective effects and to contrast pro-radical and cytotoxic compounds present in these solutions. According to these observations, in the present work, the alteration of chemical composition and bioactive properties of Lavandula angustifolia Miller essential oil, exposed to UV light, was investigated. UV induced a significant deterioration of lavender oil biochemical profile. Moreover, the antioxidant activity of this solution, in in vitro tests and directly on B16-F10 melanoma cells, greatly decreased after UV treatment. Our results also showed that essential oil was shielded from UV stress by propolis addition. Even after UV treatment, bee glue highly protected lavender oil secondary metabolites from degradation and also preserved their antiradical properties, both in in vitro antioxidant assays and in cell oxidative damage evaluations. This research proposed propolis as highly efficient UV protective and antiradical additive for sunscreens, cosmetics and alimentary or pharmaceutical products containing plant extracts. © 2013 The American Society of Photobiology.

Antioxidant Properties and Cardioprotective Mechanism of Malaysian Propolis in Rats.

PubMed

Ahmed, Romana; Tanvir, E M; Hossen, Md Sakib; Afroz, Rizwana; Ahmmed, Istiyak; Rumpa, Nur-E-Noushin; Paul, Sudip; Gan, Siew Hua; Sulaiman, Siti Amrah; Khalil, Md Ibrahim

2017-01-01

Propolis contains high concentrations of polyphenols, flavonoids, tannins, ascorbic acid, and reducing sugars and proteins. Malaysian Propolis (MP) has been reported to exhibit high 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity and ferric reducing antioxidant power (FRAP) values. Herein, we report the antioxidant properties and cardioprotective properties of MP in isoproterenol- (ISO-) induced myocardial infarction in rats. Male Wistar rats ( n = 32) were pretreated orally with an ethanol extract of MP (100 mg/kg/day) for 30 consecutive days. Subcutaneous injection of ISO (85 mg/kg in saline) for two consecutive days caused a significant increase in serum cardiac marker enzymes and cardiac troponin I levels and altered serum lipid profiles. In addition significantly increased lipid peroxides and decreased activities of cellular antioxidant defense enzymes were observed in the myocardium. However, pretreatment of ischemic rats with MP ameliorated the biochemical parameters, indicating the protective effect of MP against ISO-induced ischemia in rats. Histopathological findings obtained for the myocardium further confirmed the biochemical findings. It is concluded that MP exhibits cardioprotective activity against ISO-induced oxidative stress through its direct cytotoxic radical-scavenging activities. It is also plausible that MP contributed to endogenous antioxidant enzyme activity via inhibition of lipid peroxidation.

Harnessing Intracellular Biochemical Pathways for In Vitro Synthesis of Designer Tellurium Nanorods.

PubMed

Xiong, Ling-Hong; Cui, Ran; Zhang, Zhi-Ling; Tu, Jia-Wei; Shi, Yun-Bo; Pang, Dai-Wen

2015-10-28

Synthesizing nanomaterials of desired properties is a big challenge, which requires extremely harsh conditions and/or use of toxic materials. More recently developed in vivo methods have brought a different set of problems such as separation and purification of nanomaterials made in vivo. Here, a novel approach that harnesses cellular pathways for in vitro synthesis of high-quality tellurium nanorods with tunable lengths and optical properties is reported. It is first demonstrated that in vivo biochemical pathways could be used to synthesize Te nanorods via the intracellular reduction of TeO3(2-) in living Staphylococcus aureus cells. The pathways to set up a quasi-biological system for Te precursor formation are then utilized, which could further synthesize Te nanorods in vitro. This allows to successfully synthesize in vitro, under routine laboratory conditions, Te nanorods with uniform and tunable lengths, ranging from about 10 to 200 nm, and controllable optical properties with high molar extinction coefficients. The approach here should open new avenues for controllable, facile, and efficient synthesis of designer nanomaterials for diverse industrial and biomedical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

['Specificity' in microbiology and immunochemistry between 1880 and 1930].

PubMed

Corbellini, Gilberto

2010-01-01

During the second half of the XIX Century, microbiological sciences acquired a set of conceptual, methodological and technological tools that radically transformed theoretical and empirical knowledge of the microorganisms, with particular regard to their biochemical properties and their etiopathological role in infectious diseases. During that period, theoretical and experimental researches in general microbiology and immunochemistry addressed the nature and empirical appearances of microbes, both pathogens and not, and the origins of chemical properties of immune sera. In other words, microbiologists tried operatively explaining the origins of the morphological, physiological, and pathogenetic differences between the microbial species. At the same time physiologists and biochemists investigated the chemical basis of the selective or specific interactions between microorganisms or their chemical components and humoral factors contained into the sera produced by the body in response to the contact with microbes. During the half a century, between 1880 and 1930, qualitative and quantitative experimental studies demonstrated that the specificity of microbiological phenomena depended on the biology of microbes and that the specificity of immune reactions hinged upon the biochemical properties of special molecules synthesized by some physiological system which can recognize and react against any foreign substance.

Bovine seminal PDC-109 protein: an overview of biochemical and functional properties.

PubMed

Srivastava, N; Jerome, A; Srivastava, S K; Ghosh, S K; Kumar, Amit

2013-04-01

Although long-term storage of bovine semen is desirable for wider use, successful cryopreservation depends on several factors, including various proteins present in seminal plasma. One such group of proteins, viz. bovine seminal plasma (BSP) proteins represents the major protein fraction in bovine seminal plasma. They constitute three major heparin-binding (HB-) acidic proteins secreted by seminal vesicles, viz. BSP-A1/-A2 (PDC-109), BSP-A3 and BSP-30-kDa. By purification studies it was deduced that PDC-109 is a polypeptide of 109 amino acids and contains two tandem repeating fibronectin type-II (Fn-II) domains, preceded by a 23 residue N-terminal domain. Though BSP-A1 and BSP-A2 are biochemically similar they differ only in glycosylation and their mixture is called PDC-109 or gonadostatins. PDC-109 exists as a polydisperse, multimeric self-associated molecule and possesses multifunctional properties, viz. binding to the surface of plasma membrane of spermatozoa causing conformational change in the sperm surface proteins and enhances motility. Besides binding, PDC-109 protein provokes cholesterol efflux from sperm membrane and promotes sperm reservoir by interacting with oviductal membrane. Interaction of sperm with PDC-109 protein induces sperm capacitation and acrosome reaction. However, prolonged exposure of spermatozoa with free floating PDC-109 protein as during processing for preservation, increases cholesterol efflux from spermatozoa. The efflux of sperm membrane cholesterol and disturbance in cholesterol:phospholipids ratio causes destabilization of plasma membrane thereby inducing cryoinjury to the sperm. In this review, the biochemical, functional properties of PDC-109 protein and its role during semen cryopreservation is summarized. Copyright © 2013 Elsevier B.V. All rights reserved.

Effects of poultry manure on soil biochemical properties in phthalic acid esters contaminated soil.

PubMed

Gao, Jun; Qin, Xiaojian; Ren, Xuqin; Zhou, Haifeng

2015-12-01

This study aimed to evaluate the effects of poultry manure (PM) on soil biological properties in DBP- and DEHP-contaminated soils. An indoor incubation experiment was conducted. Soil microbial biomass C (Cmic), soil enzymatic activities, and microbial phospholipid fatty acid (PLFA) concentrations were measured during incubation period. The results indicated that except alkaline phosphatase activity, DBP and DEHP had negative effects on Cmic, dehydrogenase, urease, protease activities, and contents of total PLFA. However, 5 % PM treatment alleviated the negative effects of PAEs on the above biochemical parameters. In DBP-contaminated soil, 5 % PM amendment even resulted in dehydroenase activity and Cmic content increasing by 17.8 and 11.8 % on the day 15 of incubation, respectively. During the incubation periods, the total PLFA contents decreased maximumly by 17.2 and 11.6 % in DBP- and DEHP-contaminated soils without PM amendments, respectively. Compared with those in uncontaminated soil, the total PLFA contents increased slightly and the value of bacPLFA/fugalPLFA increased significantly in PAE-contaminated soils with 5 % PM amendment. Nevertheless, in both contaminated soils, the effects of 5 % PM amendment on the biochemical parameters were not observed with 10 % PM amendment. In 10 % PM-amended soils, DBP and DEHP had little effect on Cmic, soil enzymatic activities, and microbial community composition. At the end of incubation, the effects of PAEs on these parameters disappeared, irrespective of PM amendment. The application of PM ameliorated the negative effect of PAEs on soil biological environment. However, further work is needed to study the effect of PM on soil microbial gene expression in order to explain the change mechanisms of soil biological properties.

Similarities and differences in the biochemical and enzymological properties of the four isomaltases from Saccharomyces cerevisiae

PubMed Central

Deng, Xu; Petitjean, Marjorie; Teste, Marie-Ange; Kooli, Wafa; Tranier, Samuel; François, Jean Marie; Parrou, Jean-Luc

2014-01-01

The yeast Saccharomyces cerevisiae IMA multigene family encodes four isomaltases sharing high sequence identity from 65% to 99%. Here, we explore their functional diversity, with exhaustive in-vitro characterization of their enzymological and biochemical properties. The four isoenzymes exhibited a preference for the α-(1,6) disaccharides isomaltose and palatinose, with Michaëlis–Menten kinetics and inhibition at high substrates concentration. They were also able to hydrolyze trisaccharides bearing an α-(1,6) linkage, but also α-(1,2), α-(1,3) and α-(1,5) disaccharides including sucrose, highlighting their substrate ambiguity. While Ima1p and Ima2p presented almost identical characteristics, our results nevertheless showed many singularities within this protein family. In particular, Ima3p presented lower activities and thermostability than Ima2p despite only three different amino acids between the sequences of these two isoforms. The Ima3p_R279Q variant recovered activity levels of Ima2p, while the Leu-to-Pro substitution at position 240 significantly increased the stability of Ima3p and supported the role of prolines in thermostability. The most distant protein, Ima5p, presented the lowest optimal temperature and was also extremely sensitive to temperature. Isomaltose hydrolysis by Ima5p challenged previous conclusions about the requirement of specific amino acids for determining the specificity for α-(1,6) substrates. We finally found a mixed inhibition by maltose for Ima5p while, contrary to a previous work, Ima1p inhibition by maltose was competitive at very low isomaltose concentrations and uncompetitive as the substrate concentration increased. Altogether, this work illustrates that a gene family encoding proteins with strong sequence similarities can lead to enzyme with notable differences in biochemical and enzymological properties. PMID:24649402

Similarities and differences in the biochemical and enzymological properties of the four isomaltases from Saccharomyces cerevisiae.

PubMed

Deng, Xu; Petitjean, Marjorie; Teste, Marie-Ange; Kooli, Wafa; Tranier, Samuel; François, Jean Marie; Parrou, Jean-Luc

2014-01-01

The yeast Saccharomyces cerevisiae IMA multigene family encodes four isomaltases sharing high sequence identity from 65% to 99%. Here, we explore their functional diversity, with exhaustive in-vitro characterization of their enzymological and biochemical properties. The four isoenzymes exhibited a preference for the α-(1,6) disaccharides isomaltose and palatinose, with Michaëlis-Menten kinetics and inhibition at high substrates concentration. They were also able to hydrolyze trisaccharides bearing an α-(1,6) linkage, but also α-(1,2), α-(1,3) and α-(1,5) disaccharides including sucrose, highlighting their substrate ambiguity. While Ima1p and Ima2p presented almost identical characteristics, our results nevertheless showed many singularities within this protein family. In particular, Ima3p presented lower activities and thermostability than Ima2p despite only three different amino acids between the sequences of these two isoforms. The Ima3p_R279Q variant recovered activity levels of Ima2p, while the Leu-to-Pro substitution at position 240 significantly increased the stability of Ima3p and supported the role of prolines in thermostability. The most distant protein, Ima5p, presented the lowest optimal temperature and was also extremely sensitive to temperature. Isomaltose hydrolysis by Ima5p challenged previous conclusions about the requirement of specific amino acids for determining the specificity for α-(1,6) substrates. We finally found a mixed inhibition by maltose for Ima5p while, contrary to a previous work, Ima1p inhibition by maltose was competitive at very low isomaltose concentrations and uncompetitive as the substrate concentration increased. Altogether, this work illustrates that a gene family encoding proteins with strong sequence similarities can lead to enzyme with notable differences in biochemical and enzymological properties.

Experimental Infection of Cattle With a Novel Prion Derived From Atypical H-Type Bovine Spongiform Encephalopathy.

PubMed

Okada, Hiroyuki; Masujin, Kentaro; Miyazawa, Kohtaro; Iwamaru, Yoshihumi; Imamura, Morikazu; Matsuura, Yuichi; Arai, Shozo; Fukuda, Shigeo; Murayama, Yuichi; Yokoyama, Takashi

2017-11-01

H-type bovine spongiform encephalopathy (H-BSE) is an atypical form of BSE in cattle. During passaging of H-BSE in transgenic bovinized (TgBoPrP) mice, a novel phenotype of BSE, termed BSE-SW emerged and was characterized by a short incubation time and host weight loss. To investigate the biological and biochemical properties of the BSE-SW prion, a transmission study was conducted in cattle, which were inoculated intracerebrally with brain homogenate from BSE-SW-infected TgBoPrP mice. The disease incubation period was approximately 15 months. The animals showed characteristic neurological signs of dullness, and severe spongiform changes and a widespread, uniform distribution of disease-associated prion protein (PrP Sc ) were observed throughout the brain of infected cattle. Immunohistochemical PrP Sc staining of the brain revealed the presence of intraglial accumulations and plaque-like deposits. No remarkable differences were identified in vacuolar lesion scores, topographical distribution patterns, and staining types of PrP Sc in the brains of BSE-SW- vs H-BSE-infected cattle. PrP Sc deposition was detected in the ganglia, vagus nerve, spinal nerve, cauda equina, adrenal medulla, and ocular muscle. Western blot analysis revealed that the specific biochemical properties of the BSE-SW prion, with an additional 10- to 12-kDa fragment, were well maintained after transmission. These findings indicated that the BSE-SW prion has biochemical properties distinct from those of H-BSE in cattle, although clinical and pathologic features of BSW-SW in cattle are indistinguishable from those of H-BSE. The results suggest that the 2 infectious agents, BSE-SW and H-BSE, are closely related strains.

Music Tune Restoration Based on a Mother Wavelet Construction

NASA Astrophysics Data System (ADS)

Fadeev, A. S.; Konovalov, V. I.; Butakova, T. I.; Sobetsky, A. V.

2017-01-01

It is offered to use the mother wavelet function obtained from the local part of an analyzed music signal. Requirements for the constructed function are proposed and the implementation technique and its properties are described. The suggested approach allows construction of mother wavelet families with specified identifying properties. Consequently, this makes possible to identify the basic signal variations of complex music signals including local time-frequency characteristics of the basic one.

Differences in Physical and Biochemical Properties of Thermus scotoductus SA-01 Cultured with Dielectric or Convection Heating.

PubMed

Cockrell, Allison L; Fitzgerald, Lisa A; Cusick, Kathleen D; Barlow, Daniel E; Tsoi, Stanislav D; Soto, Carissa M; Baldwin, Jeffrey W; Dale, Jason R; Morris, Robert E; Little, Brenda J; Biffinger, Justin C

2015-09-01

A thermophile, Thermus scotoductus SA-01, was cultured within a constant-temperature (65°C) microwave (MW) digester to determine if MW-specific effects influenced the growth and physiology of the organism. As a control, T. scotoductus cells were also cultured using convection heating at the same temperature as the MW studies. Cell growth was analyzed by optical density (OD) measurements, and cell morphologies were characterized using electron microscopy imaging (scanning electron microscopy [SEM] and transmission electron microscopy [TEM]), dynamic light scattering (DLS), and atomic force microscopy (AFM). Biophysical properties (i.e., turgor pressure) were also calculated with AFM, and biochemical compositions (i.e., proteins, nucleic acids, fatty acids) were analyzed by attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. Gas chromatography-mass spectrometry (GC-MS) was used to analyze the fatty acid methyl esters extracted from cell membranes. Here we report successful cultivation of a thermophile with only dielectric heating. Under the MW conditions for growth, cell walls remained intact and there were no indications of membrane damage or cell leakage. Results from these studies also demonstrated that T. scotoductus cells grown with MW heating exhibited accelerated growth rates in addition to altered cell morphologies and biochemical compositions compared with oven-grown cells. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Identification of paraoxonase 3 in rat liver microsomes: purification and biochemical properties.

PubMed Central

Rodrigo, Lourdes; Gil, Fernando; Hernandez, Antonio F; Lopez, Olga; Pla, Antonio

2003-01-01

Three paraoxonase genes (PON1, PON2 and PON3) have been described so far in mammals. Although considerable information is available regarding PON1, little is known about PON2 and PON3. PON3 has been isolated recently from rabbit serum [Draganov, Stetson, Watson, Billecke and La Du (2000) J. Biol. Chem. 275, 33435-33442] and liver [Ozols (1999) Biochem. J. 338, 265-275]. In the present study, we have identified the presence of PON3 in rat liver microsomes and a method for the purification to homogeneity is presented. PON3 has been purified 177-fold to apparent homogeneity with a final specific activity of 461 units/mg using a method consisting of seven steps: solubilization of the microsomal fraction, hydroxyapatite adsorption, chromatography on DEAE-Sepharose CL-6B, non-specific affinity chromatography on Cibacron Blue 3GA, two DEAE-cellulose steps and a final affinity chromatography on concanavalin A-Sepharose. SDS/PAGE of the final preparation indicated a single protein-staining band with an apparent molecular mass of 43 kDa. The isolated protein was identified by nanoelectrospray MS. Internal amino acid sequences of several peptides were determined and compared with those of human, rabbit and mouse PON3, showing a high similarity. Some biochemical properties of PON3 were also studied, including optimum pH, K(m) and heat and pH stability. PMID:12946270

Polymer Basics: Classroom Activities Manipulating Paper Clips to Introduce the Structures and Properties of Polymers

ERIC Educational Resources Information Center

Umar, Yunusa

2014-01-01

A simple and effective hands-on classroom activity designed to illustrate basic polymer concepts is presented. In this activity, students build primary structures of homopolymers and different arrangements of monomers in copolymer using paper clips as monomers. The activity supports formation of a basic understanding of polymer structures,…

41 CFR 102-85.25 - What is the basic principle governing OAs?

Code of Federal Regulations, 2010 CFR

2010-07-01

... principle governing OAs? 102-85.25 Section 102-85.25 Public Contracts and Property Management Federal... POLICY FOR OCCUPANCY IN GSA SPACE Pricing Policy-General § 102-85.25 What is the basic principle governing OAs? The basic principle governing OAs is to adopt the private sector practice of capturing in a...

Contract Award on Initial Proposals

DTIC Science & Technology

1988-09-30

3 2. Competition in Contracting Act ... ......... 6 3. Federal Property and Administrative Services Act 10 B. Basic Rules for Award Without...Discussions Before CICA . 11 C. Basic Rules for Award Without Discussions After Passage of CICA .......... ........................ ... 12 D. Award...controlled by statute. This chapter will explore those statutes and their antecedents. The basic rules for awarding contracts without discussions

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

The effect of metal ions on Staphylococcus aureus revealed by biochemical and mass spectrometric analyses.

PubMed

Chudobova, Dagmar; Dostalova, Simona; Ruttkay-Nedecky, Branislav; Guran, Roman; Rodrigo, Miguel Angel Merlos; Tmejova, Katerina; Krizkova, Sona; Zitka, Ondrej; Adam, Vojtech; Kizek, Rene

2015-01-01

In this study, we focused on the effect of heavy metal ions in resistant strains of gram-positive bacteria Staphylococcus aureus using biochemical methods and mass spectrometry. Five nitrate solutions of heavy metals (Ag(+), Cu(2+), Cd(2+), Zn(2+) and Pb(2+)) were used to create S. aureus resistant strains. Biochemical changes of resistant strains in comparison with the non-resistant control strain of S. aureus were observed by microbiological (measuring - growth curves and inhibition zones) and spectrophotometric methods (antioxidant activity and alaninaminotransferase, aspartateaminotransferase, alkaline phosphatase, γ-glutamyltransferase activities). Mass spectrometry was employed for the qualitative analysis of the samples (changes in S. aureus protein composition) and for the identification of the strains database MALDI Biotyper was employed. Alterations, in terms of biochemical properties and protein composition, were observed in resistant strains compared to non-resistant control strain. Our results describe the possible option for the analysis of S. aureus resistant strains and may thus serve as a support for monitoring of changes in genetic information caused by the forming of resistance to heavy metals. Copyright © 2014 Elsevier GmbH. All rights reserved.

Physical-chemical properties and the reactivity of pyridoxine and pyrrolidone carboxylate and their protolytic forms.

PubMed

Golovenko, N Ya; Larionov, V B; Karpova, O V

2016-01-01

Preparation Methadoxine is equimolar salt, which cationic component (pyridoxine) is 3-oxypyridine derivative, possessing B6-vitamine like activity, while anionic component is the cyclic lactame of glutamic acid. Since biopharmaceutical and pharmacological properties of this drug depend on biochemical transformation its components, of the aim of this work was to determine the structure of possible ionized pyridoxine and pyrrolidone carboxylate forms and their reaction ability in biochemical processes. Physical-chemical properties of compounds (pKa, logP, logD, proton donor/acceptor quantity, solubility (g/l)) were calculated with ACD/pKaDB program or obtained from Pub-Med physical/chemical properties database. UV spectra of compounds were obtained after dissolution in different pH solutions (1.0, 4.5 and 6.8). It was found that at different pH values one can observe changes of the absorption spectra due to the presence of prevailing amount of the protonated form. An analysis of both pKa, logP and logD indicators and reactive functional groups of Methadoxine components has revealed that they can be protonated in different regions of gastro-intestinal tract, that influences their solubility in hydrophilic and lypophilic media. Pharmacological properties of pyridoxine and pyrrolidone carboxylate themselves are performed after their preliminary biotransformation to active metabolites. Only ionic interaction between Methadoxine components in the substance composition can appear, that provides its pharmaceutical stability and ensures its activity only in the organism conditions.

Isolation & characterization of Brucella melitensis isolated from patients suspected for human brucellosis in India

PubMed Central

Barua, Anita; Kumar, Ashu; Thavaselvam, Duraipandian; Mangalgi, Smita; Prakash, Archana; Tiwari, Sapana; Arora, Sonia; Sathyaseelan, Kannusamy

2016-01-01

Background & objectives: Brucellosis is endemic in the southern part of India. A combination of biochemical, serological and molecular methods is required for identification and biotyping of Brucella. The present study describes the isolation and biochemical, molecular characterization of Brucella melitensis from patients suspected for human brucellosis. Methods: The blood samples were collected from febrile patients suspected to have brucellosis. A total of 18 isolates were obtained from 102 blood samples subjected to culture. The characterization of these 18 isolates was done by growth on Brucella specific medium, biochemical reactions, CO2 requirement, H2S production, agglutination with A and M mono-specific antiserum, dye sensitivity to basic fuchsin and thionin. Further, molecular characterization of the isolates was done by amplification of B. melitensis species specific IS711 repetitive DNA fragment and 16S (rRNA) sequence analysis. PCR-restriction fragment length polymorphism (RFLP) analysis of omp2 locus and IS711 gene was also done for molecular characterization. Results: All 102 suspected samples were subjected to bacteria isolation and of these, 18 isolates could be recovered on blood culture. The biochemical, PCR and PCR-RFLP and 16s rRNA sequencing revealed that all isolates were of B. melitensis and matched exactly with reference strain B. melitensis 16M. Interpretation & conclusions: The present study showed an overall isolation rate of 17.64 per cent for B. melitensis. There is a need to establish facilities for isolation and characterization of Brucella species for effective clinical management of the disease among patients as well as surveillance and control of infection in domestic animals. Further studies are needed from different geographical areas of the country with different level of endemicity to plan and execute control strategies against human brucellosis. PMID:27488010

Mass Uncertainty and Application For Space Systems

NASA Technical Reports Server (NTRS)

Beech, Geoffrey

2013-01-01

Expected development maturity under contract (spec) should correlate with Project/Program Approved MGA Depletion Schedule in Mass Properties Control Plan. If specification NTE, MGA is inclusive of Actual MGA (A5 & A6). If specification is not an NTE Actual MGA (e.g. nominal), then MGA values are reduced by A5 values and A5 is representative of remaining uncertainty. Basic Mass = Engineering Estimate based on design and construction principles with NO embedded margin MGA Mass = Basic Mass * assessed % from approved MGA schedule. Predicted Mass = Basic + MGA. Aggregate MGA % = (Aggregate Predicted - Aggregate Basic) /Aggregate Basic.

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

Proposal for study on IR light and glucose phantom interaction for human glucose quantification applications

NASA Astrophysics Data System (ADS)

Romo-Cárdenas, Gerardo S.; Sanchez-Lopez, Juan D.; Nieto-Hipolito, Juan I.; Cosio-León, María.; Luque-Morales, Priscy; Vazquez-Briseno, Mabel

2016-09-01

It has been established the importance of a constant glucose monitoring in order to keep a regular control for diabetes patients. Several medical studies accept the necessity of exploring alternatives for the traditional digital glucometer, given the pain and discomfort related to this technique, which can lead to a compromised control of the disease. Several efforts based on the application of IR spectroscopy had been done with favorable, yet not conclusive results. Therefore it's necessary to apply a comprehensive and interdisciplinary study based on the biochemical and optical properties of the glucose in the human body, in order to understand the interaction between this substance, its surroundings and IR light. These study propose a comprehensive approach of the glucose and IR light interaction, considering and combining important biochemical, physiological and optical properties, as well as some machine learning techniques for the data analysis. The results of this work would help to define the right parameters aiming to obtain an optical glucose quantification system and protocol.

Effect of ascorbic acid on storage of Greyhound erythrocytes.

PubMed

Fontes, Jorge A; Banerjee, Uddyalok; Iazbik, M Cristina; Marín, Liliana M; Couto, C Guillermo; Palmer, Andre F

2015-09-01

To assess changes in biochemical and biophysical properties of canine RBCs during cold (1° to 6°C) storage in a licensed RBC additive solution (the RBC preservation solution designated AS-1) supplemented with ascorbic acid. Blood samples from 7 neutered male Greyhounds; all dogs had negative results when tested for dog erythrocyte antigen 1.1. Blood was collected into citrate-phosphate-dextrose and stored in AS-1. Stored RBCs were supplemented with 7.1mM ascorbic acid or with saline (0.9% NaCl) solution (control samples). Several biochemical and biophysical properties of RBCs were measured, including percentage hemolysis, oxygen-hemoglobin equilibrium, and the kinetic rate constants for O2 dissociation, carbon monoxide association, and nitric oxide dioxygenation. Greyhound RBCs stored in AS-1 supplemented with ascorbic acid did not have significantly decreased hemolysis, compared with results for the control samples, during the storage period. In this study, ascorbic acid did not reduce hemolysis during storage. Several changes in stored canine RBCs were identified as part of the hypothermic storage lesion.

Label-free cell separation and sorting in microfluidic systems

PubMed Central

Gossett, Daniel R.; Weaver, Westbrook M.; Mach, Albert J.; Hur, Soojung Claire; Tse, Henry Tat Kwong; Lee, Wonhee; Amini, Hamed

2010-01-01

Cell separation and sorting are essential steps in cell biology research and in many diagnostic and therapeutic methods. Recently, there has been interest in methods which avoid the use of biochemical labels; numerous intrinsic biomarkers have been explored to identify cells including size, electrical polarizability, and hydrodynamic properties. This review highlights microfluidic techniques used for label-free discrimination and fractionation of cell populations. Microfluidic systems have been adopted to precisely handle single cells and interface with other tools for biochemical analysis. We analyzed many of these techniques, detailing their mode of separation, while concentrating on recent developments and evaluating their prospects for application. Furthermore, this was done from a perspective where inertial effects are considered important and general performance metrics were proposed which would ease comparison of reported technologies. Lastly, we assess the current state of these technologies and suggest directions which may make them more accessible. Figure A wide range of microfluidic technologies have been developed to separate and sort cells by taking advantage of differences in their intrinsic biophysical properties PMID:20419490

Future direction in marine bacterial agarases for industrial applications.

PubMed

Jahromi, Saeid Tamadoni; Barzkar, Noora

2018-06-16

The marine ecosystem has been known to be a rich source of novel enzymes. Agarase is a key enzyme that can hydrolyze agar in the marine environment. Marine bacterial agarase has been isolated from various sources, such as sediments, coastal water, and deep sea and from the surface of crustaceans and seaweeds. This review presents an account of the agarase production of marine bacteria. General information about agar, agarase, isolation, and purification of marine bacterial agarases; the biochemical properties of native agarase from marine bacteria; the biochemical properties of recombinant marine bacterial agarases from engineered microorganisms; and the industrial future of marine bacterial agarases is analyzed. With recent biotechnological processes, researchers need novel functional enzymes like agarase from marine resources, such as marine bacteria, that can be used for diverse applications in the biotechnological industry. Marine bacterial agarases might be of significant interest to the industry because they are safe and are a natural source. This review highlights the potential of marine bacteria as important sources of agarase for application in various industries.

Impact of Thermal Pretreatment Temperatures on Woody Biomass Chemical Composition, Physical Properties and Microstructure

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

Wang, Ping; Howard, Bret H.

Thermal pretreatment of biomass by torrefaction and low temperature pyrolysis has the potential for generating high quality and more suitable fuels. To utilize a model to describe the complex and dynamic changes taking place during these two treatments for process design, optimization and scale-up, detailed data is needed on the property evolution during treatment of well-defined individual biomass particles. The objectives of this study are to investigate the influence of thermal pretreatment temperatures on wood biomass biochemical compositions, physical properties and microstructure. Wild cherry wood was selected as a model biomass and prepared for this study. The well-defined wood particlemore » samples were consecutively heated at 220, 260, 300, 350, 450 and 550 °C for 0.5 h under nitrogen. Untreated and treated samples were characterized for biochemical composition changes (cellulose, hemicellulose, and lignin) by thermogravimetric analyzer (TGA), physical properties (color, dimensions, weight, density and grindablity), chemical property (proximate analysis and heating value) and microstructural changes by scanning electron microscopy (SEM). Hemicellulose was mostly decomposed in the samples treated at 260 and 300 °C and resulted in the cell walls weakening resulting in improved grindability. The dimensions of the wood were reduced in all directions and shrinkage increased with increased treatment temperature and weight loss. With increased treatment temperature, losses of weight and volume increased and bulk density decreased. The low temperature pyrolyzed wood samples improved solid fuel property with high fuel ratio, which are close to lignite/bituminous coal. Morphology of the wood remained intact through the treatment range but the cell walls were thinner. Lastly, these results will improve the understanding of the property changes of the biomass during pretreatment and will help to develop models for process simulation and potential application of the treated biomass.« less

Impact of Thermal Pretreatment Temperatures on Woody Biomass Chemical Composition, Physical Properties and Microstructure

DOE PAGES

Wang, Ping; Howard, Bret H.

2017-12-23

Thermal pretreatment of biomass by torrefaction and low temperature pyrolysis has the potential for generating high quality and more suitable fuels. To utilize a model to describe the complex and dynamic changes taking place during these two treatments for process design, optimization and scale-up, detailed data is needed on the property evolution during treatment of well-defined individual biomass particles. The objectives of this study are to investigate the influence of thermal pretreatment temperatures on wood biomass biochemical compositions, physical properties and microstructure. Wild cherry wood was selected as a model biomass and prepared for this study. The well-defined wood particlemore » samples were consecutively heated at 220, 260, 300, 350, 450 and 550 °C for 0.5 h under nitrogen. Untreated and treated samples were characterized for biochemical composition changes (cellulose, hemicellulose, and lignin) by thermogravimetric analyzer (TGA), physical properties (color, dimensions, weight, density and grindablity), chemical property (proximate analysis and heating value) and microstructural changes by scanning electron microscopy (SEM). Hemicellulose was mostly decomposed in the samples treated at 260 and 300 °C and resulted in the cell walls weakening resulting in improved grindability. The dimensions of the wood were reduced in all directions and shrinkage increased with increased treatment temperature and weight loss. With increased treatment temperature, losses of weight and volume increased and bulk density decreased. The low temperature pyrolyzed wood samples improved solid fuel property with high fuel ratio, which are close to lignite/bituminous coal. Morphology of the wood remained intact through the treatment range but the cell walls were thinner. Lastly, these results will improve the understanding of the property changes of the biomass during pretreatment and will help to develop models for process simulation and potential application of the treated biomass.« less

The nuclear envelope from basic biology to therapy.

PubMed

Worman, Howard J; Foisner, Roland

2010-02-01

The nuclear envelope has long been a focus of basic research for a highly specialized group of cell biologists. More recently, an expanding group of scientists and physicians have developed a keen interest in the nuclear envelope since mutations in the genes encoding lamins and associated proteins have been shown to cause a diverse range of human diseases often called laminopathies or nuclear envelopathies. Most of these diseases have tissue-selective phenotypes, suggesting that the nuclear envelope must function in cell-type- and developmental-stage-specific processes such as chromatin organization, regulation of gene expression, controlled nucleocytoplasmic transport and response to stress in metazoans. On 22-23 April 2009, Professor Christopher Hutchison organized the 4th British Nuclear Envelope Disease and Chromatin Organization meeting at the College of St Hild and St Bede at Durham University, sponsored by the Biochemical Society. In attendance were investigators with one common interest, the nuclear envelope, but with diverse expertise and training in animal and plant cell biology, genetics, developmental biology and medicine. We were each honoured to be keynote speakers. This issue of Biochemical Society Transactions contains papers written by some of the presenters at this scientifically exciting meeting, held in a bucolic setting where the food was tasty and the wine flowed freely. Perhaps at the end of this excellent meeting more questions were raised than answered, which will stimulate future research. However, what became clear is that the nuclear envelope is a cellular structure with critical functions in addition to its traditional role as a barrier separating the nuclear and cytoplasmic compartments in interphase eukaryotic cells.

Creation and implementation of a flipped jigsaw activity to stimulate interest in biochemistry among medical students.

PubMed

Williams, Charlene; Perlis, Susan; Gaughan, John; Phadtare, Sangita

2018-05-06

Learner-centered pedagogical methods that are based on clinical application of basic science concepts through active learning and problem solving are shown to be effective for improving knowledge retention. As the clinical relevance of biochemistry is not always apparent to health-profession students, effective teaching of medical biochemistry should highlight the implications of biochemical concepts in pathology, minimize memorization, and make the concepts memorable for long-term retention. Here, we report the creation and successful implementation of a flipped jigsaw activity that was developed to stimulate interest in learning biochemistry among medical students. The activity combined the elements of a flipped classroom for learning concepts followed by a jigsaw activity to retrieve these concepts by solving clinical cases, answering case-based questions, and creating concept maps. The students' reception of the activity was very positive. They commented that the activity provided them an opportunity to review and synthesize information, helped to gage their learning by applying this information and work with peers. Students' improved performance especially for answering the comprehension-based questions correctly in the postquiz as well as the depth of information included in the postquiz concept maps suggested that the activity helped them to understand how different clinical scenarios develop owing to deviations in basic biochemical pathways. Although this activity was created for medical students, the format of this activity can also be useful for other health-professional students as well as undergraduate and graduate students. © 2018 by The International Union of Biochemistry and Molecular Biology, 2018. © 2018 The International Union of Biochemistry and Molecular Biology.

Is Fasting for Ramadan Safe in Patients with Mechanical Cardiac Valves?

PubMed

Yildirim, Ersin; Secen, Ozlem; Uku, Okkes; Nail Bilen, Mehmet; Kutlu Karadag, Makbule

2017-03-01

The study aim was to investigate the safety and effects of fasting during Ramadan on the International Normalized Ratio (INR) in patients with mechanical cardiac valves. A total of 105 patients admitted to the authors' hospital between June and October 2015, who had history of prosthetic valve replacement, was investigated. The patients were allocated to two groups: those fasting during Ramadan (n = 42) and those not fasting (n = 63). All patients were examined by a cardiologist, and the clinical findings and complaints for the past three months were evaluated. The INR, complete blood count (CBC) and a basic biochemical panel were monitored for all patients. The mean corpuscular volume (MCV) of the fasting group was significantly higher than that of the non- fasting group (87.59 ± 6.39 (μm3) versus 84.28 ± 6.387 (μm3); p = 0.011). Other CBC parameters and basic biochemical values did not differ significantly different between groups. Neither were significant differences noted in INR values during Ramadan (fasting group 2.87 ± 0.97; non-fasting group 2.73 ± 0.78; p = 0.50) and at routine control one month later (fasting group 3.07 ± 1.55; non-fasting group 2.94 ± 1.03; p = 0.601). No significant differences related to increased rates of hospitalization, valvular dysfunction on echocardiography, thrombus, embolism, bleeding and clinical complaints were identified between the groups. Fasting during Ramadan had no adverse effects on the INR of patients, and appears to be safe for patients with mechanical prosthetic cardiac valves.

Immortalization of cat iris sphincter smooth muscle cells by SV40 virus: growth, morphological, biochemical and pharmacological characteristics.

PubMed

Ocklind, A; Yousufzai, S Y; Ghosh, S; Coca-Prados, M; St Jernschantz, J; Abdel-Latif, A A

1995-11-01

The purpose of this study was to establish immortalized cell cultures of cat iris sphincter smooth muscle cells for a model investigating ocular receptors and their signal transduction pathways. Cultured cat iris sphincter muscle cells were immortalized by viral transformation with SV40 virus and the morphological and immunocytochemical properties of the normal and immortalized cells were investigated. The transformed cell clone, SV-CISM-2, was further characterized biochemically and pharmacologically. The normal muscle cells showed characteristics of smooth muscle cells, as judged by their growth and the presence of smooth muscle alpha-actin and desmin. After seven passages the normal cells ceased to proliferate. In contrast, the immortalized cells retained their proliferative ability for more than 220 population doublings over 55 passages. The transformation phenotype in these cells was confirmed by their expression of the large T-antigen, the incorporation of viral DNA into cellular DNA, growth in agarose and in low-serum medium, and complete loss of contact inhibition. The immortalized cells expressed smooth muscle alpha-actin, desmin and MLC protein. Biochemical and pharmacological studies on the SV-CISM cells revealed the presence of several functional receptors including muscarinic cholinergic, beta-adrenergic, peptidergic (substance P and endothelin). Platelet-activating factor, and prostaglandin (PG). Muscarinic stimulation of these cells resulted in: (a) a dose-dependent increase in the release of arachidonic acid (AA) and (PGs) and enhancement in the production of inositol trisphosphate (IP3); and (b) a substantial increase in MLC phosphorylation (118%), an indicator of smooth muscle contractility. The stimulatory effects of carbachol on these responses were completely blocked by atropine, a muscarinic receptor antagonist. This study constitutes the first successful immortalization of iris sphincter smooth muscle cells. The SV-CISM-2 cells can serve as an important model system for investigations on the biochemical and pharmacological properties of receptors and their signal transduction pathways in smooth muscle. The advantage of these cells over normal iris sphincter cells is that they can be propagated over many generations without alterations in their morphological, biochemical and physiological characteristics.

Correlation of basic TL, OSL and IRSL properties of ten K-feldspar samples of various origins

NASA Astrophysics Data System (ADS)

Sfampa, I. K.; Polymeris, G. S.; Pagonis, V.; Theodosoglou, E.; Tsirliganis, N. C.; Kitis, G.

2015-09-01

Feldspars stand among the most widely used minerals in dosimetric methods of dating using thermoluminescence (TL), optically stimulated luminescence (OSL) and infrared stimulated luminescence (IRSL). Having very good dosimetric properties, they can in principle contribute to the dating of every site of archaeological and geological interest. The present work studies basic properties of ten naturally occurring K-feldspar samples belonging to three feldspar species, namely sanidine, orthoclase and microcline. The basic properties studied are (a) the influence of blue light and infrared stimulation on the thermoluminescence glow-curves, (b) the growth of OSL, IRSL, residual TL and TL-loss as a function of OSL and IRSL bleaching time and (c) the correlation between the OSL and IRSL signals and the energy levels responsible for the TL glow-curve. All experimental data were fitted using analytical expressions derived from a recently developed tunneling recombination model. The results show that the analytical expressions provide excellent fits to all experimental results, thus verifying the tunneling recombination mechanism in these materials and providing valuable information about the concentrations of luminescence centers.

Basic functional trade-offs in cognition: An integrative framework.

PubMed

Del Giudice, Marco; Crespi, Bernard J

2018-06-14

Trade-offs between advantageous but conflicting properties (e.g., speed vs. accuracy) are ubiquitous in cognition, but the relevant literature is conceptually fragmented, scattered across disciplines, and has not been organized in a coherent framework. This paper takes an initial step toward a general theory of cognitive trade-offs by examining four key properties of goal-directed systems: performance, efficiency, robustness, and flexibility. These properties define a number of basic functional trade-offs that can be used to map the abstract "design space" of natural and artificial cognitive systems. Basic functional trade-offs provide a shared vocabulary to describe a variety of specific trade-offs including speed vs. accuracy, generalist vs. specialist, exploration vs. exploitation, and many others. By linking specific features of cognitive functioning to general properties such as robustness and efficiency, it becomes possible to harness some powerful insights from systems engineering and systems biology to suggest useful generalizations, point to under-explored but potentially important trade-offs, and prompt novel hypotheses and connections between disparate areas of research. Copyright © 2018 Elsevier B.V. All rights reserved.

The AAPM/RSNA physics tutorial for residents. Basic physics of MR imaging: an introduction.

PubMed

Hendrick, R E

1994-07-01

This article provides an introduction to the basic physical principles of magnetic resonance (MR) imaging. Essential basic concepts such as nuclear magnetism, tissue magnetization, precession, excitation, and tissue relaxation properties are presented. Hydrogen spin density and tissue relaxation times T1, T2, and T2* are explained. The basic elements of a planar MR pulse sequence are described: section selection during tissue excitation, phase encoding, and frequency encoding during signal measurement.

Refractories for high alkali environments

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

Rau, A.W.; Cloer, F.

1996-12-31

Information on refractories for high alkali environments is outlined. Information is presented on: product gallery; alkali attack; chemical reactions; basic layout of alkali cup test; criteria for rating alkali cup test samples; and basic layout of physical properties test.

New Simulation Methods to Facilitate Achieving a Mechanistic Understanding of Basic Pharmacology Principles in the Classroom

ERIC Educational Resources Information Center

Grover, Anita; Lam, Tai Ning; Hunt, C. Anthony

2008-01-01

We present a simulation tool to aid the study of basic pharmacology principles. By taking advantage of the properties of agent-based modeling, the tool facilitates taking a mechanistic approach to learning basic concepts, in contrast to the traditional empirical methods. Pharmacodynamics is a particular aspect of pharmacology that can benefit from…

Model Checking Temporal Logic Formulas Using Sticker Automata

PubMed Central

Feng, Changwei; Wu, Huanmei

2017-01-01

As an important complex problem, the temporal logic model checking problem is still far from being fully resolved under the circumstance of DNA computing, especially Computation Tree Logic (CTL), Interval Temporal Logic (ITL), and Projection Temporal Logic (PTL), because there is still a lack of approaches for DNA model checking. To address this challenge, a model checking method is proposed for checking the basic formulas in the above three temporal logic types with DNA molecules. First, one-type single-stranded DNA molecules are employed to encode the Finite State Automaton (FSA) model of the given basic formula so that a sticker automaton is obtained. On the other hand, other single-stranded DNA molecules are employed to encode the given system model so that the input strings of the sticker automaton are obtained. Next, a series of biochemical reactions are conducted between the above two types of single-stranded DNA molecules. It can then be decided whether the system satisfies the formula or not. As a result, we have developed a DNA-based approach for checking all the basic formulas of CTL, ITL, and PTL. The simulated results demonstrate the effectiveness of the new method. PMID:29119114

Basic and applied research program. Semiannual report, July-December 1978

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

Butler, B.L.

1979-12-01

The status of research projects in the Basic and Applied Research Program at SERI is presented for the semiannual period ending December 31, 1978. The five tasks in this program are grouped into Materials Research and Development, Materials Processing and Development, Photoconversion Research, Exploratory Research, and Energy Resource and Assessment and have been carried out by personnel in the Materials, Bio/Chemical Conversion, and Energy Resource and Assessment Branches. Subtask elements in the task areas include coatings and films, polymers, metallurgy and corrosion, optical materials, surfaces and interfaces in materials research and development; photochemistry, photoelectrochemistry, and photobiology in photoconversion; thin glassmore » mirror development, silver degradation of mirrors, hail resistance of thin glass, thin glass manufacturing, cellular glass development, and sorption by desiccants in materials processing and development; and thermoelectric energy conversion, desiccant cooling, photothermal degradation, and amorphous materials in exploratory research. For each task or subtask element, the overview, scope, goals, approach, apparatus and equipment, and supporting subcontracts are presented, as applicable, in addition to the status of the projects in each task or subtask. Listing of publications and reports authored by personnel associated with the Basic and Applied Research Program and prepared or published during 1978 are also included.« less

Identification, recombinant expression, and biochemical analysis of putative secondary product glucosyltransferases from Citrus paradisi

USDA-ARS?s Scientific Manuscript database

Flavonoid and limonoid glycosides influence taste properties as well as marketability of citrus fruit and products, particularly in grapefruit. In this work, nine grapefruit putative natural product glucosyltransferases (PGTs) were resolved by either using degenerate primers against the semi-conser...

Early detection of crop injury from herbicide glyphosate by leaf biochemical parameter inversion

USDA-ARS?s Scientific Manuscript database

Early detection of crop injury from glyphosate is of significant importance in crop management. In this paper, we attempt to detect glyphosate-induced crop injury by PROSPECT (leaf optical PROperty SPECTra model) inversion through leaf hyperspectral reflectance measurements for non-Glyphosate-Resist...

Unique Medicinal Properties of Withania somnifera: Phytochemical Constituents and Protein Component.

PubMed

Dar, Parvaiz A; Singh, Laishram R; Kamal, Mohammad A; Dar, Tanveer A

2016-01-01

Withania somnifera is an important medicinal herb that has been widely used for the treatment of different clinical conditions. The overall medicinal properties of Withania somnifera make it a viable therapeutic agent for addressing anxiety, cancer, microbial infection, immunomodulation, and neurodegenerative disorders. Biochemical constituents of Withania somnifera like withanolideA, withanolide D, withaferin A and withaniamides play an important role in its pharmacological properties. Proteins like Withania somnifera glycoprotein and withania lectin like-protein possess potent therapeutic properties like antimicrobial, anti-snake venom poison and antimicrobial. In this review, we have tried to present different pharmacological properties associated with different extract preparations, phytochemical constituents and protein component of Withania somnifera. Future insights in this direction have also been highlighted.

[A complexity analysis of Chinese herbal property theory: the multiple expressions of herbal property].

PubMed

Jin, Rui; Zhang, Bing

2012-12-01

Chinese herbal property is the highly summarized concept of herbal nature and pharmaceutical effect, which reflect the characteristics of herbal actions on human body. These herbal actions, also interpreted as presenting the information about pharmaceutical effect contained in herbal property on the biological carrier, are defined as herbal property expressions. However, the biological expression of herbal property is believed to possess complex features for the involved complexity of Chinese medicine and organism. Firstly, there are multiple factors which could influence the expression results of herbal property such as the growth environment, harvest season and preparing methods of medicinal herbs, and physique and syndrome of body. Secondly, there are multiple biological approaches and biochemical indicators for the expression of the same property. This paper elaborated these complexities for further understanding of herbal property. The individuality of herbs and expression factors should be well analyzed in the related studies.

The Power of Algebra.

ERIC Educational Resources Information Center

Boiteau, Denise; Stansfield, David

This document describes mathematical programs on the basic concepts of algebra produced by Louisiana Public Broadcasting. Programs included are: (1) "Inverse Operations"; (2) "The Order of Operations"; (3) "Basic Properties" (addition and multiplication of numbers and variables); (4) "The Positive and Negative…

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

PubMed

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

2017-01-01

Are telomere length and telomerase activity associated with biochemical primary ovarian insufficiency (POI)? Shortened telomere length and diminished telomerase activity were associated with biochemical POI. POI is a result of pathological reproductive aging and encompasses occult, biochemical and overt stages. Studies have indicated telomere length as a biomarker for biological aging. A total of 120 patients with biochemical POI and 279 control women were recruited by the Center for Reproductive Medicine of Shandong University. Telomere length in peripheral blood leukocytes (LTL) and granulosa cells (GTL) was measured using a modified Quantitative Polymerase Chain Reaction technique. The relative telomerase activity (RTA) in granulosa cells was detected using a modified quantitative-telomeric repeat amplification protocol assay. After adjusting for age, patients with biochemical POI (n = 120) exhibited significantly shorter LTLs (0.75 ± 0.09 vs 1.79 ± 0.12, P < 0.001; OR = 0.54, 95% CI = 0.43-0.68) and GTLs (0.78 ± 0.09 vs 1.90 ± 0.23, P < 0.001; OR = 0.54, 95% CI = 0.41-0.70) than the controls (n = 279 for LTLs; n = 90 for GTLs). Significantly diminished RTAs in granulosa cells were detected in patients with biochemical POI (n = 31) compared with the controls (n = 38) (1.57 ± 0.59 vs 4.63 ± 0.93, P = 0.025; OR = 0.84, 95% CI = 0.72-0.98). N/A. The cross-sectional nature of this study might have its limit in telomere length as well as telomerase activity along with the progressing decline in ovarian function. These findings suggest that telomere length and telomerase activity may be considered as indicators for progression of ovarian decline. This research was supported by the National Basic Research Program of China (973 Program) (2012CB944700), Science research foundation item of no-earnings health vocation (201402004) and the National Natural Science Foundation of China (31471352, 81270662, 81471509, 81300461, 81522018). The authors have no potential conflict of interest to declare. © The Author 2016. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Government Giveth and the Government Taketh Away: Federal Tax Law and Fund Raising.

ERIC Educational Resources Information Center

Holzman, Donald J.

1982-01-01

Tax laws' incentives and disincentives for charitable giving are outlined. Basics of charitable giving, partial property interests, gifts of future interest in tangible property, undivided interest gifts, ordinary income property, capital gain property, bargain sales, remainder interest gifts, estate tax, and valuation overstatement are discussed…

Property Accounting for Local and State School Systems. State Educational Records and Reports Series--Handbook III.

ERIC Educational Resources Information Center

Reason, Paul L.; Tankard, George G., Jr.

This handbook serves as a basic guide to property accounting for local and state school systems in the U.S. Information and guidelines are presented regarding--(1) classification of property accounts, (2) definitions of property accounts, (3) measures of school property, (4) supplies and equipment, (5) individual property records, and (6) summary…

A nerve guidance conduit with topographical and biochemical cues: potential application using human neural stem cells

NASA Astrophysics Data System (ADS)

Jenkins, Phillip M.; Laughter, Melissa R.; Lee, David J.; Lee, Young M.; Freed, Curt R.; Park, Daewon

2015-06-01

Despite major advances in the pathophysiological understanding of peripheral nerve damage, the treatment of nerve injuries still remains an unmet medical need. Nerve guidance conduits present a promising treatment option by providing a growth-permissive environment that 1) promotes neuronal cell survival and axon growth and 2) directs axonal extension. To this end, we designed an electrospun nerve guidance conduit using a blend of polyurea and poly-caprolactone with both biochemical and topographical cues. Biochemical cues were integrated into the conduit by functionalizing the polyurea with RGD to improve cell attachment. Topographical cues that resemble natural nerve tissue were incorporated by introducing intraluminal microchannels aligned with nanofibers. We determined that electrospinning the polymer solution across a two electrode system with dissolvable sucrose fibers produced a polymer conduit with the appropriate biomimetic properties. Human neural stem cells were cultured on the conduit to evaluate its ability to promote neuronal growth and axonal extension. The nerve guidance conduit was shown to enhance cell survival, migration, and guide neurite extension.

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.

Initial blood storage experiment

NASA Technical Reports Server (NTRS)

Surgenor, Douglas MACN.

1988-01-01

The possibility of conducting experiments with the formed elements of the blood under conditions of microgravity opens up important opportunities to improve the understanding of basic formed element physiology, as well as, contribution to improved preservation of the formed elements for use in transfusion. The physiological, biochemical, and physical changes of the membrane of the erythrocyte, platelet, and leukocyte was studied during storage under two specific conditions: standard blood bank conditions and microgravity, utilizing three FDA approved plastic bags. Storage lesions; red cell storage on Earth; platelet storage on Earth; and leukocyte storage Earth were examined. The interaction of biomaterials and blood cells was studied during storage.

Training Under-Represented Students in Biological Research at Fisk University

NASA Technical Reports Server (NTRS)

Gunasekaran, Muthukumaran

1999-01-01

The objectives of our training and research project in biology at Fisk are to motivate and train our African-American undergraduate and graduate students by (a) teaching the basic principles and applications of different biological, biochemical and biophysical research techniques; (b) providing a "hands on experience" with laboratory instrumentation (c) requiring the students to participate in the proposed research project entitled "Cyanobacterial Bioreactors for Oxygen and Ammonia Production under "CELSS" Conditions" to gain confidence in independently conducting experiments and (d) providing training in scientific data collection and presentation to peers in scientific conferences or meetings.

Respiratory Allergies: A General Overview of Remedies, Delivery Systems, and the Need to Progress

PubMed Central

Colombo, Giselda; Celenza, Cinzia

2014-01-01

The spread of respiratory allergies is increasing in parallel with the alarm of the scientific community. Evidently, our knowledge of the onset mechanisms of these diseases and, as a consequence, of the available remedies is inadequate. This review provides a brief, general description of current therapeutic resources and the state of research with regard to both drugs and medical devices in order to highlight their limits and the urgent need for progress. Increasing the amount of basic biochemical research will improve our knowledge of such onset mechanisms and the potential efficacy of therapeutic preparations. PMID:25006500

Tropospheric ozone as a fungal elicitor.

PubMed

Zuccarini, Paolo

2009-03-01

Tropospheric ozone has been proven to trigger biochemical plant responses that are similar to the ones induced by an attack of fungal pathogens,i.e. it resembles fungal elicitors.This suggests that ozone can represent a valid tool for the study of stress responses and induction of resistance to pathogens. This review provides an overview of the implications of such a phenomenon for basic and applied research. After an introduction about the environmental implications of tropospheric ozone and plant responses to biotic stresses, the biochemistry of ozone stress is analysed, pointing out its similarities with plant responses to pathogens and its possible applications.

[Development of a basic ration out of commercial foods for nutrition in ground-based simulation experiments].

PubMed

Agureev, A N; Kalandarov, S; Bogatova, R I; Krivitsina, Z A; Vasil'eva, V F

2005-01-01

Food rations composed of canned products were given the physiological and hygienic evaluation in the context of their fitness for human volunteers in experiments with head-down bedrest in isolation and confinement. As a result, the food rations were proven to contain the desired quantities of nutrients. Evaluation of food fitness for human subjects was made based on the data of clinical-physiological and biochemical investigations. The rations met the energy and anabolic metabolism demands of human subjects during extreme chamber experiments and were favorable to maintaining good level of vital processes.

The Nucleosome Remodeling and Deacetylase (NuRD) Complex in Development and Disease

PubMed Central

Basta, Jeannine; Rauchman, Michael

2014-01-01

The Nucleosome Remodeling and Deacetylase (NuRD) complex is one of the major chromatin remodeling complexes found in cells. It plays an important role in regulating gene transcription, genome integrity and cell cycle progression. Through its impact on these basic cellular processes, increasing evidence indicates that alterations in the activity of this macromolecular complex can lead to developmental defects, oncogenesis and accelerated ageing. Recent genetic and biochemical studies have elucidated the mechanisms of NuRD action in modifying the chromatin landscape. These advances have the potential to lead to new therapeutic approaches to birth defects and cancer. PMID:24880148

[Advances in isoprene synthase research].

PubMed

Gou, Yan; Liu, Zhongchuan; Wang, Ganggang

2017-11-25

Isoprene emission can lead to significant consequence for atmospheric chemistry. In addition, isoprene is a chemical compound for various industrial applications. In the organisms, isoprene is produced by isoprene synthase that eliminates the pyrophosphate from the dimethylallyl diphosphate. As a key enzyme of isoprene formation, isoprene synthase plays an important role in the process of natural emission and artificial synthesis of isoprene. So far, isoprene synthase has been found in various plants. Isoprene synthases from different sources are of conservative structural and similar biochemical properties. In this review, the biochemical and structural characteristics of isoprene synthases from different sources were compared, the catalytic mechanism of isoprene synthase was discussed, and the perspective application of the enzyme in bioengineering was proposed.

Threonine-Insensitive Homoserine Dehydrogenase From Soybean: Genomic Organization, Kinetic Mechanism, and In vivo Activity

USDA-ARS?s Scientific Manuscript database

Aspartate kinase (AK) and homoserine dehydrogenase (HSD) functions as key regulatory enzymes at branch points in the aspartate amino acid pathway and are feedback inhibited by threonine. In plants, the biochemical properties of AK and bifunctional AK-HSD enzymes have been characterized, but the mol...

Safety in the Chemical Laboratory: Is Thioacetamide a Serious Health Hazard in Inorganic Chemistry Laboratories?

ERIC Educational Resources Information Center

Elo, Hannu

1987-01-01

Describes the potential health hazards of using thioacetamide in introductory courses where students are involved in qualitative inorganic analysis. Describes the chemical as possessing carcinogenic, hepatotoxic, and mutagenic properties. Cautions that thioacetamide has caused various biochemical changes in the liver, and recommends limited uses…

Acetylcholinesterase of Rhipicephalus (Boophilus) microplus and Phlebotomus papatasi: Gene identification, expression, and biochemical properties of recombinant proteins

USDA-ARS?s Scientific Manuscript database

Rhipicephalus (Boophilus) microplus (Bm) ticks are vectors of bovine babesiosis and anaplasmosis. Tick resistance to organophosphate (OP) acaricide involves acetylcholinesterase (AChE) insensitivity to OP and metabolic detoxification. Sequencing and in vitro expression of Bm genes encoding AChE allo...

Cholera studies*†

PubMed Central

Pollitzer, R.

1955-01-01

The morphological characteristics, biochemical properties, and cultural characteristics of V. cholerae are described in great detail in this study. The author also discusses the resistance of the organism to temperature, humidity, sunlight, and various chemicals, as well as the viability of V. cholerae outside the body (in faeces, contaminated material, food, beverages, water, etc.). PMID:14379012

Acetylcholinesterase of Phlebotomus papatasi (Scopoli): expression and biochemical properties of orthologous organophosphate resistance mutations from mosquitoes

USDA-ARS?s Scientific Manuscript database

Phlebotomine sand flies are small hematophagous vectors of human and zoonotic leishmaniases present throughout tropical and subtropical areas of the world. Phlebotomus papatasi is a principal vector of human cutaneous leishmaniasis that has presented serious problems for military operations and resi...

Enzyme engineering through evolution: thermostable recombinant group II intron reverse transcriptases provide new tools for RNA research and biotechnology.

PubMed

Collins, Kathleen; Nilsen, Timothy W

2013-08-01

Current investigation of RNA transcriptomes relies heavily on the use of retroviral reverse transcriptases. It is well known that these enzymes have many limitations because of their intrinsic properties. This commentary highlights the recent biochemical characterization of a new family of reverse transcriptases, those encoded by group II intron retrohoming elements. The novel properties of these enzymes endow them with the potential to revolutionize how we approach RNA analyses.

Classification and Analysis of Regulatory Pathways Using Graph Property, Biochemical and Physicochemical Property, and Functional Property

PubMed Central

Cai, Yu-Dong; Chou, Kuo-Chen

2011-01-01

Given a regulatory pathway system consisting of a set of proteins, can we predict which pathway class it belongs to? Such a problem is closely related to the biological function of the pathway in cells and hence is quite fundamental and essential in systems biology and proteomics. This is also an extremely difficult and challenging problem due to its complexity. To address this problem, a novel approach was developed that can be used to predict query pathways among the following six functional categories: (i) “Metabolism”, (ii) “Genetic Information Processing”, (iii) “Environmental Information Processing”, (iv) “Cellular Processes”, (v) “Organismal Systems”, and (vi) “Human Diseases”. The prediction method was established trough the following procedures: (i) according to the general form of pseudo amino acid composition (PseAAC), each of the pathways concerned is formulated as a 5570-D (dimensional) vector; (ii) each of components in the 5570-D vector was derived by a series of feature extractions from the pathway system according to its graphic property, biochemical and physicochemical property, as well as functional property; (iii) the minimum redundancy maximum relevance (mRMR) method was adopted to operate the prediction. A cross-validation by the jackknife test on a benchmark dataset consisting of 146 regulatory pathways indicated that an overall success rate of 78.8% was achieved by our method in identifying query pathways among the above six classes, indicating the outcome is quite promising and encouraging. To the best of our knowledge, the current study represents the first effort in attempting to identity the type of a pathway system or its biological function. It is anticipated that our report may stimulate a series of follow-up investigations in this new and challenging area. PMID:21980418

Decellularized extracellular matrices produced from immortal cell lines derived from different parts of the placenta support primary mesenchymal stem cell expansion

PubMed Central

Kusuma, Gina D.; Brennecke, Shaun P.; O’Connor, Andrea J.; Kalionis, Bill

2017-01-01

Mesenchymal stem/stromal cells (MSCs) exhibit undesired phenotypic changes during ex vivo expansion, limiting production of the large quantities of high quality primary MSCs needed for both basic research and cell therapies. Primary MSCs retain many desired MSC properties including proliferative capacity and differentiation potential when expanded on decellularized extracellular matrix (dECM) prepared from primary MSCs. However, the need to use low passage number primary MSCs (passage 3 or lower) to produce the dECM drastically limits the utility and impact of this technology. Here, we report that primary MSCs expanded on dECM prepared from high passage number (passage 25) human telomerase reverse transcriptase (hTERT) transduced immortal MSC cell lines also exhibit increased proliferation and osteogenic differentiation. Two hTERT-transduced placenta-derived MSC cell lines, CMSC29 and DMSC23 [derived from placental chorionic villi (CMSCs) and decidua basalis (DMSCs), respectively], were used to prepare dECM-coated substrates. These dECM substrates showed structural and biochemical differences. Primary DMSCs cultured on dECM-DMSC23 showed a three-fold increase in cell number after 14 days expansion in culture and increased osteogenic differentiation compared with controls. Primary CMSCs cultured on the dECM-DMSC23 exhibited a two-fold increase in cell number and increased osteogenic differentiation. We conclude that immortal MSC cell lines derived from different parts of the placenta produce dECM with varying abilities for supporting increased primary MSC expansion while maintaining important primary MSC properties. Additionally, this is the first demonstration of using high passage number cells to produce dECM that can promote primary MSC expansion, and this advancement greatly increases the feasibility and applicability of dECM-based technologies. PMID:28152107

Biological reference materials for extracellular vesicle studies.

PubMed

Valkonen, S; van der Pol, E; Böing, A; Yuana, Y; Yliperttula, M; Nieuwland, R; Laitinen, S; Siljander, P R M

2017-02-15

Extracellular vesicles (EVs) mediate normal physiological homeostasis and pathological processes by facilitating intercellular communication. Research of EVs in basic science and clinical settings requires both methodological standardization and development of reference materials (RM). Here, we show insights and results of biological RM development for EV studies. We used a three-step approach to find and develop a biological RM. First, a literature search was done to find candidates for biological RMs. Second, a questionnaire was sent to EV researchers querying the preferences for RM and their use. Third, a biological RM was selected, developed, characterized, and evaluated. The responses to the survey demonstrated a clear and recognized need for RM optimized for the calibration of EV measurements. Based on the literature, naturally occurring and produced biological RM, such as virus particles and liposomes, were proposed as RM. However, none of these candidate RMs have properties completely matching those of EVs, such as size and refractive index distribution. Therefore, we evaluated the use of nanoerythrosomes (NanoE), vesicles produced from erythrocytes, as a potential biological RM. The strength of NanoE is their resemblance to EVs. Compared to the erythrocyte-derived EVs (eryEVs), NanoE have similar morphology, a similar refractive index (1.37), larger diameter (70% of the NanoE are over 200nm), and increased positive staining for CD235a and lipids (Di-8-ANEPPS) (58% and 67% in NanoE vs. 21% and 45% in eryEVs, respectively). Altogether, our results highlight the general need to develop and validate new RM with similar physical and biochemical properties as EVs to standardize EV measurements between instruments and laboratories. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Arc is a flexible modular protein capable of reversible self-oligomerization

PubMed Central

Myrum, Craig; Baumann, Anne; Bustad, Helene J.; Flydal, Marte Innselset; Mariaule, Vincent; Alvira, Sara; Cuéllar, Jorge; Haavik, Jan; Soulé, Jonathan; Valpuesta, José Maria; Márquez, José Antonio; Martinez, Aurora; Bramham, Clive R.

2015-01-01

The immediate early gene product Arc (activity-regulated cytoskeleton-associated protein) is posited as a master regulator of long-term synaptic plasticity and memory. However, the physicochemical and structural properties of Arc have not been elucidated. In the present study, we expressed and purified recombinant human Arc (hArc) and performed the first biochemical and biophysical analysis of hArc's structure and stability. Limited proteolysis assays and MS analysis indicate that hArc has two major domains on either side of a central more disordered linker region, consistent with in silico structure predictions. hArc's secondary structure was estimated using CD, and stability was analysed by CD-monitored thermal denaturation and differential scanning fluorimetry (DSF). Oligomerization states under different conditions were studied by dynamic light scattering (DLS) and visualized by AFM and EM. Biophysical analyses show that hArc is a modular protein with defined secondary structure and loose tertiary structure. hArc appears to be pyramid-shaped as a monomer and is capable of reversible self-association, forming large soluble oligomers. The N-terminal domain of hArc is highly basic, which may promote interaction with cytoskeletal structures or other polyanionic surfaces, whereas the C-terminal domain is acidic and stabilized by ionic conditions that promote oligomerization. Upon binding of presenilin-1 (PS1) peptide, hArc undergoes a large structural change. A non-synonymous genetic variant of hArc (V231G) showed properties similar to the wild-type (WT) protein. We conclude that hArc is a flexible multi-domain protein that exists in monomeric and oligomeric forms, compatible with a diverse, hub-like role in plasticity-related processes. PMID:25748042

Decellularized extracellular matrices produced from immortal cell lines derived from different parts of the placenta support primary mesenchymal stem cell expansion.

PubMed

Kusuma, Gina D; Brennecke, Shaun P; O'Connor, Andrea J; Kalionis, Bill; Heath, Daniel E

2017-01-01

Mesenchymal stem/stromal cells (MSCs) exhibit undesired phenotypic changes during ex vivo expansion, limiting production of the large quantities of high quality primary MSCs needed for both basic research and cell therapies. Primary MSCs retain many desired MSC properties including proliferative capacity and differentiation potential when expanded on decellularized extracellular matrix (dECM) prepared from primary MSCs. However, the need to use low passage number primary MSCs (passage 3 or lower) to produce the dECM drastically limits the utility and impact of this technology. Here, we report that primary MSCs expanded on dECM prepared from high passage number (passage 25) human telomerase reverse transcriptase (hTERT) transduced immortal MSC cell lines also exhibit increased proliferation and osteogenic differentiation. Two hTERT-transduced placenta-derived MSC cell lines, CMSC29 and DMSC23 [derived from placental chorionic villi (CMSCs) and decidua basalis (DMSCs), respectively], were used to prepare dECM-coated substrates. These dECM substrates showed structural and biochemical differences. Primary DMSCs cultured on dECM-DMSC23 showed a three-fold increase in cell number after 14 days expansion in culture and increased osteogenic differentiation compared with controls. Primary CMSCs cultured on the dECM-DMSC23 exhibited a two-fold increase in cell number and increased osteogenic differentiation. We conclude that immortal MSC cell lines derived from different parts of the placenta produce dECM with varying abilities for supporting increased primary MSC expansion while maintaining important primary MSC properties. Additionally, this is the first demonstration of using high passage number cells to produce dECM that can promote primary MSC expansion, and this advancement greatly increases the feasibility and applicability of dECM-based technologies.

Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets.

PubMed

Kielbassa, J; Bortfeldt, R; Schuster, S; Koch, I

2009-02-01

The investigation of spliceosomal processes is currently a topic of intense research in molecular biology. In the molecular mechanism of alternative splicing, a multi-protein-RNA complex - the spliceosome - plays a crucial role. To understand the biological processes of alternative splicing, it is essential to comprehend the biogenesis of the spliceosome. In this paper, we propose the first abstract model of the regulatory assembly pathway of the human spliceosomal subunit U1. Using Petri nets, we describe its highly ordered assembly that takes place in a stepwise manner. Petri net theory represents a mathematical formalism to model and analyze systems with concurrent processes at different abstraction levels with the possibility to combine them into a uniform description language. There exist many approaches to determine static and dynamic properties of Petri nets, which can be applied to analyze biochemical systems. In addition, Petri net tools usually provide intuitively understandable graphical network representations, which facilitate the dialog between experimentalists and theoreticians. Our Petri net model covers binding, transport, signaling, and covalent modification processes. Through the computation of structural and behavioral Petri net properties and their interpretation in biological terms, we validate our model and use it to get a better understanding of the complex processes of the assembly pathway. We can explain the basic network behavior, using minimal T-invariants which represent special pathways through the network. We find linear as well as cyclic pathways. We determine the P-invariants that represent conserved moieties in a network. The simulation of the net demonstrates the importance of the stability of complexes during the maturation pathway. We can show that complexes that dissociate too fast, hinder the formation of the complete U1 snRNP.

Intellectual property rights and research disclosure in the university environment: preserving the commercialization option and optimizing market interest.

PubMed

Patino, Robert

2009-03-01

Clinical and basic scientists at academic medical and biomedical research institutions often form ideas that could have both monetary and human health benefits if developed and applied to improvement of human wellbeing. However, such ideas lose much of their potential value in both regards if they are disclosed in traditional knowledge-sharing forums such as abstracts, posters, and oral presentations at research meetings. Learning the basics about intellectual property protection and obtaining professional guidance in the management of intellectual property from a knowledgeable technology management professional or intellectual property attorney can avoid such losses yet pose a minimal burden of confidentiality on the investigator. Knowing how to successfully navigate the early stages of intellectual property protection can greatly increase the likelihood that discoveries and knowledge will become available for the public good without diminishing the important mandate of disseminating knowledge through traditional knowledge-sharing forums.

Skeletal muscle mechanics, energetics and plasticity.

PubMed

Lieber, Richard L; Roberts, Thomas J; Blemker, Silvia S; Lee, Sabrina S M; Herzog, Walter

2017-10-23

The following papers by Richard Lieber (Skeletal Muscle as an Actuator), Thomas Roberts (Elastic Mechanisms and Muscle Function), Silvia Blemker (Skeletal Muscle has a Mind of its Own: a Computational Framework to Model the Complex Process of Muscle Adaptation) and Sabrina Lee (Muscle Properties of Spastic Muscle (Stroke and CP) are summaries of their representative contributions for the session on skeletal muscle mechanics, energetics and plasticity at the 2016 Biomechanics and Neural Control of Movement Conference (BANCOM 2016). Dr. Lieber revisits the topic of sarcomere length as a fundamental property of skeletal muscle contraction. Specifically, problems associated with sarcomere length non-uniformity and the role of sarcomerogenesis in diseases such as cerebral palsy are critically discussed. Dr. Roberts then makes us aware of the (often neglected) role of the passive tissues in muscles and discusses the properties of parallel elasticity and series elasticity, and their role in muscle function. Specifically, he identifies the merits of analyzing muscle deformations in three dimensions (rather than just two), because of the potential decoupling of the parallel elastic element length from the contractile element length, and reviews the associated implications for the architectural gear ratio of skeletal muscle contraction. Dr. Blemker then tackles muscle adaptation using a novel way of looking at adaptive processes and what might drive adaptation. She argues that cells do not have pre-programmed behaviors that are controlled by the nervous system. Rather, the adaptive responses of muscle fibers are determined by sub-cellular signaling pathways that are affected by mechanical and biochemical stimuli; an exciting framework with lots of potential. Finally, Dr. Lee takes on the challenging task of determining human muscle properties in vivo. She identifies the dilemma of how we can demonstrate the effectiveness of a treatment, specifically in cases of muscle spasticity following stroke or in children with cerebral palsy. She then discusses the merits of ultrasound based elastography, and the clinical possibilities this technique might hold. Overall, we are treated to a vast array of basic and clinical problems in skeletal muscle mechanics and physiology, with some solutions, and many suggestions for future research.

Influence of selected physicochemical parameters on microbiological activity of mucks.

NASA Astrophysics Data System (ADS)

Całka, A.; Sokołowska, Z.; Warchulska, P.; Dąbek-Szreniawska, M.

2009-04-01

One of the basic factor decided about soil fertility are microorganisms that together with flora, determine trend and character of biochemical processes as well totality of fundamental transformations connected with biogeochemistry and physicochemical properties of soil. Determination of general bacteria number, quantity of selected groups of microorganisms and investigation of respiration intensity let estimate microbiological activity of soil. Intensity of microbiological processes is directly connected with physicochemical soil parameters. In that case, such structural parameters as bulk density, porosity, surface or carbon content play significant role. Microbiological activity also changes within the bounds of mucks with different stage of humification and secondary transformation. Knowledge of relations between structural properties, microorganism activity and degree of transformation and humification can lead to better understanding microbiological processes as well enable to estimate microbiological activity at given physicochemical conditions and at progressing process of soil transformation. The study was carried out on two peaty-moorsh (muck) soils at different state of secondary transformation and humification degree. Soil samples were collected from Polesie Lubelskie (layer depth: 5 - 25 cm). Investigated mucks originated from soils formed from low peatbogs. Soil sample marked as I belonged to muck group weakly secondary transformed. Second sample (II) represented soil group with middle stage of secondary transformation. The main purpose of the research was to examine the relations between some physicochemical and surface properties and their biological activity. Total number and respiration activity of microorganisms were determined. The effectiveness of utilizing the carbon substances from the soil by the bacteria increased simultaneously with the transformation state of the peat-muck soils. Quantity of organic carbon decreased distinctly in the soil at the higher stage of secondary transformation and it influenced quantity and activity of soil microorganisms. Bulk density and surface increased with increasing secondary transformation degree. On the other hand, porosity decreased with increasing secondary transformation index. Process of secondary transformation influenced the soil environment for the microbes by changing the physicochemical properties. This way it influenced the number of microorganisms and caused changes of biological activity in the soils.

Biochemical acclimation, stomatal limitation and precipitation patterns underlie decreases in photosynthetic stimulation of soybean (Glycine max) at elevated [CO₂] and temperatures under fully open air field conditions.

PubMed

Rosenthal, David M; Ruiz-Vera, Ursula M; Siebers, Matthew H; Gray, Sharon B; Bernacchi, Carl J; Ort, Donald R

2014-09-01

The net effect of elevated [CO2] and temperature on photosynthetic acclimation and plant productivity is poorly resolved. We assessed the effects of canopy warming and fully open air [CO2] enrichment on (1) the acclimation of two biochemical parameters that frequently limit photosynthesis (A), the maximum carboxylation capacity of Rubisco (Vc,max) and the maximum potential linear electron flux through photosystem II (Jmax), (2) the associated responses of leaf structural and chemical properties related to A, as well as (3) the stomatal limitation (l) imposed on A, for soybean over two growing seasons in a conventionally managed agricultural field in Illinois, USA. Acclimation to elevated [CO2] was consistent over two growing seasons with respect to Vc,max and Jmax. However, elevated temperature significantly decreased Jmax contributing to lower photosynthetic stimulation by elevated CO2. Large seasonal differences in precipitation altered soil moisture availability modulating the complex effects of elevated temperature and CO2 on biochemical and structural properties related to A. Elevated temperature also reduced the benefit of elevated [CO2] by eliminating decreases in stomatal limitation at elevated [CO2]. These results highlight the critical importance of considering multiple environmental factors (i.e. temperature, moisture, [CO2]) when trying to predict plant productivity in the context of climate change. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Production and characterization of recombinant protein preparations of Endonuclease G-homologs from yeast, C. elegans and humans.

PubMed

Kieper, Jana; Lauber, Christiane; Gimadutdinow, Oleg; Urbańska, Anna; Cymerman, Iwona; Ghosh, Mahua; Szczesny, Bartosz; Meiss, Gregor

2010-09-01

Nuc1p, CPS-6, EndoG and EXOG are evolutionary conserved mitochondrial nucleases from yeast, Caenorhabditis elegans and humans, respectively. These enzymes play an important role in programmed cell death as well as mitochondrial DNA-repair and recombination. Whereas a significant interest has been given to the cell biology of these proteins, in particular their recruitment during caspase-independent apoptosis, determination of their biochemical properties has lagged behind. In part, biochemical as well as structural analysis of mitochondrial nucleases has been hampered by the fact that upon cloning and overexpression in Escherichia coli these enzymes can exert considerable toxicity and tend to aggregate and form inclusion bodies. We have, therefore, established a uniform E. coli expression system allowing us to obtain these four evolutionary related nucleases in active form from the soluble as well as insoluble fractions of E. coli cell lysates. Using preparations of recombinant Nuc1p, CPS-6, EndoG and EXOG we have compared biochemical properties and the substrate specificities of these related nucleases on selected substrates in parallel. Whereas Nuc1p and EXOG in addition to their endonuclease activity exert 5'-3'-exonuclease activity, CPS-6 and EndoG predominantly are endonucleases. These findings allow speculating that the mechanisms of action of these related nucleases in cell death as well as DNA-repair and recombination differ according to their enzyme activities and substrate specificities. Copyright 2010 Elsevier Inc. All rights reserved.

The effect of nonablative laser energy on joint capsular properties. An in vitro histologic and biochemical study using a rabbit model

NASA Technical Reports Server (NTRS)

Hayashi, K.; Thabit, G. 3rd; Vailas, A. C.; Bogdanske, J. J.; Cooley, A. J.; Markel, M. D.

1996-01-01

The purpose of this study was to evaluate the effect of laser energy at nonablative levels on joint capsular histologic and biochemical properties in an in vitro rabbit model. The medial and lateral portions of the femoropatellar joint capsule from both stifles of 12 mature New Zealand White rabbits were used. Specimens were divided into three treatment groups (5 watts, 10 watts, and 15 watt) and one control group using a randomized block design. Specimens were placed in a 37 degrees bath of lactated Ringer's solution and laser energy was applied using a holmium:yttrium-aluminum-garnet laser in four transverse passes across the tissue at a velocity of 2 mm/sec with the handpiece set 1.5 mm from the synovial surface. Histologic analysis revealed thermal alteration of collagen (fusion) and fibroblasts (pyknosis) at all energy densities, with higher laser energy causing significantly greater morphologic changes over a larger area (P < 0.05). Application of laser energy did not significantly alter the biochemical parameters evaluated, including type I collagen content and nonreducible crosslinks (P > 0.05). This study demonstrated that nonablative laser energy caused significant thermal damage to the joint capsular tissue in an energy-dependent fashion, but type I collagen content and nonreducible crosslinks (P > 0.05). This study demonstrated that nonablative laser energy caused significant thermal damage to the joint capsular tissue in an energy-dependent fashion, but type I Collagen content and nonreducible corsslinks were not significantly altered.

Evidence that Altered Cis Element Spacing Affects PpsR Mediated Redox Control of Photosynthesis Gene Expression in Rubrivivax gelatinosus.

PubMed

Shimizu, Takayuki; Cheng, Zhuo; Matsuura, Katsumi; Masuda, Shinji; Bauer, Carl E

2015-01-01

PpsR is a major regulator of photosynthesis gene expression among all characterized purple photosynthetic bacteria. This transcription regulator has been extensively characterized in Rhodobacter (Rba.) capsulatus and Rba. sphaeroides which are members of the α-proteobacteria lineage. In this study, we have investigated the biochemical properties and mutational effects of a ppsR deletion strain in the β-proteobacterium Rubrivivax (Rvi.) gelatinosus in order to reveal phylogenetically conserved mechanisms and species-specific characteristics. A deletion of the ppsR gene resulted in de-repression of photosystem synthesis showing that PpsR functions as a repressor of photosynthesis genes in this species. We also constructed a Rvi. gelatinosus PpsR mutant in which a conserved cysteine at position 436 was changed to an alanine to examine whether or not this residue is important for sensing redox, as reported in Rhodobacter species. Surprisingly, the Cys436 Ala mutant retained the ability to repress photosynthesis gene expression under aerobic conditions, suggesting that PpsR from Rvi. gelatinosus has different redox-responding characteristics. Furthermore, biochemical analyses demonstrated that Rvi. gelatinosus PpsR only shows redox-dependent binding to promoters with 9-bp spacing, but not 8-bp spacing, between two PpsR-recognition sequences. These results indicate that redox-dependent binding of PpsR requires appropriate cis configuration of PpsR target sequences in Rvi. gelatinosus. These results also indicate that PpsR homologs from different species regulate photosynthesis genes with altered biochemical properties.

Final Report 2007: DOE-FG02-87ER60561

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

Kilbourn, Michael R

2007-04-26

This project involved a multi-faceted approach to the improvement of techniques used in Positron Emission Tomography (PET), from radiochemistry to image processing and data analysis. New methods for radiochemical syntheses were examined, new radiochemicals prepared for evaluation and eventual use in human PET studies, and new pre-clinical methods examined for validation of biochemical parameters in animal studies. The value of small animal PET imaging in measuring small changes of in vivo biochemistry was examined and directly compared to traditional tissue sampling techniques. In human imaging studies, the ability to perform single experimental sessions utilizing two overlapping injections of radiopharmaceuticals wasmore » tested, and it was shown that valid biochemical measures for both radiotracers can be obtained through careful pharmacokinetic modeling of the PET emission data. Finally, improvements in reconstruction algorithms for PET data from small animal PET scanners was realized and these have been implemented in commercial releases. Together, the project represented an integrated effort to improve and extend all basic science aspects of PET imaging at both the animal and human level.« less

Quality changes in refrigerated stored minced pork wrapped with plastic cling film and the effect of glucose supplementation.

PubMed

Del Blanco, Alba; Caro, Irma; Quinto, Emiliano J; Mateo, Javier

2017-04-01

Meat spoilage greatly depends on meat composition and storage conditions. Microbial and biochemical changes in minced pork (100-g portions) wrapped with a polyvinyl chloride film during a 4-day refrigerated storage were studied. As glucose is the first substrate used by spoilage bacteria and when it is depleted bacteria could generate undesirable volatiles, the effect of the addition of glucose to minced meat was also studied. Three treatments were used: control (C), without added glucose, and low and high glucose concentration (L and H), 150mg and 750mg of glucose in 100g of meat, respectively. Spoilage bacteria, pH, redox potential, colour, basic volatile nitrogen, glucose, organic acids, and volatiles were analyzed in both recently prepared and stored pork samples. Storage resulted in increased levels of lactic acid bacteria and glucose-derived short chain alkyl volatiles, and a decrease in redox potential and volatile aldehyde levels. The addition of glucose to meat did not affect the biochemical characteristics of stored minced pork. Copyright © 2016 Elsevier Ltd. All rights reserved.

Searching for Organics, Fossils, and Biology on Mars

NASA Technical Reports Server (NTRS)

McKay, Christopher P.; DeVincenzi, Donald (Technical Monitor)

2001-01-01

One of the goals of Astrobiology is to understand life on a fundamental level. All life on Earth is constructed from the same basic biochemical building blocks consisting of 20 amino acids with left handed symmetry, five nucleotides, a few sugars of right handed symmetry and some lipids. Using the metaphor of computers this is equivalent to saying that all life shares the same hardware. Beyond hardware similarity, it is now known that all life has fundamentally the same software. The genetic code of life is common to all organisms. Some have argued that the "hammer of evolution is heavy" and life anywhere is likely to be composed of identical biochemical and genetic patterns. However, in a system as complex as biochemistry it is likely that there are numerous local optima and the details of the optimum found by evolutionary selection on another world would likely depend on the initial conditions and random developments in the early biological history on that world. To address these fundamental questions in Astrobiology we need a second example of life: a second genesis.

Vesicle encapsulation of a nonbiological photochemical system capable of reducing NAD(+) to NADH.

PubMed

Summers, David P; Rodoni, David

2015-10-06

One of the fundamental structures of a cell is the membrane. Self-assembling lipid bilayer vesicles can form the membrane of an artificial cell and could also have plausibly assembled prebiotically for the origin of life. Such cell-like structures, that encapsulate some basic subset of the functions of living cells, are important for research to infer the minimum chemistry necessary for a cell, to help understand the origin of life, and to allow the production of useful species in microscopic containers. We show that the encapsulation of TiO2 particles has the potential to provide the basis for an energy transduction system inside vesicles which can be used to drive subsequent chemistry. TiO2 encapsulated in vesicles can be used to produce biochemical species such as NADH. The NADH is formed from NAD(+) reduction and is produced in a form that is able to drive further enzymatic chemistry. This allows us to link a mineral-based, nonbiological photosystem to biochemical reactions. This is a fundamental step toward being able to use this mineral photosystem in a protocell/artificial cell.

Calcium oxalate druses affect leaf optical properties in selenium-treated Fagopyrum tataricum.

PubMed

Golob, Aleksandra; Stibilj, Vekoslava; Nečemer, Marijan; Kump, Peter; Kreft, Ivan; Hočevar, Anja; Gaberščik, Alenka; Germ, Mateja

2018-03-01

Plants of the genus Fagopyrum contain high levels of crystalline calcium oxalate (CaOx) deposits, or druses, that can affect the leaf optical properties. As selenium has been shown to modify the uptake and accumulation of metabolically important elements such as calcium, we hypothesised that the numbers of druses can be altered by selenium treatment, and this would affect the leaf optical properties. Tartary buckwheat (Fagopyrum tataricum Gaertn.) was grown outdoors in an experimental field. At the beginning of flowering, plants were foliarly sprayed with sodium selenate solution at 10 mg selenium L -1 or only with water. Plant morphological, biochemical, physiological and optical properties were examined, along with leaf elemental composition and content. Se spraying did not affect leaf biochemical and functional properties. However, it increased leaf thickness and the contents of Se in the leaves, and decreased the density of calcium oxalate druses in the leaves. Except Se content, Se spraying did not affect contents of other elements in leaves, including total calcium per dry mass of leaf tissue. Redundancy analysis showed that of all parameters tested, only the calcium oxalate druses parameters were significant in explaining the variability of the leaf reflectance and transmittance spectra. The density of CaOx druses positively correlated with the reflectance in the blue, green, yellow and UV-B regions of the spectrum, while the area of CaOx druses per mm 2 of leaf transection area positively correlated with the transmittance in the green and yellow regions of the spectrum. Copyright © 2018 Elsevier B.V. All rights reserved.

Informing Stem Cell-Based Tendon Tissue Engineering Approaches with Embryonic Tendon Development.

PubMed

Okech, William; Kuo, Catherine K

Adult tendons fail to regenerate normal tissue after injury, and instead form dysfunctional scar tissue with abnormal mechanical properties. Surgical repair with grafts is the current standard to treat injuries, but faces significant limitations including pain and high rates of re-injury. To address this, we aim to regenerate new, normal tendons to replace dysfunctional tendons. A common approach to tendon tissue engineering is to design scaffolds and bioreactors based on adult tendon properties that can direct adult stem cell tenogenesis. Despite significant progress, advances have been limited due, in part, to a need for markers and potent induction cues. Our goal is to develop novel tendon tissue engineering approaches informed by embryonic tendon development. We are characterizing structure-property relationships of embryonic tendon to identify design parameters for three-dimensional scaffolds and bioreactor mechanical loading systems to direct adult stem cell tenogenesis. We will review studies in which we quantified changes in the mechanical and biochemical properties of tendon during embryonic development and elucidated specific mechanisms of functional property elaboration. We then examined the effects of these mechanical and biochemical factors on embryonic tendon cell behavior. Using custom-designed bioreactors, we also examined the effects of dynamic mechanical loading and growth factor treatment on embryonic tendon cells. Our findings have established cues to induce tenogenesis as well as metrics to evaluate differentiation. We finish by discussing how we have evaluated the tenogenic differentiation potential of adult stem cells by comparing their responses to that of embryonic tendon cells in these culture systems.

Effect of spaceflight on the functional, biochemical, and metabolic properties of skeletal muscle

NASA Technical Reports Server (NTRS)

Baldwin, K. M.

1996-01-01

This paper summarizes the effects of spaceflight on the functional, morphological, and biochemical properties of human and rodent skeletal muscle. The findings suggest that following as little as 5-6 in space there are deficits in both human and rodent motor capacity, strength, and endurance properties of skeletal muscle. The reduced strength is associated, in part, with a reduction in muscle mass as reflected in smaller cross-sectional areas of both fast- and slow-twitch fibers. Available evidence in animal models suggests that slow-twitch fibers are more sensitive to the atrophying process. Accompanying the atrophy is a transformation of slow to fast protein phenotype involving myosin heavy chain and sarcoplasmic reticulum protein isoforms. These transformations appear to be regulated, in part, by pretranslational processes. Data on the oxidative capacity of rodent skeletal muscle suggest a bias toward preferential utilization of carbohydrate as the primary substrate. These collective findings suggest that skeletal muscles comprised chiefly of slow fibers are highly dependent on gravity for the normal expression of protein mass and slow phenotype. Future studies need to focus on elucidating the mechanisms associated with the atrophy response, as well as identifying suitable exercise and other countermeasures capable of preserving the structural and functional integrity of skeletal muscle.

Stimulating effects of two plant growth-promoting bacteria, Enterobacter ludwigii Ez-185-17 and Raoultella terrigena Ez-555-6, on flax culture

NASA Astrophysics Data System (ADS)

Sarron, Elodie; Clément, Nathalie; Pawlicki-Jullian, Nathalie; Gaillard, Isabelle; Boitel-Conti, Michèle

2018-04-01

Two bacteria, Enterobacter ludwigii Ez-185-17 and Raoultella terrigena Ez-555-6, isolated from root nodules of Medicago lupulina from the Chernobyl exclusion zone, were identified in a previous study and shown not to disturb plant growth. The main goal of this work is to elucidate the relationships between these bacteria and flax, in particular whether they display activities such as plant growth promoting bacteria (PGPB) properties or modulation hairy root development. In order to better understand their role in plants, some known PGPB properties were determined in comparison with several control bacteria. The influence of these bacteria on Linum usitatissimum growth under hydroponic conditions was also investigated. Our study shows that both bacteria belong to PGPB since they were able to increase considerably the root surface area of flax, especially Raoultella terrigena Ez-555-6. Significant IAA production and phosphate solubilization of Enterobacter ludwigii Ez-185-17 were highlighted, which enabled these biochemical PGPB properties to be correlated with their effects on flax growth. However, Raoultella terrigena Ez-555-6 did not express high biochemical activities, suggesting that other PGPB abilities should be studied in order to establish the link with flax growth improvement.

Antioxidant Properties and Cardioprotective Mechanism of Malaysian Propolis in Rats

PubMed Central

Ahmed, Romana; Hossen, Md. Sakib; Ahmmed, Istiyak; Rumpa, Nur-E-Noushin; Sulaiman, Siti Amrah

2017-01-01

Propolis contains high concentrations of polyphenols, flavonoids, tannins, ascorbic acid, and reducing sugars and proteins. Malaysian Propolis (MP) has been reported to exhibit high 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity and ferric reducing antioxidant power (FRAP) values. Herein, we report the antioxidant properties and cardioprotective properties of MP in isoproterenol- (ISO-) induced myocardial infarction in rats. Male Wistar rats (n = 32) were pretreated orally with an ethanol extract of MP (100 mg/kg/day) for 30 consecutive days. Subcutaneous injection of ISO (85 mg/kg in saline) for two consecutive days caused a significant increase in serum cardiac marker enzymes and cardiac troponin I levels and altered serum lipid profiles. In addition significantly increased lipid peroxides and decreased activities of cellular antioxidant defense enzymes were observed in the myocardium. However, pretreatment of ischemic rats with MP ameliorated the biochemical parameters, indicating the protective effect of MP against ISO-induced ischemia in rats. Histopathological findings obtained for the myocardium further confirmed the biochemical findings. It is concluded that MP exhibits cardioprotective activity against ISO-induced oxidative stress through its direct cytotoxic radical-scavenging activities. It is also plausible that MP contributed to endogenous antioxidant enzyme activity via inhibition of lipid peroxidation. PMID:28261310

Relationship between a spleen-derived immunosuppressive peptide 'SDIP' and the 'Facteur thymique sérique' (FTS): biochemical and biological comparison of the two factors.

PubMed Central

Lenfant, M; Millerioux, L; Blazsek, I; Duchange, N

1983-01-01

A spleen-derived immunosuppressive peptide (SDIP) has been purified to homogeneity. Its physicochemical properties (electrophoretic mobility, u.v. spectra, absence of dansyl derivative) and its enzymatic susceptibilities (proteolytic enzymes, RNase, and DNase) were similar to those of the thymic hormone 'FTS'. SDIP and FTS were eluted with identical retention times in high performance liquid chromatography analysis in three different systems. When tested in sheep cell rosettes, and in the FTS radioimmunoassay in J.F. Bach's laboratory, SDIP presented an activity similar to FTS. In order to compare the thymic hormone to SDIP the biological activity of FTS was determined in in vivo and in in vitro humoral immunity reactions to a T-dependent antigen. As SDIP, FTS inhibited in vivo and in vitro the 19S-bearing cell formation during the last step of the differentiation of the lymphocytes, in the same range of concentration. The two factors appeared to stimulate the incorporation of [3H]-thymidine into the DNA of short-term cultures of thymocytes. The similarity of biological properties of SDIP and FTS together with the similarity observed in the physico-chemical and biochemical properties led to the conclusion that bovine spleen contains a factor similar to FTS. PMID:6682089

Yield, quality and biochemical properties of various strawberry cultivars under water stress.

PubMed

Adak, Nafiye; Gubbuk, Hamide; Tetik, Nedim

2018-01-01

Although strawberry (Fragaria x ananassa Duch.) species are sensitive to abiotic stress conditions, some cultivars are known to be tolerant to different environmental conditions. We examined the response of different strawberry cultivars to water stress conditions in terms of yield, quality and biochemical features. The trial was conducted under two different irrigation regimes: in grow bags containing cocopeat (control, 30%; water stress, 15% drainage) with four different cultivars (Camarosa, Albion, Amiga and Rubygem). Fruit weight declined by 59.72% and the yield per unit area by 63.62% under water stress conditions as compared to control. Albion and Rubygem were found to be more tolerant and Amiga the most sensitive in terms of yield under stress conditions. Water stress increased all biochemical features in fruits such as total phenol, total anthocyanin, antioxidant activity and sugar contents. Among the cultivars, glucose and fructose was higher in Albion. Considering the rise in global warming, identification of resistant and tolerant cultivars to stress conditions are crucial for future breeding programmes. Our results showed that some of the fruit's physical features were affected negatively by stress conditions whereas many of the biochemical features such as total anthocyanin content, total phenolic content and antioxidant activity were positively modulated. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

The identification and biochemical properties of the catalytic specificity of a serine peptidase secreted by Aspergillus fumigatus Fresenius.

PubMed

da Silva, Ronivaldo Rodrigues; Caetano, Renato Cesar; Okamoto, Debora Nona; de Oliveira, Lilian Caroline Goncalves; Bertolin, Thiago Carlos; Juliano, Maria Aparecida; Juliano, Luiz; de Oliveira, Arthur H C; Rosae, Jose C; Cabral, Hamilton

2014-07-01

Aspergillus fumigatus is a saprophytic fungus as well as a so-called opportunist pathogen. Its biochemical potential and enzyme production justify intensive studies about biomolecules secreted by this microorganism. We describe the alkaline serine peptidase production, with optimum activity at 50°C and a pH of 7.5 and a reduction in proteolytic activity in the presence of the Al(+3) ions. When using intramolecularly quenched fluorogenic substrates, the highest catalytic efficiency was observed with the amino acid leucine on subsite S'(3) (60,000 mM(-1)s(-1)) and preference to non-polar amino acids on subsite S(3). In general, however, the peptidase shows non-specificity on other subsites studied. According to the biochemical characteristics, this peptidase may be an important biocatalyst for the hydrolysis of an enormous variety of proteins and can constitute an essential molecule for the saprophytic lifestyle or invasive action of the opportunistic pathogen. The peptidase described herein exhibits an estimated molecular mass of 33 kDa. Mass spectrometry analysis identified the sequence GAPWGLGSISHK displaying similarities to that of serine peptidase from Aspergillus fumigatus. These data may lead to a greater understanding of the advantageous biochemical potential, biotechnological interest, and trends of this fungus in spite of being an opportunist pathogen.

Biochemical alterations in duckweed and algae induced by carrier solvents: Selection of an appropriate solvent in toxicity testing.

PubMed

Hu, Li-Xin; Tian, Fei; Martin, Francis L; Ying, Guang-Guo

2017-10-01

Carrier solvents are often used in aquatic toxicity testing for test chemicals with hydrophobic properties. However, the knowledge of solvent effects on test organisms remains limited. The present study aimed to determine the biochemical effects of the 4 common solvents methanol, ethanol, acetone, and dimethyl sulfoxide (DMSO) on 2 test species, Lemna minor and Raphidocelis subcapitata, by applying Fourier transform infrared spectroscopy (FTIR) coupled with multivariate analysis to select appropriate solvents for toxicity testing. The results showed biochemical variations associated with solvent treatments at different doses on test species. From the infrared spectra obtained, the structures of lipid membrane and protein phosphorylation in the test species were found to be sensitive to the solvents. Methanol and ethanol mainly affected the protein secondary structure, whereas acetone and DMSO primarily induced alterations in carbohydrates and proteins in the test species. The FTIR results demonstrated that methanol and ethanol showed higher biochemical alterations in the test species than acetone and DMSO, especially at the high doses (0.1 and 1% v/v). Based on the growth inhibition displayed and FTIR spectroscopy, acetone, and DMSO can be used as carrier solvents in toxicity testing when their doses are lower than 0.1% v/v. Environ Toxicol Chem 2017;36:2631-2639. © 2017 SETAC. © 2017 SETAC.

Modelling the influence of land-use changes on biophysical and biochemical interactions at regional and global scales.

PubMed

Devaraju, N; Bala, G; Nemani, R

2015-09-01

Land-use changes since the start of the industrial era account for nearly one-third of the cumulative anthropogenic CO2 emissions. In addition to the greenhouse effect of CO2 emissions, changes in land use also affect climate via changes in surface physical properties such as albedo, evapotranspiration and roughness length. Recent modelling studies suggest that these biophysical components may be comparable with biochemical effects. In regard to climate change, the effects of these two distinct processes may counterbalance one another both regionally and, possibly, globally. In this article, through hypothetical large-scale deforestation simulations using a global climate model, we contrast the implications of afforestation on ameliorating or enhancing anthropogenic contributions from previously converted (agricultural) land surfaces. Based on our review of past studies on this subject, we conclude that the sum of both biophysical and biochemical effects should be assessed when large-scale afforestation is used for countering global warming, and the net effect on global mean temperature change depends on the location of deforestation/afforestation. Further, although biochemical effects trigger global climate change, biophysical effects often cause strong local and regional climate change. The implication of the biophysical effects for adaptation and mitigation of climate change in agriculture and agroforestry sectors is discussed. © 2014 John Wiley & Sons Ltd.

The Next Frontier: Quantitative Biochemistry in Living Cells.

PubMed

Honigmann, Alf; Nadler, André

2018-01-09

Researchers striving to convert biology into an exact science foremost rely on structural biology and biochemical reconstitution approaches to obtain quantitative data. However, cell biological research is moving at an ever-accelerating speed into areas where these approaches lose much of their edge. Intrinsically unstructured proteins and biochemical interaction networks composed of interchangeable, multivalent, and unspecific interactions pose unique challenges to quantitative biology, as do processes that occur in discrete cellular microenvironments. Here we argue that a conceptual change in our way of conducting biochemical experiments is required to take on these new challenges. We propose that reconstitution of cellular processes in vitro should be much more focused on mimicking the cellular environment in vivo, an approach that requires detailed knowledge of the material properties of cellular compartments, essentially requiring a material science of the cell. In a similar vein, we suggest that quantitative biochemical experiments in vitro should be accompanied by corresponding experiments in vivo, as many newly relevant cellular processes are highly context-dependent. In essence, this constitutes a call for chemical biologists to convert their discipline from a proof-of-principle science to an area that could rightfully be called quantitative biochemistry in living cells. In this essay, we discuss novel techniques and experimental strategies with regard to their potential to fulfill such ambitious aims.

Ground and excited state properties of high performance anthocyanidin dyes-sensitized solar cells in the basic solutions

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

Prima, Eka Cahya; Computational Material Design and Quantum Engineering Laboratory, Engineering Physics, Institut Teknologi Bandung; International Program on Science Education, Universitas Pendidikan Indonesia

2015-09-30

The aglycones of anthocyanidin dyes were previously reported to form carbinol pseudobase, cis-chalcone, and trans-chalcone due to the basic levels. The further investigations of ground and excited state properties of the dyes were characterized using density functional theory with PCM(UFF)/B3LYP/6-31+G(d,p) level in the basic solutions. However, to the best of our knowledge, the theoretical investigation of their potential photosensitizers has never been reported before. In this paper, the theoretical photovoltaic properties sensitized by dyes have been successfully investigated including the electron injections, the ground and excited state oxidation potentials, the estimated open circuit voltages, and the light harvesting efficiencies. Themore » results prove that the electronic properties represented by dyes’ LUMO-HOMO levels will affect to the photovoltaic performances. Cis-chalcone dye is the best anthocyanidin aglycone dye with the electron injection spontaneity of −1.208 eV, the theoretical open circuit voltage of 1.781 V, and light harvesting efficiency of 56.55% due to the best HOMO-LUMO levels. Moreover, the ethanol solvent slightly contributes to the better cell performance than the water solvent dye because of the better oxidation potential stabilization in the ground state as well as in the excited state. These results are in good agreement with the known experimental report that the aglycones of anthocyanidin dyes in basic solvent are the high potential photosensitizers for dye-sensitized solar cell.« less

Light sheet-based fluorescence microscopy (LSFM) reduces phototoxic effects and provides new means for the modern life sciences

NASA Astrophysics Data System (ADS)

Pampaloni, Francesco; Ansari, Nari; Girard, Philippe; Stelzer, Ernst H. K.

2011-07-01

Most optical technologies are applied to flat, basically two-dimensional cellular systems. However, physiological meaningful information relies on the morphology, the mechanical properties and the biochemistry of a cell's context. A cell requires the complex three-dimensional relationship to other cells. However, the observation of multi-cellular biological specimens remains a challenge. Specimens scatter and absorb light, thus, the delivery of the probing light and the collection of the signal light become inefficient; many endogenous biochemical compounds also absorb light and suffer degradation of some sort (photo-toxicity), which induces malfunction of a specimen. In conventional and confocal fluorescence microscopy, whenever a single plane, the entire specimen is illuminated. Recording stacks of images along the optical Z-axis thus illuminates the entire specimen once for each plane. Hence, cells are illuminated 10-20 and fish 100-300 times more often than they are observed. This can be avoided by changing the optical arrangement. The basic idea is to use light sheets, which are fed into the specimen from the side and overlap with the focal plane of a wide-field fluorescence microscope. In contrast to an epi-fluorescence arrangement, such an azimuthal fluorescence arrangement uses two independently operated lenses for illumination and detection. Optical sectioning and no photo-toxic damage or photo-bleaching outside a small volume close to the focal plane are intrinsic properties. Light sheet-based fluorescence microscopy (LSFM) takes advantage of modern camera technologies. LSFM can be operated with laser cutters and for fluorescence correlation spectroscopy. During the last few years, LSFM was used to record zebrafish development from the early 32-cell stage until late neurulation with sub-cellular resolution and short sampling periods (60-90 sec/stack). The recording speed was five 4-Megapixel large frames/sec with a dynamic range of 12-14 bit. We followed cell movements during gastrulation, revealed the development during cell migration processes and showed that an LSFM exposes an embryo to 200 times less energy than a conventional and 5,000 times less energy than a confocal fluorescence microscope. Most recently, we implemented incoherent structured illumination in our DSLM. The intensity modulated light sheets can be generated with dynamic frequencies and allow us to estimate the effect of the specimen on the image formation process at various depths in objects of different age.

Temporal development of near-native functional properties and correlations with qMRI in self-assembling fibrocartilage treated with exogenous lysyl oxidase homolog 2.

PubMed

Hadidi, Pasha; Cissell, Derek D; Hu, Jerry C; Athanasiou, Kyriacos A

2017-12-01

Advances in cartilage tissue engineering have led to constructs with mechanical integrity and biochemical composition increasingly resembling that of native tissues. In particular, collagen cross-linking with lysyl oxidase has been used to significantly enhance the mechanical properties of engineered neotissues. In this study, development of collagen cross-links over time, and correlations with tensile properties, were examined in self-assembling neotissues. Additionally, quantitative MRI metrics were examined in relation to construct mechanical properties as well as pyridinoline cross-link content and other engineered tissue components. Scaffold-free meniscus fibrocartilage was cultured in the presence of exogenous lysyl oxidase, and assessed at multiple time points over 8weeks starting from the first week of culture. Engineered constructs demonstrated a 9.9-fold increase in pyridinoline content, reaching 77% of native tissue values, after 8weeks of culture. Additionally, engineered tissues reached 66% of the Young's modulus in the radial direction of native tissues. Further, collagen cross-links were found to correlate with tensile properties, contributing 67% of the tensile strength of engineered neocartilages. Finally, examination of quantitative MRI metrics revealed several correlations with mechanical and biochemical properties of engineered constructs. This study displays the importance of culture duration for collagen cross-link formation, and demonstrates the potential of quantitative MRI in investigating properties of engineered cartilages. This is the first study to demonstrate near-native cross-link content in an engineered tissue, and the first study to quantify pyridinoline cross-link development over time in a self-assembling tissue. Additionally, this work shows the relative contributions of collagen and pyridinoline to the tensile properties of collagenous tissue for the first time. Furthermore, this is the first investigation to identify a relationship between qMRI metrics and the pyridinoline cross-link content of an engineered collagenous tissue. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Biochemical thermodynamics: applications of Mathematica.

PubMed

Alberty, Robert A

2006-01-01

The most efficient way to store thermodynamic data on enzyme-catalyzed reactions is to use matrices of species properties. Since equilibrium in enzyme-catalyzed reactions is reached at specified pH values, the thermodynamics of the reactions is discussed in terms of transformed thermodynamic properties. These transformed thermodynamic properties are complicated functions of temperature, pH, and ionic strength that can be calculated from the matrices of species values. The most important of these transformed thermodynamic properties is the standard transformed Gibbs energy of formation of a reactant (sum of species). It is the most important because when this function of temperature, pH, and ionic strength is known, all the other standard transformed properties can be calculated by taking partial derivatives. The species database in this package contains data matrices for 199 reactants. For 94 of these reactants, standard enthalpies of formation of species are known, and so standard transformed Gibbs energies, standard transformed enthalpies, standard transformed entropies, and average numbers of hydrogen atoms can be calculated as functions of temperature, pH, and ionic strength. For reactions between these 94 reactants, the changes in these properties can be calculated over a range of temperatures, pHs, and ionic strengths, and so can apparent equilibrium constants. For the other 105 reactants, only standard transformed Gibbs energies of formation and average numbers of hydrogen atoms at 298.15 K can be calculated. The loading of this package provides functions of pH and ionic strength at 298.15 K for standard transformed Gibbs energies of formation and average numbers of hydrogen atoms for 199 reactants. It also provides functions of temperature, pH, and ionic strength for the standard transformed Gibbs energies of formation, standard transformed enthalpies of formation, standard transformed entropies of formation, and average numbers of hydrogen atoms for 94 reactants. Thus loading this package makes available 774 mathematical functions for these properties. These functions can be added and subtracted to obtain changes in these properties in biochemical reactions and apparent equilibrium constants.

Propagation of kinetic uncertainties through a canonical topology of the TLR4 signaling network in different regions of biochemical reaction space

PubMed Central

2010-01-01

Background Signal transduction networks represent the information processing systems that dictate which dynamical regimes of biochemical activity can be accessible to a cell under certain circumstances. One of the major concerns in molecular systems biology is centered on the elucidation of the robustness properties and information processing capabilities of signal transduction networks. Achieving this goal requires the establishment of causal relations between the design principle of biochemical reaction systems and their emergent dynamical behaviors. Methods In this study, efforts were focused in the construction of a relatively well informed, deterministic, non-linear dynamic model, accounting for reaction mechanisms grounded on standard mass action and Hill saturation kinetics, of the canonical reaction topology underlying Toll-like receptor 4 (TLR4)-mediated signaling events. This signaling mechanism has been shown to be deployed in macrophages during a relatively short time window in response to lypopolysaccharyde (LPS) stimulation, which leads to a rapidly mounted innate immune response. An extensive computational exploration of the biochemical reaction space inhabited by this signal transduction network was performed via local and global perturbation strategies. Importantly, a broad spectrum of biologically plausible dynamical regimes accessible to the network in widely scattered regions of parameter space was reconstructed computationally. Additionally, experimentally reported transcriptional readouts of target pro-inflammatory genes, which are actively modulated by the network in response to LPS stimulation, were also simulated. This was done with the main goal of carrying out an unbiased statistical assessment of the intrinsic robustness properties of this canonical reaction topology. Results Our simulation results provide convincing numerical evidence supporting the idea that a canonical reaction mechanism of the TLR4 signaling network is capable of performing information processing in a robust manner, a functional property that is independent of the signaling task required to be executed. Nevertheless, it was found that the robust performance of the network is not solely determined by its design principle (topology), but this may be heavily dependent on the network's current position in biochemical reaction space. Ultimately, our results enabled us the identification of key rate limiting steps which most effectively control the performance of the system under diverse dynamical regimes. Conclusions Overall, our in silico study suggests that biologically relevant and non-intuitive aspects on the general behavior of a complex biomolecular network can be elucidated only when taking into account a wide spectrum of dynamical regimes attainable by the system. Most importantly, this strategy provides the means for a suitable assessment of the inherent variational constraints imposed by the structure of the system when systematically probing its parameter space. PMID:20230643

Calculations of critical misfit and thickness: An overview

NASA Technical Reports Server (NTRS)

Vandermerwe, Jan H.; Jesser, W. A.

1988-01-01

This overview stresses the equilibrium/nonequilibrium nature of the physical properties, as well as the basic properties of the models, used to calculate critical misfit and critical thickness in epitaxy.

Screening Genetic Resources of Capsicum Peppers in Their Primary Center of Diversity in Bolivia and Peru.

PubMed

van Zonneveld, Maarten; Ramirez, Marleni; Williams, David E; Petz, Michael; Meckelmann, Sven; Avila, Teresa; Bejarano, Carlos; Ríos, Llermé; Peña, Karla; Jäger, Matthias; Libreros, Dimary; Amaya, Karen; Scheldeman, Xavier

2015-01-01

For most crops, like Capsicum, their diversity remains under-researched for traits of interest for food, nutrition and other purposes. A small investment in screening this diversity for a wide range of traits is likely to reveal many traditional varieties with distinguished values. One objective of this study was to demonstrate, with Capsicum as model crop, the application of indicators of phenotypic and geographic diversity as effective criteria for selecting promising genebank accessions for multiple uses from crop centers of diversity. A second objective was to evaluate the expression of biochemical and agromorphological properties of the selected Capsicum accessions in different conditions. Four steps were involved: 1) Develop the necessary diversity by expanding genebank collections in Bolivia and Peru; 2) Establish representative subsets of ~100 accessions for biochemical screening of Capsicum fruits; 3) Select promising accessions for different uses after screening; and 4) Examine how these promising accessions express biochemical and agromorphological properties when grown in different environmental conditions. The Peruvian Capsicum collection now contains 712 accessions encompassing all five domesticated species (C. annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens). The collection in Bolivia now contains 487 accessions, representing all five domesticates plus four wild taxa (C. baccatum var. baccatum, C. caballeroi, C. cardenasii, and C. eximium). Following the biochemical screening, 44 Bolivian and 39 Peruvian accessions were selected as promising, representing wide variation in levels of antioxidant capacity, capsaicinoids, fat, flavonoids, polyphenols, quercetins, tocopherols, and color. In Peru, 23 promising accessions performed well in different environments, while each of the promising Bolivian accessions only performed well in a certain environment. Differences in Capsicum diversity and local contexts led to distinct outcomes in each country. In Peru, mild landraces with high values in health-related attributes were of interest to entrepreneurs. In Bolivia, wild Capsicum have high commercial demand.

Screening Genetic Resources of Capsicum Peppers in Their Primary Center of Diversity in Bolivia and Peru

PubMed Central

van Zonneveld, Maarten; Ramirez, Marleni; Williams, David E.; Petz, Michael; Meckelmann, Sven; Avila, Teresa; Bejarano, Carlos; Peña, Karla; Jäger, Matthias; Libreros, Dimary; Amaya, Karen; Scheldeman, Xavier

2015-01-01

For most crops, like Capsicum, their diversity remains under-researched for traits of interest for food, nutrition and other purposes. A small investment in screening this diversity for a wide range of traits is likely to reveal many traditional varieties with distinguished values. One objective of this study was to demonstrate, with Capsicum as model crop, the application of indicators of phenotypic and geographic diversity as effective criteria for selecting promising genebank accessions for multiple uses from crop centers of diversity. A second objective was to evaluate the expression of biochemical and agromorphological properties of the selected Capsicum accessions in different conditions. Four steps were involved: 1) Develop the necessary diversity by expanding genebank collections in Bolivia and Peru; 2) Establish representative subsets of ~100 accessions for biochemical screening of Capsicum fruits; 3) Select promising accessions for different uses after screening; and 4) Examine how these promising accessions express biochemical and agromorphological properties when grown in different environmental conditions. The Peruvian Capsicum collection now contains 712 accessions encompassing all five domesticated species (C. annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens). The collection in Bolivia now contains 487 accessions, representing all five domesticates plus four wild taxa (C. baccatum var. baccatum, C. caballeroi, C. cardenasii, and C. eximium). Following the biochemical screening, 44 Bolivian and 39 Peruvian accessions were selected as promising, representing wide variation in levels of antioxidant capacity, capsaicinoids, fat, flavonoids, polyphenols, quercetins, tocopherols, and color. In Peru, 23 promising accessions performed well in different environments, while each of the promising Bolivian accessions only performed well in a certain environment. Differences in Capsicum diversity and local contexts led to distinct outcomes in each country. In Peru, mild landraces with high values in health-related attributes were of interest to entrepreneurs. In Bolivia, wild Capsicum have high commercial demand. PMID:26402618

Augmented Dried versus Cryopreserved Amniotic Membrane as an Ocular Surface Dressing

PubMed Central

Allen, Claire L.; Clare, Gerry; Stewart, Elizabeth A.; Branch, Matthew J.; McIntosh, Owen D.; Dadhwal, Megha; Dua, Harminder S.; Hopkinson, Andrew

2013-01-01

Purpose Dried amniotic membrane (AM) can be a useful therapeutic adjunct in ophthalmic surgery and possesses logistical advantages over cryopreserved AM. Differences in preservation techniques can significantly influence the biochemical composition and physical properties of AM, potentially affecting clinical efficacy. This study was established to investigate the biochemical and structural effects of drying AM in the absence and presence of saccharide lyoprotectants and its biocompatibility compared to cryopreserved material. Methods AM was cryopreserved or dried with and without pre-treatment with trehalose or raffinose and the antioxidant epigallocatechin (EGCG). Structural and visual comparisons were assessed using electron microscopy. Localisation, expression and release of AM biological factors were determined using immunoassays and immunofluorescence. The biocompatibility of the AM preparations co-cultured with corneal epithelial cell (CEC) or keratocyte monolayers were assessed using cell proliferation, cytotoxicity, apoptosis and migration assays. Results Drying devitalised AM epithelium, but less than cryopreservation and cellular damage was reduced in dried AM pre-treated with trehalose or raffinose. Dried AM alone, and with trehalose or raffinose showed greater factor retention efficiencies and bioavailability compared to cryopreserved AM and demonstrated a more sustained biochemical factor time release in vitro. Cellular health assays showed that dried AM with trehalose or raffinose are compatible and superior substrates compared to cryopreserved AM for primary CEC expansion, with increased proliferation and reduced LDH and caspase-3 levels. This concept was supported by improved wound healing in an immortalised human CEC line (hiCEC) co-cultured with dried and trehalose or raffinose membranes, compared to cryopreserved and fresh AM. Conclusions Our modified preservation process and our resultant optimised dried AM has enhanced structural properties and biochemical stability and is a superior substrate to conventional cryopreserved AM. In addition this product is stable and easily transportable allowing it to be globally wide reaching for use in clinical and military sectors. PMID:24205233

Modular decomposition of metabolic reaction networks based on flux analysis and pathway projection.

PubMed

Yoon, Jeongah; Si, Yaguang; Nolan, Ryan; Lee, Kyongbum

2007-09-15

The rational decomposition of biochemical networks into sub-structures has emerged as a useful approach to study the design of these complex systems. A biochemical network is characterized by an inhomogeneous connectivity distribution, which gives rise to several organizational features, including modularity. To what extent the connectivity-based modules reflect the functional organization of the network remains to be further explored. In this work, we examine the influence of physiological perturbations on the modular organization of cellular metabolism. Modules were characterized for two model systems, liver and adipocyte primary metabolism, by applying an algorithm for top-down partition of directed graphs with non-uniform edge weights. The weights were set by the engagement of the corresponding reactions as expressed by the flux distribution. For the base case of the fasted rat liver, three modules were found, carrying out the following biochemical transformations: ketone body production, glucose synthesis and transamination. This basic organization was further modified when different flux distributions were applied that describe the liver's metabolic response to whole body inflammation. For the fully mature adipocyte, only a single module was observed, integrating all of the major pathways needed for lipid storage. Weaker levels of integration between the pathways were found for the early stages of adipocyte differentiation. Our results underscore the inhomogeneous distribution of both connectivity and connection strengths, and suggest that global activity data such as the flux distribution can be used to study the organizational flexibility of cellular metabolism. Supplementary data are available at Bioinformatics online.

Benchmarking a Visual-Basic based multi-component one-dimensional reactive transport modeling tool

NASA Astrophysics Data System (ADS)

Torlapati, Jagadish; Prabhakar Clement, T.

2013-01-01

We present the details of a comprehensive numerical modeling tool, RT1D, which can be used for simulating biochemical and geochemical reactive transport problems. The code can be run within the standard Microsoft EXCEL Visual Basic platform, and it does not require any additional software tools. The code can be easily adapted by others for simulating different types of laboratory-scale reactive transport experiments. We illustrate the capabilities of the tool by solving five benchmark problems with varying levels of reaction complexity. These literature-derived benchmarks are used to highlight the versatility of the code for solving a variety of practical reactive transport problems. The benchmarks are described in detail to provide a comprehensive database, which can be used by model developers to test other numerical codes. The VBA code presented in the study is a practical tool that can be used by laboratory researchers for analyzing both batch and column datasets within an EXCEL platform.

Proteomics Unveils Fibroblast-Cardiomyocyte Lactate Shuttle and Hexokinase Paradox in Mouse Muscles.

PubMed

Rakus, Dariusz; Gizak, Agnieszka; Wiśniewski, Jacek R

2016-08-05

Quantitative mapping, given in biochemically interpretable units such as mol per mg of total protein, of tissue-specific proteomes is prerequisite for the analysis of any process in cells. We applied label- and standard-free proteomics to characterize three types of striated muscles: white, red, and cardiac muscle. The analysis presented here uncovers several unexpected and novel features of striated muscles. In addition to differences in protein expression levels, the three muscle types substantially differ in their patterns of basic metabolic pathways and isoforms of regulatory proteins. Importantly, some of the conclusions drawn on the basis of our results, such as the potential existence of a "fibroblast-cardiomyocyte lactate shuttle" and the "hexokinase paradox" point to the necessity of reinterpretation of some basic aspects of striated muscle metabolism. The data presented here constitute a powerful database and a resource for future studies of muscle physiology and for the design of pharmaceutics for the treatment of muscular disorders.

[Assessment of prophylaxis and treatment of blood loss in patients with pre-eclampsia].

PubMed

Timokhova, S Iu; Golubtsov, V V; Zabolotskikh, I B

2014-01-01

To improve treatment results of women with massive obstetrical blood loss. Subjects and methods: 96 female patients with average and heavy degree preeclampsia worsened massive blood developing were involved into the investigation. The women were divided into two groups: main (n=55) (basic) - it's patients were treated with complex of offered wiays control (n=41) - it's patients were evaluated retrospectively. During the investigation the parameters of hemostasis system and periphery blood values were performed as dynamic evaluations, acidity-basic state and water-electrolyte balance parameters, medical history were monitored. As a result of the investigation it was found out that these offered actions complex application about reducing massive obstetric blood accelerates restoration of clinic, bio-chemical paramnleters during the early post-operating period The application of the offered methods has reduced both inltraoperative blood loss in women with preeclamsia and use of blood components and the time spent on the hemostasis system correction for all the women of the base group.

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.

Biophysics at the Boundaries: The Next Problem Sets

NASA Astrophysics Data System (ADS)

Skolnick, Malcolm

2009-03-01

The interface between physics and biology is one of the fastest growing subfields of physics. As knowledge of such topics as cellular processes and complex ecological systems advances, researchers have found that progress in understanding these and other systems requires application of more quantitative approaches. Today, there is a growing demand for quantitative and computational skills in biological research and the commercialization of that research. The fragmented teaching of science in our universities still leaves biology outside the quantitative and mathematical culture that is the foundation of physics. This is particularly inopportune at a time when the needs for quantitative thinking about biological systems are exploding. More physicists should be encouraged to become active in research and development in the growing application fields of biophysics including molecular genetics, biomedical imaging, tissue generation and regeneration, drug development, prosthetics, neural and brain function, kinetics of nonequilibrium open biological systems, metabolic networks, biological transport processes, large-scale biochemical networks and stochastic processes in biochemical systems to name a few. In addition to moving into basic research in these areas, there is increasing opportunity for physicists in industry beginning with entrepreneurial roles in taking research results out of the laboratory and in the industries who perfect and market the inventions and developments that physicists produce. In this talk we will identify and discuss emerging opportunities for physicists in biophysical and biotechnological pursuits ranging from basic research through development of applications and commercialization of results. This will include discussion of the roles of physicists in non-traditional areas apart from academia such as patent law, financial analysis and regulatory science and the problem sets assigned in education and training that will enable future biophysicists to fill these roles.

Association of the Pro12Ala polymorphism in peroxisome proliferator-activated receptor gamma2 with decreased basic metabolic rate in women with polycystic ovary syndrome.

PubMed

Koika, Vasiliki; Marioli, Dimitra J; Saltamavros, Alexandros D; Vervita, Vasiliki; Koufogiannis, Kleanthis D; Adonakis, George; Decavalas, George; Georgopoulos, Neoklis A

2009-08-01

The peroxisome proliferator-activated receptor (PPAR)gamma is a transcription factor involved in glucose homeostasis and energy metabolism. A missense mutation at codon 12 in the PPARgamma2 has been associated with increased body mass index (BMI) and attenuated insulin resistance (IR) in polycystic ovary syndrome (PCOS). We have recently shown a decreased basic metabolic rate (BMR) in PCOS. The aim of the present study is to determine the prevalence of the Pro12Ala polymorphism of the PPARgamma2 gene and its associations with indices of IR and BMR in lean and slightly overweight PCOS women. Case-control association study involving 156 PCOS women with biochemical hyperandrogenism, chronic anovulation and polycystic ovarian morphology in ultrasound and 56 unrelated healthy controls. Hormonal determinations were performed by electrochemiluminescence quantitation or RIA. BMR was measured by indirect calorimetry. All subjects were genotyped by a PCR-restriction fragment length polymorphism assay. Genotype frequencies of the Pro12Ala polymorphism in PPARgamma2 did not differ among PCOS women and control subjects. The presence of Pro12Ala polymorphism of PPARgamma2 was associated with lower BMR (P=0.04). This finding was valid in our subgroup of lean PCOS (BMI<25 kg/m(2)), in which the Ala variant was also associated with higher total testosterone values. The Pro12Ala polymorphism in the PPARgamma2 gene is associated with decreased BMR in women with PCOS and biochemical hyperandrogenemia. These young women are therefore at risk to increase their body weight and should restrict their energy intake by diet and enhance their energy expenditure by exercise.

Thermodynamic and Kinetic Properties of the Electrochemical Cell.

ERIC Educational Resources Information Center

Smith, Donald E.

1983-01-01

Describes basic characteristics of the electrochemical cell. Also describes basic principles of electrochemical procedures and use of these concepts to explain use of the term "primarily" in discussions of methods primarily responsive to equilibrium cell potential, bulk ohmic resistance, and the Faradaic impedance. (JN)

Properties of the ion-ion hybrid resonator in fusion plasmas

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

Morales, George J.

2015-10-06

The project developed theoretical and numerical descriptions of the properties of ion-ion hybrid Alfvén resonators that are expected to arise in the operation of a fusion reactor. The methodology and theoretical concepts were successfully compared to observations made in basic experiments in the LAPD device at UCLA. An assessment was made of the excitation of resonator modes by energetic alpha particles for burning plasma conditions expected in the ITER device. The broader impacts included the generation of basic insight useful to magnetic fusion and space science researchers, defining new avenues for exploration in basic laboratory experiments, establishing broader contacts betweenmore » experimentalists and theoreticians, completion of a Ph.D. dissertation, and promotion of interest in science through community outreach events and classroom instruction.« less

Differentiation of live and dead salmonella cells using fourier transform infrared (FTIR) spectroscopy and principle component analysis (PCA) technique

USDA-ARS?s Scientific Manuscript database

Various technologies have been developed for pathogen detection using optical, electrochemical, biochemical and physical properties. Conventional microbiological methods need time from days to week to get the result. Though this method is very sensitive and accurate, a rapid detection of pathogens i...

Recombinant acetylcholinesterase 1 of the sand fly Phlebotomus papatasi (Scopoli): expression, biochemical properties, and insensitivity to organophosphate inhibition

USDA-ARS?s Scientific Manuscript database

Phlebotomine sand flies are small hematophagous vectors of human and zoonotic leishmaniases present throughout tropical and subtropical areas of the world. These flies present serious problems for military operations and resident populations in the Middle East and other areas where they are endemic....

Acetylcholinesterase of the Sand Fly Phlebotomus papatasi (Scopoli): cDNA Sequence, Baculovirus Expression and Biochemical Properties

USDA-ARS?s Scientific Manuscript database

Millions of people and domestic animals around the world are affected by leishmaniasis, a disease caused by various species of flagellated protozoans in the genus Leishmania that are transmitted by several sand fly species. Insecticides are widely used for sand fly population control to try to reduc...

Expression and Biochemical Properties of a Recombinant Acetylcholinesterase 1 of the Sand Fly, Phlebotomus papatasi (Scopoli) Insensitive to Organophosphate Inhibition

USDA-ARS?s Scientific Manuscript database

Phlebotomine sand flies are small hematophagous flies present throughout tropical and subtropical areas of the world and are vectors of human and zoonotic leishmaniases. Human cutaneous leishmaniasis is a debilitating disease presenting major problems for U.S. military operations in the Middle East,...

Discovery of an acidic, thermostable and highly NADP+ dependent formate dehydrogenase from Lactobacillus buchneri NRRL B-30929

USDA-ARS?s Scientific Manuscript database

Objectives: To identify a robust NADP+ dependent formate dehydrogenase from Lactobacillus buchneri NRRL B-30929 (LbFDH) with unique biochemical properties. Results: A new NADP+ dependent formate dehydrogenase gene (fdh) was cloned from genomic DNA of L. buchneri NRRL B-30929. The recombinant constru...

Determining the biochemical properties of the Oxalate Biosynthetic Component (Obc)1 from Burkholderia mallei

USDA-ARS?s Scientific Manuscript database

Oxalic acid is produced by a variety of organisms ranging from simple microbes to complex animals. This acid has been proposed to fulfill various physiological and pathological functions which vary between organisms. In bacteria from the Burkholderia genus, oxalate secretion has been shown to be quo...

Fundamentals of biomechanics in tissue engineering of bone.

PubMed

Athanasiou, K A; Zhu, C; Lanctot, D R; Agrawal, C M; Wang, X

2000-08-01

The objective of this review is to provide basic information pertaining to biomechanical aspects of bone as they relate to tissue engineering. The review is written for the general tissue engineering reader, who may not have a biomechanical engineering background. To this end, biomechanical characteristics and properties of normal and repair cortical and cancellous bone are presented. Also, this chapter intends to describe basic structure-function relationships of these two types of bone. Special emphasis is placed on salient classical and modern testing methods, with both material and structural properties described.

Couplings

NASA Astrophysics Data System (ADS)

Stošić, Dušan; Auroux, Aline

Basic principles of calorimetry coupled with other techniques are introduced. These methods are used in heterogeneous catalysis for characterization of acidic, basic and red-ox properties of solid catalysts. Estimation of these features is achieved by monitoring the interaction of various probe molecules with the surface of such materials. Overview of gas phase, as well as liquid phase techniques is given. Special attention is devoted to coupled calorimetry-volumetry method. Furthermore, the influence of different experimental parameters on the results of these techniques is discussed, since it is known that they can significantly influence the evaluation of catalytic properties of investigated materials.

Tailoring (bio)chemical activity of semiconducting nanoparticles: critical role of deposition and aggregation.

PubMed

Chernyshova, Irina V; Ponnurangam, Sathish; Somasundaran, Ponisseril

2011-06-22

The impact of deposition and aggregation on (bio)chemical properties of semiconducting nanoparticles (NPs) is perhaps among the least studied aspects of aquatic chemistry of solids. Employing a combination of in situ FTIR and ex situ X-ray photoelectron spectroscopy (XPS) and using the Mn(II) oxygenation on hematite (α-Fe(2)O(3)) and anatase (TiO(2)) NPs as a model catalytic reaction, we discovered that the catalytic and sorption performance of the semiconducting NPs in the dark can be manipulated by depositing them on different supports or mixing them with other NPs. We introduce the electrochemical concept of the catalytic redox activity to explain the findings and to predict the effects of (co)aggregation and deposition on the catalytic and corrosion properties of ferric (hydr)oxides. These results offer new possibilities for rationally tailoring the technological performance of semiconducting metal oxide NPs, provide a new framework for modeling their fate and transport in the environment and living organisms, and can be helpful in discriminating between weakly and strongly adsorbed species in spectra.

The perspective effects of various seed coating substances on rice seed variety Khao Dawk Mali 105 storability II: the case study of chemical and biochemical properties.

PubMed

Thobunluepop, P; Pan-in, W; Pawelzik, E; Vearasilp, S

2009-04-01

The aim of this study was to investigate the effects of seed coating substances; chemical fungicide (CA) and biological fungicide polymers [chitosan-lignosulphonate polymer (CL) and eugenol incorporated into chitosan-lignosulphonate polymer (E+CL)] on chemical and biochemical changes of rice seeds cv. KDML 105, which have been studied during storage for 12 months. CA significantly affected the rice seed chemical properties and the associated seed deterioration. After 12 months storage, protein content decreased accompanied by declined of lipid content, increased free fatty acids and activated lipoxygenase enzyme. In the case of biological fungicide coated seeds, the antioxidative scavenging enzymes were ascorbate peroxidase and superoxide dismutase and a high antioxidant activity protected them. Moreover, the sugar content was positive correlated with seed germination and vigor. The biological coated seeds were found to maintain high sugar contents inside the seeds, which resulted high seed storability significantly. In contrast, under fungicide stress (CA), those compounds were lost that directly affected seed vigor during storage.

Modification of measurement methods for evaluation of tissue-engineered cartilage function and biochemical properties using nanosecond pulsed laser

NASA Astrophysics Data System (ADS)

Ishihara, Miya; Sato, Masato; Kutsuna, Toshiharu; Ishihara, Masayuki; Mochida, Joji; Kikuchi, Makoto

2008-02-01

There is a demand in the field of regenerative medicine for measurement technology that enables determination of functions and components of engineered tissue. To meet this demand, we developed a method for extracellular matrix characterization using time-resolved autofluorescence spectroscopy, which enabled simultaneous measurements with mechanical properties using relaxation of laser-induced stress wave. In this study, in addition to time-resolved fluorescent spectroscopy, hyperspectral sensor, which enables to capture both spectral and spatial information, was used for evaluation of biochemical characterization of tissue-engineered cartilage. Hyperspectral imaging system provides spectral resolution of 1.2 nm and image rate of 100 images/sec. The imaging system consisted of the hyperspectral sensor, a scanner for x-y plane imaging, magnifying optics and Xenon lamp for transmmissive lighting. Cellular imaging using the hyperspectral image system has been achieved by improvement in spatial resolution up to 9 micrometer. The spectroscopic cellular imaging could be observed using cultured chondrocytes as sample. At early stage of culture, the hyperspectral imaging offered information about cellular function associated with endogeneous fluorescent biomolecules.

Efficiency of C3 and C4 Plant Derived-Biochar for Cd Mobility, Nutrient Cycling and Microbial Biomass in Contaminated Soil.

PubMed

Bashir, Saqib; Shaaban, Muhammad; Mehmood, Sajid; Zhu, Jun; Fu, Qingling; Hu, Hongqing

2018-06-01

Biochar is considered a novel soil amendment to reduce metal mobility, but its influence on soil chemical and biochemical properties is not fully understood. In the present study, biochar derived from rice straw (RSB), rice hull (RHB), and maize stover (MSB) was used to evaluate comparative efficiency on Cd mobility and soil biochemical properties. Ammonium nitrate extractable Cd significantly decreased among all the applied biochar types and application rates. The European Community Bureau of Reference (BCR) technique showed significant decrease in acid-soluble Cd by 24%-32%, 19%-23%, and 22%-27% for RSB, RHB, and MSB, respectively at the 1.5% and 3% rate. However, the concentration of Cd in the residual increased by 38%, 35% and 36% for RSB, RHB and MSB, respectively at a 3% application rate. Soil microbial biomass (C and N) and inorganic nitrogen forms (NH 4 and NO 3 ) significantly increased among all biochar applications. Overall, RSB demonstrated positive results as soil amendments for Cd immobilization, increasing soil nutrient availability, and enhancing soil microbial biomass.

Cold-adapted digestive aspartic protease of the clawed lobsters Homarus americanus and Homarus gammarus: biochemical characterization.

PubMed

Rojo, Liliana; García-Carreño, Fernando; de Los Angeles Navarrete del Toro, Maria

2013-02-01

Aspartic proteinases in the gastric fluid of clawed lobsters Homarus americanus and Homarus gammarus were isolated to homogeneity by single-step pepstatin-A affinity chromatography; such enzymes have been previously identified as cathepsin D-like enzymes based on their deduced amino acid sequence. Here, we describe their biochemical characteristics; the properties of the lobster enzymes were compared with those of its homolog, bovine cathepsin D, and found to be unique in a number of ways. The lobster enzymes demonstrated hydrolytic activity against synthetic and natural substrates at a wider range of pH; they were more temperature-sensitive, showed no changes in the K(M) value at 4°C, 10°C, and 25°C, and had 20-fold higher k(cat)/K(M) values than bovine enzyme. The bovine enzyme was temperature-dependent. We propose that both properties arose from an increase in molecular flexibility required to compensate for the reduction of reaction rates at low habitat temperatures. This is supported by the fast denaturation rates induced by temperature.

Hydrogel Based Biosensors for In Vitro Diagnostics of Biochemicals, Proteins, and Genes.

PubMed

Jung, Il Young; Kim, Ji Su; Choi, Bo Ram; Lee, Kyuri; Lee, Hyukjin

2017-06-01

Hydrogel-based biosensors have drawn considerable attention due to their various advantages over conventional detection systems. Recent studies have shown that hydrogel biosensors can be excellent alternative systems to detect a wide range of biomolecules, including small biochemicals, pathogenic proteins, and disease specific genes. Due to the excellent physical properties of hydrogels such as the high water content and stimuli-responsive behavior of cross-linked network structures, this system can offer substantial improvement for the design of novel detection systems for various diagnostic applications. The other main advantage of hydrogels is the role of biomimetic three-dimensional (3D) matrix immobilizing enzymes and aptamers within the detection systems, which enhances their stability. This provides ideal reaction conditions for enzymes and aptamers to interact with substrates within the aqueous environment of the hydrogel. In this review, we have highlighted various novel detection approaches utilizing the outstanding properties of the hydrogel. This review summarizes the recent progress of hydrogel-based biosensors and discusses their future perspectives and clinical limitations to overcome. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microcin Amyloid Fibrils A Are Reservoir of Toxic Oligomeric Species

PubMed Central

Shahnawaz, Mohammad; Soto, Claudio

2012-01-01

Microcin E492 (Mcc), a low molecular weight bacteriocin produced by Klebsiella pneumoniae RYC492, has been shown to exist in two forms: soluble forms that are believed to be toxic to the bacterial cell by forming pores and non-toxic fibrillar forms that share similar biochemical and biophysical properties with amyloids associated with several human diseases. Here we report that fibrils polymerized in vitro from soluble forms sequester toxic species that can be released upon changing environmental conditions such as pH, ionic strength, and upon dilution. Our results indicate that basic pH (≥8.5), low NaCl concentrations (≤50 mm), and dilution (>10-fold) destabilize Mcc fibrils into more soluble species that are found to be toxic to the target cells. Additionally, we also found a similar conversion of non-toxic fibrils into highly toxic oligomers using Mcc aggregates produced in vivo. Moreover, the soluble protein released from fibrils is able to rapidly polymerize into amyloid fibrils under fibril-forming conditions and to efficiently seed aggregation of monomeric Mcc. Our findings indicate that fibrillar forms of Mcc constitute a reservoir of toxic oligomeric species that is released into the medium upon changing the environmental conditions. These findings may have substantial implications to understand the dynamic process of interconversion between toxic and non-toxic aggregated species implicated in protein misfolding diseases. PMID:22337880

Regulation of yeast DNA polymerase δ-mediated strand displacement synthesis by 5′-flaps

PubMed Central

Koc, Katrina N.; Stodola, Joseph L.; Burgers, Peter M.; Galletto, Roberto

2015-01-01

The strand displacement activity of DNA polymerase δ is strongly stimulated by its interaction with proliferating cell nuclear antigen (PCNA). However, inactivation of the 3′–5′ exonuclease activity is sufficient to allow the polymerase to carry out strand displacement even in the absence of PCNA. We have examined in vitro the basic biochemical properties that allow Pol δ-exo− to carry out strand displacement synthesis and discovered that it is regulated by the 5′-flaps in the DNA strand to be displaced. Under conditions where Pol δ carries out strand displacement synthesis, the presence of long 5′-flaps or addition in trans of ssDNA suppress this activity. This suggests the presence of a secondary DNA binding site on the enzyme that is responsible for modulation of strand displacement activity. The inhibitory effect of a long 5′-flap can be suppressed by its interaction with single-stranded DNA binding proteins. However, this relief of flap-inhibition does not simply originate from binding of Replication Protein A to the flap and sequestering it. Interaction of Pol δ with PCNA eliminates flap-mediated inhibition of strand displacement synthesis by masking the secondary DNA site on the polymerase. These data suggest that in addition to enhancing the processivity of the polymerase PCNA is an allosteric modulator of other Pol δ activities. PMID:25813050

Predicting Functions of Proteins in Mouse Based on Weighted Protein-Protein Interaction Network and Protein Hybrid Properties

PubMed Central

Shi, Xiaohe; Lu, Wen-Cong; Cai, Yu-Dong; Chou, Kuo-Chen

2011-01-01

Background With the huge amount of uncharacterized protein sequences generated in the post-genomic age, it is highly desirable to develop effective computational methods for quickly and accurately predicting their functions. The information thus obtained would be very useful for both basic research and drug development in a timely manner. Methodology/Principal Findings Although many efforts have been made in this regard, most of them were based on either sequence similarity or protein-protein interaction (PPI) information. However, the former often fails to work if a query protein has no or very little sequence similarity to any function-known proteins, while the latter had similar problem if the relevant PPI information is not available. In view of this, a new approach is proposed by hybridizing the PPI information and the biochemical/physicochemical features of protein sequences. The overall first-order success rates by the new predictor for the functions of mouse proteins on training set and test set were 69.1% and 70.2%, respectively, and the success rate covered by the results of the top-4 order from a total of 24 orders was 65.2%. Conclusions/Significance The results indicate that the new approach is quite promising that may open a new avenue or direction for addressing the difficult and complicated problem. PMID:21283518

The influence of leaf anatomy on the internal light environment and photosynthetic electron transport rate: exploration with a new leaf ray tracing model.

PubMed

Xiao, Yi; Tholen, Danny; Zhu, Xin-Guang

2016-11-01

Leaf photosynthesis is determined by biochemical properties and anatomical features. Here we developed a three-dimensional leaf model that can be used to evaluate the internal light environment of a leaf and its implications for whole-leaf electron transport rates (J). This model includes (i) the basic components of a leaf, such as the epidermis, palisade and spongy tissues, as well as the physical dimensions and arrangements of cell walls, vacuoles and chloroplasts; and (ii) an efficient forward ray-tracing algorithm, predicting the internal light environment for light of wavelengths between 400 and 2500nm. We studied the influence of leaf anatomy and ambient light on internal light conditions and J The results show that (i) different chloroplasts can experience drastically different light conditions, even when they are located at the same distance from the leaf surface; (ii) bundle sheath extensions, which are strips of parenchyma, collenchyma or sclerenchyma cells connecting the vascular bundles with the epidermis, can influence photosynthetic light-use efficiency of leaves; and (iii) chloroplast positioning can also influence the light-use efficiency of leaves. Mechanisms underlying leaf internal light heterogeneity and implications of the heterogeneity for photoprotection and for the convexity of the light response curves are discussed. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Southeastern Community College Annual Progress Report, December 1995.

ERIC Educational Resources Information Center

Gardner, R. Gene

Presenting information on the status of Southeastern Community College (SCC), in Iowa, this annual progress report highlights basic institutional data, financial information, and improvements and planned changes of the college as of 1995. Part 1 presents basic data on SCC, including facility locations, assessed property valuation, district…