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Effects of detergent environments on the photocycle of purified monomeric bacteriorhodopsin.

Time-resolved difference spectra have been obtained for the photocycle of delipidated bacteriorhodopsin monomers (d-BR) in six different detergent micelle environments that were prepared by two new detergent-exchange techniques. A global kinetic analysis of the photocycle spectra for d-BR in each detergent environment was performed. Comparison of these results with those obtained for the photocycle of bacteriorhodopsin in purple membrane (PM) shows that there is one fewer kinetically distinguishable process for monomeric BR between the decay of the K intermediate and the rise of the M intermediate. Assuming a sequential pathway occurs in the photocycle, it appears that the equilibrium between the L and M intermediates is reached much more rapidly in the detergent micelles. This is attributed to a more direct interaction between Asp-85 and the proton on the nitrogen of the Schiff base of retinal for BR in the detergents. Equilibrium concentrations of late photocycle intermediates are also altered in detergents. The later steps of the photocycle, including the decay of the M intermediate, are slowed in detergents with rings in their hydrocarbon region. This is attributed to effects on conformational changes occurring during the decay of M and/or other later photocycle intermediates. The lifetime of dark adaptation of light-adapted d-BR in different detergent environments increases in environments where the lifetime of the M intermediate increases. These results suggest that the high percentage of either unsaturated or methyl-branched lipids in PM and the membranes of other retinal proteins may be important for their effective functioning.

Bacteriorhodopsins↗

Molecular dynamics study of the structure and dynamics of a protein molecule in a crystalline ionic environment, Streptomyces griseus protease A.

A large-scale molecular dynamics simulation of the behavior of a serine protease (Streptomyces griseus protease A) in a crystalline environment has been performed. All atoms (including hydrogens) of two protein molecules and the surrounding solvent of crystallization, consisting of both water and salt ions, were explicitly represented, and a relatively long range of interactions (up to 15 A) were included. The simulation is the longest so far reported for a protein in such an environment (60 ps). The use of the full crystalline environment allows a direct comparison of the structure and dynamic properties of the protein and surrounding solvent to be made with the experimental X-ray structure. Here we report the comparison of the protein structures and analyze the energetics of the system, including interaction with the aqueous environment. Subsequent papers will deal with other aspects of the simulation. The overall root mean square differences between the time-averaged molecular dynamics structure and that from crystallography, for all well-ordered, non-hydrogen atoms, are 1.67 and 1.25 A for the two molecules taken as the asymmetric unit. An extensive analysis of the conformation of substructural elements and individual residues and their deviation from experiment has revealed a strong influence of the ionic medium on their behavior. Implications of the results for free energy calculations and for future directions are also discussed.

Algorithms↗

Resonance Raman study on the oxidized and anionic semiquinone forms of flavocytochrome b2 and L-lactate monooxygenase. Influence of the structure and environment of the isoalloxazine ring on the flavin function.

The oxidized and semiquinone anion radical forms of flavin mononucleotide carried by flavocytochrome b2 and L-lactate monooxygenase have been studied by resonance Raman (RR) spectroscopy. The RR spectra of their oxidized forms are compared with previously published RR data on various flavins and flavoproteins. Taking as a support available X-ray crystallographic data on flavoproteins, we have found correlations between the frequencies of RR bands II (1575-1588 cm-1), III (1534-1557 cm-1), and X (1244-1266 cm-1) and the H-bonding environment and/or the structure of the flavin ring. The present RR data provide strong evidence that the electron density, the conformation, and the H-bonding environment of the oxidized flavin mononucleotide of flavocytochrome b2 and L-lactate monooxygenase are different. As far as the anionic semiquinone form of flavoproteins is concerned, the behavior of two bands observed at 1280-1300 and 1320-1350 cm-1 suggests that they have vibrational origins similar to those of RR bands II and III of oxidized compounds. On this basis, the differences in conformation and H-bonding environment of the isoalloxazine ring, observed for the oxidized form of flavocytochrome b2 and L-lactate monooxygenase, appear to be preserved upon one-electron reduction of the flavin. For both flavoproteins, the RR spectra of the semiquinone form are affected by pyruvate binding. The data are interpreted in the frame of a change in H-bonding interaction of the C4&dbd;O carbonyl group of the flavin without significant alteration of the isoalloxazine conformation. This modification in electrostatic interaction quantitatively accounts for the pyruvate-induced changes of the oxidized/semiquinone and semiquinone/reduced redox potentials of the flavoproteins. Considering the high homology in the flavin catalytic sites of flavocytochrome b2 and L-lactate monooxygenase, the observed differences in H-bonding environment and conformation of the FMN ring are related to the different biological functions of the two flavoproteins.

Benzoquinones↗

Change in environment of the P1 side chain upon progression from the Michaelis complex to the covalent serpin-proteinase complex.

Serpins inhibit proteinases by forming a kinetically trapped intermediate during a suicide substrate inhibition reaction. To determine whether the kinetic trap involves a repositioning of the P1 side chain of the serpin following formation of the initial Michaelis complex, we used the tryptophan of a P1 M-->W variant of human alpha1-proteinase inhibitor as a fluorescent reporter group of the environment of the P1 side chain. The P1W variant was a valid model serpin and formed SDS-stable complexes with both trypsin and chymotrypsin with a stoichiometry of inhibition close to 1.0. Rates of inhibition of chymotrypsin for wild-type and variant alpha1-proteinase inhibitor differred only approximately 1.8-fold. Rates of inhibition of trypsin were, however, 25-fold lower for the variant than for the wild-type inhibitor. Steady-state fluorescence spectra showed a change in environment for the P1 side chain upon forming both covalent complex with trypsin or chymotrypsin and noncovalent complex with anhydrochymotrypsin. The P1 environments in the chymotrypsin and anhydrochymotrypsin complexes were, however, different. Fluorescence quenching studies confirmed the burial of the P1 side chain upon formation of both the noncovalent and covalent complexes, but were not able to discriminate between the solvent accessibility in these complexes. Stopped-flow fluorescence measurements resolved the covalent intramolecular reaction that led to covalent complex and showed that, during the course of the covalent reaction, the environment of the P1 side chain changed consistent with a repositioning relative to residues of the proteinase active site as part of formation of the trap. This repositioning is likely to be a crucial part of the trapping mechanism.

Binding Sites↗

Road map and principles for built environment sustainability.

The built environment, defined by the facilities and civil infrastructure systems that people use, is the fundamental foundation upon which a society exists, develops, and survives. As the main provider and the life cycle custodian of the built environment, the Architecture, Engineering, and Construction (AEC) industry plays a critical role in determining the quality, integrity, and longevity of this foundation. In the execution of these two roles, provider and custodian, the AEC industry has had a major direct and indirect impact on the natural environment, contributing both directly and indirectly to natural resource depletion and degradation, waste generation and accumulation, and environmental impact and degradation. These impacts are not unique to the AEC industry. Other industries face similar challenges, and for many years, a wide range of constituencies within them have been attempting the implementation of the concept of sustainability within what these industries do, how they do it, and with what as a possible mechanism to slow, reduce, eliminate these impacts, and even restore conditions to a better state. In the pursuit of sustainability, the AEC industry faces challenges posed by the unique attributes and characteristics nature of facilities and civil infrastructure systems, the complexities of the current processes for their delivery and use, and the diverse set of resources required for both their delivery and their use. This paper offers a road map and an initial set of principles to implement built environment sustainability as a starting point for an ongoing, industry-wide dialogue and debate.

Conservation of Natural Resources↗

Dry matter, lipids, and proteins of canola seeds as affected by germination and seedling growth under illuminated and dark environments.

The effect of germination and growth under illuminated and dark environments on canola seed reserves was investigated. Depletion of proteins and lipids in whole seedlings and their top (leaf/cotyledons) and bottom parts (stem/roots/seed coat) was independent of light, whereas the protein solubility increased at a faster rate under an illuminated environment than in the dark. A rapid increase in free fatty acids but a net decrease of dry matter content in seedlings grown in the dark environment was observed. The dry matter content of seedlings grown in the illuminated environment increased due to photosynthetic biomass accumulation.

Brassica napus↗

Proteomic analysis of mice hippocampus in simulated microgravity environment.

Space travel induces many deleterious effects on the flight crew due to the '0' g environment. The brain experiences a tremendous fluid shift, which is responsible for many of the detrimental changes in physical behavior seen in astronauts. It therefore indicates that the brain may undergo major changes in its protein levels in a '0' g environment to counteract the stress. Analysis of these global changes in proteins may explain to better understand the functioning of brain in a '0' g condition. Toward such an effort, we have screened proteins in the hippocampus of mice kept in simulated microgravity environment for 7 days and have observed a few changes in major proteins as compared to control mice. Essentially, the results show a major loss of proteins in the hippocampus of mice subjected to simulated microgravity. These changes occur in structural proteins such as tubulin, coupled with the loss of proteins involved in metabolism. This preliminary investigation leads to an understanding of the alteration of proteins in the hippocampus in response to the microgravity environment.

Animals↗

The relationship of adolescent personality and family environment to psychiatric diagnosis.

This study examines the relationship of adolescent personality and family environment to psychiatric diagnosis in 170 adolescents admitted to a psychiatric inpatient unit. Patients were administered the Child Assessment Schedule (CAS), the family Environment Scale (FES), and the Millon Adolescent Personality Inventory (MAPI). Adolescent personality and/or family environment were related to 1) major depression, conduct disorder, and attention deficit/hyperactivity disorder in both boys and girls, 2) oppositional defiant disorder, post traumatic stress disorder and overanxious disorder in girls, and 3) dysthymic disorder and alcohol use in boys. The study empirically shows the relationship of both personality and family environment in psychiatric diagnoses.

Adolescent↗

Biogeochemistry and microbial ecology of methane oxidation in anoxic environments: a review.

Evidence supporting a key role for anaerobic methane oxidation in the global methane cycle is reviewed. Emphasis is on recent microbiological advances. The driving force for research on this process continues to be the fact that microbial communities intercept and consume methane from anoxic environments, methane that would otherwise enter the atmosphere. Anaerobic methane oxidation is biogeochemically important because methane is a potent greenhouse gas in the atmosphere and is abundant in anoxic environments. Geochemical evidence for this process has been observed in numerous marine sediments along the continental margins, in methane seeps and vents, around methane hydrate deposits, and in anoxic waters. The anaerobic oxidation of methane is performed by at least two phylogenetically distinct groups of archaea, the ANME-1 and ANME-2. These archaea are frequently observed as consortia with sulfate-reducing bacteria, and the metabolism of these consortia presumably involves a syntrophic association based on interspecies electron transfer. The archaeal member of a consortium apparently oxidizes methane and shuttles reduced compounds to the sulfate-reducing bacteria. Despite recent advances in understanding anaerobic methane oxidation, uncertainties still remain regarding the nature and necessity of the syntrophic association, the biochemical pathway of methane oxidation, and the interaction of the process with the local chemical and physical environment. This review will consider the microbial ecology and biogeochemistry of anaerobic methane oxidation with a special emphasis on the interactions between the responsible organisms and their environment.

Anaerobiosis↗

Classification of the environment of protein residues.

We have studied the classification of the environment of residues within protein structures. Eisenberg's original idea created environmental categories to discriminate between similar residues [Bowie et al., Science (1991), 253, 164-170]. These environments grouped residues based upon their buried surface area, polarity of the surrounding environment, and secondary structure element in which the residue is found. However, Eisenberg's original categories led to incomplete discrimination between residues that only partially substitute for each other. We have expanded on Eisenberg's original idea of environmental categories, by both considering additional contacts in the calculation of the solvent-accessible molecular surface area and by subdividing the environmental plot into regions based upon its theoretical features. Our alternative surface area calculations were used in conjunction with the polarity of the environment of the residue to define a new set of environmental categories. These new categories were able to discriminate between residues such as threonine, valine, and aspartic acid while reflecting the propensity of these residues to substitute for each other.

Amino Acids↗

Construct validity of a Physical Work Environment Satisfaction Questionnaire.

Many theories of behavior at work fail to consider the effects of the physical environment on employees' behavior and attitudes. The purpose of this research was to gather evidence of the construct validity of the Physical Work Environment Satisfaction Questionnaire (PWESQ) and of the validity of the physical work environment satisfaction construct. Evidence of the construct validity of the PWESQ was sought through its administration, along with a number of established measures of work attitudes, to 641 employees in 8 organizations. The data provided evidence of the validity of both the physical work environment satisfaction construct and the PWESQ as a valid measure of that construct. Practical and theoretical implications, as well as implications for future research, are discussed.

Adult↗

Multicultural competency in research: examining the relationships among multicultural competencies, research training and self-efficacy, and the multicultural environment.

Research on multicultural competencies has mainly focused on the practice dimension of psychology training and practice. Little theoretical or empirical research has examined multicultural research training and self-efficacy. In this study, 119 psychology graduate students filled out a Web survey focusing on the research training environment, research self-efficacy, multicultural competency, the multicultural environment, and social desirability. Results showed that multicultural competency, research training, and the multicultural environment were related to multicultural research self-efficacy. Hierarchical regressions showed that multicultural competency predicted students' research anxiety; social desirability predicted multicultural research utility, multicultural competency, and the research training environment; and multicultural competency predicted students' confidence in research and perceptions that their graduate training programs were multicultural. Implications are discussed.

Attitude of Health Personnel↗

Probing the phagolysosomal environment of human macrophages with a Ca2+-responsive operon fusion in Yersinia pestis.

Several microorganisms, including Yersinia sp., Salmonella sp., Brucella sp., Mycobacterium sp. and Leishmania sp., have successfully adapted to grow within macrophage phagolysosomes. Infections caused by these intracellular pathogens are among the most difficult to treat. As part of an antimicrobial strategy directed at modifying the phagolysosomal environment to the disadvantage of these important pathogens, we are defining the ambient conditions within the organism-containing phagolysosome. To probe this environment, we have used Yersinia pestis, whose expression of several virulence attributes is highly dependent on the Ca2+ concentration in its growth environment. We first genetically engineered a strain of Y. pestis which responds to a low-calcium environment by transcription of inserted structural genes of the Escherichia coli lac operon. Using this mutant organism as a relevant biological probe, we demonstrate here that the calcium concentration in Y. pestis-containing phagolysosomes is sufficiently low to permit virulence gene expression; this resolves the question of where Y. pestis might express its Ca2+-regulated genes in vivo.

Antigens, Bacterial↗

Compartment modeling of MTBE in the generic environment and estimations of the aquatic MTBE input in Germany using the EQC model.

The use of the gasoline additive methyl tert-butyl ether (MTBE) has caused serious concern about groundwater and surface water contamination. The behavior of MTBE in the two most relevant compartments, surface water and air in a generic environment and in a simulated German environment is investigated using the equilibrium criterion (EQC) model. Due to lack of literature data, the half-life time of MTBE in river water is estimated to about 80-120 d (105 d) at 18 degrees C and roughly 1.5 a (year)(533 d) at 4 degrees C from a batch experiment. The EQC model considers four compartments, air, surface water, soil and sediment in an environment of typically 100,000 km2 with about 10% of the area covered with water. The user can progress through the tiered sequence of Level I to III with increasing complexity which reveals more information about the the fate of the considered chemical. The equilibrium mass distribution of MTBE calculated with the Level I model shows that 87% partitions into air and 13% into surface water at 10 degrees C. The results of the Level II calculations indicate that 50% of MTBE in the air is transported from the system and 38% in the air is degraded at 10 degrees C. The resulting total persistence time of 3 d for MTBE in the generic environment of the Level II model can be compared to the calculated value for chlorobenzene. The MTBE input into water is significantly more sensitive to the 'mode of entry' than input into air. The MTBE concentration in surface water is almost exclusively the result of direct emission into water, whereas the atmosphere can additionally be loaded by volatilization from water. The total aquatic MTBE emission in Germany and the average MTBE concentration in German surface waters were roughly estimated to 20-80 t a(-1) (tons per year)(50 t a(-1)) and 50 ng L(-1), respectively. Surface water concentrations calculated with the underlying assumptions of the model can neither be explained by exposure through waste water and industrial effluents nor with an estimated loss of industrially used MTBE in Germany. For the year-round scenario at 10 degrees C, MTBE concentrations of 19 ng L(-1) (surface water) and 167 ng m(-3) (air) result. However, it remains unclear whether the assumptions of the model, the lack of analyses from industrial effluents or both are responsible for the difference. Additional aquatic emission sources could result from gasoline transport on and storage near rivers. The comparison of winter and summer scenarios shows that in summer, atmospheric (25%) and aqueous (50%) concentrations are lower than in winter due to higher degradation rates.

Air Pollutants↗

Raman spectroscopy of endoliths from Antarctic cold desert environments.

Six endolithic communities from Antarctic cold desert environments have been analysed by Raman spectroscopy. The extreme conditions that the organisms have to withstand in cold environments leads to the adoption of different survival strategies and adaptation of the geological environment. Production of radiation- and desiccation-protective biomolecules is identifiable but the displacement of potentially protective minerals onto the rock surface has also been detected as a protective mechanism against UV-radiation. In this work, Raman spectroscopy is demonstrated as a valuable technique to determine the organic and inorganic compounds used by microorganisms as protective mechanisms against extreme stress conditions. The data from this study will be useful for construction of molecular recognition biomarkers and remote Raman spectral sensing experiments proposed for terrestrial extremophiles in stressed environments.

Antarctic Regions↗

Organophosphorus flame retardants and plasticizers in air from various indoor environments.

Eleven organophosphorus compounds (OPs) that are used as plasticizers and flame retardants were analysed in duplicate samples of indoor air from 17 domestic and occupational environments. Solid-phase extraction (SPE) columns were used as adsorbents and analysis was performed using GC with a nitrogen phosphorus selective detector. The total amounts of OPs in the air samples ranged between 36 and 950 ng m(-3); tris(chloropropyl) phosphate (TCPP) and tris(2-chloroethyl) phosphate (TCEP) being the most abundant (0.4 to 730 ng m(-3)), followed by tributyl phosphate (0.5-120 ng m(-3)). Public buildings tended to have about 3-4 times higher levels of OPs than domestic buildings. The relative amounts of individual OPs varied between the sites and generally reflected the building materials, furniture and consumer products used in the sampled environments. Potential sources of these compounds include, inter alia, acoustic ceilings, upholstered furniture, wall coverings, floor polish and polyvinylchloride floor coverings. A correlation was observed between the TCEP concentrations in the air in the sampled environments and previously reported concentrations in dust, but no such correlation was seen for the heavier and less volatile tris(2-butoxyethyl) phosphate (TBEP). Based on estimated amounts of indoor air inhaled and dust ingested, adults and children in the sampled environments would be exposed to up to 5.8 microg kg(-1) day(-1) and 57 microg kg(-1) day(-1) total OPs, respectively.

Adult↗

Preferred hearing-aid frequency responses in simulated listening environments.

This study was designed to determine if an adaptive strategy could be used to select frequency/gain characteristics that would be considered appropriate across a variety of listening environments. In Experiment I, the test-retest reliability of the paired comparison procedure used in Experiment II was assessed in quiet for nine subjects and in speech noise for six subjects. For both conditions, results revealed mean standard deviations of < 3 dB from 200 through 4000 Hz. In Experiment II, four subjects selected frequency/gain characteristics for five different listening environments (quiet, speech noise, quiet conference room, reverberant lecture hall, and reverberant lecture hall in noise). In general, subjects did not tend to select different frequency/gain characteristics across the five simulated environments used in this study. When differences in frequency responses were observed, they tended to be alterations in overall gain rather than changes in relative frequency response. Findings support additional evaluation in more diverse listening environments, possibly with systems that incorporate nonlinear signal processing.

Acoustic Stimulation↗

Effects of age, education, and living environment on Boston Naming Test performance.

The 60-item Boston Naming Test (BNT; Kaplan, Goodglass, & Weintraub, 1983) was administered to 323 normal elderly subjects between the ages of 65 and 97. The combined effects of age, education, and living environment (institutionalized/independent living) on total test score was determined. These three variables accounted for 32% of the variance in BNT performance. Educational background accounted for the greatest proportion of the variance, followed by age and living environment. There was also a significant interaction between age, education, and living environment. Overall, increased age adversely affected BNT scores. However, institutionalized subjects with a sixth-ninth grade education performed poorly on the BNT regardless of age. In addition, there was little difference in BNT performance according to age or living environment for the well educated. (The only exceptions were the oldest institutionalized subjects, who performed poorly on the BNT regardless of level of education.) The data presented in this study should be helpful for those clinicians who administer the BNT to elderly patients who are institutionalized or who have a limited educational background.

Activities of Daily Living↗