A model for the 77 K excited state dynamics in Chlamydomonas reinhardtii in state 1 and state 2

The regulatory mechanism of state transitions was studied in Chlamydomonas reinhardtii (C.r.) wild type (WT) as well as mutant strains deficient in the photosystem I (PSI) or the photosystem II (PSII) core. Time-resolved fluorescence measurements were obtained on instantly frozen cells incubated beforehand in the dark in aerobic or anaerobic conditions which leads to state 1 (S1) or state 2 (S2). WT data contains information on the light-harvesting complex (LHC) connected to PSI and PSII. The mutants' data contain information on either LHCII-LHCI-PSI or LHCII-PSII, plus information on LHC antennas devoid of a PS core. In a simultaneous analysis of the data from all strains under S1 or S2 conditions a unified model for the excited state dynamics at 77 K was created. This yielded the completely resolved LHCII-LHCI-PSI and LHCII-PSII dynamics and quantified the state transitions. In WT cells the fraction of light absorbed by LHCII connected to PSII decreases from 45% in S1 to 29% in S2, while it increases from 0% to 16% for LHCII connected to PSI. Thus (16/45 =) 36% of all LHCII is involved in the state transition. In the mutant strains deficient in the PSI core, the red most species peaking at 716 nm disappears completely, indicating that this far red Chl pigment is located in the PSI core. In the mutant strain deficient in the PSII core, red shifted species with maxima at 684 and 686 nm appear in the LHCII antenna. LHCII-684 is quenched and decays with a rate of (310 ps)^? 1.     

Solid state fermentation for production of α-amylase byBacillus megaterium 16M

Summary The ratio of buffer to wheat bran, incubation temperature and initial pH influence -amylase production byBacillus megaterium 16M under solid state fermentation. The enzyme, with pH and temperature optima at 6.0 and 70°C, is formed at a level of 30,000 units/g dry bacterial bran without coproduction of proteases and cellulases.     

Solid state fermentation for cellulases and β-glucosidase production by Aspergillus niger

Production of cellulases and β-glucosidase was studied using locally-isolated Aspergillus niger on various cheap sources of cellulose like bagasse, corn corbs, computer cards and sawdust, by solid state fermentation (SSF) and by liquid state fermentation (LSF). Enzyme activities were increased about 30–80% by SSF in comparison with conventional LSF. Enzyme production was further improved by various pretreatments, making cellulosic material easily accessible. The best results were obtained with 5 M NaOH treatment.     

‘Initial state’ coordinations reproduce the instant flexibility for human walking

An important feature of human locomotor control is the instant adaptability to unpredictable changes of conditions surrounding the locomotion. Humans, for example, can seamlessly adapt their walking gait following a sudden ankle impairment (e.g., as a result of an injury). In this paper, we propose a theoretical study of the mechanisms underlying flexible locomotor control. We hypothesize that flexibility is achieved by modulating the posture at the beginning of the stance phase—the initial state. Using a walking model, we validate our hypothesis through computer simulations     

Solid state fermentation of straw withNeurospora crassa for CMCase and β-glucosidase production

Summary CMCase and -glucosidase were produced by the mutantNeurospora crassa 40b cultivated on untreated wheat straw in a solid state fermentation. Best enzyme activities were observed when the growth medium was composed of wheat straw mixed with certain mineral solutions at a ratio 1:2 (w/v). A partially purified enzyme preparation showed optimum enzyme activities of CMCase and -glucosidase at pH 4.0 and 5.0 and temperature 50 and 60°C respectively. The apparent Km values for the same enzymes were 16.8 g/l and 1.03x10^–4 M respectively. At optimum growth and enzyme assay conditions yields as high as 586.2 U CMCase and 58.4 U -glucosidase per gram of straw were obtained.     

The transition state of coupled folding and binding for a flexible β-finger

Flexible and fully disordered protein regions that fold upon binding mediate numerous protein-protein interactions. However, little is known about their mechanism of interaction. One such coupled folding and binding occurs when a flexible region of neuronal nitric oxide synthase adopts a β-finger structure upon binding to its protein ligand, a PDZ [PSD-95 (postsynaptic density protein-95)/Discs large/ZO-1] domain from PSD-95. We have analyzed this binding reaction by protein engineering combined with kinetic experiments. Mutational destabilization of the β-finger changed mainly the dissociation rate constant of the proteins and, to a lesser extent, the association rate constant. Thus, mutation affected late events in the coupled folding and binding reaction. Our results therefore suggest that the native binding interactions of the β-finger are not present in the rate-limiting transition state for binding but form on the downhill side in a cooperative manner. However, by mutation, we could destabilize the β-finger further and change the rate-limiting step such that an initial conformational change becomes rate limiting. This switch in rate-limiting step shows that multistep binding mechanisms are likely to be found among flexible and intrinsically disordered regions of proteins.     

OECD pressure–state–response indicators for managing biodiversity: a realistic perspective for a French biosphere reserve

Sustainability is said to be the science of integration, be it integration of scale, discipline or of stakeholders’ interests. One way to integrate such diverse elements is to develop sustainable development indicators. Numerous national and international organizations have attempted to develop such indicators, among which interaction indicators are of critical importance because they enable us to link up human activities, ecological dynamics, and social goals. Among the various ways to develop such indicators, the most common ones are the pressure–state–response (PSR) indicators, as well as others coming from this framework. With realistic methodology one shall observe how PSR indicators might appear as an operational tool to face rapid social and ecological changes within a French biosphere reserve in Brittany. Results suggest that such a framework is insufficient to describe, understand and manage social and ecological interactions.

Prepared for change? An assessment of the current state of knowledge to support climate adaptation for Australian fisheries

Fisheries and marine ecosystems are challenged globally by climate change with subsequent biological and socio-ecological implications. Adaptation represents one pathway by which management agencies can seek to ensure sustainability of these resources for societal well-being, particularly when based on strong scientific evidence. Here, we examined the extent of primary scientific literature that is currently available to inform climate adaption initiatives for Australian fisheries. This is achieved via a systematic literature review for 99 harvested Australian marine species, aimed at identifying primary scientific articles that reported new knowledge of climate-driven biological changes and/or socio-ecological implications. We then assessed the quantity of scientific literature against estimated relative climate sensitivity scores for each species (from a previous study), and investigated factors that may influence relative research effort. We found that two-thirds of species had no peer-reviewed climate-related literature available, and that research effort among Australian fisheries species is most closely related to the number of commercial fish stocks per species, and commercial catch weight. We also found that the south-east and western Australian regions had the most climate-related biological information to support climate adaptation in fisheries management. Nonetheless, although accumulating knowledge of the biological and socio-ecological implications of climate change is important, increasing knowledge alone is insufficient to maintain the productivity and profitability of Australian fisheries in light of projected climate impacts. We suggest that the further use of this knowledge to inform decision-making processes is essential to ensure that climate adaptation options are fully explored, to allow sustainable and productive fisheries.

     

Identification of the heterozygous state for the α1-antitrypsin deficiency gene in man

Alpha₁-antitrypsin (₁-at) of individuals homozygous for a gene determining low serum concentrations of this protein can be distinguished electrophoretically from ₁-at of homozygotes for the more common gene. Heterozygotes possess both electrophoretic species, and they may have ₁-at levels intermediate between those of both homozygotes or may be in the range of the homozygotes for the common gene. The frequency of the gene determining a deficiency of ₁-at in a population sample of 100 individuals was 0.075.This work was supported in part by NIH Program Project Grant HE-06285 from the National Heart Institute.     

A Förster-resonance-energy transfer-based method for fluorescence detection of the protein redox state

A method for fluorescence detection of a protein's redox state based on resonance energy transfer from an attached fluorescence label to the prosthetic group of the redox protein is described and tested for proteins containing three types of prosthetic groups: a type-1 copper site (azurin, amicyanin, plastocyanin, and pseudoazurin), a heme group (cytochrome c550), and a flavin mononucleotide (flavodoxin). This method permits one to reliably distinguish between reduced and oxidized proteins and to perform potentiometric titrations at submicromolar concentrations.     

The current state of GMO governance: Are we ready for GM animals?

Given the history of GMO conflict and debate, the GM animal future is dependent on the response of the regulatory landscape and its associated range of interest groups at national, regional and international levels. Focusing on the EU and the USA, this article examines the likely form of that multi-level response, the increased role of cultural values, the contribution of new and existing interest groups and the consequent implications for the commercialization of both green and red GM animal biotechnology.     

Backbone resonance assignments for G protein αi3 subunit in the GTP-bound state

Guanine-nucleotide binding proteins (G proteins) act as molecular switches in signaling pathways, by coupling the activation of G protein-coupled receptors (GPCRs) at the cell surface to intracellular responses. In the resting state, G protein forms a heterotrimer, consisting of GDP-bound form of the G protein α subunit (Gα(GDP)) and G protein βγ subunit (Gβγ). Ligand binding to GPCRs promotes the GDP-GTP exchange on Gα, leading to the dissociation of the GTP-bound form of Gα (Gα(GTP)) and Gβγ. Then, Gα(GTP) and Gβγ bind to their downstream effector enzymes or ion channels and regulate their activities, leading to a variety of cellular responses. Finally, Gα hydrolyzes the bound GTP to GDP and returns to the resting state by re-associating with Gβγ. G proteins are classified with four major families based on the amino acid sequences of Gα: i/o, s, q/11, and 12/13. Each family transduces the signaling from different GPCRs to the specific effectors. Here, we established the backbone resonance assignments of human Gα_i3, a member of the i/o family, with a molecular weight of 41 K in complex with a GTP analogue, GTPγS.     

Backbone resonance assignments for G protein αi3 subunit in the GDP-bound state

Guanine-nucleotide binding proteins (G proteins) serve as molecular switches in signaling pathways, by coupling the activation of G protein-coupled receptors (GPCRs) at the cell surface to intracellular responses. In the resting state, G protein forms a heterotrimer, consisting of the G protein α subunit with GDP (Gα·GDP) and the G protein βγ subunit (Gβγ). Ligand binding to GPCRs promotes the GDP–GTP exchange on Gα, leading to the dissociation of the GTP-bound form of Gα (Gα·GTP) and Gβγ. Then, Gα·GTP and Gβγ bind to their downstream effector enzymes or ion channels and regulate their activities, leading to a variety of cellular responses. Finally, Gα hydrolyzes the bound GTP to GDP and returns to the resting state by re-associating with Gβγ. The G proteins are classified with four major families based on the amino acid sequences of Gα: i/o, s, q/11, and 12/13. Here, we established the backbone resonance assignments of human Gα_i3, a member of the i/o family with a molecular weight of 41 K, in complex with GDP. The chemical shifts were compared with those of Gα_i3 in complex with a GTP-analogue, GTPγS, which we recently reported, indicating that the residues with significant chemical shift differences are mostly consistent with the regions with the structural differences between the GDP- and GTPγS-bound states, as indicated in the crystal structures. The assignments of Gα_i3·GDP would be useful for the analyses of the dynamics of Gα_i3 and its interactions with various target molecules.     

Distributions of activation energy barriers that produce stretched exponential probability distributions for the time spent in each state of the two state reaction A⇌B

Many biochemical reactions consist of the spontaneous fluctuation between two states: A⇌B. For example these two states could be a ligand bound to an enzyme and the ligand and the enzyme separated from each other. A typical case would be the unbinding of CO from myoglobin (Mb), namely, MbCO⇌Mb+CO. Another example is the fluctuation in the ion channel protein in the cell membrane between conformations that are closed to the passage of ions and those that are open to the passage of ions, namely, closed⇌open. Such chemical reactions can be described as two energy levels corresponding to the two states, separated by a distribution of activation energy barriers. Since a kinetic rate can be associated with each energy barrier, this is also equivalent to a distribution of kinetic rate constants. We derive the distribution of the kinetic rates that produces the stretched exponential probability distribution, exp(−at ^b ) where 0<b≤1, which has been observed for such reactions. We also derive the form of the cumulative probability distribution when the pathways connecting the states have minimum or maximum rate constants.     

What is the best reference state for designing statistical atomic potentials in protein structure prediction?

Many statistical potentials were developed in last two decades for protein folding and protein structure recognition. The major difference of these potentials is on the selection of reference states to offset sampling bias. However, since these potentials used different databases and parameter cutoffs, it is difficult to judge what the best reference states are by examining the original programs. In this study, we aim to address this issue and evaluate the reference states by a unified database and programming environment. We constructed distance-specific atomic potentials using six widely-used reference states based on 1022 high-resolution protein structures, which are applied to rank modeling in six sets of structure decoys. The reference state on random-walk chain outperforms others in three decoy sets while those using ideal-gas, quasi-chemical approximation and averaging sample stand out in one set separately. Nevertheless, the performance of the potentials relies on the origin of decoy generations and no reference state can clearly outperform others in all decoy sets. Further analysis reveals that the statistical potentials have a contradiction between the universality and pertinence, and optimal reference states should be extracted based on specific application environments and decoy spaces.     

Potato peel as a solid state substrate for thermostable α-amylase production by thermophilic Bacillus isolates

Summary Potato peel was found to be a superior substrate for solid state fermentation, compared to wheat bran, for the production of α-amylase by two thermophilic isolates of Bacillus licheniformis and Bacillus subtilis. Under optimal conditions, B. licheniformis produced 270 units/ml and 175 units/ml of α-amylase on potato peel and wheat bran, respectively, while the corresponding values for B. subtilis were 600 units/ml and 265 units/ml. The enzyme from B.␣licheniformis was optimally active at 90 °C and pH 9.0, while that from B. subtilis at 60 °C and pH 7.0. The nature of the experimental data permitted excellent polynomial fits, on the basis of which, two master equations, corresponding to the isolated strains, were derived for estimation of enzyme activity for any set of values of temperature, particle size, moisture, and incubation time within the indicated ranges.