Protein Brownian Rotation at the Glass Transition Temperature of a Freeze-Concentrated Buffer Probed by Superparamagnetic Nanoparticles

For applications from food science to the freeze-thawing of proteins it is important to understand the often complex freezing behavior of solutions of biomolecules. Here we use a magnetic method to monitor the Brownian rotation of a quasi-spherical cage-shaped protein, apoferritin, approaching the glass transition T_g in a freeze-concentrated buffer (Tris-HCl). The protein incorporates a synthetic magnetic nanoparticle (Co-doped Fe₃O₄ (magnetite)). We use the magnetic signal from the nanoparticles to monitor the protein orientation. As T decreases toward T_g of the buffer solution the protein’s rotational relaxation time increases exponentially, taking values in the range from a few seconds up to thousands of seconds, i.e., orders of magnitude greater than usually accessed, e.g., by NMR. The longest relaxation times measured correspond to estimated viscosities >2 MPa s. As well as being a means to study low-temperature, high-viscosity environments, our method provides evidence that, for the cooling protocol used, the following applies: 1), the concentration of the freeze-concentrated buffer at T_g is independent of its initial concentration; 2), little protein adsorption takes place at the interface between ice and buffer; and 3), the protein is free to rotate even at temperatures as low as 207 K.     

Protein Brownian Rotation at the Glass Transition Temperature of a Freeze-Concentrated Buffer Probed by Superparamagnetic Nanoparticles

For applications from food science to the freeze-thawing of proteins it is important to understand the often complex freezing behavior of solutions of biomolecules. Here we use a magnetic method to monitor the Brownian rotation of a quasi-spherical cage-shaped protein, apoferritin, approaching the glass transition T_g in a freeze-concentrated buffer (Tris-HCl). The protein incorporates a synthetic magnetic nanoparticle (Co-doped Fe₃O₄ (magnetite)). We use the magnetic signal from the nanoparticles to monitor the protein orientation. As T decreases toward T_g of the buffer solution the protein’s rotational relaxation time increases exponentially, taking values in the range from a few seconds up to thousands of seconds, i.e., orders of magnitude greater than usually accessed, e.g., by NMR. The longest relaxation times measured correspond to estimated viscosities >2 MPa s. As well as being a means to study low-temperature, high-viscosity environments, our method provides evidence that, for the cooling protocol used, the following applies: 1), the concentration of the freeze-concentrated buffer at T_g is independent of its initial concentration; 2), little protein adsorption takes place at the interface between ice and buffer; and 3), the protein is free to rotate even at temperatures as low as 207 K.     

Influence of Gold Nanoparticles on the Tolerance of Wheat to Low Temperature

Doklady Biochemistry and Biophysics - It was shown for the first time that the treatment of winter wheat (Triticum aestivum L.) seeds with gold nanoparticles (average diameter 15.3 nm; solution...     

High-Oleate Oilseeds Fail to Develop at Low Temperature

The fad2 mutants of Arabidopsis thaliana are deficient in activity of the endoplasmic reticulum oleate desaturase that is the main enzyme responsible for polyunsaturated lipid synthesis in developing seeds of oil crops. A comparison of wild-type and fad2 seeds developing on heterozygous (FAD2/-) plants was used as a model for genetically engineered high-oleate oilseeds of species such as soybean and canola. When fad2 seeds developed at normal temperatures (22[deg]C), they showed high viability compared to wild-type seeds. When a portion of seed development took place at 6[deg]C, germination of the wild-type siblings remained high but germination of fad2 segregants declined considerably. This was true even when exposure to low temperature was limited to the final stages of seed filling and maturation. Compared to wild-type seeds, fully viable fad2 seeds produced at 22[deg]C had reduced lipid contents and were slower to germinate at 10 and 6[deg]C. Taken together, these results indicate that for some oilseed species at least, molecular genetic manipulation of oleate levels in the oil may result in plant lines with unacceptable performance in the field.     

Evaluation of Disulfide Bond Position to Enhance the Thermal Stability of a Highly Stable Single Domain Antibody

Single domain antibodies are the small recombinant variable domains derived from camelid heavy-chain-only antibodies. They are renowned for their stability, in large part due to their ability to refold following thermal or chemical denaturation. In addition to refolding after heat denaturation, A3, a high affinity anti-Staphylococcal Enterotoxin B single domain antibody, possesses a melting temperature of ∼84°C, among the highest reported for a single domain antibody. In this work we utilized the recently described crystal structure of A3 to select locations for the insertion of a second disulfide bond and evaluated the impact that the addition of this second bond had on the melting temperature. Four double-disulfide versions of A3 were constructed and each was found to improve the melting temperature relative to the native structure without reducing affinity. Placement of the disulfide bond at a previously published position between framework regions 2 and 3 yielded the largest improvement (>6°C), suggesting this location is optimal, and seemingly provides a universal route to raise the melting temperature of single domain antibodies. This study further demonstrates that even single domain antibodies with extremely high melting points can be further stabilized by addition of disulfide bonds.     

The Evolution of Insect-Fungus Associations: From Contact to Stable Symbiosis

Insect-fungus interactions range from agonistic to mutualistic,and include several spectacular examples of complex symbioses.A potential benefit of mycophagy (the ingestion of fungal tissue)is the augmentation of digestive capacity by the ingestion offungal enzymes that remain active in the gut following ingestion.Cellulose digestion is mediated by ingested fungal enzymes inthe wood-boring larvae of cerambycid beetles and siricid woodwasps,in detritus-feeding stonefly nymphs, and in the workers of fungus-growingtermites. In this paper I discuss a plausible scenario for theevolution of stable symbiotic insect-fungus associations, inwhich the augmentation of digestive capacity through the ingestionof fungal enzymes is an important factor leading to the establishmentof interdependence between the interacting partners in a mutualism.Ingested fungal enzymes play a different role in the mutualisticassociation of the attine ants and their symbiotic fungi. Analyses of the associations of the siricid woodwasps, fungus-growingtermites, and fungus-growing ants with their symbiotic fungipermit the testing of Law's (1985) predictions concerning theconsequences of evolution in a mutualistic environment. As predicted,the rate of speciation has been slower in the protected partnerthan in the host partner, selection has favored asexual reproductionin the protected partner, and, at least in the attine ant-fungussymbiosis, the protected partner exhibits a low degree of specificitytoward different host species. Insect-fungus interactions provide rich material for the studyof both mechanistic and theoretical aspects of mutualism.     

Gentle Lysis of Staphylococcus aureus at Low Temperature

A low-temperature lysis procedure for Staphylococcus aureus is described. It is simple and requires no special equipment.     

Identification of Listeria monocytogenes Genes Expressed in Response to Growth at Low Temperature

Listeria monocytogenes is a food-borne bacterial pathogen that is able to grow at refrigeration temperatures. To investigate microbial gene expression associated with cold acclimation, we used a differential cDNA cloning procedure known as selective capture of transcribed sequences (SCOTS) to identify bacterial RNAs that were expressed at elevated levels in bacteria grown at 10°C compared to those grown at 37°C. A total of 24 different cDNA clones corresponding to open reading frames in the L. monocytogenes strain EGD-e genome were obtained by SCOTS. These included cDNAs for L. monocytogenes genes involved in previously described cold-adaptive responses (flaA and flp), regulatory adaptive responses (rpoN, lhkA, yycJ, bglG, adaB, and psr), general microbial stress responses (groEL, clpP, clpB, flp, and trxB), amino acid metabolism (hisJ, trpG, cysS, and aroA), cell surface alterations (fbp, psr, and flaA), and degradative metabolism (eutB, celD, and mleA). Four additional cDNAs were obtained corresponding to genes potentially unique to L. monocytogenes and showing no significant similarity to any other previously described genes. Northern blot analyses confirmed increased steady-state levels of RNA for all members of a subset of genes examined during growth at a low temperature. These results indicated that L. monocytogenes acclimation to growth at 10°C likely involves amino acid starvation, oxidative stress, aberrant protein synthesis, cell surface remodeling, alterations in degradative metabolism, and induction of global regulatory responses.     

Sclerotial Formation of Polyporus umbellatus by Low Temperature Treatment under Artificial Conditions

Background

Polyporus umbellatus sclerotia have been used as a diuretic agent in China for over two thousand years. A shortage of the natural P. umbellatus has prompted researchers to induce sclerotial formation in the laboratory.

Methodology/Principal Finding

P. umbellatus cultivation in a sawdust-based substrate was investigated to evaluate the effect of low temperature conditions on sclerotial formation. A phenol-sulfuric acid method was employed to determine the polysaccharide content of wild P. umbellatus sclerotia and mycelia and sclerotia grown in low-temperature treatments. In addition, reactive oxygen species (ROS) content, expressed as the fluorescence intensity of mycelia during sclerotial differentiation was determined. Analysis of ROS generation and sclerotial formation in mycelia after treatment with the antioxidants such as diphenyleneiodonium chloride (DPI), apocynin (Apo), or vitamin C were studied. Furthermore, macroscopic and microscopic characteristics of sclerotial differentiation were observed. Sclerotia were not induced by continuous cultivation at 25°C. The polysaccharide content of the artificial sclerotia is 78% of that of wild sclerotia. In the low-temperature treatment group, the fluorescent intensity of ROS was higher than that of the room temperature (25°C) group which did not induce sclerotial formation all through the cultivation. The antioxidants DPI and Apo reduced ROS levels and did not induce sclerotial formation. Although the concentration-dependent effects of vitamin C (5–15 mg mL⁻¹) also reduced ROS generation and inhibited sclerotial formation, using a low concentration of vitamin C (1 mg mL⁻¹) successfully induced sclerotial differentiation and increased ROS production.

Conclusions/Significance

Exposure to low temperatures induced P. umbellatus sclerotial morphogenesis during cultivation. Low temperature treatment enhanced ROS in mycelia, which may be important in triggering sclerotial differentiation in P. umbellatus. Moreover, the application of antioxidants impaired ROS generation and inhibited sclerotial formation. Our findings may help to provide new insights into the biological mechanisms underlying sclerotial morphogenesis in P. umbellatus.     

From DARPins to LoopDARPins: Novel LoopDARPin Design Allows the Selection of Low Picomolar Binders in a Single Round of Ribosome Display

Antibodies are the most versatile binding proteins in nature with six loops creating a flexible continuous interaction surface. However, in some molecular formats, antibodies are aggregation prone. Designed ankyrin repeat proteins (DARPins) were successfully created as alternative design solutions. Nevertheless, their concave shape, rigidity and incompletely randomized binding surface may limit the epitopes that can be targeted by this extremely stable scaffold. Combining conformational diversity and a continuous convex paratope found in many antibodies with the beneficial biophysical properties of DARPins, we created LoopDARPins, a next generation of DARPins with extended epitope binding properties. We employed X-ray structure determination of a LoopDARPin for design validation. Biophysical characterizations show that the introduction of an elongated loop through consensus design does not decrease the stability of the scaffold, consistent with molecular dynamics simulations. Ribosome-display selections against extracellular signal-regulated kinase 2 (ERK2) and four members of the BCL-2 family (BCL-2, BCL-XL, BCL-W and MCL-1) of anti-apoptotic regulators yielded LoopDARPins with affinities in the mid-picomolar to low nanomolar range against all targets. The BCL-2 family binders block the interaction with their natural interaction partner and will be valuable reagents to test the apoptotic response in functional assays. With the LoopDARPin scaffold, binders for BCL-2 with an affinity of 30 pM were isolated with only a single round of ribosome display, an enrichment that has not been described for any scaffold. Identical stringent one-round selections with conventional DARPins without loop yielded no binders. The LoopDARPin scaffold may become a highly valuable tool for biotechnological high-throughput applications.     

Selective Formation of Photosystem 1 under Illumination at Low Intensity

Analyses of chlorophylls a and b and P700 in the wheat leaves grown for 8 days under illumination with white light at different intensities suggested selective formation of photosystem 1 of the photosynthesis at low light intensities. This was confirmed for the two types of chloroplasts isolated from leaves grown at light intensities of 1.1 and 240 μ W/cm², respectively, by measuring their pigment compositions, activities of photosystems 1 and 2, and absorption and fluorescence spectra. The chloroplasts developed at the low intensity showed properties only of photosystem 1 while those developed at the high intensity showed properties of both photosystems 1 and 2. Only photosystem 1 particles were obtained by fractionation of low intensity chloroplasts by treatment with digitonin followed by centrifugation, while high intensity chloroplasts could be fractionated into photosystem-1 and photosystem-2 particles. When the leaves grown at low light intensity were illuminated with strong light, photosystem 2 was developed. The fluorescence emission spectrum of low intensity chloroplasts at 77°K showed two peaks at 685 and 734 nm, and the spectrum of high intensity chloroplasts showed three peaks at 685, 697 and 740 nm.     

Hepatic Gene Expression Changes in Rats Internally Exposed to Radioactive 56MnO2 Particles at Low Doses

We have studied the biological effects of the internal exposure to radioactive manganese-56 dioxide (⁵⁶MnO₂), the major radioisotope dust found in soil after atomic bomb explosions. Our previous study of blood chemistry indicated a possible adverse effect of ⁵⁶MnO₂ on the liver. In the present study, we further examined the effects on the liver by determining changes in hepatic gene expressions. Male Wistar rats were exposed to ⁵⁶MnO₂ particles (three groups with the whole-body doses of 41, 90, and 100 mGy), stable MnO₂ particles, or external ⁶⁰Co γ-rays (2 Gy), and were examined together with the non-treated control group on postexposure day 3 and day 61. No histopathological changes were observed in the liver. The mRNA expression of a p53-related gene, the cyclin-dependent kinase inhibitor 1A, increased in ⁵⁶MnO₂ as well as in γ-ray irradiated groups on postexposure day 3 and day 61. The expression of a stress-responsive gene, nuclear factor κB, was also increased by ⁵⁶MnO₂ and γ-rays on postexposure day 3. However, the expression of cytokine genes (interleukin-6 or chemokine ligand 2) or fibrosis-related TGF-β/Smad genes (Tgfb1, Smad3, or Smad4) was not altered by the exposure. Our data demonstrated that the internal exposure to ⁵⁶MnO₂ particles at less than 0.1 Gy significantly affected the short-term gene expressions in the liver in a similar manner with 2 Gy of external γ-irradiation. These changes may be adaptive responses because no changes occurred in cytokine or TGF-β/Smad gene expressions.     

Opinion Formation by Social Influence: From Experiments to Modeling

Predicting different forms of collective behavior in human populations, as the outcome of individual attitudes and their mutual influence, is a question of major interest in social sciences. In particular, processes of opinion formation have been theoretically modeled on the basis of a formal similarity with the dynamics of certain physical systems, giving rise to an extensive collection of mathematical models amenable to numerical simulation or even to exact solution. Empirical ground for these models is however largely missing, which confine them to the level of mere metaphors of the real phenomena they aim at explaining. In this paper we present results of an experiment which quantifies the change in the opinions given by a subject on a set of specific matters under the influence of others. The setup is a variant of a recently proposed experiment, where the subject’s confidence on his or her opinion was evaluated as well. In our realization, which records the quantitative answers of 85 subjects to 20 questions before and after an influence event, the focus is put on characterizing the change in answers and confidence induced by such influence. Similarities and differences with the previous version of the experiment are highlighted. We find that confidence changes are to a large extent independent of any other recorded quantity, while opinion changes are strongly modulated by the original confidence. On the other hand, opinion changes are not influenced by the initial difference with the reference opinion. The typical time scales on which opinion varies are moreover substantially longer than those of confidence change. Experimental results are then used to estimate parameters for a dynamical agent-based model of opinion formation in a large population. In the context of the model, we study the convergence to full consensus and the effect of opinion leaders on the collective distribution of opinions.     

The Stress of Protein Misfolding: From Single Cells to Multicellular Organisms

Organisms survive changes in the environment by altering their rates of metabolism, growth, and reproduction. At the same time, the system must ensure the stability and functionality of its macromolecules. Fluctuations in the environment are sensed by highly conserved stress responses and homeostatic mechanisms, and of these, the heat shock response (HSR) represents an essential response to acute and chronic proteotoxic damage. However, unlike the strategies employed to maintain the integrity of the genome, protection of the proteome must be tailored to accommodate the normal flux of nonnative proteins and the differences in protein composition between cells, and among individuals. Moreover, adult cells are likely to have significant differences in the rates of synthesis and clearance that are influenced by intrinsic errors in protein expression, genetic polymorphisms, and fluctuations in physiological and environmental conditions. Here, we will address how protein homeostasis (proteostasis) is achieved at the level of the cell and organism, and how the threshold of the stress response is set to detect and combat protein misfolding. For metazoans, the requirement for coordinated function and growth imposes additional constraints on the detection, signaling, and response to misfolding, and requires that the HSR is integrated into various aspects of organismal physiology, such as lifespan. This is achieved by hierarchical regulation of heat shock factor 1 (HSF1) by the metabolic state of the cell and centralized neuronal control that could allow optimal resource allocation between cells and tissues. We will examine how protein folding quality control mechanisms in individual cells may be integrated into a multicellular level of control, and further, even custom-designed to support individual variability and impose additional constraints on evolutionary adaptation.     

Bacterial Adaptation to Low Temperature: Implications for Cold-Inducible Genes

Escherichia coli and later found to be a cold-shock response common to many bacterial species. CspA of 7.4 kD, a major cold-shock protein in E. coli, has been shown to share structural similarity with a class of eukaryotic Y box proteins which have RNA-binding domains. Transient synthesis of CspA upon cold shock is mediated by increased stabilization of the mRNA at low temperatures. The proposed role of some cold-shock proteins including CspA in the bacterial adaptation to low temperatures is to function as a RNA chaperone in the regulation of translation. Some enzymes of psychrotrophic or psychrophilic bacteria exhibit unique features of a cold-adapted enzyme, high catalytic activity at a low temperature and rapid inactivation at a moderate temperature. A monomeric isocitrate dehydrogenase isozyme (IDH-II) of a psychrophilic bacterium, Vibrio sp. strain ABE-1, is a typical cold-adapted enzyme. In addition, this enzyme is induced at low temperatures. Low temperature-dependent expression of icdll encoding IDH-II is controlled by two different cis-elements located at the untranslated upstream region of the gene, one is a silencer and the other is essential for the low temperature response. The physiological role of IDH-II is evaluated by transforming E. coli with icdll. The growth rate of the E. coli transformants at low temperatures is dependent on the level of expressed IDH-II activity. Received 11 January 1999/ Accepted in revised form 6 April 1999     

东乡野生稻苗期响应低温胁迫的转录组分析

为了解东乡野生稻（Oryza rufipogon）对低温胁迫的响应机制,对苗期的RNA-seq转录表达谱进行了研究。结果表明,与对照相比,共检测到10 200个差异表达基因（DEGs）,其中5 201个上调表达,4 999个下调表达,其中有426个DEGs位于已报道的水稻耐冷QTL区间,且37个为耐冷调控相关的家族基因。GO功能分类和KEGG代谢路径分析表明,核酸结合转录因子活性、氨基酸生物合成以及光合作用代谢等均参与响应低温胁迫过程。实时荧光定量分析表明,ABA响应蛋白基因、MYB转录因子和40S核糖体蛋白SA基因等12个可能与低温胁迫响应相关的DEGs表达模式与RNA-seq的一致。可见,植物激素传导途径和转录因子相关调控基因在东乡野生稻苗期响应低温胁迫过程中起重要作用。     

低能离子注入对大豆种子吸胀冷害的影响

本文分别从浸种液中无机离子的浓度、可溶性糖的浓度以及溶液的pH值,研究了低能离子注入对大豆种子吸胀冷害的影响。结果发现一定剂量的氮离子注入大豆种子后,其无机离子、可溶性糖、酸性物质的泄漏量均有低于对照组的趋势,而且其长势好于对照组,说明离子注入能在一定程度上减轻大豆遭受的吸胀冷害。