Anisotropic intersubunit and inter-ring interactions revealed in the native bullet-shaped chaperonin complex from Thermus thermophilus

Background

The recent morphological studies on chaperonins have revealed that nearly equivalent amount of symmetric GroEL–(GroES)₂ (football-shaped) and asymmetric GroEL–GroES (bullet-shaped) complexes coexist during the chaperonin reaction cycle, which prompted us to reexamine the equatorial split observed for chaperonin from Thermus thermophilus by implementing semi-empirical molecular orbital (MO) calculations, since it is now believed that the symmetric formation is a precursor to the equatorial split.

Methods

Semi-empirical MO calculations were employed to investigate the intersubunit interactions within the bullet-shaped T. thermophilus chaperonin capturing the substrate of folding intermediates. Interaction energies between each cis-GroEL subunit and closely related remaining subunits in cis-GroEL ring, or in trans-GroEL ring across the equatorial plane, and further, interaction energies between each GroES subunit and adjacent subunits in the same GroES ring and in cis-GroEL ring were simulated.

Results

Anisotropic intensities and energy distribution of the subunits were revealed by the calculations, which are consistent with two conformations of the subunits forming cis-GroEL ring as revealed by X-ray crystal structure, and with an anisotropic critical binding site on cis-GroEL ring for chaperonin functioning.

Conclusions

This is the first application of semi-empirical MO calculations to the macromolecular complex of the native bullet-shaped chaperonin (GroEL–GroES–ADP homolog) from T. thermophilus.

General significance

The results also appear to support the occurrence of the equatorial split for T. thermophilus chaperonin observed via electron microscopy, but has not yet been fully observed for Escherichia coli GroEL–GroES system.     

Distribution of antimicrobial‐resistant lactic acid bacteria in natural cheese in Japan

To determine and compare the extent of contamination caused by antimicrobial‐resistant lactic acid bacteria (LAB) in imported and domestic natural cheeses on the Japanese market, LAB were isolated using deMan, Rogosa and Sharpe (MRS) agar and MRS agar supplemented with six antimicrobials. From 38 imported and 24 Japanese cheeses, 409 LAB isolates were obtained and their antimicrobial resistance was tested. The percentage of LAB resistant to dihydrostreptomycin, erythromycin, and/or oxytetracycline isolated from imported cheeses (42.1%) was significantly higher than that of LAB resistant to dihydrostreptomycin or oxytetracycline from cheeses produced in Japan (16.7%; P = 0.04). Antimicrobial resistance genes were detected in Enterococcus faecalis (tetL, tetM, and ermB; tetL and ermB; tetM) E. faecium (tetM), Lactococcus lactis (tetS), Lactobacillus (Lb.), casei/paracasei (tetM or tetW), and Lb. rhamnosus (ermB) isolated from seven imported cheeses. Moreover, these E. faecalis isolates were able to transfer antimicrobial resistance gene(s). Although antimicrobial resistance genes were not detected in any LAB isolates from Japanese cheeses, Lb. casei/paracasei and Lb. coryniformis isolates from a Japanese farm‐made cheese were resistant to oxytetracycline (minimal inhibitory concentration [MIC], 32 µg/mL). Leuconostoc isolates from three Japanese farm‐made cheeses were also resistant to dihydrostreptomycin (MIC, 32 to > 512 µg/mL). In conclusion, the present study demonstrated contamination with antimicrobial‐resistant LAB in imported and Japanese farm‐made cheeses on the Japanese market, but not in Japanese commercial cheeses.     

Molecular Dynamics Calculations of Wild Type vs. Mutant Protein C: Relationship Between Binding Affinity to Endothelial Cell Protein C Receptor and Hereditary Disease

Abstract

Molecular dynamics simulations of the protein C γ-carboxyglutamic acid (Gla) domain and endothelial cell protein C receptor (EPCR) complex were performed to determine the effect of a hereditary disease, which results in a mutation (Gla 25 → Lys) in the protein C Gla domain. Our results suggest that the Gla 25 → Lys mutation causes a significant reduction in the binding force between protein C Gla domain and EPCR due to destabilization of the helix structure of EPCR and displacement of a Ca²⁺ ion.     

Root orientation can affect detection accuracy of ground-penetrating radar

Aim

Ground-penetrating radar (GPR) has been applied to detect coarse tree roots. The horizontal angle of a root crossing a scanning line is a factor that affects both root detection and waveform parameter values. The purpose of this study was to quantitatively evaluate the influence of root orientation (x, degree) on two major waveform parameters, amplitude area (A, dB × ns) and time interval between zero crossings (T, ns).

Methods

We scanned four diameter classes of dowels in a sandy bed as simulated roots using a 900 MHz antenna from multiple angles to clarify the relationships between the parameters and x.

Results

Angle x strongly affected reflection images and A values. The variation in A(x) fitted a sinusoidal waveform, whereas T was independent of x. The value of A scanning at 90° was estimated by A values of arbitrary x in two orthogonal transects. The sum of T in all reflected waveforms showed a significant linear correlation with dowel diameter.

Conclusions

We clarified that root orientation dramatically affected root detection and A values. The sum of T of all reflected waveforms was a suitable parameter for estimating root diameter. Applying grid transects can overcome the effects of root orientation.     

Chicken- and duck-associated Bacteroides–Prevotella genetic markers for detecting fecal contamination in environmental water

Bacteroides–Prevotella group is one of the most promising targets for detecting fecal contamination in water environments, principally due to its host-specific distributions and high concentrations in feces of warm-blooded animals. We developed real-time PCR assays for quantifying chicken/duck-, chicken-, and duck-associated Bacteroides–Prevotella 16S rRNA genetic markers (Chicken/Duck-Bac, Chicken-Bac, and Duck-Bac). A reference collection of DNA extracts from 143 individual fecal samples and wastewater treatment plant influent was tested by the newly established markers. The quantification limits of Chicken/Duck-Bac, Chicken-Bac, and Duck-Bac markers in environmental water were 54, 57, and 12 copies/reaction, respectively. It was possible to detect possible fecal contaminations from wild ducks in environmental water with the constructed genetic marker assays, even though the density of total coliforms in the identical water samples was below the detection limit. Chicken/Duck-Bac marker was amplified from feces of wild duck and chicken with the positive ratio of 96 and 61 %, respectively, and no cross-reaction was observed for the other animal feces. Chicken-Bac marker was detected from 70 % of chicken feces, while detected from 39 % of cow feces, 8.3 % of pig feces, and 12 % of swan feces. Duck-Bac marker was detected from 85 % of wild duck feces and cross-reacted with 31 % of cow feces. These levels of detection specificity are common in avian-associated genetic markers previously proposed, which implies that there is a practical limitation in the independent application of avian-associated Bacteroides–Prevotella 16S rRNA genetic markers and a combination with other fecal contamination markers is preferable for detecting fecal contamination in water environments.     

Adipose‐derived mesenchymal stem cells and regenerative medicine

Adipose tissue‐derived mesenchymal stem cells (ADSCs) are multipotent and can differentiate into various cell types, including osteocytes, adipocytes, neural cells, vascular endothelial cells, cardiomyocytes, pancreatic β‐cells, and hepatocytes. Compared with the extraction of other stem cells such as bone marrow‐derived mesenchymal stem cells (BMSCs), that of ADSCs requires minimally invasive techniques. In the field of regenerative medicine, the use of autologous cells is preferable to embryonic stem cells or induced pluripotent stem cells. Therefore, ADSCs are a useful resource for drug screening and regenerative medicine. Here we present the methods and mechanisms underlying the induction of multilineage cells from ADSCs.     

Connexin-43 hemichannels contribute to the propagation of μ-calpain-mediated neuronal death in a cortical ablation injury model

We investigated the role of the astrocytic and neuronal hemichannels (HCs) in the spread of cortical neuronal death in a rat cortical injury model. Over time (by 6 h), propidium iodide (PI)-positive cells with labeling either with anti-neuron specific enolase or anti-parvalbumin (indicating GABAnergic interneurons) antibody spread in the deep cortical layers adjacent to the injury and co-localized with activated μ-calpain. Connexin (Cx)-43, glial fibrillary acidic protein (GFAP), activated μ-calpain and α-fodrin breakdown product (FBP) increased post-injury, peaking at 1 h, in the injury and adjacent areas. GFAP-Cx43-positive reactivated astrocytes exhibited similar distribution to the dead neurons. Cx43 and Cx36 primarily comprise HCs in the astrocyte and neuron, respectively. Ethidium bromide (EtBr) uptake was enhanced post-injury, and confirmed in the Cx43- and Cx36-positive cells. A Cx43-HC inhibitor Gap26 prevented the opening of the Cx43-HC and Cx36-HC, μ-calpain activation, α-fodrin proteolysis and death in the deep cortical neurons. Collectively, opening of the astrocytic Cx43-HC and neuronal Cx36-HC would induce the regional spread of cortical neuronal death through μ-calpain activation in the rat brain injury model.     

Community-dependent foraging habits of flower visitors: cascading indirect interactions among five bumble bee species

Despite the ubiquity and the importance of interspecific interactions among flower visitors, few studies have examined their effects on the realized feeding niches of visitor species in a community context. To evaluate the community-wide effects of interactions among flower visitors, I have examined changes in the flower utilization patterns of each visitor species at several sites where the component of the visitor’s community differed. Specifically, I compared the flower preferences and foraging habits (legitimate foraging vs. primary nectar robbing vs. secondary nectar robbing) of five bumble bee species in flower patches consisting of Trifolium pratense L. (red clover) and T. repens L. (white clover) on Hokkaido Island, Japan. I also examined the nectar production and standing crops of each flower species to evaluate the exploitation competition based on nectar. The bumble bee species exhibited different flower utilization patterns among sites. At sites where the long-tongued Bombus diversus tersatus was common and the exotic short-tongued B. terrestris was rare, B. diversus tersatus visited red clover (long-tubed flowers) exclusively, whereas medium-tongued B. pseudobaicalensis and short-tongued B. hypocrita sapporoensis and B. hypnorum koropokkrus preferentially visited white clover (short-tubed flowers). Conversely, at sites where the long-tongued bee was rare, four other species frequently visited red clover in different modes: B. pseudobaicalensis visited legitimately, B. hypocrita sapporoensis and B. terrestris visited as primary nectar robbers, and B. hypnorum koropokkrus visited as a secondary nectar robber. The presence or absence of resource exploitation by the long-tongued species and the interaction between primary and secondary nectar robbers via robbing holes was the major ecological sources of these differences. Diverse effects of interactions among flower visitors played important roles in shaping pattern of plant and flower visitor interactions.     

The Preparation and Geometrical Isomerism of Substituted α-Methylthio-Cinnamic Acids

α-Methylthio-cinnamic acid and its substituted analogues (III) were synthesized from their respective β-aryl-α-thiopyruvic acids (II). In connection with the study on the tautomeric ene-thiol structure of β-aryl-α-thiopyruvic acids (II), 4-arylidenerl,3-oxathiolan-5-one (IV) were prepared from compounds II.