Bacterial signal transduction networks via connectors and development of the inhibitors as alternative antibiotics

Bacterial cells possess a signal transduction system that differs from those described in higher organisms, including human cells. These so-called two-component signal transduction systems (TCSs) consist of a sensor (histidine kinase, HK) and a response regulator, and are involved in cellular functions, such as virulence, drug resistance, biofilm formation, cell wall synthesis, cell division. They are conserved in bacteria across all species. Although TCSs are often studied and characterized individually, they are assumed to interact with each other and form signal transduction networks within the cell. In this review, I focus on the formation of TCS networks via connectors. I also explore the possibility of using TCS inhibitors, especially HK inhibitors, as alternative antimicrobial agents.     

Cessation of annual apical growth and partial death of cambium in stem of Abies sachalinensis under intensive shading

Journal of Plant Research - This study evaluated variation in the height at which absent rings and internodes were detected along stem of Abies sachalinensis trees grown under shade for...     

Laser Impact on Marine Planktonic Diatoms: An Experimental Study Using a Flow Cytometry System

A flow cytometry system was used to evaluate the impact of pulsed laser irradiations from an Nd:YAG laser on two marine coastal water diatoms, Chaetoceros gracilis and Skeletonema costatum. Three flow speeds, i.e. 9, 18 and 27 ml min^{m 1} and three laser fluences, i.e. 0.025, 0.05 and 0.1 J cm^{m 2} pulse^{m 1} were tested during this study. The reduction in cell density and chlorophyll a (chl a) concentrations were monitored by reference to non-irradiated samples as controls. Upon irradiation, the cell density and the chl a concentrations became reduced significantly compared to the control (one way ANOVA p <0.001 for the cell density in both the species and p <0.05 for chl a concentrations in both species). A maximum mortality of 0.77 log₁₀ (about 83%) for C. gracilis and 0.68 log₁₀ (about 78%) for S. costatum was observed at 9 ml min^{m 1} flow speed and 0.1 J cm^{m 2} laser fluence. The maximum reduction observed in the chl a concentration was about 26% (control 0.413 and sample 0.306 mg ml^{m 1}) for C. gracilis and 27% (control 0.222 and sample 0.16 mg ml^{m 1}) for S. costatum, when the flow rate was 9 ml min^{m 1} and the fluence 0.1 J cm^{m 2}. In general, mortality increased with an increase in the laser fluence. The results thus show if the cooling water is laser-irradiated to mitigate biofouling, this could result in significant damage to the planktonic flora of the flowing seawater system, which in turn might reduce algal biofilm formation on industrially important structures. The reduction in the chl a concentration showed that the laser irradiations also could result in a significant reduction in the primary productivity of the cooling water.     

The 1st step initiation essential for allergen‐specific IgE antibody production upon the 2nd step: Induction of non‐specific IgE+ small B cells containing secondly‐sensitized allergen‐specific ones in mice firstly‐sensitized with an allergen

There was a significant amount of non‐specific, but not of allergen (e.g., papain, mite feces and four kinds of pollen)‐specific, IgE antibodies (Abs) in the sera of normal mice. An i.n. injection of each allergen without adjuvant into mice caused an increase in total IgE Ab titers with a similar time course in the serum. However, the stage of initiation of allergy varied from allergen to allergen. Submandibular lymph node cells from normal mice contained papain‐, but not mite feces‐ or pollen‐specific IgE⁺ cells and an i.n. injection of papain induced papain‐specific IgE Abs in the serum. In contrast, one (i.n.) or two (i.n. and s.c) injections of mite feces induced neither mite feces‐specific IgE⁺ cells in the lymph nodes nor mite feces‐specific IgE Abs in the serum. I.n. sensitization with cedar pollen induced cedar pollen‐specific IgE⁺ small B cells in the lymph nodes on Day 10, when non‐specific IgE Ab titers reached a peak in the serum, implying induction of related allergen‐specific IgE⁺ small cells as well. In fact, a second (s.c.) injection of ragweed (or cedar) pollen into mice sensitized i.n. once with cedar (or ragweed) pollen, but not with mite feces, induced a large amount of ragweed (or cedar) pollen‐specific IgE Abs in the serum. These results indicate that when firstly‐sensitized non‐specific IgE⁺ small B cells in mouse lymph nodes include some secondly‐sensitized allergen‐specific ones, mice produce IgE Abs specific for the secondly‐injected allergen.

     

Concentration dependence of nitroxyl spin probes in liposomal solution: electron spin resonance and overhauser-enhanced magnetic resonance studies

In this work, the detailed studies of electron spin resonance (ESR) and overhauser-enhanced magnetic resonance imaging (OMRI) were carried out for permeable nitroxyl spin probe, MC-PROXYL as a function of agent concentration in liposomal solution. In order to compare the impermeable nature of nitroxyl radical, the study was also carried out only at 2?mM concentration of carboxy-PROXYL. The ESR parameters were estimated using L-band and 300?MHz ESR spectrometers. The line width broadening was measured as a function of agent concentration in liposomal solution. The estimated rotational correlation time is proportional to the agent concentration, which indicates that less mobile nature of nitroxyl spin probe in liposomal solution. The partition parameter and permeability values indicate that the diffusion of nitroxyl spin probe distribution into the lipid phase is maximum at 2?mM concentration of MC-PROXYL. The dynamic nuclear polarization (DNP) parameters such as DNP factor, longitudinal relaxivity, saturation parameter, leakage factor and coupling factor were estimated for 2?mM MC-PROXYL in 400?mM liposomal dispersion. The spin lattice relaxation time was shortened in liposomal solution, which leads to the high relaxivity. Reduction in coupling factor is due to less interaction between the electron and nuclear spins, which causes the reduction in enhancement. The leakage factor increases with increasing agent concentration. The increase in DNP enhancement was significant up to 2?mM in liposomal solution. These results paves the way for choosing optimum agent concentration and OMRI scan parameters used in intra and extra membrane water by loading the liposome vesicles with a lipid permeable nitroxyl spin probes in OMRI experiments.     

Insight into the recognition mechanism of DNA cytosine-5 methyltransferases (DNMTs) by incorporation of acyclic 5-fluorocytosine (FC) nucleosides into DNA

DNA cytosine-5 methyltransferase (DNMT) catalyzes methylation at the C5 position of cytosine in the CpG sequence in double stranded DNA to give 5-methylCpG (mCpG) in the epigenetic regulation step in human cells. The entire reaction mechanism of DNMT is divided into six steps, which are scanning, recognition, flipping, loop locking, methylation, and releasing. The methylation and releasing mechanism are well-investigated; however, few reports are known about other reaction steps. To obtain insight into the reaction mechanism, we planned the incorporation of acyclic nucleosides, which make it easy to flip out the target nucleobase, into oligodeoxynucleotides (ODNs) and investigated the interaction between the ODN and DNMT. Here, we describe the design and synthesis of ODNs containing new acyclic 5-fluorocytosine nucleosides and their physiological and biological properties, including their interactions with DNMT. We found that the ODNs containing the acyclic 5-fluorocytosine nucleoside showed higher flexibility than those that contain 5-fluoro-2′-deoxycytidine. The observed flexibility of ODNs is expected to influence the scanning and recognition steps due to the decrease in helicity of the B-form.     

Genetic Engineering of the Processing Site of D1 Precursor Protein of Photosystem II Reaction Center in Chlamydomonas reinhardtii

The D1 protein (D1) of photosystem II (PSII) reaction centeris synthesized as a precursor (pD1) and then processed at itscarboxyl terminus to establish the function of water cleavage.The amino acid sequence of the carboxyl terminal extension excisedby this process is poorly conserved except for a residue afterthe cleavage site at position of 345. We have constructed avector for site-directed mutagenesis of the chloroplast psbAgene encoding D1 of the green alga, Chlamydomonas reinhardtii.The vector enables one to transform the chloroplasts of a psbAdeletion mutant (Fud7) and directly select transformants forresistance to spectinomycin. Using this transforming vector,we have substituted Ser345 to Gly, Cys, Val and Phe in orderto investigate effects of the amino acid side chain at thisposition on the processing rate. All of the resulting transformantsexhibited the PSII activity as wild type and grew normally underphotoautotrophic conditions even under strong light where rapidturnover of Dl protein is expected to occur. Western blottinganalysis demonstrated that mature D1 accumulates in these transformantsat wild type level. Pulse and chase labeling of chloroplast-encodedproteins using [³⁵S]sulfate revealed that the processing ofD1 precursor protein occurs in all four transformants as efficientlyas in wild type, at least under the experimental conditionsexamined. The results suggest that either the amino acid sidechain at position of 345 (+1 position) is not crucial to theenzymatic cleavage of pD1 in vivo or the apparent rate of processingin vivo is not limited by the enzymatic cleavage. (Received September 22, 1995; Accepted December 25, 1995)     

Age-Dependent changes of mineral contents in men and women’s calcanei

To elucidate age-related change of mineral contents in human bones, the mineral content and density of human calcanei were determined by inductively coupled plasma atomic emission spectrometry and dual-energy X-ray absorptiometry. Calcanei were removed from 27 subjects (17 men and 10 women) who died in the age range from 40–98 yr old. Both the inductively coupled plasma emission spectrometry and dual-energy X-ray absorptiometry indicated that there were agedependent decreases of the mineral contents and density in the men’s calcaneus in the age range from 40–98 yr, but not in the women’s calcaneus in the age range from 42–87 yr. It was also found that the calcanean masses of the men and women remained constant within the same age range until 98 yr.     

Cytochemical detection of endogenous peroxidase in the acinar cells of the hamster submandibular gland

The presence of endogenous peroxidase activity in the hamster submandibular gland was investigated cytochemically by light and electron microscopy using diaminobenzidine methods. After fixation of tissue with 2% paraformaldehyde--2.5% glutaraldehyde and incubation in a DAB reaction medium containing 0.01% H₂O₂, the peroxidase reaction product was localized in the nuclear envelope, the cisternae of the endoplasmic reticulum, secretory granules and the Golgi apparatus in both the acinar and granular duct cells of the submandibular gland. This is in contrast to earlier investigators who failed to detect peroxidase activity in acinar cells of the hamster submandibular gland and reported that peroxidase is localized only in the granular duct cells. The discrepancy may be caused by differences in experimental procedures. It is suggested that fixation of tissue with a high concentration of glutaral dehyde and incubation in a DAB reaction medium containing a high concentration of H₂O₂ inhibits the peroxidase activity of acinar cells in the hamster submandibular gland     

Comprehensive analysis of motions in molecular dynamics trajectories of the actin capping protein and its inhibitor complexes

The actin capping protein (CP) binds to actin filaments to block further elongation. The capping activity is inhibited by proteins V‐1 and CARMIL interacting with CP via steric and allosteric mechanisms, respectively. The crystal structures of free CP, CP/V‐1, and CP/CARMIL complexes suggest that the binding of CARMIL alters the flexibility of CP rather than the overall structure of CP, and this is an allosteric inhibition mechanism. Here, we performed molecular dynamics (MD) simulations of CP in the free form, and in complex with CARMIL or V‐1. The resulting trajectories were analyzed exhaustively using Motion Tree, which identifies various rigid‐body motions ranging from small local motions to large domain motions. After enumerating all the motions, CP flexibilities with different ligands were characterized by a list of frequencies for 20 dominant rigid‐body motions, some of which were not identified in previous studies. The comparative analysis highlights the influence of the binding of the CARMIL peptide to CP flexibility. In free CP and the CP/V‐1 complex, domain motions around a large crevice between the N‐stalk and the CP‐S domain occur frequently. The CARMIL peptide binds the crevice and suppresses the motions effectively. In addition, the binding of the CARMIL peptide enhances and alters local motions around the pocket that participates in V‐1 binding. These newly identified motions are likely to suppress the binding of V‐1 to CP. The observed changes in CP motion provide insights that describe the mechanism of allosteric regulation by CARMIL through modulating CP flexibility. Proteins 2016; 84:948–956. © 2016 Wiley Periodicals, Inc.