Complementary hydrophobic interaction of the redox enzyme maturation protein NarJ with the signal peptide of the respiratory nitrate reductase NarG.

In bacteria, NarJ plays an essential role as a redox enzyme maturation protein in the assembly of the nitrate reductase NarGHI by interacting with the N-terminal signal peptide of NarG to facilitate cofactor incorporation into NarG. The purpose of our research was to elucidate the exact mechanism of NarG signal peptide recognition by NarJ. We determined the structures of NarJ alone and in complex with the signal peptide of NarG via X-ray crystallography and verified the NarJ-NarG interaction through mutational, binding, and molecular dynamics simulation studies. NarJ adopts a curved α-helix bundle structure with a U-shaped hydrophobic groove on its concave side. This groove accommodates the signal peptide of NarG via a dual binding mode in which the left and right parts of the NarJ groove each interact with two consecutive hydrophobic residues from the N- and C-terminal regions of the NarG signal peptide, respectively, through shape and chemical complementarity. This binding is accompanied by unwinding of the helical structure of the NarG signal peptide and by stabilization of the NarG-binding loop of NarJ. We conclude that NarJ recognizes the NarG signal peptide through a complementary hydrophobic interaction mechanism that mediates a structural rearrangement.

Structural and Biochemical Analysis of the Recombination Mediator Protein RecR from Campylobacter jejuni.

The recombination mediator complex RecFOR, consisting of the RecF, RecO, and RecR proteins, is needed to initiate homologous recombination in bacteria by positioning the recombinase protein RecA on damaged DNA. Bacteria from the phylum Campylobacterota, such as the pathogen Campylobacter jejuni, lack the recF gene and trigger homologous recombination using only RecR and RecO. To elucidate the functional properties of C. jejuni RecR (cjRecR) in recombination initiation that differ from or are similar to those in RecF-expressing bacteria, we determined the crystal structure of cjRecR and performed structure-based binding analyses. cjRecR forms a rectangular ring-like tetrameric structure and coordinates a zinc ion using four cysteine residues, as observed for RecR proteins from RecF-expressing bacteria. However, the loop of RecR that has been shown to recognize RecO and RecF in RecF-expressing bacteria is substantially shorter in cjRecR as a canonical feature of Campylobacterota RecR proteins, indicating that cjRecR lost a part of the loop in evolution due to the lack of RecF and has a low RecO-binding affinity. Furthermore, cjRecR features a larger positive patch and exhibits substantially higher ssDNA-binding affinity than RecR from RecF-expressing bacteria. Our study provides a framework for a deeper understanding of the RecOR-mediated recombination pathway.

Hexameric structure of the flagellar master regulator FlhDC from Cupriavidus necator and its interaction with flagellar promoter DNA.

Bacterial flagella are assembled with ∼30 different proteins in a defined order via diverse regulatory systems. In gram-negative bacteria from the Gammaproteobacteria and Betaproteobacteria classes, the transcription of flagellar genes is strictly controlled by the master regulator FlhDC. In Gammaproteobacteria species, the FlhDC complex has been shown to activate flagellar expression by directly interacting with the promoter region in flagellar genes. To obtain the DNA-binding mechanism of FlhDC and determine the conserved and distinct structural features of Betaproteobacteria and Gammaproteobacteria FlhDCs that are necessary for their functions, we determined the crystal structure of Betaproteobacteria Cupriavidus necator FlhDC (cnFlhDC) and biochemically analyzed its DNA-binding capacity. cnFlhDC specifically recognized the promoter DNA of the class II flagellar genes flgB and flhB. cnFlhDC adopts a ring-like heterohexameric structure (cnFlhD4C2) and harbors two Zn-Cys clusters, as observed for Gammaproteobacteria Escherichia coli FlhDC (ecFlhDC). The cnFlhDC structure exhibits positively charged surfaces across two FlhDC subunits as a putative DNA-binding site. Noticeably, the positive patch of cnFlhDC is continuous, in contrast to the separated patches of ecFlhDC. Moreover, the ternary intersection of cnFlhD4C2 behind the Zn-Cys cluster forms a unique protruding neutral structure, which is replaced with a charged cavity in the ecFlhDC structure.

Structural basis of flagellar motility regulation by the MogR repressor and the GmaR antirepressor in Listeria monocytogenes.

The pathogenic Listeria monocytogenes bacterium produces the flagellum as a locomotive organelle at or below 30°C outside the host, but it halts flagellar expression at 37°C inside the human host to evade the flagellum-induced immune response. Listeria monocytogenes GmaR is a thermosensor protein that coordinates flagellar expression by binding the master transcriptional repressor of flagellar genes (MogR) in a temperature-responsive manner. To understand the regulatory mechanism whereby GmaR exerts the antirepression activity on flagellar expression, we performed structural and mutational analyses of the GmaR-MogR system. At or below 30°C, GmaR exists as a functional monomer and forms a circularly enclosed multidomain structure via an interdomain interaction. GmaR in this conformation recognizes MogR using the C-terminal antirepressor domain in a unique dual binding mode and mediates the antirepressor function through direct competition and spatial restraint mechanisms. Surprisingly, at 37°C, GmaR rapidly forms autologous aggregates that are deficient in MogR neutralization capabilities.

Crystal Structure of the Recombination Mediator Protein RecO from Campylobacter jejuni and Its Interaction with DNA and a Zinc Ion.

Homologous recombination is involved in repairing DNA damage, contributing to maintaining the integrity and stability of viral and cellular genomes. In bacteria, the recombination mediator proteins RecO and RecR are required to load the RecA recombinase on ssDNA for homologous recombination. To structurally and functionally characterize RecO, we determined the crystal structure of RecO from Campylobacter jejuni (cjRecO) at a 1.8 Å resolution and biochemically assessed its capacity to interact with DNA and a metal ion. cjRecO folds into a curved rod-like structure that consists of an N-terminal domain (NTD), C-terminal domain (CTD), and Zn2+-binding domain (ZnD). The ZnD at the end of the rod-like structure coordinates three cysteine residues and one histidine residue to accommodate a Zn2+ ion. Based on an extensive comparative analysis of RecO structures and sequences, we propose that the Zn2+-binding consensus sequence of RecO is CxxC…C/HxxC/H/D. The interaction with Zn2+ is indispensable for the protein stability of cjRecO but does not seem to be required for the recombination mediator function. cjRecO also interacts with ssDNA as part of its biological function, potentially using the positively charged patch in the NTD and CTD. However, cjRecO displays a low ssDNA-binding affinity, suggesting that cjRecO requires RecR to efficiently recognize ssDNA for homologous recombination.

Structural and biochemical analyses of the flagellar expression regulator DegU from Listeria monocytogenes.

Listeria monocytogenes is a pathogenic bacterium that produces flagella, the locomotory organelles, in a temperature-dependent manner. At 37 °C inside humans, L. monocytogenes employs MogR to repress the expression of flagellar proteins, thereby preventing the production of flagella. However, in the low-temperature environment outside of the host, the antirepressor GmaR inactivates MogR, allowing flagellar formation. Additionally, DegU is necessary for flagellar expression at low temperatures. DegU transcriptionally activates the expression of GmaR and flagellar proteins by binding the operator DNA in the fliN-gmaR promoter as a response regulator of a two-component regulatory system. To determine the DegU-mediated regulation mechanism, we performed structural and biochemical analyses on the recognition of operator DNA by DegU. The DegU-DNA interaction is primarily mediated by a C-terminal DNA-binding domain (DBD) and can be fortified by an N-terminal receiver domain (RD). The DegU DBD adopts a tetrahelical helix-turn-helix structure and assembles into a dimer. The DegU DBD dimer recognizes the operator DNA using a positive patch. Unexpectedly, unlike typical response regulators, DegU interacts with operator DNA in both unphosphorylated and phosphorylated states with similar binding affinities. Therefore, we conclude that DegU is a noncanonical response regulator that is constitutively active irrespective of phosphorylation.

Structural analysis of the dNTP triphosphohydrolase PA1124 from Pseudomonas aeruginosa.

dNTP triphosphohydrolase (TPH) belongs to the histidine/aspartate (HD) superfamily and catalyzes the hydrolysis of dNTPs into 2'-deoxyribonucleoside and inorganic triphosphate. TPHs are required for cellular dNTP homeostasis and DNA replication fidelity and are employed as a host defense mechanism. PA1124 from the pathogenic Pseudomonas aeruginosa bacterium functions as a dGTP and dTTP triphosphohydrolase. To reveal how PA1124 drives dNTP hydrolysis and is regulated, we performed a structural study of PA1124. PA1124 assembles into a hexameric architecture as a trimer of dimers. Each monomer has an interdomain dent where a metal ion is coordinated by conserved histidine and aspartate residues. A structure-based comparative analysis suggests that PA1124 accommodates the dNTP substrate into the interdomain dent near the metal ion. Interestingly, PA1124 interacts with ssDNA, presumably as an allosteric regulator, using a positively charged intersubunit cleft that is generated via dimerization. Furthermore, our phylogenetic analysis highlights similar or distinct oligomerization profiles across the TPH family.

Structural analysis of a Simpl-like protein from Campylobacter jejuni.

Signaling molecule that interacts with mouse pelle-like kinase (Simpl) is an animal protein that contributes to the regulation of inflammatory responses. Although Simpl-like proteins (SLPs) are mainly found in bacteria, functional and structural studies on bacterial SLPs are limited to BP26, a periplasmic protein from Brucella species. We identified a group of bacterial SLPs, including Campylobacter jejuni SLP (cjSLP) and Shewanella putrefaciens SLP (spSLP), that exhibit significant sequence variation from Simpl and BP26. To address the structural and oligomeric diversities of SLPs, we determined the crystal structure of cjSLP and performed a comparative analysis of SLP structures. cjSLP adopts a boomerang-shaped, two-domain structure, and each domain of cjSLP adopts an α-helix-decorated ß-sheet structure as observed in BP26. This observation suggests that the duplicated α/ß structure would be the canonical fold of the Simpl family. Despite the fold similarity, cjSLP exhibits a more open interdomain organization than BP26 and displays unique local structural features that are not observed in BP26. Furthermore, cjSLP and its ortholog spSLP are monomeric in solution in contrast to the hexadecameric assembly of BP26. Therefore, we conclude that cjSLP represents a unique bacterial SLP group that is distinct from BP26 in both structures and oligomeric states.

Structural analysis of the flagellar capping protein FliD from Helicobacter pylori.

Helicobacter pylori is a pathogenic flagellated bacterium that infects the gastroduodenal mucosa and causes peptic ulcers in humans. FliD caps the distal end of the flagellar filament and is essential in filament growth. Moreover, FliD has been studied to diagnose and prevent H. pylori infection. Here, we report structure-based molecular studies of H. pylori FliD (hpFliD). A crystal structure of hpFliD at 2.6 Šresolution presents a four-domain (D2-D5) structure, where the D3 domain forms a central platform surrounded by the other three domains (D2, D4, and D5). hpFliD domains D2 and D3 structurally resemble those of FliD orthologs, whereas the D4 and D5 domains are exclusive to hpFliD. Moreover, our ELISA analysis using anti-H. pylori antibodies demonstrated that the hpFliD-specific D4 and D5 domains are highly antigenic compared to the D2 and D3 domains. Collectively, our structural and serological analyses underscore the structural role of hpFliD domains and provide a molecular basis for vaccine and diagnosis development.

Development of Latent Fingermarks on Surfaces of Food-A More Realistic Approach.

Latent fingermark developing methods from food (mandarin, egg, banana, apple, potato, carrot, eggplant, onion, bell pepper, and tomato) surface has been studied by 10 methods, including powdering method, small particle reagent method, and cyanoacrylate fuming method. The foods were stored under two conditions (room temperature and refrigerator) before fingermark deposition and aged for 2, 24, 48, and 72 h before fingermark development. In most of the food surfaces used in this study, cyanoacrylate fuming with 80% relative humidity was superior to the powder or small particle reagent methods. The quality of the fingermarks varied depending on the storage conditions before the fingermark deposition (in the refrigerator or at ambient temperature) and the time elapsed since the fingermark deposition. However, the storage conditions before the fingermark deposition and the time elapsed since the fingermark deposition did not show any correlation with the quality of the fingermark.

Inhaled nitric oxide therapy was not associated with postoperative acute kidney injury in patients undergoing lung transplantation: A retrospective pilot study.

Inhaled nitric oxide (iNO) therapy is commonly used in lung transplantation (LT) recipients during the perioperative periods. However, previous studies report that the use of iNO may increase the risk of renal dysfunction. Post-LT acute kidney injury (AKI) can lead to critical situations, including prolonged intensive care unit or hospital stays and increased morbidity and mortality. Accordingly, the aim of this study was to investigate the relationship between iNO therapy and incidence of post-LT AKI in LT recipients.The medical data of 36 patients who underwent LT surgery from January 2012 to July 2017 in a single university hospital setting were retrospectively collected and analyzed. Patients were divided into 2 groups: iNO (n = 14) and control (n = 19). The demographic data, anesthetic methods, complications, and perioperative laboratory test values of each patient were assessed. Patients were categorized according to changes in plasma creatinine (Cr) concentration levels within 48 hours after LT using Acute Kidney Injury Network criteria.There was no significant difference in the occurrence (P = .13) and severity (P = .9) of post-LT AKI between iNO and control groups. The mean serum Cr levels after surgery were 0.91 ±â€Š0.44 and 0.81 ±â€Š0.37 mg/dL in the iNO and control groups, respectively (P = .50).AKI plays a critical role in the prognosis of LT recipients. Our results revealed that iNO therapy was not associated with the incidence of post-LT AKI. Therefore, if iNO treatment is indicated, active use under close monitoring of renal function is recommended in LT-patients concerned about AKI after surgery.

Laser parameters for efficient biomedical stimulation: A study to increase cognitive response rate.

BACKGROUND: The laser is able to irradiate the exact amount of stimulation to an area by a non contact method, and has the advantage of being able to stimulate the local target area. OBJECTIVE: This study examined an efficient method of laser tactile stimulation using laser parameter combinations. METHODS: The laser parameters that could cause an increase in the cognitive response rate of human subjects were examined without increasing the amount of total laser energy. RESULTS: As a result, the appropriate matching parameters such as duty ratio, pulse frequency, and exposure time of laser pulses showed a dominant influence in effectively increasing the tactile response rate of subjects with limited amount of total laser energy. CONCLUSIONS: This study can be applied to neurophysiology, cognitive research, and clinical laser application.

Effect of transforaminal epidural polydeoxyribonucleotide injections on lumbosacral radiculopathy: A case report.

RATIONALE: Transforaminal epidural glucocorticoids administration is widely performed for the management of lumbosacral radiculopathy. However, it may worsen the condition of patients with type 2 diabetes mellitus (DM). Polydeoxyribonucleotide (PDRN) was recently noted as a substitute for glucocorticoids. PATIENT CONCERNS: A 44-year-old male patient was admitted to our pain clinic with symptoms of low back pain with severe pain and tingling sensation of left posterolateral leg. He had type 2 DM medicated with Glimepiride and Metformin. Blood glucose level was 367 mg/dL. He declined to use glucocorticoid. DIAGNOSES: He was diagnosed as left foraminal disc protrusion at L4-5, left subarticular disc protrusion at L5-S1. INTERVENTIONS: Fluoroscopically guided transforaminal epidural PDRN injections were carried out. OUTCOMES: The patient was followed up for more than 6 months and demonstrated good improvement in lumbosacral radiculopathy without any complications. LESSONS: This is the first successful report on epidural injection of PDRN.

A study on detection of glucose concentration using changes in color coordinates.

Glucose concentration is closely related to the metabolic activity of cells and it is the most important substance as the energy source of a living body which plays an important role in the human body. This paper proposes an optical method that can measure the concentration of glucose. The change in glucose concentration was observed by using CIE diagram, and wavelength and purity values were detected. Also, even small changes in glucose concentration can be evaluated through mathematical modeling. This system is simple, economical, and capable of quantifying optical signals with numerical values for glucose sensing. This method can be applicable to the clinical field that examines diabetes mellitus or metabolic syndrome.

Responses of human sensory characteristics to 532 nm pulse laser stimuli.

BACKGROUND: Lasers are advantageous in some applications to stimulate a small target area and is used in various fields such as optogenetic, photoimmunological and neurophysiological studies. OBJECTIVE: This study aims to implement a non-contact sense of touch without damaging biological tissues using laser. METHODS: Various laser parameters were utilized in safety range to induce a sense of touch and investigate the human responses. With heat distribution simulation, the amount of changes in the temperature and the tendency in laser parameters of sensory stimulation were analyzed. RESULTS: The results showed the identified tactile responses in safety range with various laser parameters and temperature distribution for the laser stimulus was obtained through the simulation. CONCLUSIONS: This study can be applied to the areas of sensory receptor stimulation, neurophysiology and clinical medicine.

Mid-Air Tactile Stimulation Using Indirect Laser Radiation.

In this paper, we demonstrate that a laser irradiated on a thin light-absorbing elastic medium attached on the skin can elicit a tactile sensation of mechanical tap. First, we present simulation results that show laser irradiation to the elastic medium creates inner elastic waves on the basis of thermoelastic effects and these elastic waves trigger the bending deformation of the medium, which then stimulates the skin. Second, we analyze the physical properties of the associated stimulus by measuring its force profile. Third, we identify the perceptual characteristics of the stimulus in comparison to those of mechanical and electrical stimuli by means of a perceptual experiment employing dissimilarity rating. All the evidence indicates that indirect laser radiation provides a sensation of short mechanical tap. Furthermore, little individual difference was observed in the results of the perceptual experiment. To the best of our knowledge, this study is the first in reporting the feasibility of indirect laser radiation for mid-air tactile rendering.

Study of somesthesis according to change in pulse diode laser parameters.

Laser can precisely deliver quantitative energy to a desired region in a non-contact way. Since it can stimulate regions and minutely control parameters such as the intensity, duration and frequency of stimulus, laser is often used for the areas such as low power laser treatment and clinical physiology. This study proposes simulation using pulse diode laser with reliable output and identifies laser parameters that can present a variety of somesthesis. It is found that typically, as frequency and energy increase, the ratio of feeling senses increases, and dominant sense moves from the sense of heat through tactile sense to pain. This study will be baseline data for studies of the sense of heat, tactile sense and pain, contribute to studying neurophysiology sector and be applied to basic clinical research.

Simple LED spectrophotometer for analysis of color information.

A spectrophotometer is the basic measuring equipment essential to most research activity fields requiring samples to be measured, such as physics, biotechnology and food engineering. This paper proposes a system that is able to detect sample concentration and color information by using LED and color sensor. Purity and wavelength information can be detected by CIE diagram, and the concentration can be estimated with purity information. This method is more economical and efficient than existing spectrophotometry, and can also be used by ordinary persons. This contribution is applicable to a number of fields because it can be used as a colorimeter to detect the wavelength and purity of samples.

A new optical technique to monitor joint motion using position sensitive detector.

BACKGROUND: Evaluation of joint movements is essential to choose an appropriate rehabilitation protocol for a patient. OBJECTIVE: The aim of this study is to suggest an alternative optical technique for measurement of joint angle which is convenient, inexpensive, and can be operated in real time. METHODS: According to the principle of the triangulation method, position sensitive detector (PSD) converts reflected light signals into distance-related voltages. Various parameters were investigated to increase detection range and resolution of joint angle measurements. RESULTS: The accuracy of the suggested optical sensor was verified by comparing with a commercial goniometer and 3D motion capture system. CONCLUSIONS: This method can be applied to monitor recovery progress for the patient in rehabilitation and sport science.

Development of multi-colored LED system for therapeutic application.

BACKGROUND: The evaluation and control of lighting is crucial in physiological, biomedical, and industrial fields. Many kinds of lighting techniques based on LED have been developed due to its advantages. OBJECTIVE: The aim of this study is to develop the multi-colored LED system for healing purposes. METHODS: Light source with three-color chip LEDs was investigated to detect the dominant wavelength. RESULTS: The results show that the additive principle by three-color LEDs can be successfully applied to lighting system by generating a variety of colors. CONCLUSIONS: The results are expected to be useful in the field of light therapy and medicine. Applications of the developed light system are lighting therapies such as stimulating blood circulation and digestive processes, and controlling inflammation.