Exploring the antibacterial potential of Lactococcus lactis subsp. lactis bv. diacetylactis BGBU1-4 by genome mining, bacteriocin gene overexpression, and chemical protein synthesis of lactolisterin BU variants.

Lactic acid bacterium Lactococcus lactis BGBU1-4 produces 43 amino acids (aa) long bacteriocin, lactolisterin BU (LBU), a 5.161 kDa peptide with potent antibacterial activity against many Gram-positive pathogens. In addition, BGBU1-4 produces an additional unknown product of 3.642 kDa with antibacterial activity. Here, we determined that the significant amount of naturally produced LBU breaks down to create a 3.642 kDa truncated form of LBU bacteriocin consisting of 31 N-terminal aa (LBU1-31) that exhibits 12.5% the antibacterial activity of the full-length LBU. We showed that chemically synthesized LBU is stable and 50% less active than native LBU, and so we used the synthetic peptides of LBU and its variants to further study their activities and antibacterial potential. Deletion analysis of LBU revealed that the 24 N-terminal aa of LBU (LBU1-24) are responsible for antibacterial activity, while downstream aa (25-43) determine the species-specific effectiveness of LBU. Although LBU1-31 contains aa 1-24, the truncation at position 31 is predicted to change the structure within aa 15-31 and might impact on antibacterial activity. Intriguingly, whole genome sequencing and genome mining established that BGBU1-4 is abundant in genes that encode potential antibacterials, but produces LBU and its breakdown product LBU1-31 exclusively.

Correlation Theory of the Maxillary Central Incisor, Face and Dental Arch Shape in the Serbian Population.

Background and Objectives: According to the modified Williams theory, the shape of the maxillary central incisor corresponds to the shape of the maxillary alveolar ridge (dental arch) and the shape of the face. Moreover, the standards of beauty suggest that the center of the face of an individual with a full set of teeth should match the center of the maxillary and mandibular dental arches. The purpose of this study is to conduct a comparative cross-sectional study on the matching of the shape of the face, maxillary central incisor and maxillary dental arch as well as the matching of the midfacial line and dental arches in subjects with complete dentition. Materials and Methods: The study included 90 subjects of both sexes. The matching of the shape of the face and midfacial line, i.e., dental arches and maxillary incisors, was determined by analysing photographs, whereas the shape of the dental arch was determined by analysing plaster models. Results: No significant gender-related differences were found either in the shape of the maxillary central incisor that matched the shape of the maxillary dental arch (p = 0.349) or in the shape of the dental arch that matched the shape of the face (p = 0.697). However, a significant difference was noted in the shape of the teeth that matched the shape of the face (p = 0.043), which was more significantly impaired in men. In addition, the matching of the mid-face and the mid-dental arch was significantly greater in women (p = 0.016). Conclusions: The modified Williams theory was confirmed in most subjects, thus it can be considered a relevant guideline when determining the shape of teeth after their loss. The highest percentage of matching in both sexes was with the shape of the face and dental arch. There was no positive correlation between the middle of the maxillary and mandibular dental arch in most cases.

Redesigned pMAL expression vector for easy and fast purification of active native antimicrobial peptides.

AIMS: The aim of this study was to construct the improved pMAL expression vector to increase the efficacy of purification of small native peptides and their clear-cut separation from MBP tag. The modifications we introduced can be applied to many expression vectors. METHODS AND RESULTS: To improve the pMAL expression vector, we introduced the His6 tag and the enterokinase cleavage site (Ek) downstream from the MBP tag and Xa cleavage site on the original vector. For cloning of a desired peptide DNA, the enterokinase site contains a unique BsaBI restriction site adjacent to the original multi-cloning site. This redesigned pMAL vector was optimized for the purification of cytoplasmic (pMALc5HisEk) and periplasmic (pMALp5HisEk) peptides. The purification of native and active peptide (P) was obtained following two-step affinity chromatography. In the first step, the entire MBP-His6 -Ek-P fusion protein is purified using the Ni-NTA agarose column. This fusion protein was cleaved with active His6 tagged enterokinase. In the second step, the further purification was performed by column containing the mixture of amylose and Ni-NTA agarose resins. This removes both the MBP-His6 and His6 -enterokinase leaving pure native protein in solution. These new vectors and the two-step purification protocol were successfully applied in purification of active native small antimicrobial peptides (AMPs), lactococcin A and human ß-defensin. CONCLUSIONS: We constructed the improved pMAL expression vectors and established the pipeline and optimal conditions for their use in efficient purification of large amounts of active native small peptides. SIGNIFICANCE AND IMPACT OF THE STUDY: Choice of expression vector impacts on the efficiency of expression and purification of desired proteins. The idea of redesigning pMAL vector was driven by the need for rapid purification of larger amounts of active native AMPs. This newly improved pMAL vector, the cloning strategy, expression conditions and two-step purification protocol represent a unique simple approach which can be applied in every laboratory.

Structure and function of PspA and Vipp1 N-terminal peptides: Insights into the membrane stress sensing and mitigation.

The phage shock protein (Psp) response maintains integrity of the inner membrane (IM) in response to extracytoplasmic stress conditions and is widely distributed amongst enterobacteria. Its central component PspA, a member of the IM30 peripheral membrane protein family, acts as a major effector of the system through its direct association with the IM. Under non-stress conditions PspA also negatively regulates its own expression via direct interaction with the AAA+ ATPase PspF. PspA has a counterpart in cyanobacteria called Vipp1, which is implicated in protection of the thylakoid membranes. PspA's and Vipp1's conserved N-terminal regions contain a putative amphipathic helix a (AHa) required for membrane binding. An adjacent amphipathic helix b (AHb) in PspA is required for imposing negative control upon PspF. Here, purified peptides derived from the putative AH regions of PspA and Vipp1 were used to directly probe their effector and regulatory functions. We observed direct membrane-binding of AHa derived peptides and an accompanying change in secondary structure from unstructured to alpha-helical establishing them as bona fide membrane-sensing AH's. The peptide-binding specificities and their effects on membrane stability depend on membrane anionic lipid content and stored curvature elastic stress, in agreement with full length PspA and Vipp1 protein functionalities. AHb of PspA inhibited the ATPase activity of PspF demonstrating its direct regulatory role. These findings provide new insight into the membrane binding and function of PspA and Vipp1 and establish that synthetic peptides can be used to probe the structure-function of the IM30 protein family.

Single-step method for ß-galactosidase assays in Escherichia coli using a 96-well microplate reader.

Historically, the lacZ gene is one of the most universally used reporters of gene expression in molecular biology. Its activity can be quantified using an artificial substrate, o-nitrophenyl-ß-d-galactopyranoside (ONPG). However, the traditional method for measuring LacZ activity (first described by J. H. Miller in 1972) can be challenging for a large number of samples, is prone to variability, and involves hazardous compounds for lysis (e.g., chloroform, toluene). Here we describe a single-step assay using a 96-well microplate reader with a proven alternative cell permeabilization method. This modified protocol reduces handling time by 90%.

Transcription Regulation and Membrane Stress Management in Enterobacterial Pathogens.

Transcription regulation in a temporal and conditional manner underpins the lifecycle of enterobacterial pathogens. Upon exposure to a wide array of environmental cues, these pathogens modulate their gene expression via the RNA polymerase and associated sigma factors. Different sigma factors, either involved in general 'house-keeping' or specific responses, guide the RNA polymerase to their cognate promoter DNAs. The major alternative sigma54 factor when activated helps pathogens manage stresses and proliferate in their ecological niches. In this chapter, we review the function and regulation of the sigma54-dependent Phage shock protein (Psp) system-a major stress response when Gram-negative pathogens encounter damages to their inner membranes. We discuss the recent development on mechanisms of gene regulation, signal transduction and stress mitigation in light of different biophysical and biochemical approaches.

Is the cellular and molecular machinery docile in the stationary phase of Escherichia coli?

The bacterial cell envelope retains a highly dense cytoplasm. The properties of the cytoplasm change with the metabolic state of the cell, the logarithmic phase (log) being highly active and the stationary phase metabolically much slower. Under the differing growth phases, many different types of stress mechanisms are activated in order to maintain cellular integrity. One such response in enterobacteria is the phage shock protein (Psp) response that enables adaptation to the inner membrane (IM) stress. The Psp system consists of a transcriptional activator PspF, negative regulator PspA, signal sensors PspBC, with PspA and PspG acting as effectors. The single molecule imaging of the PspF showed the existence of dynamic communication between the nucleoid-bound states of PspF and membrane via negative regulator PspA and PspBC sensors. The movement of proteins in the cytoplasm of bacterial cells is often by passive diffusion. It is plausible that the dynamics of the biomolecules differs with the state of the cytoplasm depending on the growth phase. Therefore, the Psp response proteins might encounter the densely packed glass-like properties of the cytoplasm in the stationary phase, which can influence their cellular dynamics and function. By comparing the properties of the log and stationary phases, we find that the dynamics of PspF are influenced by the growth phase and may be controlled by the changes in the cytoplasmic fluidity.

Anionic lipids and the cytoskeletal proteins MreB and RodZ define the spatio-temporal distribution and function of membrane stress controller PspA in Escherichia coli.

All cell types must maintain the integrity of their membranes. The conserved bacterial membrane-associated protein PspA is a major effector acting upon extracytoplasmic stress and is implicated in protection of the inner membrane of pathogens, formation of biofilms and multi-drug-resistant persister cells. PspA and its homologues in Gram-positive bacteria and archaea protect the cell envelope whilst also supporting thylakoid biogenesis in cyanobacteria and higher plants. In enterobacteria, PspA is a dual function protein negatively regulating the Psp system in the absence of stress and acting as an effector of membrane integrity upon stress. We show that in Escherichia coli the low-order oligomeric PspA regulatory complex associates with cardiolipin-rich, curved polar inner membrane regions. There, cardiolipin and the flotillin 1 homologue YqiK support the PspBC sensors in transducing a membrane stress signal to the PspA-PspF inhibitory complex. After stress perception, PspA high-order oligomeric effector complexes initially assemble in polar membrane regions. Subsequently, the discrete spatial distribution and dynamics of PspA effector(s) in lateral membrane regions depend on the actin homologue MreB and the peptidoglycan machinery protein RodZ. The consequences of loss of cytoplasmic membrane anionic lipids, MreB, RodZ and/or YqiK suggest that the mode of action of the PspA effector is closely associated with cell envelope organization.

Enzyme-functionalized hydrogel film for extracorporeal uric acid reduction.

Enzyme replacement therapy for hyperuricemia treatment has been proven effective for critical state hyperuricemia patients. Still, direct administration of recombinant uricase can induce several fatal side effects. To circumvent this drawback, hydrogel protein carriers can be used in platforms for extracorporeal treatment such as microscale-based devices. In this work, calcium alginate and poly-(vinyl alcohol) hydrogel films were studied for their urate oxidase immobilization and uric acid reduction, which could be implemented in microscale-based extracorporeal devices. A mathematical model was developed in conjunction with uric acid reduction experiments to evaluate the influence of mass transfer and reaction parameters in the Michaelis-Menten kinetic expression. Alginate hydrogels prepared with crosslinker 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-(hydroxysuccinimide) offered superior diffusivity of uric acid in the gel matrix at the maximum value of D g , UA ≈ $$ {D}_{\mathrm{g},\mathrm{UA}}\approx $$ 1.98 × 10-11 m2 /s compared with alginate prepared solely from ionic crosslinking with D g , UA ≈ $$ {D}_{\mathrm{g},\mathrm{UA}}\approx $$ 5.31 × 10-12 m2 /s at the same alginate concentration. The maximum value of νmax was experimentally determined at 7.78 × 10-5 mol/(m3 s). A 3% sodium alginate hydrogel with crosslinkers yielded the highest reduction of uric acid at 92.70%. The mathematical model demonstrated an excellent prediction of uric acid conversion suggesting potential use of the model for formulation and maximizing the therapeutic performance of functionalized hydrogels.

A histological evaluation of a low-level laser therapy as an adjunct to periodontal therapy in patients with diabetes mellitus.

Diabetes mellitus (DM) and chronic periodontitis are common chronic diseases in adults in the world population. DM has a strong influence on the oral cavity and represents a risk factor for gingivitis and periodontitis. Low-level laser therapy (LLLT) has proven effective in the reduction of inflammation and swelling. The aim of the present study was to evaluate the efficacy of LLLT in diabetic periodontitis through histological analysis. A total of 300 diabetics with chronic periodontal disease and teeth indicated for extraction were assigned into six equal groups. In the groups 1 and 4, indicated teeth were extracted before treatment, and in the rest of the groups upon completion of the entire treatment. All patients received oral hygiene instructions and full-mouth conservative periodontal treatment. In groups 3 and 6, LLLT was applied (670 nm, 5 mW, 2 J/cm(2), 16 min, 5 days). Histologic findings of gingival tissue treated with LLLT showed expressed healing, as is evident by the absence of inflammatory cells. Tissue edema could not be seen, and the number of blood vessels was reduced. In the gingival lamina, propria pronounced collagenization and homogenization were present. It can be concluded that LLLT has shown efficacy in the treatment of periodontitis in diabetics. Because of more pronounced alterations of periodontium in diabetics, the use of LLLT is of particular importance.

Longevity Demonstration of Methane to C2 via a Nonthermal Plasma Microreactor.

Hydrocarbon processing using plasmas has tremendous potential, yet there still exist many uncertainties pertaining to practical operation over long durations. Previously, it has been demonstrated that a nonthermal plasma operating in a DC glow regime can transform methane into C2 species (acetylene, ethylene, ethane) in a microreactor. Using a DC glow regime in a microchannel reactor allows for lower power consumption, at the expense of greater consequence of fouling. Since biogas can be a source of methane, a longevity study was undertaken to understand how the microreactor system would change over time with a feed mixture of simulated biogas (CO2, CH4) and air. Two different biogas mixtures were used, one of which contained 300 ppm H2S, while the other had no H2S. Potential difficulties observed from previous experiments included carbon deposition on the electrodes, which could interfere with the electrical characteristics of the plasma discharge as well as material deposition in the microchannel, which could affect gas flow. It was found that raising the temperature of the system to 120 °C helped prevent hydrocarbon deposition in the reactor. Purging the reactor periodically with dry air was also found to have positive effects as it removed carbon buildup on the electrodes themselves. Successful operation over a 50 h time period without any significant deterioration was demonstrated.

Urea separation in flat-plate microchannel hemodialyzer; experiment and modeling.

Two flat-plate microchannel hemodialyzers were constructed consisting of two identical laminae separated by a 20[µm] thick ultrafiltration membrane (Gambro AN69). Each lamina contains a parallel array of microchannels 100[µm] deep, 200[µm] wide, and 5.6[cm] or 9.9[cm] in length respectively. Urea was removed from the aqueous stream containing 1.0[g] urea per liter de-ionized water in the blood side, by countercurrent contact with pure de-ionized water in the dialysate side of the flat-plate hemodialyzer. In all cases volumetric flow rate of water in the dialysate side was equal or less than the volumetric flow rate in the blood side, which is in large contrast to commercial applications of hollow-fiber hemodialyzers where dialysate flow is severalfold larger than blood flow rate. A three-dimensional finite volume mass transport model, built entirely from the first principles with no adjustable parameters, was written in FORTRAN. The results of the mathematical model excellently predict experimental results. The fractional removals of urea predicted by the model are within 2.7%-11% of experimentally obtained values for different blood and dialysate velocities/flow rates in microchannels, and for different transmembrane pressures. The overall mass transfer coefficient was calculated using the urea outlet concentrations obtained at various average velocities (1.0-5.0[cm/s]) in the blood and dialysate, and two nominal transmembrane pressures (∆P(tm) = 0 and 10,000.[Pa]). Overall mass transfer coefficients obtained experimentally ranged from 0.068 to 0.14 [cm/min]. The numerical model predicted an average overall mass transfer coefficient of 0.08 [cm/min]. This value is 60% higher than those found in commercial dialyzers (~0.05[cm/min]).

Dissipation of proton motive force is not sufficient to induce the phage shock protein response in Escherichia coli.

Phage shock proteins (Psp) and their homologues are found in species from the three domains of life: Bacteria, Archaea and Eukarya (e.g. higher plants). In enterobacteria, the Psp response helps to maintain the proton motive force (PMF) of the cell when the inner membrane integrity is impaired. The presumed ability of ArcB to sense redox changes in the cellular quinone pool and the strong decrease of psp induction in ΔubiG or ΔarcAB backgrounds suggest a link between the Psp response and the quinone pool. The authors now provide evidence indicating that the physiological signal for inducing psp by secretin-induced stress is neither the quinone redox state nor a drop in PMF. Neither the loss of the H(+)-gradient nor the dissipation of the electrical potential alone is sufficient to induce the Psp response. A set of electron transport mutants differing in their redox states due to the lack of a NADH dehydrogenase and a quinol oxidase, but retaining a normal PMF displayed low levels of psp induction inversely related to oxidised ubiquinone levels under microaerobic growth and independent of PMF. In contrast, cells displaying higher secretin induced psp expression showed increased levels of ubiquinone. Taken together, this study suggests that not a single but likely multiple signals are needed to be integrated to induce the Psp response.

Physical, functional and conditional interactions between ArcAB and phage shock proteins upon secretin-induced stress in Escherichia coli.

The phage shock protein (Psp) system found in enterobacteria is induced in response to impaired inner membrane integrity (where the Psp response is thought to help maintain the proton motive force of the cell) and is implicated in the virulence of pathogens such as Yersinia and Salmonella. We provided evidence that the two-component ArcAB system was involved in induction of the Psp response in Escherichia coli and now report that role of ArcAB is conditional. ArcAB, predominantly through the action of ArcA regulated genes, but also via a direct ArcB-Psp interaction, is required to propagate the protein IV (pIV)-dependent psp-inducing signal(s) during microaerobiosis, but not during aerobiosis or anaerobiosis. We show that ArcB directly interacts with the PspB, possibly by means of the PspB leucine zipper motif, thereby allowing cross-communication between the two systems. In addition we demonstrate that the pIV-dependent induction of psp expression in anaerobiosis is independent of PspBC, establishing that PspA and PspF can function as a minimal Psp system responsive to inner membrane stress.

In vivo localizations of membrane stress controllers PspA and PspG in Escherichia coli.

The phage shock protein (Psp) response in Gram-negative bacteria counteracts membrane stress. Transcription of the PspF regulon (pspABCDE and pspG) in Escherichia coli is induced upon stresses that dissipate the proton motive force (pmf). Using GFP fusions we have visualized the subcellular localizations of PspA (a negative regulator and effector of Psp) and PspG (an effector of Psp). It has previously been proposed that PspA evenly coates the inner membrane of the cell. We now demonstrate that instead of uniformly covering the entire cell, PspA (and PspG) is highly organized into what appear to be distinct functional classes (complexes at the cell pole and the lateral cell wall). Real-time observations revealed lateral PspA and PspG complexes are highly mobile, but absent in cells lacking MreB. Without the MreB cytoskeleton, induction of the Psp response is still observed, yet these cells fail to maintain pmf under stress conditions. The two spatial subspecies therefore appear to be dynamically and functionally distinct with the polar clusters being associated with sensory function and the mobile complexes with maintenance of pmf.

Properties of the phage-shock-protein (Psp) regulatory complex that govern signal transduction and induction of the Psp response in Escherichia coli.

The phage-shock-protein (Psp) response maintains the proton-motive force (pmf) under extracytoplasmic stress conditions that impair the inner membrane (IM) in bacterial cells. In Escherichia coli transcription of the pspABCDE and pspG genes requires activation of σ(54)-RNA polymerase by the enhancer-binding protein PspF. A regulatory network comprising PspF-A-C-B-ArcB controls psp expression. One key regulatory point is the negative control of PspF imposed by its binding to PspA. It has been proposed that under stress conditions, the IM-bound sensors PspB and PspC receive and transduce the signal(s) to PspA via protein-protein interactions, resulting in the release of the PspA-PspF inhibitory complex and the consequent induction of psp. In this work we demonstrate that PspB self-associates and interacts with PspC via putative IM regions. We present evidence suggesting that PspC has two topologies and that conserved residue G48 and the putative leucine zipper motif are determinants required for PspA interaction and signal transduction upon stress. We also establish that PspC directly interacts with the effector PspG, and show that PspG self-associates. These results are discussed in the context of formation and function of the Psp regulatory complex.

The route to transcription initiation determines the mode of transcriptional bursting in E. coli.

Transcription is fundamentally noisy, leading to significant heterogeneity across bacterial populations. Noise is often attributed to burstiness, but the underlying mechanisms and their dependence on the mode of promotor regulation remain unclear. Here, we measure E. coli single cell mRNA levels for two stress responses that depend on bacterial sigma factors with different mode of transcription initiation (σ70 and σ54). By fitting a stochastic model to the observed mRNA distributions, we show that the transition from low to high expression of the σ70-controlled stress response is regulated via the burst size, while that of the σ54-controlled stress response is regulated via the burst frequency. Therefore, transcription initiation involving σ54 differs from other bacterial systems, and yields bursting kinetics characteristic of eukaryotic systems.

Comparative antiradical activity and molecular Docking/Dynamics analysis of octopamine and norepinephrine: the role of OH groups.

Octopamine is a neurotransmitter in invertebrates and a phenol analog of norepinephrine. The crystallographic and spectral (UV-visUV, and NMR) characteristics of octopamine were investigated experimentally and theoretically by applying appropriate level of theory, B3LYP-D3BJ/6-311++G(d,p), which reproduced well the experimental bond lengths and angles. The intramolecular interactions governing the stability of conformers were described by NBO and QTAIM analyses. The antiradical potencies of octopamine and norepinephrine towards DPPH and ABTS+ were examined with special emphasis on the preferred mechanism and effect of catechol moiety. Several techniques were used to distinguish Hydrogen Atom Transfer (HAT) and Proton Coupled Electron Transfer (PCET) mechanisms for reaction with DPPH. The calculated rate constants of the reactions with both radicals showed that Sequential Proton Loss Electron Transfer (SPLET) mechanism was dominant both thermodynamically and kinetically, with values of thermodynamic functions and rate constants clearly proving the importance of the second hydroxyl group in structure. The Molecular Docking and afterward Molecular Dynamics calculations of formed complexes between octopamine/norepinephrine with ß1- and ß2- adrenergic receptors examined in details the interactions that lead to the formation of stable complexes. The number of strong interactions of amino acids with norepinephrine was higher, but the absence of hydroxyl group in octopamine did not lead to a significant change in the type of interactions and stability. The formed complexes showed higher flexibility of amino acids, similar compactness of structure as proteins and increased interatomic distances of the backbone when compared to pure proteins.

Model-based evolutionary analysis: the natural history of phage-shock stress response.

The evolution of proteins is inseparably linked to their function. Because most biological processes involve a number of different proteins, it may become impossible to study the evolutionary properties of proteins in isolation. In the present article, we show how simple mechanistic models of biological processes can complement conventional comparative analyses of biological traits. We use the specific example of the phage-shock stress response, which has been well characterized in Escherichia coli, to elucidate patterns of gene sharing and sequence conservation across bacterial species.

Effects of coenzyme Q10 encapsulated in nanoliposomes on wound healing processes after tooth extraction.

BACKGROUND/PURPOSE: Tooth extraction is often followed by a number of different complications that demand additional treatment. In order to accelerate healing processes and decrease the complication occurrence various agents, growth factors, natural and synthetic antioxidants (e.g coenzyme Q10-CoQ10), are applied. Due to the partially known health-promoting effects of CoQ10 we decided to assess potential of it's encapsulated in nanoliposomes form on wound healing process following tooth extraction. MATERIALS AND METHODS: Effects of free and encapsulated form of CoQ10 on wound healing processes after tooth extraction in rats, 3 and 7 days following surgical procedure, was studied by means of tissue biochemical (myeloperoxidase activity and nitric oxide (NO) concentrations) and pathohistological analysis. RESULTS: The obtained results indicate that the encapsulated form of CoQ10 compared to control and CoQ10 treated animals statistically significantly decreases inflammatory process estimated through myeloperoxidase activity and NO concentrations, as well as based on histopathological analysis 3 and 7 days following surgery. CONCLUSION: The results of this study unequivocally prove that the encapsulation of CoQ10 in nanoliposomes enhances CoQ10 activity by accelerating wound healing process after tooth extraction.