Gold-Deposited Graphene Nanosheets for Self-Cleaning Graphene Surface-Enhanced Raman Spectroscopy with Superior Charge-Transfer Contribution

The interaction of graphene with metals initiates charge-transfer interaction-induced chemical enhancements, which critically depend on the doping effect from deposited metallic configurations. In this paper, we have explored the gold nanoparticle-decorated monolayer graphene nanosheets for the large graphene-induced Raman enhancement of adsorbed analytes, indicating the surface-enhanced Raman spectroscopy (SERS) capabilities of metal-doped graphene (G-SERS). Here, the systematically sputtered Au thickness optimization procedure revealed noticeable modifications in the graphene Raman spectra and photoluminescence (PL) background quenching, which indicated favorable charge transfer through n-type doping of chemical vapor deposition-grown graphene nanosheets. The highly consistent, individually distributed morphology of the gold nanoislands over graphene nanosheets depicted a reproducibly uniform G-SERS signal with excellent relative standard deviation values (<5%), resulting in the strongest Raman intensity enhancement factors of ∼108 (MB) (methylene blue) and 107 (DPA) (2,6-pyridinedicarboxylic acid) composed of the weakest PL background. The combined charge-transfer-induced chemical enhancement and electromagnetic enhancement from individual Au nanoislands result in a lowering of detectability down to 10-16 M (MB) and 10-11 M (DPA) concentrations with efficient time-dependent signal stability. Additionally, the GAu demonstrated its effective (∼94.4%) photocatalytic degradation capabilities by decomposing MB dye molecules from a concentration of 1 μM to 2.52 fM within 60 min. Therefore, the prominent charge-transfer contribution through controlled Au decoration over graphene nanosheets provides a potential strategy for fabricating superior SERS sensors and photocatalysts exhibiting adequate signal consistency, stability, and photodegradation efficiency through overcoming the limitations of the traditional sensing platforms.

Spectroscopic and molecular docking investigation on the interaction of a water-soluble Cu(II) complex containing diethanolamine and dipicolinic acid ligands with human serum albumin

Under physiological conditions, spectroscopic techniques as well as molecular docking simulation have been used to investigate the binding interaction mechanism between Cu(II) complex containing Pyridine-2,6-dicarboxylic acid (PDCA) and Diethanolamine (DEA) ligands, [Cu(DEA)(PDCA)] and human serum albumin (HSA). UV spectral changes of protein in the presence of the Cu(II) complex suggested the formation of a Protein-Cu(II) complex conjugate with specific new structure. The Cu(II) complex quenches the intrinsic fluorescence of the HSA via a static mechanism in which van der Waals interactions along with hydrogen bonds are fundamental binding forces. Displacement experiments performed by warfarin and ibuprofen site probes predict that the Cu(II) complex is located in subdomain IIA, Sudlow site 1 of HSA. Molecular docking results showed close resemblance with experimental data.Communicated by Ramaswamy H. Sarma.

The Detection of Anthrax Biomarker DPA by Ratiometric Fluorescence Probe of Carbon Quantum Dots and Europium Hybrid Material Based on Poly(ionic)- Liquid

Bacillus anthracis has gained international attention as a deadly bacterium and a potentially deadly biological warfare agent. Dipicolinic acid (DPA) is the main component of the protective layer of anthracis spores, and is also an anthrax biomarker. Therefore, it is of great significance to explore an efficient and sensitive DPA detection method. Herein, a novel ratio hybrid probe (CQDs-PIL-Eu3+) was prepared by a simple one-step hydrothermal method using carbon quantum dots (CQDs) as an internal reference fluorescence and a covalent bond between CQDs and Eu3+ by using a polyionic liquid (PIL) as a bridge molecule. The ratiometric fluorescence probe was found to have the characteristics of sensitive fluorescence visual sensing in detecting DPA. The structure and the sensing properties of CQDs-PIL-Eu3+ were investigated in detail. In particular, the fluorescence intensity ratio of Eu3+ to CQDs (I616/I440) was linear with the concentration of DPA in the range of 0-50 μM, so the detection limit of the probe was as low as 32 nm, which was far lower than the DPA dose released by the number of anthrax spores in human body (60 μM) and, thus, can achieve sensitive detection. Therefore, the ratiometric fluorescence probe in this work has the characteristics of strong anti-interference, visual sensing, and high sensitivity, which provides a very promising scheme for the realization of anthrax biomarker DPA detection.

Development of Copper Complexes with Diimines and Dipicolinate as Anticancer Cytotoxic Agents

Coordination complexes may act as anticancer agents. Among others, the formation of the complex may facilitate the ligand uptake by the cell. Searching for new copper compounds with cytotoxic activity, the complex Cu-dipicolinate was studied as a neutral scaffold to form ternary complexes with diimines. A series of [Cu(dipicolinate)(diimine)] complexes (where diimine: Phenanthroline, phen, 5-NO₂-phenanthroline, 4-methyl-phenanthroline, neocuproine, 3,4,7,8-tetramethyl-phenanthroline, tmp, bathophenanthroline, bipyridine, dimethyl-bipyridine, as well as the ligand 2,2-dipyridil-amine, bam) were synthesized and characterized both in the solid state, including a new crystal structure of [Cu₂(dipicolinate)₂(tmp)₂]·7H₂O. Their chemistry in aqueous solution was explored by UV/vis spectroscopy, conductivity, cyclic voltammetry, and electron paramagnetic resonance studies. Their DNA binding was analyzed by electronic spectroscopy (determining K_b values), circular dichroism, and viscosity methods. The cytotoxicity of the complexes was assessed on human cancer cell lines MDA-MB-231, MCF-7 (breast, the first triple negative), A549 (lung epithelial) and A2780cis (ovarian, Cisplatin-resistant), and non-tumor cell lines MRC-5 (lung) and MCF-10A (breast). The major species are ternary, in solution and solid state. Complexes are highly cytotoxic as compared to Cisplatin. Complexes containing bam and phen are interesting candidates to study their in vivo activity in triple-negative breast cancer treatment.

Zwitterionic or Not? Fast and Reliable Structure Determination by Combining Crystal Structure Prediction and Solid-State NMR

When it comes to crystal structure determination, computational approaches such as Crystal Structure Prediction (CSP) have gained more and more attention since they offer some insight on how atoms and molecules are packed in the solid state, starting from only very basic information without diffraction data. Furthermore, it is well known that the coupling of CSP with solid-state NMR (SSNMR) greatly enhances the performance and the accuracy of the predictive method, leading to the so-called CSP-NMR crystallography (CSP-NMRX). In this paper, we present the successful application of CSP-NMRX to determine the crystal structure of three structural isomers of pyridine dicarboxylic acid, namely quinolinic, dipicolinic and dinicotinic acids, which can be in a zwitterionic form, or not, in the solid state. In a first step, mono- and bidimensional SSNMR spectra, i.e., ¹H Magic-Angle Spinning (MAS), ¹³C and ¹⁵N Cross Polarisation Magic-Angle Spinning (CPMAS), ¹H Double Quantum (DQ) MAS, ¹H-¹³C HETeronuclear CORrelation (HETCOR), were used to determine the correct molecular structure (i.e., zwitterionic or not) and the local molecular arrangement; at the end, the RMSEs between experimental and computed ¹H and ¹³C chemical shifts allowed the selection of the correct predicted structure for each system. Interestingly, while quinolinic and dipicolinic acids are zwitterionic and non-zwitterionic, respectively, in the solid state, dinicotinic acid exhibits in its crystal structure a "zwitterionic-non-zwitterionic continuum state" in which the proton is shared between the carboxylic moiety and the pyridinic nitrogen. Very refined SSNMR experiments were carried out, i.e., ¹⁴N-¹H Phase-Modulated (PM) pulse and Rotational-Echo Saturation-Pulse Double-Resonance (RESPDOR), to provide an accurate N-H distance value confirming the hybrid nature of the molecule. The CSP-NMRX method showed a remarkable match between the selected structures and the experimental ones. The correct molecular input provided by SSNMR reduced the number of CSP calculations to be performed, leading to different predicted structures, while RMSEs provided an independent parameter with respect to the computed energy for the selection of the best candidate.

The Novel Monooxygenase Gene dipD in the dip Gene Cluster of Alcaligenes faecalis JQ135 Is Essential for the Initial Catabolism of Dipicolinic Acid

Dipicolinic acid (DPA), an essential pyridine derivative biosynthesized in Bacillus spores, constitutes a major proportion of global biomass carbon pool. Alcaligenes faecalis strain JQ135 could catabolize DPA through the "3HDPA (3-hydroxydipicolinic acid) pathway." However, the genes involved in this 3HDPA pathway are still unknown. In this study, a dip gene cluster responsible for DPA degradation was cloned from strain JQ135. The expression of dip genes was induced by DPA and negatively regulated by DipR. A novel monooxygenase gene, dipD, was crucial for the initial hydroxylation of DPA into 3HDPA and proposed to encode the key catalytic component of the multicomponent DPA monooxygenase. The heme binding protein gene dipF, ferredoxin reductase gene dipG, and ferredoxin genes dipJ/dipK/dipL were also involved in the DPA hydroxylation and proposed to encode other components of the multicomponent DPA monooxygenase. The ¹⁸O₂ stable isotope labeling experiments confirmed that the oxygen atom in the hydroxyl group of 3HDPA came from dioxygen molecule rather than water. The protein sequence of DipD exhibits no significant sequence similarities with known oxygenases, suggesting that DipD was a new member of oxygenase family. Moreover, bioinformatic survey suggested that the dip gene cluster was widely distributed in many Alpha-, Beta-, and Gammaproteobacteria, including soil bacteria, aquatic bacteria, and pathogens. This study provides new molecular insights into the catabolism of DPA in bacteria. IMPORTANCE Dipicolinic acid (DPA) is a natural pyridine derivative that serves as an essential component of the Bacillus spore. DPA accounts for 5 to 15% of the dry weight of spores. Due to the huge number of spores in the environment, DPA is also considered to be an important component of the global biomass carbon pool. DPA could be decomposed by microorganisms and enter the global carbon cycling; however, the underlying molecular mechanisms are rarely studied. In this study, a DPA catabolic gene cluster (dip) was cloned and found to be widespread in Alpha-, Beta-, and Gammaproteobacteria. The genes responsible for the initial hydroxylation of DPA to 3-hydroxyl-dipicolinic acid were investigated in Alcaligenes faecalis strain JQ135. The present study opens a door to elucidate the mechanism of DPA degradation and its possible role in DPA-based carbon biotransformation on earth.

The SpoVA membrane complex is required for dipicolinic acid import during sporulation and export during germination

In response to starvation, endospore-forming bacteria differentiate into stress-resistant spores that can remain dormant for years yet rapidly germinate and resume growth in response to nutrients. The small molecule dipicolinic acid (DPA) plays a central role in both the stress resistance of the dormant spore and its exit from dormancy during germination. The spoVA locus is required for DPA import during sporulation and has been implicated in its export during germination, but the molecular bases are unclear. Here, we define the minimal set of proteins encoded in the Bacillus subtilis spoVA operon required for DPA import and demonstrate that these proteins form a membrane complex. Structural modeling of these components combined with mutagenesis and in vivo analysis reveal that the C and Eb subunits form a membrane channel, while the D subunit functions as a cytoplasmic plug. We show that point mutations that impair the interactions between D and the C-Eb membrane complex reduce the efficiency of DPA import during sporulation and reciprocally accelerate DPA release during germination. Our data support a model in which DPA transport into spores involves cycles of unplugging and then replugging the C-Eb membrane channel, while nutrient detection during germination triggers DPA release by unplugging it.

Multi-Functional Silver Nanoparticles for High-Throughput Endospore Sensing

In spore-forming bacteria such as Bacillus and Clostridium, the vegetative cells form highly durable hard shells called endospores inside the bacteria to survive as the growth environment deteriorates. Because of these properties, endospores can cause food poisoning and medical accidents if they contaminate food, medicine, or other products, and it is required for technology to detect the spores at the manufacturing site. In this study, we focused on the surface-enhanced Raman scattering (SERS) method for the sensitive detection of dipicolinic acid (DPA), a molecular marker of endospores. We constructed Fe₃O₄/Ag core-shell functional silver nanoparticles that specifically bind to DPA, and investigated a method for the qualitative detection of DPA by SERS and the quantitative detection of DPA by fluorescence method using a terbium complex formed on the surface. As a result, the concentration of the functional silver nanoparticles constructed could detect spore-derived DPA by fluorescence detection method, and SERS was several tens of nM. The functionalized nanoparticles can detect DPA quantitatively and qualitatively, and are expected to be applied to detection technology in the production of food and pharmaceuticals.

Contactless and robust dielectric microspheres-assisted surface-enhanced Raman scattering sensitivity improvement for anthrax biomarker detection

This report presents a contactless and robust dielectric microspheres (DMs)-assisted surface enhanced Raman scattering (SERS) enhancement method to improve SERS detection sensitivity detection sensitivity. DMs that could focus and collect light were embedded within the polydimethylsiloxane (PDMS) film to avoid direct contact with the analytical solution and improve detection reliability. The as prepared DMs embedded PDMS DMs PD MS film was integrated with a microfluidic technique to enhance the SERS signal of a liquid substrate. Detection in microfluidic systems can reduce reagent consumption, shorten assay time, and avoid evaporation of the colloid substrate solution. The robustness and potential influencing factors of DMs PDMS film assisted SERS enhancement (DERS) were evaluated using 4-aminothiophenol (4-ATP) as the Raman probe. The sensing performance of the proposed method toward dipicolinic acid (DPA) was evaluated, and an evident signal intensification was obtained. Remarkably, the DMs PDMS film can also be implemented on solid substrates. A proof-of-concept experiment was performed by covering the DMs PDMS film directly over an AgNPs@Si solid substrate wherein a 5.7-fold sensitivity improvement was achieved.

Carbapenemase-Producing Gram-Negative Bacteria in Andalusia, Spain, 2014-2018

The emergence and spread of carbapenemase-producing gram-negative bacteria is a major public health concern. We used data collected from microbiology laboratories as part of the PIRASOA program during 2014-2018 to study the epidemiology of carbapenemase-producing bacteria in Andalusia, Spain. Our findings highlight the importance of ongoing surveillance and epidemiologic studies for these bacteria.

Antifungal Mechanism of Dipicolinic Acid and Its Efficacy for the Biocontrol of Pear Valsa Canker

Valsa pyri is a fatal canker pathogen that causes significant reduction of crop yield in pear orchards. V. pyri invades the trunk phloem, and is difficult to control by chemical treatment. In this work, it was found for the first time that Bacillus subtilis-produced dipicolinic acid (DPA) exhibits antifungal activity against different canker pathogens, including Alteraria alternata, Botryosphaeria dothidea, Rhizoctonia solani, and V. pyri. Growth inhibition of V. pyri was observed at less than 5 mM concentration (pH = 5.6). DPA showed the highest antifungal activity at acidic pH values and in the presence of bivalent metals, such as zinc(II), cobalt(II), and copper(II). Measurement of mRNA expression levels and scanning electron microscope (SEM) observations revealed that DPA causes V. pyri apoptosis via inhibition of chitin biosynthesis and subsequent cell lysis. Interestingly, DPA showed high stability in the pear bark and was able to cross the pear tree bark into the phloem, protecting the internal phases of the pear trunk. In preventive applications, DPA reduced the canker symptoms of V. pyri on Cuigan pear trees by 90%. Taken together, an efficient strategy for the management of V. pyri-caused canker disease was developed using a novel antifungal agent, DPA, with strong antifungal activity and particular diffusion properties.

Evaluation of inhibitor-combination mCIM for detecting MBL-producing Enterobacterales using three MBL inhibitors

The increase in carbapenemase-producing Enterobacterales (CPE), including metallo-β-lactamase (MBL) producers, is a severe global health concern. Thus, highly sensitive and specific methods for detecting MBL producers are needed. In this study, we tested the detectability of MBL-producing Enterobacterales against three types of MBL inhibitors (sodium mercaptoacetate, SMA; ethylenediaminetetraacetic acid, EDTA; and dipicolinic acid, DPA) used in combination with a modified carbapenem inactivation method (mCIM). These inhibitor-combination mCIMs were tested against 129 CPE (IMP, 93; NDM, 11; KPC, 13; NMC, 1; OXA-48, 11) and 75 non-CPE. For evaluation of MBL inhibitors, we used two concentrations for each of the three inhibitors: DPA (200 and 300 mg l^{- 1}), EDTA (5 and 10 mM), and SMA (1500 and 3000 mg l^{- 1}). The overall sensitivities of SMA, EDTA and DPA were 97.1-99.0 %, 81.7-99.0 % and 88.5-96.2 %, respectively. Moreover, each method showed high specificity (99.0-100 %). Although inhibitor-combination mCIMs were highly sensitive and specific for the detection of MBL producers, we found that sensitivity was dependent on the concentration of inhibitors.

Design of dipicolinic acid derivatives as New Delhi metallo-β-lactamase-1 inhibitors using a combined computational approach

New Delhi metallo-β-lactamase (NDM-1) is the most recent addition to the class of metallo-β-lactamases (MBLs). This enzyme leads to antibiotic resistance in clinical treatments owing to its exertion of hydrolysis activity in almost all clinically available β-lactam antibiotics. Consequently, inhibitors targeting NDM-1 have attracted considerable research attention. However, progress has been slow regarding the study of the quantitative structure-activity relationship (QSAR) of NDM-1 inhibitors. In this study, a three-dimensional QSAR (3 D-QSAR) for NDM-1 inhibitors was established using Topomer CoMFA. The multiple correlation coefficients of the fitting model, leave-one-out cross validation, and external validation were found to be 0.761, 0.976, and 0.972, respectively. Topomer Search was used to design 16 new molecules that inhibit NDM-1 using R-group search from ZINC databases, 10 of which had comparatively high activities against NDM-1. The results indicate that Topomer CoMFA and Topomer Search can be used to design new NDM-1 inhibitors and guide the design of new NDM-1 drugs with good predictive capability. Furthermore, from molecular modeling and binding free-energy calculation, it was found that the newly designed molecules can bind to the catalytic region of NDM-1. Additionally, the newly designed inhibitors formed strong interactions with Ile35, Met67, Phe70, Trp93, His122, His189, Cys208, and His250 around the Zn²⁺-centered active region of NDM-1. These findings will facilitate the development of more effective NDM-1 inhibitors for use as potential antibacterial agents.Communicated by Ramaswamy H. Sarma.

Terbium Functionalized Schizochytrium-Derived Carbon Dots for Ratiometric Fluorescence Determination of the Anthrax Biomarker

Efficient and instant detection of biological threat-agent anthrax is highly desired in the fields of medical care and anti-terrorism. Herein, a new ratiometric fluorescence (FL) nanoprobe was elaborately tailored for the determination of 2,6-dipicolinic acid (DPA), a biomarker of anthrax spores, by grafting terbium ions (Tb³⁺) to the surface of carbon dots (CDs). CDs with blue FL were fabricated by a simple and green method using schizochytrium as precursor and served as an FL reference and a supporting substrate for coordination with Tb³⁺. On account of the absorbance energy transfer emission effect (AETE), green emission peaks of Tb³⁺ in CDs-Tb nanoprobe appeared at 545 nm upon the addition of DPA. Under optimal conditions, good linearity between the ratio FL intensity of F₅₄₅/F₄₄₅ and the concentrations of DPA was observed within the experimental concentration range of 0.5–6 μM with the detection limit of 35.9 nM, which is superior to several literature studies and significantly lower than the infectious dosage of the Bacillus anthracis spores. Moreover, the CDs-Tb nanoprobe could sensitively detect DPA in the lake water sample. This work offers an efficient self-calibrating and background-free method for the determination of DPA.

Determination of Dipicolinic Acid in "Natto" by High-Performance Liquid Chromatography Coupled With Postcolumn Photoirradiation With Zinc Acetate

A system was developed for determining dipicolinic acid in “natto” using liquid chromatography with fluorometric detection. The compound was separated by reversed-phase chromatography using a mobile phase of 0.1 mol/L disodium hydrogen phosphate, 0.05 mol/L citric acid buffer (adjusted to pH 3.0) containing 3.0 mmol/L zinc acetate and 35 mmol/L perchloric acid. The compound in the column effluent was irradiated with ultraviolet light to produce fluorescence. This fluorescence was monitored at an excitation at 336 nm and an emission at 448 nm. The calibration curve for dipicolinic acid was observed to be linear in a range of 0.2 to 112 ng. The dipicolinic acid content of natto was 7.24 ± 0.54 mg/100 g (wet weight, mean ± standard deviation [SD], n = 6).

Investigation of Dipicolinic Acid Isosteres for the Inhibition of Metallo-β-Lactamases

New Delhi metallo-β-lactamase-1 (NDM-1) poses an immediate threat to our most effective and widely prescribed drugs, the β-lactam-containing class of antibiotics. There are no clinically relevant inhibitors to combat NDM-1, despite significant efforts toward their development. Inhibitors that use a carboxylic acid motif for binding the Zn^II ions in the active site of NDM-1 make up a large portion of the >500 inhibitors reported to date. New and structurally diverse scaffolds for inhibitor development are needed urgently. Herein we report the isosteric replacement of one carboxylate group of dipicolinic acid (DPA) to obtain DPA isosteres with good inhibitory activity against NDM-1 (and related metallo-β-lactamases, IMP-1 and VIM-2). It was determined that the choice of carboxylate isostere influences both the potency of NDM-1 inhibition and the mechanism of action. Additionally, we show that an isostere with a metal-stripping mechanism can be re-engineered into an inhibitor that favors ternary complex formation. This work provides a roadmap for future isosteric replacement of routinely used metal binding motifs (i.e., carboxylic acids) for the generation of new entities in NDM-1 inhibitor design and development.

GdPO4-Based Nanoprobe for Bioimaging and Selective Recognition of Dipicolinic Acid and Cysteine by a Sensing Ensemble Approach

Multiple functions incorporated in one single-component nanoplatform pave the way for important biomedicine applications. Herein, a multifunctional terbium-doped gadolinium orthophosphate (GdPO₄:Tb-EDTA) nanoplatform was prepared through a simple, ecofriendly, one-step hydrothermal method. Results showed that dipicolinic acid (DPA), the biomarker of bacterial spores, significantly increased the fluorescence intensity of this nanoplatform and conferred it with rapid response and excellent selectivity. Subsequently, the fluorescence of the ensemble GdPO₄:Tb-EDTA-DPA can be remarkably quenched by Cu²⁺, which led to a rewritable nanosensor used in the detection of cysteine (Cys) with excellent sensitivity. In addition, GdPO₄:Tb-EDTA can also be a potential T₁-weighted magnetic resonance imaging (MRI) contrast agent, which indicated a satisfactory in vitro MRI with r₁ relaxivity values of 13.9 mM^-1 s^-1 and in vivo MRI through intravenous administration on a rat model. Overall, the proposed assay may have great theoretical and practical significance for designing multifunctional biomaterials.

Terbium (III) coordination polymer-copper (II) compound as fluorescent probe for time-resolved fluorescence 'turn-on' detection of hydrogen sulfide

With recognition of the biological importance of hydrogen sulfide (H₂ S), we present a simple and effective fluorescent probe for H₂ S using a Tb³⁺ coordination polymer-Cu²⁺ compound (DPA/Tb/G-Cu²⁺ ). Dipicolinic acid (DPA) and guanosine (G) can coordinate with Tb³⁺ to form a macromolecular coordination polymer (DPA/Tb/G). DPA/Tb/G specifically binds to Cu²⁺ in the presence of coexisting cations, and obvious fluorescence quenching is observed. The quenched fluorescence can be exclusively recovered upon the addition of sulfide, which is measured in the mode of time-resolved fluorescence. The fluorescence intensities of the DPA/Tb/G-Cu²⁺ compound enhance linearly with increasing sulfide concentrations from 1 to 30 μM. The detection limit for sulfide in aqueous solution is estimated to be 0.3 μM (at 3σ). The DPA/Tb/G-Cu²⁺ compound was successfully applied to sense H₂ S in human serum samples and exhibited a satisfactory result. It displays some desirable properties, such as fast detection procedure, high selectivity and excellent sensitivity. This method is very promising to be utilized for practical detection of H₂ S in biological and environmental samples.

Germination of Spores of the Orders Bacillales and Clostridiales

Dormant Bacillales and Clostridiales spores begin to grow when small molecules (germinants) trigger germination, potentially leading to food spoilage or disease. Germination-specific proteins sense germinants, transport small molecules, and hydrolyze specific bonds in cortex peptidoglycan and specific proteins. Major events in germination include (a) germinant sensing; (b) commitment to germinate; (c) release of spores' depot of dipicolinic acid (DPA); (d) hydrolysis of spores' peptidoglycan cortex; and (e) spore core swelling and water uptake, cell wall peptidoglycan remodeling, and restoration of core protein and inner spore membrane lipid mobility. Germination is similar between Bacillales and Clostridiales, but some species differ in how germinants are sensed and how cortex hydrolysis and DPA release are triggered. Despite detailed knowledge of the proteins and signal transduction pathways involved in germination, precisely what some germination proteins do and how they do it remain unclear.

Genetic Characterization of the Exceptionally High Heat Resistance of the Non-toxic Surrogate Clostridium sporogenes PA 3679

Clostridium sporogenes PA 3679 is a non-toxic endospore former that is widely used as a surrogate for Clostridium botulinum by the food processing industry to validate thermal processing strategies. PA 3679 produces spores of exceptionally high heat resistance without botulinum neurotoxins, permitting the use of PA 3679 in inoculated pack studies while ensuring the safety of food processing facilities. To identify genes associated with this heat resistance, the genomes of C. sporogenes PA 3679 isolates were compared to several other C. sporogenes strains. The most significant difference was the acquisition of a second spoVA operon, spoVA2, which is responsible for transport of dipicolinic acid into the spore core during sporulation. Interestingly, spoVA2 was also found in some C. botulinum species which phylogenetically cluster with PA 3679. Most other C. sporogenes strains examined both lack the spoVA2 locus and are phylogenetically distant within the group I Clostridium, adding to the understanding that C. sporogenes are dispersed C. botulinum strains which lack toxin genes. C. sporogenes strains are thus a very eclectic group, and few strains possess the characteristic heat resistance of PA 3679.

Dipicolinic Acid Release and the Germination of Alicyclobacillus acidoterrestris Spores under Nutrient Germinants

The presence of Alicyclobacillus, a thermoacidophilic and spore-forming bacterium, in acidic fruit juices poses a serious problem for the processing industry. A typical sign of spoilage in contaminated juices is a characteristic phenolic off-flavour associated with the production of guaiacol. Spores are formed in response to starvation and in a natural environment re-access the nutrients, e.g.: L-alanine and AGFK - a mixture of asparagine, glucose, fructose and potassium, triggers germination. The aim of this study was to estimate the impact of L-alanine and AGFK on the germination of the spores of two Alicyclobacillus acidoterrestris strains and to evaluate the relationship of the germination rate with dipicolinic acid (DPA) release. The spores were suspended in apple juice or in buffers at pH 4 and pH 7, followed by the addition of L-alanine and AGFK. Suspensions were or were not subjected, to a temperature of 80°C/10 min and incubated for various periods of time at 45°C. Optical density (OD660) was used to estimate the number of germinated spores. The amount of DPA released was determined using HPLC. The results indicate that the degree of germination of A. acidoterrestris spores depended on the strain and time of incubation and the nutritious compounds used. The data obtained show that the amount of DPA released correlated to the number of A. acidoterrestris spores germinated.

Identity, Abundance, and Reactivation Kinetics of Thermophilic Fermentative Endospores in Cold Marine Sediment and Seawater

Cold marine sediments harbor endospores of fermentative and sulfate-reducing, thermophilic bacteria. These dormant populations of endospores are believed to accumulate in the seabed via passive dispersal by ocean currents followed by sedimentation from the water column. However, the magnitude of this process is poorly understood because the endospores present in seawater were so far not identified, and only the abundance of thermophilic sulfate-reducing endospores in the seabed has been quantified. We investigated the distribution of thermophilic fermentative endospores (TFEs) in water column and sediment of Aarhus Bay, Denmark, to test the role of suspended dispersal and determine the rate of endospore deposition and the endospore abundance in the sediment. We furthermore aimed to determine the time course of reactivation of the germinating TFEs. TFEs were induced to germinate and grow by incubating pasteurized sediment and water samples anaerobically at 50°C. We observed a sudden release of the endospore component dipicolinic acid immediately upon incubation suggesting fast endospore reactivation in response to heating. Volatile fatty acids (VFAs) and H2 began to accumulate exponentially after 3.5 h of incubation showing that reactivation was followed by a short phase of outgrowth before germinated cells began to divide. Thermophilic fermenters were mainly present in the sediment as endospores because the rate of VFA accumulation was identical in pasteurized and non-pasteurized samples. Germinating TFEs were identified taxonomically by reverse transcription, PCR amplification and sequencing of 16S rRNA. The water column and sediment shared the same phylotypes, thereby confirming the potential for seawater dispersal. The abundance of TFEs was estimated by most probable number enumeration, rates of VFA production, and released amounts of dipicolinic acid during germination. The surface sediment contained ∼105-106 inducible TFEs cm-3. TFEs thus outnumber thermophilic sulfate-reducing endospores by an order of magnitude. The abundance of cultivable TFEs decreased exponentially with sediment depth with a half-life of 350 years. We estimate that 6 × 109 anaerobic thermophilic endospores are deposited on the seafloor per m2 per year in Aarhus Bay, and that these thermophiles represent >10% of the total endospore community in the surface sediment.

Dipicolinic Acid Release by Germinating Clostridium difficile Spores Occurs through a Mechanosensing Mechanism

Clostridium difficile is transmitted between hosts in the form of a dormant spore, and germination by C. difficile spores is required to initiate infection, because the toxins that are necessary for disease are not deposited on the spore form. Importantly, the C. difficile spore germination pathway represents a novel pathway for bacterial spore germination. Prior work has shown that the order of events during C. difficile spore germination (cortex degradation and DPA release) is flipped compared to the events during B. subtilis spore germination, a model organism. Here, we further characterize the C. difficile spore germination pathway and summarize our findings indicating that DPA release by germinating C. difficile spores occurs through a mechanosensing mechanism in response to the degradation of the spore cortex.

Classically, dormant endospores are defined by their resistance properties, particularly their resistance to heat. Much of the heat resistance is due to the large amount of dipicolinic acid (DPA) stored within the spore core. During spore germination, DPA is released and allows for rehydration of the otherwise-dehydrated core. In Bacillus subtilis, 7 proteins are encoded by the spoVA operon and are important for DPA release. These proteins receive a signal from the activated germinant receptor and release DPA. This DPA activates the cortex lytic enzyme CwlJ, and cortex degradation begins. In Clostridium difficile, spore germination is initiated in response to certain bile acids and amino acids. These bile acids interact with the CspC germinant receptor, which then transfers the signal to the CspB protease. Activated CspB cleaves the cortex lytic enzyme, pro-SleC, to its active form. Subsequently, DPA is released from the core. C. difficile encodes orthologues of spoVAC, spoVAD, and spoVAE. Of these, the B. subtilis SpoVAC protein was shown to be capable of mechanosensing. Because cortex degradation precedes DPA release during C. difficile spore germination (opposite of what occurs in B. subtilis), we hypothesized that cortex degradation would relieve the osmotic constraints placed on the inner spore membrane and permit DPA release. Here, we assayed germination in the presence of osmolytes, and we found that they can delay DPA release from germinating C. difficile spores while still permitting cortex degradation. Together, our results suggest that DPA release during C. difficile spore germination occurs though a mechanosensing mechanism.

IMPORTANCEClostridium difficile is transmitted between hosts in the form of a dormant spore, and germination by C. difficile spores is required to initiate infection, because the toxins that are necessary for disease are not deposited on the spore form. Importantly, the C. difficile spore germination pathway represents a novel pathway for bacterial spore germination. Prior work has shown that the order of events during C. difficile spore germination (cortex degradation and DPA release) is flipped compared to the events during B. subtilis spore germination, a model organism. Here, we further characterize the C. difficile spore germination pathway and summarize our findings indicating that DPA release by germinating C. difficile spores occurs through a mechanosensing mechanism in response to the degradation of the spore cortex.

Variability in DPA and Calcium Content in the Spores of Clostridium Species

Spores of a number of clostridial species, and their resistance to thermal treatment is a major concern for the food industry. Spore resistance to wet heat is related to the level of spore hydration, which is inversely correlated with the content of calcium and dipicolinic acid (DPA) in the spore core. It is widely believed that the accumulation of DPA and calcium in the spore core is a fundamental component of the sporulation process for all endospore forming species. We have noticed heterogeneity in the heat resistance capacity and overall DPA/calcium content among the spores of several species belonging to Clostridium sensu stricto group: two C. acetobutylicum strains (DSM 792 and 1731), two C. beijerinckii strains (DSM 791 and NCIMB 8052), and a C. collagenovorans strain (DSM 3089). A C. beijerinckii strain (DSM 791) and a C. acetobutylicum strain (DSM 792) display low Ca and DPA levels. In addition, these two species, with the lowest average Ca/DPA content amongst the strains considered, also exhibit minimal heat resistance. There appears to be no correlation between the Ca/DPA content and the phylogenetic distribution of the C. acetobutylicum and C. beijerinckii species based either on the 16S rRNA or the spoVA gene. This finding suggests that a subset of Clostridium sensu stricto species produce spores with low resistance to wet heat. Additionally, analysis of individual spores using STEM-EDS and STXM revealed that DPA and calcium levels can also vary amongst individual spores in a single spore population.

A new three-dimensional coordination polymer of Sr(II) based on dipicolinic acid, with different coordination environments for Sr(II)

A three-dimensional coordination polymer of Sr(II) based on dipicolinic acid (pydcH2) has been synthesized and characterized, namely poly[[diaquabis(μ3-6-carboxypyridine-2-carboxylato)bis(μ4-pyridine-2,6-dicarboxylato)tristrontium(II)] dihydrate], {[Sr3(C7H3NO4)2(C7H4NO4)2(H2O)2]·2H2O}n. The asymmetric unit consists of two unique Sr(II) centres (one of them situated on an inversion centre), two independent pydc(2-) ligands, and one coordinated and one uncoordinated water molecule. The two independent Sr(II) cations are surrounded by water and dipicolinate molecules in distorted square-antiprism and distorted tricapped trigonal prismatic geometries. The dipicolinate ligands adopt μ3- and μ4-bridging modes, linking the alkaline earth metal centres into a three-dimensional coordination framework. One dipicolinate ligand is doubly deprotonated, while the other is singly deprotonated.

A disc diffusion assay for detection of class A, B and OXA-48 carbapenemases in Enterobacteriaceae using phenyl boronic acid, dipicolinic acid and temocillin

Class A and B carbapenemases in Enterobacteriaceae may be detected using carbapenemase inhibition tests with boronic acid derivatives (BA) and dipicolinic acid (DPA)/EDTA, respectively. However, for OXA-48 (like) carbapenemases, no specific inhibitor is available. Because OXA-48 confers high-level temocillin resistance, a disc diffusion assay using temocillin as well as BA and DPA inhibition tests was evaluated for detection of class A, B and OXA-48 carbapenemases. The test collection included 128 well-characterized non-repeat Enterobacteriaceae isolates suspected of carbapenemase production; that is, with meropenem MICs ≥ 0.5 mg/L, including 99 carbapenemase producers (36 KPC, one GES, 31 MBL, four KPC plus VIM, 25 OXA-48, two OXA-162), and 29 ESBL and/or AmpC-producing isolates. PCR and sequencing of beta-lactamase genes was used as a reference test. Phenotypic carbapenemase detection was performed with discs (Rosco) containing meropenem (10 μg), temocillin (30 μg), meropenem + phenyl boronic acid (PBA), meropenem + DPA, meropenem + BA + DPA, and meropenem + cloxacillin (CL). Absence of synergy between meropenem and BA and/or DPA and a temocillin zone ≤10 mm was used to identify OXA-48. The sensitivity for identification of class A, B and OXA-48 carbapenemases was 95%, 90% and 100%, with 96-100% specificity. In non-Proteus species, the sensitivity for class B carbapenemase detection was 97%. All isolates without PBA or DPA synergy and a temocillin disc zone ≤10 mm were OXA-48 (like) positive. In conclusion, carbapenemase inhibition tests with PBA and DPA combined with a temocillin disc provide a reliable phenotypic confirmation method for class A, B and OXA-48 carbapenemases in Enterobacteriaceae.

The GerW protein is essential for L-alanine-stimulated germination of Bacillus subtilis spores

GerW (formerly called YtfJ) is a protein found in dormant spores of Bacillus subtilis. We have studied spore proteins in B. subtilis before, and here we report the characterization of GerW protein. Northern blot analysis revealed that gerW mRNA was transcribed by SigF-containing RNA polymerase beginning 1 h after the initiation of sporulation. Fluorescence was detected in forespores and dormant spores of B. subtilis recombinant strains expressing GerW-GFP. During germination in the presence of L-alanine or a mixture of L-asparagine, D-glucose, D-fructose and potassium ions (AGFK), normal spores of B. subtilis became darkened, stained positive with Hoechst 33342 and carboxyfluorescein diacetate succinimidyl ester (CFDA-SE), and released dipicolinic acid (DPA). In the case of gerW-deficient spores, AGFK triggered germination in a manner similar to that seen in the wild-type spores, whereas spores stimulated by L-alanine remained refractive under the phase contrast microscope, failed to stain positive with Hoechst 33342 or CFDA-SE, and released almost no DPA. These results indicate that GerW is essential for the L-alanine-induced breakdown of spore dormancy followed by core rehydration and the resumption of enzymatic activity, and suggest that GerW is involved in the early stages of germination in the presence of l-alanine.

Revisiting zinc coordination in human carbonic anhydrase II

Carbonic anhydrase (CA, general abbreviation for human carbonic anhydrase II) is a well-studied, zinc-dependent metalloenzyme that catalyzes hydrolysis of carbon dioxide to the bicarbonate ion. The apo-form of CA (apoCA, CA where Zn(2+) ion has been removed) is relatively easy to generate, and reconstitution of the human erythrocyte CA has been initially investigated. In the past, these studies have continually relied on equilibrium dialysis measurements to ascertain an extremely strong association constant (K(a) ≈ 1.2 × 10(12)) for Zn(2+). However, new reactivity data and isothermal titration calorimetry (ITC) data reported herein call that number into question. As shown in the ITC experiments, the catalytic site binds a stoichiometric quantity of Zn(2+) with a strong equilibrium constant (K(a) ≈ 2 × 10(9)) that is 3 orders of magnitude lower than the previously established value. Thermodynamic parameters associated with Zn(2+) binding to apoCA are unraveled from a series of complex equilibria associated with the in vitro metal binding event. This in-depth analysis adds clarity to the complex ion chemistry associated with zinc binding to carbonic anhydrase and validates thermochemical methods that accurately measure association constants and thermodynamic parameters for complex-ion and coordination chemistry observed in vitro. Additionally, the zinc sites in both the as-isolated and the reconstituted ZnCA (active CA containing a mononuclear Zn(2+) center) were probed using X-ray absorption spectroscopy. Both X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analyses indicate the zinc center in the reconstituted carbonic anhydrase is nearly identical to that of the as-isolated protein and confirm the notion that the metal binding data reported herein is the reconstitution of the zinc active site of human CA II.

Anti-diabetic effects of a series of vanadium dipicolinate complexes in rats with streptozotocin-induced diabetes

The effects of oral treatment of rats with streptozotocin-induced diabetes with a range of vanadium dipicolinate complexes (Vdipic) and derivatives are reviewed. Structure-reactivity relationships are explored aiming to correlate properties such as stability, to their insulin-enhancing effects. Three types of modifications are investigated; first, substitutions on the aromatic ring, second, coordination of a hydroxylamido group to the vanadium, and third, changes in the oxidation state of the vanadium ion. These studies allowed us to address the importance of coordination chemistry, and redox chemistry, as modes of action. Dipicolinate was originally chosen as a ligand because the dipicolinatooxovanadium(V) complex (V5dipic), is a potent inhibitor of phosphatases. The effect of vanadium oxidation state (3, 4 or 5), on the insulin-enhancing properties was studied in both the Vdipic and VdipicCl series. Effects on blood glucose, body weight, serum lipids, alkaline phosphatase and aspartate transaminase were selectively monitored. Statistically distinct differences in activity were found, however, the trends observed were not the same in the Vdipic and VdipicCl series. Interperitoneal administration of the Vdipic series was used to compare the effect of administration mode. Correlations were observed for blood vanadium and plasma glucose levels after V5dipic treatment, but not after treatment with corresponding V4dipic and V3dipic complexes. Modifications of the aromatic ring structure with chloride, amine or hydroxyl groups had limited effects. Global gene expression was measured using Affymetrix oligonucleotide chips. All diabetic animals treated with hydroxyl substituted V5dipic (V5dipicOH) and some diabetic rats treated with vanadyl sulfate had normalized hyperlipidemia yet uncontrolled hyperglycemia and showed abnormal gene expression patterns. In contrast to the normal gene expression profiles previously reported for some diabetic rats treated with vanadyl sulfate, where both hyperlipidemia and hyperglycemia were normalized. Modification of the metal, changing the coordination chemistry to form a hydroxylamine ternary complex, had the most influence on the anti-diabetic action. Vanadium absorption into serum was determined by atomic absorption spectroscopy for selected vanadium complexes. Only diabetic rats treated with the ternary V5dipicOH hydroxylamine complex showed statistically significant increases in accumulation of vanadium into serum compared to diabetic rats treated with vanadyl sulfate. The chemistry and physical properties of the Vdipic complexes correlated with their anti-diabetic properties. Here, we propose that compound stability and ability to interact with cellular redox reactions are key components for the insulin-enhancing activity of vanadium compounds. Specifically, we found that the most overall effective anti-diabetic Vdipic compounds were obtained when the compound administered had an increased coordination number in the vanadium complex.

Recent Advances in Real-time Mass Spectrometry Detection of Bacteria

The analysis of bio-aerosols poses a technology challenge, particularly when sampling and analysis are done in situ. Mass spectrometry laboratory technology has been modified to achieve quick bacteria typing of aerosols in the field. Initially, aerosol material was collected and subjected off-line to minimum sample treatment and mass spectrometry analysis. More recently, sampling and analysis were combined in a single process for the real-time analysis of bio-aerosols in the field. This chapter discusses the development of technology for the mass spectrometry of bio-aerosols, with a focus on bacteria aerosols. Merits and drawbacks of the various technologies and their typing signatures are discussed. The chapter concludes with a brief view of future developments in bio-aerosol mass spectrometry.

Investigating the vanadium environments in hydroxylamido V(V) dipicolinate complexes using 51V NMR spectroscopy and density functional theory

Using (51)V magic angle spinning solid-state NMR, SSNMR, spectroscopy and quantum chemical DFT calculations we have characterized the chemical shift and quadrupolar coupling parameters of a series of eight hydroxylamido vanadium(V) dipicolinate complexes of the general formula VO(dipic)(ONR1R2)(H2O) where R1 and R2 can be H, CH3, or CH2CH3. This class of vanadium compounds was chosen for investigation because of their seven-coordinate vanadium atom, a geometry for which there is limited (51)V SSNMR data. Furthermore, a systematic series of compounds with different electronic properties are available and allows for the effects of ligand substitution on the NMR parameters to be studied. The quadrupolar coupling constants, C(Q), are small, 3.0-3.9 MHz, but exhibit variations as a function of the ligand substitution. The chemical shift tensors in the solid state are sensitive to changes in both the hydroxylamide substituent and the dipic ligand, a sensitivity which is not observed for isotropic chemical shifts in solution. The chemical shift tensors span approximately 1000 ppm and are nearly axially symmetric. On the basis of DFT calculations of the chemical shift tensors, one of the largest contributors to the magnetic shielding anisotropy is an occupied molecular orbital with significant vanadium d(z)2 character along the V=O bond.

Sporostatic, Sporicidal, and Heat-Sensitizing Action of Maleic Acid against Spores of Proteolytic Clostridium botulinum

The antibotulinal potential of maleic acid was investigated in an uncured turkey product and model systems. There was a dose-related delay in neurotoxin detection, with no toxin developing after 40 days at 28°C with 500 or 1,500 Clostridium botulinum spores per g and 2% maleic acid. Anaerobic and aerobic microflora were suppressed by maleic acid, and pH remained constant during the incubation period. Sporicidal and sporostatic concentrations were 19.5 and 2.4 mM, respectively, in broth. The 8-day sporostatic levels were >5 and 2 mM for canned chicken and beef broths, respectively. Dipicolinic acid release was reduced by 50% with 0.25 mM maleic acid. Maleic acid also lowered spore thermal resistance at 80°C. These data indicate that maleic acid inactivates C. botulinum spores, delays spore outgrowth, and reduces thermal resistance.