Quantification of polyprenyl diphosphates in Escherichia coli cells using high-performance liquid chromatography

Dephosphorylation of undecaprenyl diphosphate is a crucial step in the synthesis of undecaprenyl phosphate, which is essential for cell wall synthesis. We have developed a method for the quantification of intracellular polyprenyl diphosphates, which have never before been measured directly. Polyprenyl phosphates and diphosphates prepared by chemical phosphorylation of polyprenols from Staphylococcus aureus were used to establish the conditions for fractionation by ion-exchange chromatography and high-performance liquid chromatography (HPLC). By using an elution solvent containing tetraethylammonium phosphate as an ion-pair reagent for HPLC, polyprenyl phosphate and polyprenyl diphosphate with carbon numbers from 40 to 55 could be detected as separate peaks from the reversed-phase column. This analytical method was applied to lipids extracted from Escherichia coli to determine the intracellular levels of octaprenyl phosphate, undecaprenyl phosphate, octaprenyl diphosphate, and undecaprenyl diphosphate. This is the first report of separate measurement of cellular levels of polyprenyl phosphates and polyprenyl diphosphates.

CaM kinase phosphatase (CaMKP/PPM1F/POPX2) is specifically inactivated through gallate-mediated protein carbonylation

CaMK phosphatase (CaMKP/PPM1F/POPX2) is a Mn²⁺-dependent, calyculin A/okadaic acid-insensitive Ser/Thr protein phosphatase that belongs to the PPM family. CaMKP is thought to be involved in regulation of not only various protein kinases, such as CaM kinases and p21-activated protein kinase, but also of cellular proteins regulated by phosphorylation. A large-scale screening of a chemical library identified gallic acid and some of its alkyl esters as novel CaMKP inhibitors highly specific to CaMKP. Surprisingly, they caused specific carbonylation of CaMKP, leading to its inactivation. Under the same conditions, no carbonylation nor inactivation was observed when PPM1A, which is affiliated with the same family as CaMKP, and λ-phosphatase were used. The carbonylation reaction was inhibited by SH compounds such as cysteamine in a dose-dependent manner with a concomitant decrease in CaMKP inhibition by ethyl gallate. The pyrogallol structure of gallate was necessary for the gallate-mediated carbonylation of CaMKP. Point mutations of CaMKP leading to impairment of phosphatase activity did not significantly affect the gallate-mediated carbonylation. Ethyl gallate resulted in almost complete inhibition of CaMKP under the conditions where the carbonylation level was nearly identical to that of CaMKP carbonylation via metal-catalyzed oxidation with ascorbic acid/FeSO₄, which resulted in only a partial inhibition of CaMKP. The gallate-mediated carbonylation of CaMKP absolutely required divalent cations such as Mn²⁺, Cu²⁺, Co²⁺ and Fe²⁺, and was markedly enhanced by a phosphopeptide substrate. When MDA-MB-231 cells transiently expressing CaM kinase I, a CaMKP substrate, were treated by ethyl gallate, significant enhancement of phosphorylation of CaM kinase I was observed, suggesting that ethyl gallate can penetrate into cells to inactivate cellular CaMKP. All the presented data strongly support the hypothesis that CaMKP undergoes carbonylation of its specific amino acid residues by incubation with alkyl gallates and the divalent metal cations, leading to inactivation specific to CaMKP.

A nation-wide survey of Japanese pediatric MOG antibody-associated diseases

OBJECTIVE

To elucidate the clinical characteristics of Japanese pediatric patients with acquired demyelinating diseases (ADS), positive for myelin oligodendrocyte glycoprotein antibody (MOG-IgG), we conducted a nation-wide survey.

METHODS

Information about pediatric patients under 18 years old with ADS was solicited with surveys sent to 323 facilities. In an initial survey, we asked whether the center had any patients with ADS, and the MOG-IgG serostatus of the patients. In a follow-up survey, we requested more precise information on patients with ADS.

RESULTS

Initial survey: 263 replies providing information on 175 patients were received. MOG-IgG were examined in 78 patients and 54 of those (69%) were positive for MOG-IgG. Follow-up survey: The characteristic involvement was optic neuritis, with visual disturbance and optic pain as characteristic symptoms. The relapse rate was 44% in patients positive for MOG-IgG, which was higher than that in seronegative patients (38%). For acute phase treatments, corticosteroid (CS), plasma exchange, and intravenous immunoglobulin (IVIG) were useful. To prevent relapse, CS, intermittent IVIG, immunosuppressants, and monoclonal antibodies were useful, but the efficacies of disease modifying drugs were uncertain. Sequelae such as visual disturbance, cognitive impairment, motor dysfunction, and epilepsy were observed in 11% of patients with MOG-IgG.

CONCLUSIONS

MOG antibody-associated diseases were found to be common among pediatric ADS patients. Since a variety of sequelae were observed in these patients, it is important to identify the appropriate treatment to ensure the best outcome. The presence of the MOG autoantibody should be taken into consideration as part of the diagnostic criteria for pediatric ADS.

Identification of Novel Proteins in Foam Nests of the Japanese Forest Green Tree Frog, Rhacophorus arboreus

Foam nests of frogs are natural biosurfactants that contain potential compounds for biocompatible materials, Drug Delivery System (DDS), emulsifiers, and bioremediation. To elucidate the protein components in the foam nests of Rhacophorus arboreus, which is an endemic Japanese frog species commonly seen during the rainy season, we performed amino acid analysis, SDS-PAGE electrophoresis, and matrix-assisted laser desorption/ionization mass spectrometry using intact foam nests. Many proteins were detected in these foam nests, ranging from a few to several hundred kDa, with both essential and non-essential amino acids. Next, we performed transcriptome analysis using a next-generation sequencer on total RNAs extracted from oviducts before egg-laying. The soluble foam nests were purified by LC-MS and analyzed using Edman degradation, and the identified N-terminal sequences were matched to the transcriptome data. Four proteins that shared significant sequence homologies with extracellular superoxide dismutase of Nanorana parkeri, vitelline membrane outer layer protein 1 homolog of Xenopus tropicalis, ranasmurfin of Polypedates leucomystax, and alpha-1-antichymotrypsin of Sorex araneus were identified. Prior to purification of the foam nests, they were treated with both a reducing reagent and an alkylating agent, and LC-MS/ MS analyses were performed. We identified 22 proteins in the foam nests that were homologous with proteinase inhibitors, ribonuclease, glycoproteins, antimicrobial protein and barrier, immunoglobulin-binding proteins, glycoprotein binding protein, colored protein, and keratin-associated protein. The presence of these proteins in foam nests, along with small molecules, such as carbohydrates and sugars, would protect them against microbial and parasitic attack, oxidative stress, and a shortage of moisture.

Complete mitochondrial genome sequence of Japanese forest green tree frog (Rhacophorus arboreus)

We determined the complete mitochondrial genome sequence of the Japanese forest green tree frog (Rhacophorus arboreus). The mitochondrial genome is 22,236 bp in length, which encodes 13 protein-coding genes, 2 rRNA, and 22 tRNA genes, and two control regions (D-loops). The whole gene arrangement of R. arboreus was the same as that of Rhacophorus omeimontis and Rhacophorus schlegelii.

Photoluminescent Ozone Sensor with Enhanced Sensitivity by Using CdSe/ZnS Quantum Dots Modified with Gold and Platinum

We report photoluminescence-based ozone sensing using composite films composed of gold or platinum and red-emitting CdSe/ZnS core-shell quantum dots. The sensing efficiency of quantum dots is enhanced by the addition of noble metals. The composite films undergo reversible changes in photoluminescence intensity (measured at excitation/emission wavelengths of 365/652 - 659 nm) in the presence of ppm levels of ozone in air at 25°C and at atmospheric pressure. The sensitivity of the composite films does not saturate with ozone in the 0.5 - 200 ppm concentration range. When compared with a quantum dot-only film, the composite films show higher sensitivities to 0.5 ppm ozone of 27% (gold) and 43% (platinum). When compared with a quantum dot-only film, the photoluminescence of the gold- or platinum-palladium alloy-based film recovers faster after the removal of ozone in the surrounding atmosphere. Thus, platinum- or gold-conjugated quantum-dot films form sensor modules for the reversible and highly sensitive detection of ozone under the tested ambient conditions.

Dual phosphorylation of protein phosphatase PPM1H promotes dephosphorylation of Smad1 in cellulo

Protein phosphatase PPM1H is known to participate in various biological or pathophysiological mechanisms. However, little is known about the molecular mechanisms of its regulation. In this study, we investigated the protein kinases that directly phosphorylate PPM1H, identifying them as cAMP-dependent protein kinase (PKA) and Ca²⁺/calmodulin-dependent protein kinase I (CaMKI). In vitro and in silico analyses showed that the phosphorylation sites of PPM1H by PKA and CaMKI were Ser-123 and Ser-210, respectively. The phosphorylation state of PPM1H in cells exhibited the kinase activator- and inhibitor-dependent changes. In mouse neuroblastoma Neuro2a cells, phosphorylation of Ser-210 was much higher in the phospho-mimetic mutant (S123D) than in the non-phosphorylatable mutant (S123A) when they were treated with ionomycin. This suggests that a hierarchical phosphorylation, with initial phosphorylation of Ser-123 promoting subsequent phosphorylation of Ser-210, occurs in these neuron-like cells. Moreover, in cell-based assay a PPM1H(S123A/S210A) double mutant barely dephosphorylated Smad1, a transcription factor known as an endogenous substrate of PPM1H. These results suggest that cAMP and Ca²⁺/calmodulin regulate dephosphorylation of Smad1 through the dual phosphorylation of PPM1H at Ser-123 and Ser-210.

Mass Spectrometry Analysis and Biological Characterization of the Predatory Ant Odontomachus monticola Venom and Venom Sac Components

We previously identified 92 toxin-like peptides and proteins, including pilosulin-like peptides 1–6 from the predatory ant Odontomachus monticola, by transcriptome analysis. Here, to further characterize venom components, we analyzed the venom and venom sac extract by ESI-MS/MS with or without trypsin digestion and reducing agent. As the low-molecular-mass components, we found amino acids (leucine/isoleucine, phenylalanine, and tryptophan) and biogenic amines (histamine and tyramine) in the venom and venom sac extract. As the higher molecular mass components, we found peptides and proteins such as pilosulin-like peptides, phospholipase A₂s, hyaluronidase, venom dipeptidyl peptidases, conotoxin-like peptide, and icarapin-like peptide. In addition to pilosulin-like peptides 1–6, we found three novel pilosulin-like peptides that were overlooked by transcriptome analysis. Moreover, pilosulin-like peptides 1–6 were chemically synthesized, and some of them displayed antimicrobial, hemolytic, and histamine-releasing activities.

Lipid Nanodisc Formation using Pxt-5 Peptide Isolated from Amphibian (Xenopus tropicalis) Skin, and its Altered Form, Modify-Pxt-5

Nanodiscs are self-assembled discoidal nanoparticles composed of amphiphilic α-helical scaffold proteins or peptides that accumulate around the circumference of a lipid bilayer. In this study, Pxt-5, which is an antimicrobial peptide isolated from the skin of Xenopus tropicalis, and its modified peptide (Modify-Pxt-5) were synthesized by solid-phase peptide synthesis (SPPS).Their surface properties, which are an important factor in inducing nanodisc formation, were investigated by circular dichroism (CD) spectroscopy, surface tension measurement, phospholipid vesicle clearance assay, and negative-staining transmission electron microscopy (NS-TEM). The α-helicity of Pxt-5 (8.4%) improved drastically to 45.6% by four amino-acid substitutions (Modify-Pxt-5). Both the peptides, having hydrophobic and hydrophilic faces, behaved like general surfactants, and the surface activity of Modify-Pxt-5 (CAC: 9.5×10^-5 M, γ_CAC: 30.3 mN·m^-1) was much higher than that of Pxt-5 (CAC: 7.9×10^-5 M, γ_CAC: 38.1 mN·m^-1). A turbid L-α-dimyristoylphosphatidylcholine (DMPC) vesicle solution (T = 0.3%) quickly turned transparent upon addition of Pxt-5 or Modify-Pxt-5. After twelve hours, the transmittance of vesicle solution with Modify-Pxt-5 (T = 96.2%) was found to be higher than that of vesicle solution with Pxt-5 (T = 83.5%), and then the micro-solubilized solutions were observed by NS-TEM. Interestingly, nanodisc structures were found in the vicinity of DMPC vesicles in both the images, and the average diameter of the nanodiscs was 11.2 ± 6.0 nm for those containing Pxt-5 and 10.8 ± 5.8 nm for those containing Modify-Pxt-5. It was also found that Modify-Pxt-5 effectively self-assembles into nanodiscs compared to Pxt-5 without any substitutions.

Characterization of CoPK02, a Ca2+/calmodulin-dependent protein kinase in mushroom Coprinopsis cinerea

We surveyed genome sequences from the basidiomycetous mushroom Coprinopsis cinerea and isolated a cDNA homologous to CMKA, a calmodulin-dependent protein kinase (CaMK) in Aspergillus nidulans. We designated this sequence, encoding 580 amino acids with a molecular weight of 63,987, as CoPK02. CoPK02 possessed twelve subdomains specific to protein kinases and exhibited 43, 35, 40% identity with rat CaMKI, CaMKII, CaMKIV, respectively, and 40% identity with CoPK12, one of the CaMK orthologs in C. cinerea. CoPK02 showed significant autophosphorylation activity and phosphorylated exogenous proteins in the presence of Ca²⁺/CaM. By the CaM-overlay assay we confirmed that the C-terminal sequence (Trp346-Arg358) was the calmodulin-binding site, and that the binding of Ca²⁺/CaM to CoPK02 was reduced by the autophosphorylation of CoPK02. Since CoPK02 evolved in a different clade from CoPK12, and showed different gene expression compared to that of CoPK32, which is homologous to mitogen-activated protein kinase-activated protein kinase, CoPK02 and CoPK12 might cooperatively regulate Ca²⁺-signaling in C. cinerea.

Development of Technologies for Sensing Ozone in Ambient Air

Ozone (O₃) gas is widely used as a strong oxidizing agent for many purposes, such as the decomposition/removal of organic contaminants and photoresist, and the deodorization/disinfection of air and water. However, ozone is highly toxic to the human body when the air concentration exceeds about 1 ppm. Therefore, there is increasing demand for simple, sensitive, reliable, and cost-effective techniques for sensing ozone gas. This article describes the features, advantages, and disadvantages of the available, practical techniques for sensing ozone gas in ambient air. The advantages of optical gas sensors as next-generation sensors is specifically introduced. The features of photoluminescent, semiconductor nanoparticles (quantum dots, QDs) as bright phosphors with the potential for various applications is further explored. Lastly, recent research results demonstrating the ozone sensitivity of photoluminescent CdSe-based core-shell quantum dots are presented. These results strongly suggest that optical ozone sensing using photoluminescent quantum dots is a promising technique.

Isolation of biologically active peptides from the venom of Japanese carpenter bee, Xylocopa appendiculata

Background

Mass spectrometry-guided venom peptide profiling is a powerful tool to explore novel substances from venomous animals in a highly sensitive manner. In this study, this peptide profiling approach is successfully applied to explore the venom peptides of a Japanese solitary carpenter bee, Xylocopa appendiculata (Hymenoptera: Apoidea: Apidae: Anthophila: Xylocopinae: Xylocopini). Although interesting biological effects of the crude venom of carpenter bees have been reported, the structure and biological function of the venom peptides have not been elucidated yet.

Methods

The venom peptide profiling of the crude venom of X. appendiculata was performed by matrix-assisted laser desorption/ionization-time of flight mass spectroscopy. The venom was purified by a reverse-phase HPLC. The purified peptides were subjected to the Edman degradation, MS/MS analysis, and/or molecular cloning methods for peptide sequencing. Biological and functional characterization was performed by circular dichroism analysis, liposome leakage assay, and antimicrobial, histamine releasing and hemolytic activity tests.

Results

Three novel peptides with m/z 16508, 1939.3, and 1900.3 were isolated from the venom of X. appendiculata. The peptide with m/z 16508 was characterized as a secretory phospholipase A₂ (PLA₂) homolog in which the characteristic cysteine residues as well as the active site residues found in bee PLA₂s are highly conserved. Two novel peptides with m/z 1939.3 and m/z 1900.3 were named as Xac-1 and Xac-2, respectively. These peptides are found to be amphiphilic and displayed antimicrobial and hemolytic activities. The potency was almost the same as that of mastoparan isolated from the wasp venom.

Conclusion

We found three novel biologically active peptides in the venom of X. appendiculata and analyzed their molecular functions, and compared their sequential homology to discuss their molecular diversity. Highly sensitive mass analysis plays an important role in this study.

Electronic supplementary material

The online version of this article (doi:10.1186/s40409-017-0119-6) contains supplementary material, which is available to authorized users.

Draft Genome Sequence of Caenibacillus caldisaponilyticus B157T, a Thermophilic and Phospholipase-Producing Bacterium Isolated from Acidulocompost

Caenibacillus caldisaponilyticus B157T (= NBRC 111400T = DSM 101100T), in the family Sporolactobacillaceae, was isolated from acidulocompost as a thermophilic and phospholipid-degrading bacterium. Here, we report the 3.36-Mb draft genome sequence, with a G+C content of 51.8%, to provide the genetic information coding for phospholipases.

Post-vaccination MDEM associated with MOG antibody in a subclinical Chlamydia infected boy

The mechanism of post-vaccination acute disseminated encephalomyelitis (ADEM) has been hypothesized as resulting from vaccination-injected antigens cross-reacting with myelin components, however, a precise etiology has been uncertain. In this report, we describe the case of a 6-year-old Japanese boy who had multiphasic disseminated encephalomyelitis (MDEM), and was positive for both anti-myelin oligodendrocyte glycoprotein (MOG) antibodies and Chlamydophila pneumoniae antibodies. After vaccinations that were the second one for measles and rubella, and the booster immunization for Japanese encephalitis, the patient presented with fever, headache, vomiting, and a change in personality. He was treated with a high-dose of intravenous methylprednisolone in the diagnosis of ADEM. However, these symptoms recurred with different magnetic resonance imaging lesion, and he was diagnosed as MDEM. Retrospective testing for pathogens revealed C. pneumoniae IgM and IgG antibodies, and it was considered that he was infected with C. pneumoniae subclinically. The patient's serum indicated a positive response for the anti-MOG antibody from the onset of the ADEM diagnosis and in all recurrent episodes. Chlamydia species infection has been known to play a role in demyelinating diseases. It is also known that the anti-MOG antibody may be present but not exhibit its pathogenesis in the absence of a cell-mediated inflammatory response; however, the precise mechanism of action of the anti-MOG antibodies is not yet determined. We propose the possibility that post-vaccination demyelinating disease may result from the synergistic effects of a preceding anti-MOG antibody, possibly produced in response to a subclinical Chlamydia species infection.

Caenibacillus caldisaponilyticus gen. nov., sp. nov., a thermophilic, spore-forming and phospholipid-degrading bacterium isolated from acidulocompost

A thermophilic and phospholipid-degrading bacterium, designated strain B157T, was isolated from acidulocompost, a garbage compost processed under acidic conditions at moderately high temperature. The organism was Gram-stain-positive, aerobic, spore-forming and rod-shaped. Growth was observed to occur at 40-65 °C and pH 4.8-8.1 (optimum growth: 50-60 °C, pH 6.2). The strain was catalase- and oxidase-positive. The cell wall contained meso-diaminopimelic acid, alanine, glutamic acid and galactose. The predominant respiratory quinone was menaquinone-7 (MK-7) and the major fatty acids were anteiso-C17 : 0 and iso-C17 : 0. Comparative 16S rRNA gene sequence analysis showed that strain B157T was related most closely to Tuberibacillus calidus 607T (94.8 % identity), and the phylogenetic analysis revealed that it belonged to the family Sporolactobacillaceae. The DNA G+C content was determined as 51.8 mol%. In spite of many similarities with the type strains of members of the family Sporolactobacillaceae, genotypic analyses suggest that strain B157T represents a novel species of a new genus, Caenibacilluscaldisaponilyticus gen. nov., sp. nov. The type strain of Caenibacilluscaldisaponilyticus is B157T (=NBRC 111400T=DSM 101100T).

Physicochemical and biological characterizations of Pxt peptides from amphibian (Xenopus tropicalis) skin

Pxt peptides (Pxt-1 through Pxt-12) have been isolated from amphibian, Xenopus tropicalis Pxt-related peptides (Pxt-2, Pxt-5, Pxt-12, reverse Pxt-2, reverse Pxt-5 and reverse Pxt-12) with significant foaming properties were further characterized. In the physicochemical experiments, all Pxt-related peptides formed significant amphiphilic α-helices in 50% 2,2,2-trifluoroethanol by circular dichroism measurements. Among Pxt-related peptides, both Pxt-5 and reverse Pxt-5 were the most effective in reducing their surface tensions. Moreover, Pxt-2, Pxt-5 and reverse Pxt-5 produced constant surface tensions above their critical association concentrations, suggesting the micelle-like assemblies. In the biological experiments, Pxt-5 possessed the most potent hemolytic activity, while reverse Pxt-5 exhibited the most remarkable gene expression of interleukin 8 and heme oxygenase 1 and the most potent cytotoxicity in HaCaT cells. In contrast, Pxt-12 and reverse Pxt-12 were much weaker in antimicrobial assays for Gram-negative bacteria, Gram-positive bacteria and yeasts, as well as in hemolytic, cell viability and cytotoxicity assays in HaCaT cells. All Pxt-related peptides exhibited about 20-50% of the total cellular histamine release at 10(-5) M, as well as mastoparan and melittin in mast cells. Real-time polymerase chain reaction analysis confirmed the gene expressions of Pxt-5 in testis and Pxt-12 in muscle, in addition to skin, while Pxt-2 was only in skin.

Cytotoxicity of CdSe-based quantum dots incorporated in glass nanoparticles evaluated using human keratinocyte HaCaT cells

CdSe quantum dots (QDs) are potential fluorescent reagents, but leakage of Cd and Se often induces cytotoxicity. Here we prepared CdSe-based QDs with glass to reduce their leakage and examined their cytotoxicity using keratinocyte cells. The cytotoxicity of the QDs with glass was obviously lower than that of the commercial QDs with polymer, suggesting their safety for biological applications.

Molecular Cloning of Secreted Luciferases from Marine Planktonic Copepods

Secreted luciferases isolated from copepod crustaceans are frequently used for nondisruptive reporter-gene assays, such as the continuous, automated and/or high-throughput monitoring of gene expression in living cells. All known copepod luciferases share highly conserved amino acid residues in two similar, repeated domains in the sequence. The similarity in the domains are ideal nature for designing PCR primers to amplify cDNA fragments of unidentified copepod luciferases from bioluminescent copepod crustaceans. Here, we introduce how to establish a cDNA encoding novel copepod luciferases from a copepod specimen by PCR with degenerated primers.

Dynamics of hydroxyoctadecadienoic acid in epilepsy patients treated with valproic acid

BACKGROUND

The effects of valproic acid (VPA) on oxidative stress are controversial due to differences in experimental conditions. Recently, total hydroxyoctadecadienoic acid (tHODE), derived from linoleic acid, was proposed as a potent biomarker to evaluate oxidative stress.

METHODS

The subjects consisted of 10 new-onset epilepsy patients treated with VPA. We measured plasma tHODE consecutively for 1 year to evaluate the degree of oxidative stress and then compared plasma tHODE at the beginning and the end of experiments with the peak level. Ten age-matched healthy subjects were recruited as a control group and their plasma tHODE was compared to the initial plasma tHODE of the epilepsy group. Measurements were done using liquid chromatography-tandem mass spectrometry.

RESULTS

Mean initial plasma tHODE in the epilepsy group was 165.2 ± 76.8 nmol/L, which was not significantly different from that of the control group (199.3 ± 62.5 nmol/L). In five epilepsy patients, plasma tHODE increased above the pathological level in 6 months, but returned to normal within 1 year. In the whole group, the difference plasma tHODE between peak, at the beginning and 1 year later, was significant.

CONCLUSION

Oxidative stress generated by VPA increased temporarily, but decreased to normal after 1 year. it is reasonable to be concerned about the effects of oxidative stress, especially at the start of VPA treatment.

(7S)-Kaitocephalin as a potent NMDA receptor selective ligand

A structure–activity relationship (SAR) study of kaitocephalin, known to be a potent naturally occurring NMDA receptor ligand, was performed.

2-Hydrazinoquinoline: a reactive matrix for matrix-assisted laser desorption/ionization mass spectrometry to detect gaseous carbonyl compounds

The sensitivity, range of applications, and reaction mechanism of 2-hydrazinoquinoline as a reactive matrix for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) were examined. Using a reaction chamber (125L) equipped with a stirring fan and a window for moving the MALDI-MS plate and volatile samples in and out, the sensitivities of 2-hydrazinoquinoline to gaseous aldehydes (formaldehyde, acetaldehyde, propionaldehyde, and n-butyraldehyde) and ketones (acetone, methyl ethyl ketone, and methyl isobutyl ketone) were determined to be at least parts per million (ppm) levels. On the other hand, carboxylic acids (formic acid, acetic acid, propionic acid, and butyric acid) and esters (ethyl acetate, pentyl acetate, isoamyl acetate, and methyl salicylate) could not be detected by 2-hydrazinoquinoline in MALDI-MS. In addition to 2,4-dinitrophenylhydrazine, a common derivatization reagent for analyzing carbonyl compounds quantitatively in gas chromatography and liquid chromatography, the dissolution of 2-hydrazinoquinoline in an acidic solution, such as trifluoroacetic acid, was essential for its function as a reactive matrix for MALDI- MS.

Hydrazide and hydrazine reagents as reactive matrices for matrix-assisted laser desorption/ionization mass spectrometry to detect steroids with carbonyl groups

Fifty-one reagents (37 hydrazides and 14 hydrazines) were examined to determine if they could function as reactive matrices for the detection of steroids with carbonyl groups in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Among these reagents, 3-hydroxy-2-naphthoic acid hydrazide reacted most efficiently with steroids with carbonyl groups, allowing detection of them at the 1pmol level. Results from accurate mass measurement with a JMS-S3000 Spiral-TOF suggested that the ion peaks corresponding to the protonated fragment of a hydrazone were observed, in addition to the protonated molecular peaks of the resulting hydrazones ([M(D)+H](+)) and their sodium adduct ([M(D)+Na](+)). 3-Hydroxy-2-naphthoic acid hydrazide also could detect cortisol (1.93ng) spiked in a human serum certified reference material, as well as cortisone and cortisol in a human saliva sample collected in the morning. Using a combination of 3-hydroxy-2-naphthoic acid hydrazide and α- cyano-4-hydroxycinammic acid (CHCA) (3-hydroxy-2-naphthoic acid hydrazide:CHCA=4:1, v/v), even cortisone and cortisol in a human saliva sample collected in the afternoon, when levels are typically low, could be detected effectively.

Identification of novel peptides from amphibian (Xenopus tropicalis) skin by direct tissue MALDI-MS analysis

Twelve novel peptides (Pxt-1 to Pxt-12) were isolated from the skin of Xenopus tropicalis, diploid frogs, using topological MS analysis. Among them, Pxt-8, Pxt-9, and Pxt-10 were the N terminus of Pxt-1, N terminus of Pxt-3 and C terminus of Pxt-11, respectively. The Pxt-3 and Pxt-11 peptides shared significant sequence homologies with magainins 1, -2 and levitide, respectively, which all isolated from X. laevis. Pxt-12 was identical to the X. tropicalis XT-6-like precursor previously isolated by ESI-MS/MS. None of the Pxt peptides contained any Cys, Asp, Tyr or Trp, although Leu and Lys were frequently found as typical frog-skin peptides. RT-PCR analysis confirmed the gene expressions of Pxt-2, Pxt-3, Pxt-4, Pxt-5, Pxt-7 and Pxt-11 in X. tropicalis skin. Several ion peaks corresponding to all identified Pxt peptides were observed with MALDI-MS analysis of X. tropicalis secretory fluids, collected after in vivo stimulation, which suggested that Pxt peptides were definitely secretory molecules. CD studies and Schiffer-Edmundson helical wheel projections suggested that Pxt-5, as well as mastoparan, at least, could form a typical amphiphilic α helix without a phospholipid or a membrane-mimetic solvent (trifluoroethanol). Moreover, Pxt-2 and Pxt-5 showed growth inhibitory effects on both Escherichia coli (Gram-negative) and Staphylococcus aureus (Gram-positive). Measurements of dynamic light scattering and the surface tensions of Pxt peptides solutions suggested that both Pxt-2 and Pxt-5 could form associations as micelles and behave like a general surfactant. Moreover, the remarkable foaming properties of Pxt-2 and Pxt-5 were observed, as well as those of the secretory fluids of X. tropicalis.

DHA concentration of red blood cells is inversely associated with markers of lipid peroxidation in men taking DHA supplement

An increase in the proportion of fatty acids with higher numbers of double bonds is believed to increase lipid peroxidation, which augments the risk for many chronic diseases. (n-3) Polyunsaturated fatty acids provide various health benefits, but there is a concern that they might increase lipid peroxidation. We examined the effects of docosahexaenoic acid [22:6 (n-3)] supplementation on lipid peroxidation markers in plasma and red blood cells (RBC) and their associations with red blood cell and plasma fatty acids. Hypertriglyceridemic men (n = 17 per group) aged 39–66 years participated in a double-blind, randomized, placebo-controlled, parallel study. They received no supplements for the first 8 days and then received 7.5 g/day docosahexaenoic acid oil (3 g/day docosahexaenoic acid) or olive oil (placebo) for 90 days. Fasting blood samples were collected 0, 45, and 91 days after supplementation. Docosahexaenoic acid supplementation did not change plasma or RBC concentrations of lipid peroxidation markers (total hydroxyoctadecadienoic acid, total hydroxyeicosatetraenoic acid, total 8-isoprostaglandin F_2α, 7α-hydroxycholesterol, 7β-hydroxycholesterol) when pre- and post-supplement values were compared. However, the post-supplement docosahexaenoic acid (DHA) concentration was inversely associated with RBC concentrations of ZE-HODE, EE-HODE, t-HODE, and total 8-isoprostaglandin F_2α, (p<0.05). RBC concentration of hydroxycholesterol was also inversely associated with DHA but it did not attain significance (p = 0.07). Our results suggest that increased concentration of DHA in RBC lipids reduced lipid peroxidation. This may be another health benefit of DHA in addition to its many other health promoting effects.

Meiothermus ruber H328 enhances the production of membrane vesicles for feather degradation

The thermophilic bacterium Meiothermus ruber H328 aggressively degrades chicken feathers. When feathers were added to culture medium, the cells significantly exfoliated membrane vesicles from the outer membrane as observed by electron microscopy of ultrathin sections. This is the first report of membrane vesicle production associated with keratinolytic activity by Meiothermus sp.

Hydrazide and hydrazine reagents as reactive matrices for MALDI-MS to detect gaseous aldehydes

The reagents 19 hydrazide and 14 hydrazine were examined to function as reactive matrices for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to detect gaseous aldehydes. Among them, two hydrazide (2-hydroxybenzohydrazide and 3-hydroxy-2-naphthoic acid hydrazide) and two hydrazine reagents [2-hydrazinoquinoline and 2,4-dinitrophenylhydrazine (DNPH)] were found to react efficiently with carbonyl groups of gaseous aldehydes (formaldehyde, acetaldehyde and propionaldehyde); these are the main factors for sick building syndrome and operate as reactive matrices for MALDI-MS. Results from accurate mass measurements by JMS-S3000 Spiral-TOF suggested that protonated ion peaks corresponding to [M + H](+) from the resulting derivatives were observed in all cases with the gaseous aldehydes in an incubation, time-dependent manner. The two hydrazide and two hydrazine reagents all possessed absorbances at 337 nm (wavelength of MALDI nitrogen laser), with, significant electrical conductivity of the matrix crystal and functional groups, such as hydroxy group and amino group, being important for desorption/ionization efficiency in MALDI-MS. To our knowledge, this is the first report that gaseous molecules could be derivatized and detected directly in a single step by MALDI-MS using novel reactive matrices that were derivatizing agents with the ability to enhance desorption/ionization efficiency.

The multiplicity of post-translational modifications in pro-opiomelanocortin-derived peptides

The precursor protein, pro-opiomelanocortin (POMC) undergoes extensive post-translational processing in a tissue-specific manner to yield various biologically active peptides involved in diverse cellular functions. The recently developed method of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for direct tissue analysis has proved to be a powerful tool for investigating the distribution of peptides and proteins. In particular, topological mass spectrometry analysis using MALDI-MS can selectively provide a mass profile of the hormones included in cell secretory granules. An advantage of this technology is that it is possible to analyze a frozen thin slice section, avoiding an extraction procedure. Subsequently, tandem mass spectrometry (MS/MS) has a profound impact on addressing the modified residues in the hormone molecules. Based on these strategies with mass spectrometry, several interesting molecular forms of POMC-derived peptides have been found in the fish pituitary, such as novel sites of acetylation in α-melanocyte-stimulating hormone (MSH), hydroxylation of a proline residue in β-MSH, and the phosphorylated form of corticotropin-like intermediate lobe peptide.

Photouncaging nanoparticles for MRI and fluorescence imaging in vitro and in vivo

Multimodal and multifunctional nanomaterials are promising candidates for bioimaging and therapeutic applications in the nanomedicine settings. Here we report the preparation of photouncaging nanoparticles with fluorescence and magnetic modalities and evaluation of their potentials for in vitro and in vivo bioimaging. Photoactivation of such bimodal nanoparticles prepared using photouncaging ligands, CdSe/ZnS quantum dots, and super paramagnetic iron oxide nanoparticles results in the systematic uncaging of the particles, which is correlated with continuous changes in the absorption, mass and NMR spectra of the ligands. Fluorescence and magnetic components of the bimodal nanoparticles are characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and elemental analyses using energy dispersive X-ray (EDX) spectroscopy and X-ray photoelectron spectroscopy (XPS). Bioconjugation of the nanoparticles with peptide hormones renders them with biocompatibility and efficient intracellular transport as seen in the fluorescence and MRI images of mouse melanoma cells (B16) or human lung epithelial adenocarcinoma cells (H1650). Biocompatibility of the nanoparticles is evaluated using MTT cytotoxicity assays, which show cell viability over 90%. Further, we combine MRI and NIR fluorescence imaging in C57BL/6 (B6) mice subcutaneously or intravenously injected with the photouncaging nanoparticles and follow the in vivo fate of the nanoparticles. Interestingly, the intravenously injected nanoparticles initially accumulate in the liver within 30 min post injection and subsequently clear by the renal excretion within 48 h as seen in the time-dependent MRI and fluorescence images of the liver, urinary bladder, and urine samples. Photouncaging ligands such as the ones reported in this article are promising candidates for not only the site-specific delivery of nanomaterials-based contrast agents and drugs but also the systematic uncaging and renal clearance of nanomaterials after the desired in vivo application.

A C69-family cysteine dipeptidase from Lactobacillus farciminis JCM1097 possesses strong Gly-Pro hydrolytic activity

Dipeptide Gly-Pro, a hard-to-degrade and collagenous peptide, is thought to be hydrolysed by prolidases that can work on various X-Pro dipeptides. Here, we found an entirely different type of dipeptidase from Lactobacillus farciminis JCM1097 that cleaves Gly-Pro far more efficiently and with higher specificity than prolidases, and then investigated its properties by use of a recombinant enzyme. Although L. farciminis dipeptidase was expressed in the form of an inclusion body in Escherichia coli at 37 °C, it was smoothly over-expressed in a soluble form at a lower temperature. The maximal Gly-Pro hydrolytic activity was attained in E. coli at 30 °C. In contrast to prolidases that are metallopeptidases showing the modest or marginal activity toward Gly-Pro, this L. farciminis dipeptidase belongs to the cysteine peptidase family C69. Lactobacillus farciminis dipeptidase occurs in cytoplasm and utilizes the side chain of an amino-terminal cysteine residue to perform the nucleophilic attack on the target amide bond between Gly-Pro after processing eight amino acid residues at the N-terminus. Furthermore, L. farciminis dipeptidase is potent enough to synthesize Gly-Pro from Gly and Pro by a reverse reaction. These novel properties could be revealed by virtue of the success in preparing recombinant enzymes in higher yield and in a stable form.

A thiophene-containing compound as a matrix for matrix-assisted laser desorption/ ionization mass spectrometry and the electrical conductivity of matrix crystals

The electrical conductivity of the matrix crystal might be a new factor to enhance matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) sensitivity. In MALDI-MS, several compounds are used as a standard matrix. Utilization of such compounds is based on an a posteriori approach, but there is no theoretical guidance for selecting a matrix. In an attempt to further understand performance in MALDI-MS, we utilized peptide detection for random screening of a chemical library (12,383 compounds) for compounds with matrix functions in MALDI-MS. A lot of thiophene compounds were found to be a matrix, in which 2-[5-(2,4-dichlorobenzoyl)-2-thienyl] acetic acid (DCBTA) provided an important clue to measure the electrical conductivity of the matrix crystal, because the structure of DCBTA is analogous to conductive polymers and organic solar cells. Most of the crystals of standard matrices, such as alpha-cyano-4-hydroxycinnamic acid (CHCA), 3,5-dimethoxy-4-hydroxycinnamic acid [sinapinic acid, (SA)], and DCBTA showed electrical conductivity, whereas the conductivity of crystal was not observed in 2,5-dihydroxybenzoic acid (2,5-DHB). On the other hand, super-DHB using 2-hydroxy-5-methoxybenzoic acid [5-methoxysalicylic acid, (MSA)] as an additive to 2,5-DHB, improved the electrical conductivity of the crystal, that followed the enhancement of peak intensity in MS spectrum. These observations might indicate that the electrical conductivity of matrix crystals is a key consideration in obtaining efficient MALDI performance.

Efficient secreted production of (R)-3-hydroxybutyric acid from living Halomonas sp. KM-1 under successive aerobic and microaerobic conditions

Production of (R)-3-hydroxybutyric acid [(R)-3-HB] by strain Halomonas sp. KM-1 under successive aeration conditions was investigated. The first aerobic condition allowed both cell growth and intracellular storage of poly-(R)-3-hydroxybutyric acid (PHB). The second microaerobic condition, achieved by reducing the culture agitation rate, lead to the degradation of PHB to (R)-3-HB. The amount of PHB stored in KM-1 cells after 48-h cultivation under aerobic conditions was 16.4 g/l. In contrast, after a shift from aerobic to microaerobic conditions and a further 18-h cultivation, PHB content in KM-1 cells decreased to 0.9 g/l. Numerous intracellular PHB-containing granules were observed in cells under aerobic conditions by electron microscopy. After the shift to microaerobic conditions, the number and size of granules were significantly reduced, in agreement with the degradation of prestored PHB. On the other hand, under microaerobic conditions, the concentration of (R)-3-HB in the medium reached a maximum of 15.2 g/l, indicating the production and extracellular secretion of (R)-3-HB as a result of PHB digestion. Notably, cell lysis was not observed during the successive aeration conditions as assessed by elution of genomic DNA to the culture supernatant, cell morphology observed by electron microscopy and counts of colony formation. In this simple system utilizing a change of aeration during cultivation of strain Halomonas sp. KM-1, we obtained one of the highest levels of microbiological production of (R)-3-HB reported to date.

Characterization of triacetyl-α-melanocyte-stimulating hormone in carp and goldfish

A triacetyl form of α-melanocyte-stimulating hormone (MSH) was found in carp (Cyprinus carpio) and goldfish (Carassius auratus), by selective detection of mass profile for cell secretory granules using direct tissue matrix-assisted laser desorption ionization with time-of-flight mass spectrometry (MALDI-TOF MS) analysis during the investigation of fish pituitaries. The structure of triacetyl-α-MSH in carp and goldfish was further analyzed using a collision-induced dissociation with electrospray ionization mass spectrometry, and determined to be N,O-diacetyl Ser as the N-terminal residue and O-acetyl Tyr at position 2. These modifications for α-MSH in carp and goldfish are structurally different from that of medaka hormone, in which [N,O-diacetyl Ser(1), O-acetyl Ser(3)]-α-MSH has been identified. The profiles of four α-MSH variants, des-, mono-, di- and tri-acetyl forms in goldfish and medaka pituitaries were also examined by direct tissue MALDI-TOF MS analysis, and the percentages as a total of α-MSH molecules were compared for fish reared in a white or black tank for 5 days. Among structural variants, diacetyl-α-MSH was the predominant form in goldfish and N-desacetyl-α-MSH in medaka, respectively. In both species, the relative level of the predominant form in the pituitary of white-adapted fish tended to be lower than that of black-adapted fish. In goldfish, no significant difference was observed in the relative content of triacetyl-α-MSH in both backgrounds, whereas the lowest content of triacetyl-α-MSH was found in black-adapted medaka. These preliminary data indicate that it is difficult to elucidate the relations between the physiological roles and acetylated pattern of α-MSH molecule, depending on species.

Evolution of bioluminescence in marine planktonic copepods

Copepods are the dominant taxa in zooplankton communities of the ocean worldwide. Although bioluminescence of certain copepods has been known for more than a 100 years, there is very limited information about the structure and evolutionary history of copepod luciferase genes. Here, we report the cDNA sequences of 11 copepod luciferases isolated from the superfamily Augaptiloidea in the order Calanoida. Highly conserved amino acid residues in two similar repeat sequences were confirmed by the multiple alignment of all known copepod luciferases. Copepod luciferases were classified into two groups of Metridinidae and Heterorhabdidae/Lucicutiidae families based on phylogenetic analyses, with confirmation of the interrelationships within the Calanoida using 18S ribosomal DNA sequences. The large diversity in the specific activity of planktonic homogenates and copepod luciferases that we were able to express in mammalian cultured cells illustrates the importance of bioluminescence as a protective function against predators. We also discuss the relationship between the evolution of copepod bioluminescence and the aspects of their ecological characteristics, such as swimming activity and vertical habitat.