Dual antioxidant and antibacterial potential of β-cryptoxanthin and a novel biosurfactant from Kocuria marina DAGII.

Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne disease in cattle and other ruminants, is proposed to be at least one of the causes of Crohn disease in humans. MAP and Mycobacterium avium subspecies avium, a closely related opportunistic environmental bacterium, share 95% of their genes and exhibit homologies of more than 99% between these genes. The identification of molecules specific for MAP is essential for understanding its pathogenicity and for development of useful diagnostic tools. The application of gas chromatography, mass spectrometry, and nuclear magnetic resonance led to the structural identification of a major cell wall lipopeptide of MAP, termed Para-LP-01, defined as C20 fatty acyl-D-Phe-N-Me-L-Val-L-Ile-L-Phe-L-Ala methyl ester. Variations of this lipopeptide with different fatty acyl moieties (C16 fatty acyl through C17, C18, C19, C21 to C22) were also identified. Besides the specificity of this lipopeptide for MAP, the presence of an N-Me-L-valine represents the first reported N-methylated amino acid within an immunogenic lipopeptide of mycobacteria. Sera from animals with Johne disease, but not sera from uninfected cattle, reacted with this lipopeptide, indicating potential biological importance.

There are challenges in viridans group streptococci (VGS) identification especially for the mitis group. Few studies have investigated the performance of MALDI-TOF MS system in VGS identification. Using 16S rRNA gene and gyrB gene sequencing as a gold standard, the performance of two MALDI-TOF MS instruments in the identification of 181 VGS clinical isolates was studied. The Bruker Biotyper and Vitek MS IVD systems correctly identified 88.4% and 98.9% of the 181 isolates, respectively. The Vitek MS RUO system was the least reliable, only correctly identifying 38.7% of the isolates to species level with several misidentifications and invalid results. The Bruker Biotyper system was very unreliable in the identification of species within the mitis group. Among 22 non-pneumococci isolates (S. mitis/S. oralis/S. pseudopneumoniae), Biotyper misidentified 21 of them as S. pneumoniae leading to a low sensitivity and low positive predictive value in these species. In contrast, the Vitek MS IVD demonstrated a better resolution for pneumococci and non-pneumococci despite the inability to distinguish between S. mitis/S. oralis. For more accurate species-level identification, further improvements in the VGS spectra databases are needed. Based on MALDI-TOF analysis and selected 16S rRNA gene plus gyrB genes sequencing, we designed a practical VGS identification algorithm.

Matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MALDI-TOF MS) is a revolutionary technique with multiple applications. Its use in clinical microbiology is now becoming widespread as the method is an easy, rapid, effective, accurate, and cheap way to identify cultured bacteria and fungi. It is, therefore, an ideal tool to replace conventional methods still used in Africa and tropical areas for routine microbiological diagnosis. The recent installation of a MALDI-TOF MS for diagnostic purposes in a hospital in Senegal has confirmed that this tool is not only valuable but also robust in tropical Africa, providing further evidence that this technique should be widely distributed there. However, despite its value for clinical microbiology in Africa, the acquisition and installation of MALDI-TOF MS is subject to several constraints. This review provides general information on aspects of MALDI-TOF MS. The specific aspects and constraints observed in Africa and tropical countries are also addressed with suggestions for appropriate solutions. Key words: Microorganism, infectious diseases, quick identification, matrix-assisted laser desorption-ionization time-of-flight, matrix assisted laser desorption ionization-time of flight (MALDI-TOF).

The serine/threonine kinase Akt is a key mediator of cell survival and growth, but its precise mechanism of action, and more specifically, the nature of its signaling partners largely remain to be elucidated. We show, using a proteomics-based approach, that the valosin-containing protein (VCP), a member of the AAA (ATPases associated with a variety of cellular activities) family, is a target of Akt signaling. SDS-PAGE of Akt co-immunoprecipitated proteins obtained from MCF-7 breast cancer cells revealed the increase of a 97-kDa band under Akt activation. Mass spectrometry analysis allowed the identification of VCP, and we have shown a serine/threonine phosphorylation on an Akt consensus site upon activation by growth factors. Site-directed mutagenesis identified Ser-351, Ser-745, and Ser-747 as Akt phosphorylation sites on VCP. Confocal microscopy indicated a co-localization between Akt and VCP upon Akt stimulation. Interestingly, small interfering RNA against VCP induced an inhibition of the growth factor-induced activation of NF-kappaB and a potent pro-apoptotic effect. Together, these data identify VCP as an essential target of Akt signaling.

Tenascin-R (TN-R) is a member of the tenascin family of multidomain matrix glycoproteins that is expressed exclusively in the central nervous system by oligodendrocytes and small neurons during postnatal development and in the adult. TN-R contributes to the regulation of axon extension and regeneration, neurite formation and synaptogenesis, and neuronal growth and migration. TN-R can be modified with three distinct sulfated oligosaccharide structures: HNK-1 (SO(4)-3-GlcUAbeta1,3Galbeta1,4GlcNAc), GalNAc-4-SO(4), and chondroitin sulfate. We have determined that TN-R expressed in dendrite-rich regions of the rat cerebellum, hippocampus, and cerebral cortex is one of the major matrix glycoproteins that bears N-linked carbohydrates terminating with beta1,4-linked GalNAc-4-SO(4). The syntheses of these unique sulfated structures on TN-R are differentially regulated. Levels of HNK-1 on TN-R rise and fall in parallel to the levels of TN-R during postnatal development of the cerebellum. In contrast, levels of GalNAc-4-SO(4) are regulated independently from those of TN-R, rising late in cerebellar development and continuing into adulthood. As a result, the pattern of TN-R modification with distinct sulfated carbohydrate structures changes dramatically over the course of postnatal cerebellar development in the rat. Because TN-R interacts with a number of different matrix components and, depending on the circumstances, can either activate or inhibit neurite outgrowth, the highly regulated addition of these unique sulfated structures may modulate the adhesive properties of TN-R over the course of development and during synapse maintenance. In addition, the 160-kDa form of TN-R is particularly enriched for terminal GalNAc-4-SO(4) later in development and in the adult, suggesting additional levels of regulation.

Cytoplasmic lipids play key roles during oocyte and embryo development. However, there is little information on the changes in lipid types during intraovarian follicular and oocyte growth. Here, we used matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry to understand lipid composition in the cat oocyte during differing stages of folliculogenesis. Follicles at different developmental stages were mechanically isolated from cat ovaries within 4 h after routine ovariohysterectomy. Oocytes with granulosa cells were recovered from secondary (preantral stage, n = 387), early antral (<0.5 mm diameter, n = 177), small antral (0.5–1 mm, n = 144), and antral (>1 mm, n = 120) follicles, then subjected to lipid extraction and MALDI-TOF analysis (n = 3 replicates). Resulting mass spectra data were evaluated using MALDIquant in R package to eliminate baseline (background) and to identify peak values. The latter maximal values for each follicle stage were selected and subjected to principal component analysis to identify similarities and differences in mass spectra profile among oocytes from varying developmental stages. Peaks were compared to those calculated molecular formulae available in the Lipid MAP database. Error estimates were calculated using Excel (Microsoft Corp., Redmond, WA), and lipid species identification performed using Lipid MS Predict. Twenty-nine lipid species from six glycerophospholipids groups (glycerophosphates, PA; glycerophosphoserines, PS; glycerophosphoinositols, PI; glycerophosphoglycerols, PG; glycerophosphoinositol monophosphates, PIP; and glycerophosphoethanolamines, PE) were identified, 15 being found in more than 1 developmental stage. Two species in particular, [PI(29:4)+Na]+ and [PIP(23:0)+Na]+, were the most abundant lipids and were identified in oocytes from all developmental stages. There were dynamic shifts in lipid species expressed at different follicle stages. Oocytes from secondary and antral follicles contained more lipid types (15 and 22, respectively) than early (10) and small antral (4) counterparts. Four (PA, PS, PI, and PIP) of the 6 glycerophospholipids were found only in oocytes from secondary and antral follicles. Oocytes from small antral follicles also lacked PA, PS, and PG, whereas PG was not found in early antral stage oocytes. In summary, we showed for the first time in the cat that, similar to goats and rats, there are temporal changes in lipid types within the oocyte during folliculogenesis. We suspect that these changing dynamics, including shifts in presence or absence of lipid species with follicle stage, may be playing key roles in oocyte growth and viability. Our findings also serve as in vivo benchmarks for parallel studies focused on enhancing an in vitro culture system for early-stage ovarian follicles to preserve fertility of genetically valuable domestic and wild felids.

PurposeSexually transmitted infections (STIs), representing a major global health problem, are caused by different microbes, including bacteria, viruses, and protozoa. Unfortunately, infections of different sexually transmitted pathogens often present similar clinical symptoms, so it is almost impossible to distinguish them clinically. Therefore, the aim of the current study was to develop a sensitive, multitarget, and high-throughput method that can detect various agents responsible for STIs.MethodsWe developed and tested a 23-plex PCR coupled with matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) assay (sexually transmitted infection-mass spectrometry, STI-MS) that simultaneously targets 11 different agents, including 8 most common clinical pathogens related to STIs (HSV-1, HSV-2, Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema pallidum, Trichomonas vaginalis, Mycoplasma genitalium, and Haemophilus ducreyi) and 3 controversial microorganisms as pathogens (Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum).ResultsThe results showed that the STI-MS approach can accurately detect the expected agents, without cross-reaction with other organisms. The limit of detection of each STI-MS assay was ranged from 1.739 to 10.009 copies/reaction, using probit analyses. The verification rate for each target organism of the STI-MS ranged from a minimum of 89.3% to a maximum of 100%, using conventional assays and ultrasensitive digital PCR to confirm the STI-MS-positive results. To further evaluate the clinical performance of this assay, 241 clinical specimens (124 urethral/cervical swabs and 117 urine) were tested in parallel using the STI-MS assay and monoplex real-time PCR for each agent. The overall validation parameters of STI-MS were extremely high including sensitivity (from 85.7% to 100%), specificity (from 92.3% to 100%), PPV (from 50% to 100%), and NPV (from 99.1% to 100%) for each target.ConclusionSTI-MS is a useful high-throughput screening tool for detecting mixed infections of STIs and has great potential for application in large-scale epidemiological programs for specific microorganisms of STI.

Porcine cumulus cell layers are thought to influence various fundamental functions during oocyte maturation. The expansion of cumulus-oocyte complexes (COCs) is known to highly correlate with oocyte maturation, fertilization, and embryonic development. In this study, we performed two dimensional electrophoresis (2-DE) and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analysis using porcine COCs proteins. Porcine COCs were collected from ovary follicles and classified as the good-quality group and the poor-quality group based on cumulus cell layers around oocyte. The COCs protein samples were separated in a pH 3.0–10.0 IPG gels for the first dimension, and then 8%–16% SDS-PAGE gel for the second dimension. Gel image analysis was performed in protein spots between good- and poor-quality groups, and then differential protein spots were identified using MALDI-TOF analysis. There were more than 300 protein spots in the 2-DE gel image obtained from 1 mg protein samples of COCs. Five differential protein spots were identified by gel image analysis with more than 1.5-fold differences. All 5 protein spots were up-regulated in good quality group and revealed as transferrin, tight junction protein ZO-2, tubulin beta chain, meiosis-specific nuclear structural protein 1 and dynamin 1-like isoform 4 in good. Our results indicated the identification of 5 differentially expressed proteins in the porcine good-quality COCs and these protein profiles will make available important guides for porcine good oocyte selection for the production of in vitro embryos.

White spot syndrome virus (WSSV) is at present one of the major pathogens in shrimp culture worldwide. The complete genome of this virus has been sequenced recently. To identify the structural and functional proteins of WSSV, the purified virions were separated by SDS-PAGE. Twenty-four protein bands were excised, in-gel digested with trypsin, and subjected to matrix-assisted laser desorption ionization-time of flight mass spectrometry and electrospray ionization tandem mass spectrometry, respectively. Eighteen proteins matching the open reading frames of WSSV genome were identified. Except for three known structural proteins and collagen, the functions of the remaining 14 proteins were unknown. Temporal analysis revealed that all the genes were transcribed in the late stage of WSSV infection except for vp121. Of the newly identified proteins, VP466 (derived from band 16) was further characterized. The cDNA encoding VP466 was expressed in Escherichia coli as a glutathione S-transferase (GST) fusion protein. Specific antibody was generated with the purified GST-VP466 fusion protein. Western blot showed that the mouse anti-GST-VP466 antibody bound specifically to a 51-kDa protein of WSSV. Immunogold labeling revealed that VP466 protein is a component of the viral envelope. Results in this investigation thus proved the effectiveness of proteomic approaches for discovering new proteins of WSSV.

The predisposition of patients with cystic fibrosis (CF) for recurrent pulmonary infections can result in poor prognosis of the disease. Although the clinical significance in CF of micro-organisms, such as Staphylococcus aureus, Haemophilus influenzae and Pseudomonas aeruginosa, is well established, the implication of uncommon glucose non-fermenting Gram-negative bacilli (UGNF-GNB) in respiratory samples from CF patients is still unclear. Because of limitations of traditional methods used in most clinical laboratories, the accurate identification of these microbes is a challenge. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) is an alternative tool for efficient identification of bacteria. This was a retrospective study to evaluate different identification methods in a collection of UGNF-GNB isolated from children with CF during a period of three years. The performance of MALDI-TOF was compared to that of 16S rDNA gene sequencing and to a conventional and automated phenotypic identification. The discriminatory power of MALDI-TOF (75.0 % agreement) was superior to automated techniques (67.1 % agreement) and to conventional phenotypical identification (50.0 % agreement). MALDI-TOF also demonstrated high accuracy in identifying Stenotrophomonas maltophilia, Achromobacter xylosoxidans and Chryseobacterium indologenes, but had limited utility in identifying Pandoraea spp. and some species of Acinetobacter and Chryseobacterium (other than C. indologenes). Although MALDI-TOF identified only 75 % of the isolates in comparison with 16S rDNA gene sequencing, the prompt identification and high discriminatory power exhibited by MALDI-TOF make it a useful tool for the characterization of micro-organisms that are difficult to identify using routine methods.

The identification of bacteria by means of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry directly using whole cells has become a standard method in clinical diagnosis due to its rapidity and simplicity. Nevertheless, the analysis of environmental samples with this approach still represents a challenge due to the enormous microbial diversity existing on earth and the lack of a comprehensive database. Most of the environmentally relevant species comprise only one unique strain, while pathogens such as Escherichia coli, with 667 described strains, are well documented. In such case, identification of the proteins responsible for the peak signals within MALDI-TOF spectra can give crucial information for species discrimination. To give higher confidence in MALDI-TOF biomarker description we exploited information from proteins identified by shotgun nanoLC-MS/MS, consisting of the identification and quantification of low-molecular-weight proteins after SDS-PAGE, in-gel trypsin proteolysis and analysis of tryptic peptides. We also proposed the standardization of the inclusion of internal calibrants in the bacterial sample to improve the accuracy of the MALDI-TOF measurements. In this way, nine candidate biomarkers were tentatively proposed for Ruegeria lacuscaerulensis ITI-1157. The conserved biomarkers were theoretically deduced for all other Ruegeria strains whose genomes have been sequenced and their corresponding m/z MALDI-TOF signals were estimated. Among these, DNA-binding protein, HU, and ribosomal proteins, L29, L30, L32 and S17, were shown experimentally to be also the most prominent and conserved signals in the other strain tested, Ruegeria pomeroyi DSS-3. Thus, we suggested that these five biomarkers, which give rise to 10 m/z peak signals derived from the mono- and doubly protonated proteins, are the best candidates for identifying bacteria belonging to the Ruegeria genus, and quickly assessed their phylogenetic proximity to described species. As an application of these biomarkers, we quickly screened 30 seawater bacterial isolates by MALDI-TOF and found one belonging to the Ruegeria genus, as further confirmed by 16S RNA sequencing. Due to its simplicity and effectiveness, this technique could be of immense value in monitoring bacteria in the environment in the near future.

Value of matrix-assisted laser desorption ionization-time of flight for routine identification of viridans group streptococci causing bloodstream infections

Two highly similar plastidic NADP-malic enzymes (NADP-MEs) are found in the C(4) species maize (Zea mays); one exclusively expressed in the bundle sheath cells (BSCs) and involved in C(4) photosynthesis (ZmC(4)-NADP-ME); and the other (ZmnonC(4)-NADP-ME) with housekeeping roles. In the present work, these two NADP-MEs were analyzed regarding their redox-dependent activity modulation. The results clearly show that ZmC(4)-NADP-ME is the only one modulated by redox status, and that its oxidation produces a conformational change limiting the catalytic process, although inducing higher affinity binding of the substrates. The reversal of ZmC(4)-NADP-ME oxidation by chemical reductants suggests the presence of thiol groups able to form disulfide bonds. In order to identify the cysteine residues involved in the activity modulation, site-directed mutagenesis and MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) analysis of ZmC(4)-NADP-ME were performed. The results obtained allowed the identification of Cys192, Cys246 (not conserved in ZmnonC(4)-NADP-ME), Cys270 and Cys410 as directly or indirectly implicated in ZmC(4)-NADP-ME redox modulation. These residues may be involved in forming disulfide bridge(s) or in the modulation of the oxidation of critical residues. Overall, the results indicate that, besides having acquired a high level of expression and localization in BSCs, ZmC(4)-NADP-ME displays a particular redox modulation, which may be required to accomplish the C(4) photosynthetic metabolism. Therefore, the present work could provide new insights into the regulatory mechanisms potentially involved in the recruitment of genes for the C(4) pathway during evolution.

Nitration of tyrosine (Y) residues of proteins is a low abundant post-translational modification that modulates protein function or fate in animal systems. However, very little is known about the in vivo prevalence of this modification and its corresponding targets in plants. Immunoprecipitation, based on an anti-3-nitroY antibody, was performed to pull-down potential in vivo targets of Y nitration in the Arabidopsis thaliana proteome. Further shotgun liquid chromatography–mass spectrometry (LC-MS/MS) proteomic analysis of the immunoprecipitated proteins allowed the identification of 127 proteins. Around 35% of them corresponded to homologues of proteins that have been previously reported to be Y nitrated in other non-plant organisms. Some of the putative in vivo Y-nitrated proteins were further confirmed by western blot with specific antibodies. Furthermore, MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) analysis of protein spots, separated by two-dimensional electrophoresis from immunoprecipitated proteins, led to the identification of seven nitrated peptides corresponding to six different proteins. However, in vivo nitration sites among putative targets could not be identified by MS/MS. Nevertheless, an MS/MS spectrum with 3-aminoY318 instead of the expected 3-nitroY was found for cytosolic glyceraldehyde-3-phosphate dehydrogenase. Reduction of nitroY to aminoY during MS-based proteomic analysis together with the in vivo low abundance of these modifications made the identification of nitration sites difficult. In turn, in vitro nitration of methionine synthase, which was also found in the shotgun proteomic screening, allowed unequivocal identification of a nitration site at Y287.

Background: In the last few years, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) has emerged as a useful tool for identification of microorganisms. Identification of the various bacterial genera has been found to be challenging using the routine phenotypic tests or commercially available automated systems relying on the biochemical identification of bacteria. Objectives: In this study, we aimed to evaluate the possible role of the MALDI-TOF system with its Biotyper software as an accurate and rapid method of bacterial identification. Methodology: This study was conducted over a period of one month, where 299 isolates were retrieved from 523 clinical samples. Results: MALDI TOF identified 275 (92%) isolates to the species level, 287 isolates (96%) to the genus level and no reliable identification for 12 (4%) isolates using the direct formic acid application method. When protein extraction was applied, valid results for species and genus identification were obtained for 296 and 299 isolates respectively, so the overall rate of identification rose to 99% and 100% respectively. Discordant results between MALDI TOF and conventional methods were confirmed by Vitek 2 and 16s rRNA sequencing. Conclusions: MALDI-TOF is a rapid, accurate and inexpensive method for microbial identification that rivals other identification systems available. Its relative ease of use and rapid turnaround time makes it a powerful tool in the microbiology laboratory.