Improving the Detection of Epidemic Clones in Candida parapsilosis Outbreaks by Combining MALDI-TOF Mass Spectrometry and Deep Learning Approaches

Identifying fungal clones propagated during outbreaks in hospital settings is a problem that increasingly confronts biologists. Current tools based on DNA sequencing or microsatellite analysis require specific manipulations that are difficult to implement in the context of routine diagnosis. Using deep learning to classify the mass spectra obtained during the routine identification of fungi by MALDI-TOF mass spectrometry could be of interest to differentiate isolates belonging to epidemic clones from others. As part of the management of a nosocomial outbreak due to Candida parapsilosis in two Parisian hospitals, we studied the impact of the preparation of the spectra on the performance of a deep neural network. Our purpose was to differentiate 39 otherwise fluconazole-resistant isolates belonging to a clonal subset from 56 other isolates, most of which were fluconazole-susceptible, collected during the same period and not belonging to the clonal subset. Our study carried out on spectra obtained on four different machines from isolates cultured for 24 or 48 h on three different culture media showed that each of these parameters had a significant impact on the performance of the classifier. In particular, using different culture times between learning and testing steps could lead to a collapse in the accuracy of the predictions. On the other hand, including spectra obtained after 24 and 48 h of growth during the learning step restored the good results. Finally, we showed that the deleterious effect of the device variability used for learning and testing could be largely improved by including a spectra alignment step during preprocessing before submitting them to the neural network. Taken together, these experiments show the great potential of deep learning models to identify spectra of specific clones, providing that crucial parameters are controlled during both culture and preparation steps before submitting spectra to a classifier.

First Report of Curtobacterium flaccumfaciens pv. flaccumfaciens Causing Bacterial Wilt and Blight on Sunflower in Russia

In the summer of 2018, wilt and leaf spots were observed on sunflower (Helianthus annuus L.) plants in fields near Kursk (51.74°N, 36.02°E) in Russia. In the following years, incidence of this disease was 5 to 20% in the inspected fields. Marginal chlorosis on seedling leaves developed into wilt and necrosis about one week later (Fig. 1). Mature plants had leaves with blight and reduced height compared to symptomless plants. Pathogen isolation from seeds was done by the method of Tegli et al. (2002) with modifications. Bacteria from diseased plants were isolated by streaking inoculum from symptomatic tissues on nutrient dextrose agar (NDA) (Schaad et al. 1988). The plates were incubated at 30°C for 7 to 10 days. Isolates consistently formed slow-growing, yellow, circular, smooth colonies without soluble pigment. The isolated bacteria were aerobic, gram-positive, and rod-shaped. Eight strains, CF-20 to CF-26 from plants, and Curt1 and Curt3 from seeds, were identified by MALDI TOF MS analysis as Curtobacterium flaccumfaciens pv. flaccumfaciens or C. flaccumfaciens pv. poinsettiae. All strains had GENIII MicroPlate (BIOLOG) test results identical to C. flaccumfaciens pv. flaccumfaciens strain DSM20129T. Further analysis was done by specific PCR (Tegli et al. 2002) and 16S rDNA, gyrB, and atpD gene sequencing. For PCR amplification, DNA was extracted by the CitoSorb Kit (Syntol Co., Moscow). Primers 27F/1492R (16S rRNA) (Marchesi et al. 1998), 2F/6R (gyrB) (Richert et al. 2005), and aptD2F/aptD2R (Jacques et al. 2012) were used to amplify the target gene sequences. The PCR products were sequenced by Evrogen (Moscow). The 16S rRNA sequences (OL584192.1 to OL584199.1) were identical to that of C. flaccumfaciens pv. flaccumfaciens strain DSM20129T (AM410688.1; 1,477/1,477 bp). The phylogenetic tree of concatenated gyrB (560 bp) and atpD (716 bp) sequences (OL548915.1 to OL548922.1 and OL548923.1 to OL548930.1, respectively) clustered the strains from sunflower among C. flaccumfaciens pv. flaccumfaciens, C. flaccumfaciens pv. betae, and C. flaccumfaciens pv. oortii (Fig. 2) with high genetic similarity to other C. flaccumfaciens strains: 96.3 to 100% for atpD and 95 to 100% for gyrB. A pathogenicity test for each of the strains was performed by injecting 5 μl of a bacterial suspension (108 CFU/ml) grown for 72 h on NDA into the stems of five plantlets (four true leaf stage) of the sunflower cv. Tunka (Limagrain, France) and soybean cv. Kasatka (VIM, Russia). Strain DSM20129T was a positive control, while sterile water was a negative control. The plants were incubated at 24°C, 80% relative humidity, and 14-h light/day. Wilting and blight on sunflower (Fig. 3) and tan spots on soybean were observed in 15 to 20 days after inoculation for all sunflower strains and strain DSM20129T. The negative control plants were asymptomatic. The bacteria re-isolated from the inoculated plants exhibited the same morphological characteristics and 16S rDNA sequence as the original culture, thus fulfilling Koch's postulates. The presence of C. flaccumfaciens pv. flaccumfaciens in sunflower seeds indicated that the bacterium was transmitted via seed. Sunflower has been previously reported as a host for the pathogen (Harveson et al. 2015). The presence of C. flaccumfaciens pv. flaccumfaciens on beans in Russia was suggested from the disease symptoms (Nikitina and Korsakov 1978), but, to our knowledge, this is the first report of the pathogen affecting sunflower in Russia. Phytosanitary categorization placed C. flaccumfaciens pv. flaccumfaciens in the EPPO A2 list (EPPO 2011). Thus, sunflower seeds should be tested to protect pathogen-free areas from introduction of this pathogen.

Pulmonary nocardiosis: Risk factors and species distribution from a high burden centre

Nocardiosis is a clinical and diagnostic challenge. This was a retrospective study carried out on cases of pulmonary nocardiosis presenting over 15 years. Clinical data was retrieved using the electronic patient records. Vitek MS 3.2 (MALDI TOF MS) was carried out on 22 isolates and sequencing on another 9 isolates. Of 71 patients presenting with pulmonary nocardiosis, 58 (81.6%) were on immunosuppressant therapy, 26 (46%) had a previous lung pathology, 11 (8%) were HIV associated. Disseminated disease was seen in 6 (8.4%). There were 8 (11.26%) deaths in this cohort of patients. Of 31/71 identified to species, the most common were Nocardia cyriacigeorgica (n ​= ​11) followed by Nocardia farcinica (n ​= ​9).

Antibacterial activity of Bacillus licheniformis B6 against viability and biofilm formation of foodborne pathogens of health importance

We studied a strain of Bacillus isolated from an artisanal tannery in Salta, Argentina. It was identified as Bacillus licheniformis B6 by 16 S phylogenetic analysis and MALDI TOF (GenBank accession code No. KP776730). The synthesis of lipopeptides by B6 and their antibacterial activity against clinical pathogenic strains was analyzed both in the cell-free supernatant (CFS) and in the crude fraction of lipopeptides (LF). Overall, the CFS did not significantly reduce the viability of the studied strains (Staphylococcus aureus 269 and ATCC 43,300, Escherichia coli 4591 and 25,922, Klebsiella sp. 1087 and 1101). However, LF at 9 mg/mL reduced the viability of those pathogenic strains by 2 and 3 log orders compared to those of the control. When the effects of LF and ampicillin were compared, they showed different sensitivity against pathogenic strains. For example, E. coli 4591 was the strain most resistant to ampicillin, requiring 250 mg/mL of antibiotic to achieve the same inhibitory effect as 9 mg/mL of B6 LF. SEM observations of the effect of LF on biofilm formation by E. coli 4591 and Klebsiella sp. 1087 clearly showed that biofilm structures were destabilized, these strains turning into weak biofilm formers. Signals in the CFS and LF corresponding to kurstakin and iturin were identified by MALDI TOF. Interestingly, surfactin was detected, rather than lichenysin, the expected lipopeptide in B. licheniformis species. Signals of bacitracin and fengycins were also found, the latter with a higher number of homologues and relative intensity in the LF than the other lipopeptides. These results show that the lipopeptides synthesized by B. licheniformis B6 have both potential antibacterial and anti-biofilm activity against pathogenic bacteria of health importance.

Faster and accurate identification of clinically important Trichosporon using MALDI TOF MS

PURPOSE

Trichosporon species are emerging human pathogens, accounting for the second most common cause of non-candidal mycosis. Rapid and reliable identification of these agents allows a better understanding of their epidemiology and therapeutic management. The Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) technique has the potential to be precise, fast and cost-effective. However, the precision of identification totally depends upon the type of protein extraction method used and embedded database in the system. Our objectives were to standardize the protein extraction technique and expand the present Bruker database by creating an in-house database and validating it with diverse clinical Trichosporon species of Indian origin.

METHODS

Two different protein extraction protocols (on-plate and off-plate) were evaluated. The off-plate protocol was finalized for the identification. MALDI TOF MS with the existing Bruker database was evaluated for its ability to identify a total of 79 intergenic spacer 1 (IGS1) gene sequence confirmed clinical isolates of 5 different Trichosporon species.

RESULTS

As outcome, off plate protocol yielded higher accuracy (73% on the species level and 95% on the genus level) than on-plate (25% on the genus level) in terms of log scores. The existing database for Trichosporon species was enriched with 28 sequence confirmed isolates, which improved accuracy from 73% to 100% and were identified up to species level with a log score >2.3.

CONCLUSIONS

Used with standardized protein-extraction protocol along with an expanded database, MALDI-TOF MS could be a rapid and reliable approach to identify clinical Trichosporon species routinely in the laboratory.

A Case Report of Mycoplasma hominis Subdural Empyema Following Decompressive Craniotomy, and a Review of Central Nervous System Mycoplasma hominis Infections

Background

Mycoplasma hominis is a small cell-wall-free organism, part of the normal microbiota of the genitourinary tract. It is rarely involved in extragenital infections, mainly joint, surgical-site, and respiratory infections.

Methods

We describe a case of M. hominis subdural empyema and lower limb surgical site infections, following decompressive craniotomy, after traumatic brain and extremities injury. In addition, a literature review of 34 cases M. hominis CNS infections was done.

Results

Our case depicts a 25-years old patient who developed subdural empyema and surgical site infections in his cranium and fibula. Both sites were cultured, and small pinpoint colonies grew on blood agar. MALDI-TOF MS identified M. hominis. Simultaneously 16S-rDNA PCR from CSF detected M. hominis. Antimicrobial treatment was switched to doxycycline with improvement. Literature review revealed 21 adults and 13 pediatric cases of M. hominis CNS infection. Risk factors in adults were head trauma, neurosurgery, or post-partum period.

Conclusions

Based upon the literature reviewed, we postulate that adult patients with head trauma or neurosurgical procedure, rarely are infected either through direct contamination during the trauma, or by undergoing urgent, urinary catheterization, and may experience distant infection due to translocation of M. hominis into the bloodstream. In such cases diagnosis is delayed due to difficulties in growing and identifying the bacteria. Empiric antimicrobials are usually not effective against mycoplasmas. These factors contributed to the mortality in adult cases (15%). Our rare case highlights the necessity of combining classical microbiology routines with advanced molecular techniques to establish a diagnosis in complicated cases.

Chemically heterogeneous carbon dots enhanced cholesterol detection by MALDI TOF mass spectrometry

A binary system composed of carbon dots (CDs) and N-doped CDs (N-CDs) embedded in an organic matrix was used for the analysis of cholesterol by MALDI (matrix-assisted laser desorption and ionization time-of-flight) mass spectrometry, as a model for detection of small, biologically relevant molecules. The results showed that both CDs are sensitive to the cholesterol and can be used either alone or in a binary system with 2,5-dihydroxybenzoic acid (DHB) to enhance the detection process. It was found that both COOH and NH₂ groups on CDs surface contributed to the enhancement in the cholesterol detection by MALDI mass spectrometry in the presence of inorganic cations. Nevertheless, in the presence of NaCl, N-CDs led to a better reproducibility of results. It was due to the coexistence of positive and negative charge on N-CDs surface that led to a homogeneous analyte/substrate distribution, which is an important detection parameter. The enhancing effect of carbon dots was linked to a negative Gibbs energy of the complex formation between CDs, Na⁺, cholesterol and DHB, and it was supported by theoretical calculations. Moreover, upon the addition of CDs/N-CDs, such features as a low ionization potential, vertical excitation, dipole moment and oscillator strength positively affected the cholesterol detection by MALDI in the presence of Na⁺.

Identifying novel allergens from a common indoor mould Aspergillus ochraceus

The increasing burden of respiratory disease is a rising concern in India. Although chronic colonisation is primarily caused by pathogenic fungi, the common environmental fungi also play an important role in developing sensitisation. This study aims to examine the allergenic potency of mycelial proteins of a common indoor fungus Aspergillus ochraceus to a selected atopic patient cohort as well as to identify the novel IgE-binding proteins through an immunoproteomic approach. 1-D and 2-D IgE specific western blot detected the IgE reactive proteins which were identified through MALDI-TOF/TOF and manual de novo peptide sequencing. The results revealed the detection of 10 cross-reactive IgE-binding proteins. Cluster analysis of 1-D immunoblot with individual patient sera identified NADP(+)-dependent glycerol dehydrogenase (GldB) homologous protein as a major allergen, which was further purified and the allergenicity was assessed. Other IgE-binding proteins showed homology with allergens like short-chain dehydrogenase, NAD-dependent mannitol dehydrogenase, and subtilisin-like serine protease. GldB purified under native conditions showed IgE reactivity amongst the selected patient cohort, which is reported for the first time in this study. The identified IgE-binding proteins can act as candidate molecules for developing hypoallergenic vaccines for designing specific immunotherapeutic techniques to fungal allergy. THE SIGNIFICANCE OF THE STUDY: Exposure to environmental fungal allergens is directly associated with promoting allergic response as well as complicating existing respiratory disease, leading to poor respiratory health. Amongst others, Aspergillus spp. contributes to the majority of the fungal derived atopic diseases. Aspergillus ochraceus is a common indoor mould in India, however, its allergenic potency was not explored till date. In this study, we establish A. ochraceus responsible to cause an allergic response to susceptible individuals and identified 10 IgE-binding proteins using an immunoproteomics approach for the first time. A. ochraceus being unsequenced, a homology-driven proteomics approach was used to identify the IgE-binding proteins which can be extended to identify proteins from other unsequenced species. The information on the IgE-binding proteins could be used as a step towards characterising them by molecular and structural methods to investigate the molecular basis of allergenicity. This will also help to enrich the existing database of allergenic proteins and pave a way towards developing therapeutic avenues.

MALDI TOF Mass Spectrometry Imaging of Blood Smear: Method Development and Evaluation

The aim of this study was to develop and evaluate matrix assisted LASER desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry imaging (MSI) of blood smear. Integrated light microscope and MALDI IT-TOF mass spectrometer, together with a matrix sublimation device, were used for analysis of blood smears coming from healthy male donors. Different blood plasma removal, matrix deposition, and instrumental settings were evaluated using the negative and positive ionization modes while agreement between the light microscopy images and the lateral distributions of cellular marker compounds served as the MSI quality indicator. Red and white blood cells chemical composition was analyzed using the differential m/z expression. Five seconds of exposure to ethanol followed by the 5 min of 9-aminoacridine or α-cyano-4-hydroxycinnamic acid deposition, together with two sets of instrumental settings, were selected for the MALDI TOF MSI experiments. Application of the thin and transparent matrix layers assured good correspondence between the LASER footprints and the preselected regions of interest. Cellular marker m/z signals coincided well with the appropriate cells. A metabolite databases search using the differentially expressed m/z produced hits which were consistent with the respective cell types. This study sets the foundations for application of blood smear MALDI TOF MSI in clinical diagnostics and research.

Automation and validation of a MALDI-TOF MS (Mass-Fix) replacement of immunofixation electrophoresis in the clinical lab

Objectives

A matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) method (Mass-Fix) as a replacement for gel-based immunofixation (IFE) has been recently described. To utilize Mass-Fix clinically, a validated automated method was required. Our aim was to automate the pre-analytical processing, improve positive specimen identification and ergonomics, reduce paper data storage and increase resource utilization without increasing turnaround time.

Methods

Serum samples were batched and loaded onto a liquid handler along with reagents and a barcoded sample plate. The pre-analytical steps included: (1) Plating immunopurification beads. (2) Adding 10 μl of serum. (3) Bead washing. (4) Eluting the immunoglobulins (Igs), and reducing to separate the heavy and light Ig chains. The resulting plate was transferred to a second low-volume liquid handler for MALDI plate spotting. MALDI-TOF mass spectra were collected. Integrated in-house developed software was utilized for sample tracking, driving data acquisition, data analysis, history tracking, and result reporting. A total of 1,029 residual serum samples were run using the automated system and results were compared to prior electrophoretic results.

Results

The automated Mass-Fix method was capable of meeting the validation requirements of concordance with IFE, limit of detection (LOD), sample stability and reproducibility with a low repeat rate. Automation and integrated software allowed a single user to process 320 samples in an 8 h shift. Software display facilitated identification of monoclonal proteins. Additionally, the process maintains positive specimen identification, reduces manual pipetting, allows for paper free tracking, and does not significantly impact turnaround time (TAT).

Conclusions

Mass-Fix is ready for implementation in a high-throughput clinical laboratory.

New insights into the zinc-α2-glycoprotein (ZAG) scaffold and its metal ions binding abilities using spectroscopic techniques

AIMS

Zinc-α2-glycoprotein (ZAG) is soluble lipid mobilizing protein and a noval adipokine associated with cancer cachexia. ZAG is an omnipresent protein and represent a fold of MHC class I proteins. Although ZAG's metal binding capacity has already been reported, no other metal has been mapped to date besides the complex formation with zinc.

MAIN METHODOLOGY

In this study, fluorescence emission spectroscopy and mass spectrometry (MALDI-TOF) were employed to define the putative interaction sites and their accessibility for the biologically important metals of Irving William Series.

KEY FINDINGS

Several hotspot residues in the ZAG scaffold involved in these interactions were mapped and their binding affinity score for each metal has been determined. Thebinding abilities of these sites and aggregation propensities of ZAG were monitored by fluorescence emission spectroscopy.

SIGNIFICANCE

The prediction of such binding affinity with metals on the active sites and its impact on the conformational states to accelerate aggregation was discussed as an important finding that may be involved in several other biochemical processes such as lipid binding, β-adrenergic receptors, cancer cachexia and association with plasma cholesterol and obesity.

Species identification of Enterococcus spp: Whole genome sequencing compared to three biochemical test-based systems and two Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) systems

Aim

Here, we evaluated the performance of two commercial MALDI‐TOF MS systems and three biochemical‐based systems and compared them to WGS as the gold standard for identifying isolates of vancomycin‐resistant enterococci (VRE).

Methods

A total of 87 VRE clinical isolates were included. The mass spectrometers were the Microflex system with Biotyper software 3.1 and the Vitek MS system. The biochemical‐based systems included the Vitek 2, Phoenix, and MicroScan WalkAway systems. WGS was performed on an Illumina MiSeq instrument using the MiSeq v3 reagent kit. Vancomycin resistance was determined according to CLSI criteria.

Results

Among the 87 VRE, 71 and 16 were identified as Enterococcus faecium and Enterococcus faecalis by WGS. All 71 E faecium were correctly identified by both mass spectrometers, as well as the Vitek 2 and Phoenix instruments. However, only 51 E faecium isolates were correctly identified by the MicroScan system. The most frequent misidentification was Enterococcus casseliflavus (n = 20). For vancomycin‐resistant E faecium, the Microflex Biotyper system had the highest sensitivity (85.54%), and all instruments (except for the Microscan) had a 100% specificity and PPV. Up to 87% of E faecalis isolates were misidentified by VITEK MS and VITEK2, 81% by Microscan and Phoenix, and 75% by Bruker biotyper.

Conclusion

As the coverage of type strain‐genome sequence database continues to grow and the cost of DNA sequencing continues to decrease, genome‐based identification can be a useful tool for diagnostic laboratories, with its superior accuracy even over MALDI‐TOF and database‐driven operations.

Differentiation between Streptococcus pneumoniae and other viridans group streptococci by matrix-assisted laser desorption/ionization time of flight mass spectrometry

OBJECTIVES

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is becoming the method of choice for bacterial identification. However, correct identification by MALDI-TOF of closely related microorganisms such as viridans streptococci is still cumbersome, especially in the identification of S. pneumoniae. By making use of additional spectra peaks for S. pneumoniae and other viridans group streptococci (VGS). We re-identified viridans streptococci that had been identified and characterized by molecular and phenotypic techniques by MALDI-TOF.

METHODS

VGS isolates (n = 579), 496 S. pneumoniae and 83 non-S. pneumoniae were analysed using MALDI-TOF MS and the sensitivity and specificity of MALDI-TOF MS was assessed. Hereafter, mass spectra analysis was performed. Presumptive identification of proteins represented by discriminatory peaks was performed by molecular weight matching and the corresponding nucleotides sequences against different protein databases.

RESULTS

Using the Bruker reference library, 495 of 496 S. pneumoniae isolates were identified as S. pneumoniae and one isolate was identified as non-S. pneumoniae. Of the 83 non-S. pneumoniae isolates, 37 were correctly identified as non-S. pneumoniae, and 46 isolates as S. pneumoniae. The sensitivity of the MALDI-TOF MS was 99.8% (95% confidence interval (CI) 98.9-100) and the specificity was 44.6% (95% CI 33.7-55.9). Eight spectra peaks were mostly present in one category (S. pneumoniae or other VGS) and absent in the other category and inversely. Two spectra peaks of these (m/z 3420 and 3436) were selected by logistic regression to generate three identification profiles. These profiles could differentiate between S. pneumoniae and other VGS with high sensitivity and specificity (99.4% and 98.8%, respectively).

CONCLUSIONS

Spectral peaks analysis based identification is a powerful tool to differentiate S. pneumoniae from other VGS species with high specificity and sensitivity and is a useful method for pneumococcal identification in carriage studies. More research is needed to further confirm our findings. Extrapolation of these results to clinical strains need to be deeply investigated.

Distinguishing two species of Cavernicola (Hemiptera, Reduviidae, Triatominae) with matrix-assisted laser desorption ionization time-of-flight mass spectrometry

The blood-sucking insects of the subfamily Triatominae are vectors of Chagas disease, the most impairing protozoan parasitic infection in Latin America. Among the five tribes known in the subfamily, one of the least studied is Cavernicolini. It has only two species within Cavernicola genus (Barber, 1937), little is known about the biochemistry of the species of this genus, therefore, using MALDI-TOF MS we provide a better understanding of the two species and differentiates them. The distinction was made by the different spectral profile of the species, where C. lenti presents unique signals in many regions, while the C. pilosa shows high-intensity signals and m/z in high bands. The application of digital mass spectrometry combined with chemometric methods was able to accurately distinguish two species of the genus Cavernicola.

Trichosporon japonicum Fungemia and Ventricular Assist Device Infection in an Immunocompetent Patient

Trichosporon species are emerging opportunistic yeasts that cause life-threatening disseminated disease in severely immunocompromised patients. Trichosporon japonicum is a very rare cause of invasive trichosporonosis. We describe a case of Trichosporon japonicum fungemia in an immunocompetent patient with a transcutaneous biventricular assist device.

Evaluation of Protein Profiling in a Cohort of Egyptian Population with Renal Cell Carcinoma and Benign Kidney Neoplasms

Section Title

Abdominal imaging leads to the detection of a large number of renal tumors without the ability to distinguish the type of tumor detected. It is necessary to find a precise way to know the type of tumor to determine the appropriate treatment. The use of urine samples for detecting new biomarkers especially proteins has a great potential. In this work we assessed the proteomic profiling difference in a cohort of Egyptian population with renal neoplasms.

Methods:

This cohort study was conducted on 85 subjects. They were classified as 40 RCC, 15 benign kidney patients, and 30 healthy controls. Morning urine samples were used for peptidome separation using magnetic beads. Matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) was applied Using FlexControlTM software.

Results:

Benign tumors were differentiated from controls by 5 integrated peaks, 12 significant and 2 integrated significant peaks, 17:3,418.8 and 25:4,173.41. While RCC were differentiated from benign by 5 integrated, 28 significant and one integrated significant peak. The RCC group was discriminated from the controls by 5 peaks which were integrated from which 1 was integrated and significant (with mass to charge ratio of 12:3,408.97). The three groups showed protein profiles ranging from 1 to 10 kDa. The external validation was performed for the RCC group versus the control reveled sensitivity of 88.7% and specificity of 73.2% by genetic algorithm.

Conclusion:

Proteomic approach can be used as a sensitive urinary marker differentiating renal masses in an early diagnostic approach.

Amino Acid Analysis by Means of MALDI TOF Mass Spectrometry or MALDI TOF/TOF Tandem Mass Spectrometry

Here we describe two different AAA protocols based on application of matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectrometry (MS). First protocol describes a MALDI TOF MS-based method for a routine simultaneous qualitative and quantitative analysis of free amino acids and protein hydrolysates. Linear responses between the amino acid concentration and the peak intensity ratio of corresponding amino acid to internal standard were observed for all amino acids analyzed in the range of concentrations from 20 to 300 μM. Limit of quantitation varied from 0.03 μM for arginine to 3.7 μM for histidine and homocysteine. This method has one inherent limitation: the analysis of isomeric and isobaric amino acids. To solve this problem, a second protocol based on the use of MALDI TOF/TOF MS/MS for qualitative analysis of amino and organic acids was developed. This technique is capable of distinguishing isobaric and isomeric compounds. Both methods do not require amino acid derivatization or chromatographic separation, and the data acquisition time is decreased to several seconds for a single sample.

Identifying Inhibitors of Inflammation: A Novel High-Throughput MALDI-TOF Screening Assay for Salt-Inducible Kinases (SIKs)

Matrix-assisted laser desorption/ionization time-of-flight (MALDI TOF) mass spectrometry has become a promising alternative for high-throughput drug discovery as new instruments offer high speed, flexibility and sensitivity, and the ability to measure physiological substrates label free. Here we developed and applied high-throughput MALDI TOF mass spectrometry to identify inhibitors of the salt-inducible kinase (SIK) family, which are interesting drug targets in the field of inflammatory disease as they control production of the anti-inflammatory cytokine interleukin-10 (IL-10) in macrophages. Using peptide substrates in in vitro kinase assays, we can show that hit identification of the MALDI TOF kinase assay correlates with indirect ADP-Hunter kinase assays. Moreover, we can show that both techniques generate comparable IC50 data for a number of hit compounds and known inhibitors of SIK kinases. We further take these inhibitors to a fluorescence-based cellular assay using the SIK activity-dependent translocation of CRTC3 into the nucleus, thereby providing a complete assay pipeline for the identification of SIK kinase inhibitors in vitro and in cells. Our data demonstrate that MALDI TOF mass spectrometry is fully applicable to high-throughput kinase screening, providing label-free data comparable to that of current high-throughput fluorescence assays.

Sugar cane spirit (cachaça): Effects of mixed inoculum of yeasts on the sensory and chemical characteristics

The main goal of this study was to produce cachaça using a mixed inoculum of Saccharomyces cerevisiae and Meyerozyma caribbica and characterize the produced beverage using HPLC, GC-FID, GC-MS and sensorial analysis. Additionally, the use of MALDI-TOF as a tool to characterize and monitor pure and mixed inocula fermenting sugar cane juice was also evaluated. Vat fermentations were carried out for three consecutive batches using autoclaved 16°Brix sugar cane juice fermented by a mixed inoculum of M. caribbica 10⁷ cells/mL and S. cerevisiae 10⁸ cells/mL. The cachaça produced by the mixed culture of M. caribbica and S. cerevisiae showed the highest concentration of volatile compounds associated with good sensory descriptors such as ethyl hexanoate (114.11μg/L), 2-phenylethyl acetate (2.77μg/L), a-terpineol (0.45μg/L), b-citronellol (2.47μg/L), and geraniol (0.24μg/L). This beverage consequently showed greater acceptance in the sensorial analysis for taste and aroma, especially by younger panelists. The feasibility of MALDI-TOF use under studied conditions was demonstrated by the comparison of the results obtained from yeast cultivation in YPD broth, YPD agar and sugar cane juice, showing that there was no interference of sugar cane juice in protein profile. The results obtained from MALDI-TOF analysis showed that the protein extraction directly from sugar cane juice under fermentation, without the traditional plating step, allowed the distinction between mixed and pure inocula even under different M. caribbica populations and Brix degrees.

Acid Ionic Liquids as a New Hardener in Urea-Glyoxal Adhesive Resins

The effect of acidic ionic liquid (IL) as a new catalyst on the properties of wood-based panels bonded with urea-glyoxal (UG) resins was investigated. Different levels of N-methyl-2-pyrrolidone hydrogen sulfate ([HNMP] HSO₄ (0, 1, 2, 3 wt %)) were added to prepared UG resin. The resin was then used for preparing laboratory particleboard panels. Then, the properties of the prepared panels were evaluated. The structure of the prepared UG resin was studied by ¹³C NMR, and thermal curing behavior of the resin before and after the addition of IL was measured by DSC. Additionally, the main oligomers formed in the UG reaction were identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI TOF) mass spectroscopy. The results indicated that IL can be used as an efficient catalyst for UG resin. The physicochemical tests indicated that the addition of [HNMP] HSO₄ from 0 to 3 wt % decreased the pH value of the glue-mix, and the pH decreased on curing to the same level as urea-formaldehyde resins. The gel accelerated with increasing catalyst content and with the decreasing of the pH in the UG resin. The panels prepared with IL had higher mechanical strength and dimensional stability compared to those made from UG resins containing NH₄Cl. Scanning electron microscope (SEM) micrographs showed that the panels prepared with ionic liquid presented low porous. DSC analysis showed that the addition of IL to the UG resin decrease the energy of activation of the curing reaction to render possible cross-linking. The MALDI TOF results indicated a preponderant linearity of the oligomers formed, implying a high energy of activation of curing for UG resins.

Mechanical Modulation of Phonon-Assisted Field Emission in a Silicon Nanomembrane Detector for Time-of-Flight Mass Spectrometry

We demonstrate mechanical modulation of phonon-assisted field emission in a free-standing silicon nanomembrane detector for time-of-flight mass spectrometry of proteins. The impacts of ion bombardment on the silicon nanomembrane have been explored in both mechanical and electrical points of view. Locally elevated lattice temperature in the silicon nanomembrane, resulting from the transduction of ion kinetic energy into thermal energy through the ion bombardment, induces not only phonon-assisted field emission but also a mechanical vibration in the silicon nanomembrane. The coupling of these mechanical and electrical phenomenon leads to mechanical modulation of phonon-assisted field emission. The thermal energy relaxation through mechanical vibration in addition to the lateral heat conduction and field emission in the silicon nanomembrane offers effective cooling of the nanomembrane, thereby allowing high resolution mass analysis.

Pure human butyrylcholinesterase hydrolyzes octanoyl ghrelin to desacyl ghrelin

The ghrelin hormone is a 28 amino acid peptide esterified on serine 3 with octanoic acid. Ghrelin is inactivated by hydrolysis of the ester bond. Previous studies have relied on inhibitors to identify human butyrylcholinesterase (BChE) as the hydrolase in human plasma that converts ghrelin to desacyl ghrelin. The reaction of BChE with ghrelin is unusual because the rate of hydrolysis is very slow and the substrate is ten times larger than standard BChE substrates. These unusual features prompted us to re-examine the reaction, using human BChE preparations that were more than 98% pure. Conversion of ghrelin to desacyl ghrelin was monitored by MALDI TOF mass spectrometry. It was found that 5 different preparations of pure human BChE all hydrolyzed ghrelin, including BChE purified from human plasma, from Cohn fraction IV-4, BChE immunopurified by binding to monoclonals mAb2 and B2 18-5, and recombinant human BChE purified from culture medium. We reasoned that it was unlikely that a common contaminant that could be responsible for ghrelin hydrolysis would appear in all of these preparations. km was <1 μM, and kcat was ~1.4 min(-1). A Michaelis-Menten analysis employing these kinetic values together with serum concentrations of ghrelin and BChE demonstrated that BChE could hydrolyze all of the ghrelin in serum in ~1 h. It was concluded that BChE is physiologically relevant for the hydrolysis of ghrelin.

Enzymatic attributes of an l-isoaspartyl methyltransferase from Candida utilis and its role in cell survival

BACKGROUNDS

Spontaneous deamidation and isoaspartate (IsoAsp) formation contributes to aging and reduced longevity in cells. A protein-l-isoaspartate (d-aspartate) O-methyltransferase (PCMT) is responsible for minimizing IsoAsp moieties in most organisms.

METHODS

PCMT was purified in its native form from yeast Candida utilis. The role of the native PCMT in cell survival and protein repair was investigated by manipulating intracellular PCMT levels with Oxidized Adenosine (AdOx) and Lithium Chloride (LiCl). Proteomic Identification of possible cellular targets was carried out using 2-dimensional gel electrophoresis, followed by on-Blot methylation and mass spectrometric analysis.

RESULTS

The 25.4 kDa native PCMT from C. utilis was found to have a Km of 3.5 µM for AdoMet and 33.36 µM for IsoAsp containing Delta Sleep Inducing Peptide (DSIP) at pH 7.0. Native PCMT comprises of 232 amino acids which is coded by a 698 bp long nucleotide sequence. Phylogenetic comparison revealed the PCMT to be related more closely with the prokaryotic homologs. Increase in PCMT levels in vivo correlated with increased cell survival under physiological stresses. PCMT expression was seen to be linked with increased intracellular reactive oxygen species (ROS) concentration. Proteomic identification of possible cellular substrates revealed that PCMT interacts with proteins mainly involved with cellular housekeeping. PCMT effected both functional and structural repair in aged proteins in vitro.

GENERAL SIGNIFICANCE

Identification of PCMT in unicellular eukaryotes like C. utilis promises to make investigations into its control machinery easier owing to the familiarity and flexibility of the system.

A simple non-invasive technique for venom milking from a solitary wasp Delta conoideum Gmelin (Hymenoptera: Vespidae)

Prospecting wasp, ant and bee venom for active bio-molecules has gained considerable interest among researchers in recent years. Collecting sufficient quantity of venom from solitary wasps without sacrificing them is often difficult. Here we describe a non-invasive technique for collecting venom from a solitary wasp Delta conoideum Gmelin (Red-backed potter wasp). Venom was milked by presenting an agar block to a single female wasp for stinging. The venom was extracted from the agar block using ACN: water solvent system. The total protein in venom was estimated quantitatively and the presence of peptides in the venom was confirmed by MALDI-TOF analysis. The proposed technique is non-invasive and pure venom can be repeatedly 'milked' using this method from other wasps and also bees without the need for sacrificing a large number of individuals.

Identification of Protein Markers Specific for Papillary Renal Cell Carcinoma Using Imaging Mass Spectrometry

Since the emergence of proteomics methods, many proteins specific for renal cell carcinoma (RCC) have been identified. Despite their usefulness for the specific diagnosis of RCC, such proteins do not provide spatial information on the diseased tissue. Therefore, the identification of cancer-specific proteins that include information on their specific location is needed. Recently, matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) based imaging mass spectrometry (IMS) has emerged as a new tool for the analysis of spatial distribution as well as identification of either proteins or small molecules in tissues. In this report, surgical tissue sections of papillary RCC were analyzed using MALDI-IMS. Statistical analysis revealed several discriminative cancer-specific m/z-species between normal and diseased tissues. Among these m/z-species, two particular proteins, S100A11 and ferritin light chain, which are specific for papillary RCC cancer regions, were successfully identified using LC-MS/MS following protein extraction from independent RCC samples. The expressions of S100A11 and ferritin light chain were further validated by immunohistochemistry of human tissues and tissue microarrays (TMAs) of RCC. In conclusion, MALDI-IMS followed by LC-MS/MS analysis in human tissue identified that S100A11 and ferritin light chain are differentially expressed proteins in papillary RCC cancer regions.

A peptide targeted against phosphoprotein and leader RNA interaction inhibits growth of Chandipura virus -- an emerging rhabdovirus

The fatal illness caused by Chandipura virus (CHPV), an emerging pathogen, presently lacks any therapeutic option. Previous research suggested that interaction between the virally encoded phosphoprotein (P) and the positive sense leader RNA (le-RNA) may play an important role in the viral lifecycle. In this report, we have identified a β-sheet/loop motif in the C-terminal domain of the CHPV P protein as essential for this interaction. A synthetic peptide encompassing this motif and spanning a continuous stretch of 36 amino acids (Pep208-243) was found to bind the le-RNA in vitro and inhibit CHPV growth in infected cells. Furthermore, a stretch of three amino acid residues at position 217-219 was identified as essential for this interaction, both in vitro and in infected cells. siRNA knockdown-rescue experiments demonstrated that these three amino acid residues are crucial for the leader RNA binding function of P protein in the CHPV life cycle. Mutations of these three amino acid residues render the peptide completely ineffective against CHPV. Effect of inhibition of phosphoprotein-leader RNA interaction on viral replication was assayed. Peptide Pep208-243 tagged with a cell penetrating peptide was found to inhibit CHPV replication as ascertained by real time RT-PCR. The specific inhibition of viral growth observed using this peptide suggests a new possibility for designing of anti-viral agents against Mononegavirale group of human viruses.

Improving the identification of anaerobes in the clinical microbiology laboratory through MALDI-TOF mass spectrometry

In this study, 1325 anaerobes were analyzed by MALDI-TOF MS. Of these, 92.5% were correctly identified at the species level. One unidentified species and several uncommon and rare species were identified. These results show that this technique has become the new gold standard for the routine identification of clinical anaerobes.

Determination of Serum Ferritin Glycosylation in Hyperferritinemia Associated to Iron Overload and Inflammation

BACKGROUND

Serum ferritin is a commonly used clinical biochemical parameter and hyperferritinemia is used as a surrogate marker for iron overload, acute or chronic inflammation, malignancy or cell death. The aim of the present study was to develop purification strategies of ferritin from sera to determine if micro-heterogeneity of serum ferritin can be used to differentiate the underlying cause of the hyperferritinemia.

PATIENTS MATERIALS AND METHODS

Sera from patients with hemochromatosis, rheumatologic diseases, aceruloplasminemia, ferroportin disease or iron loading anemia have been collected and stored and ferritin purified by negative affinity followed by ion exchange and size exclusion chromatography. Purified serum ferritin was analyzed by western blotting and MALDI TOF mass spectrometry and the spectra compared with the results from ferritin isolated from human liver, spleen and placenta.

RESULTS

By Western blotting a major band of 19kD has been found in most sera, suggesting that the L-ferritin is the predominant isoform present in serum regardless of the cause of hyperferritinemia. Multistep chromatography can be used for significant enrichment and purification of ferritin from serum, which can be further analyzed by MALDI TOF MS. Tryptic digestion and peptide mass finger-printing by MALDI TOF MS of ferritin purified from human tissues shows differential spectra.

DISCUSSION AND CONCLUSIONS

Analysis of ferritin micro-heterogeneity by MALDI TOF allows determination of the tissue origin of ferritin, which could be applied in the differential diagnostic workup of hyperferritinemia.