Alternative strategies for the recombinant synthesis, DOPA modification and analysis of mussel foot proteins - A case study for Mefp-3 from Mytilus edulis

Mussel foot proteins (Mfps) possess unique binding properties to various surfaces due to the presence of L-3,4-dihydroxyphenylalanine (DOPA). Mytilus edulis foot protein-3 (Mefp-3) is one of several proteins in the byssal adhesive plaque. Its localization at the plaque-substrate interface approved that Mefp-3 plays a key role in adhesion. Therefore, the protein is suitable for the development of innovative bio-based binders. However, recombinant Mfp-3s are mainly purified from inclusion bodies under denaturing conditions. Here, we describe a robust and reproducible protocol for obtaining soluble and tag-free Mefp-3 using the SUMO-fusion technology. Additionally, a microbial tyrosinase from Verrucomicrobium spinosum was used for the in vitro hydroxylation of peptide-bound tyrosines in Mefp-3 for the first time. The highly hydroxylated Mefp-3, confirmed by MALDI-TOF-MS, exhibited excellent adhesive properties comparable to a commercial glue. These results demonstrate a concerted and simplified high yield production process for recombinant soluble and tag-free Mfp3-based proteins with on demand DOPA modification.

Convenient preparation of indigo from the Ieaves of Baphicacanthus cusia(Nees) Bremek by enzymatic method and its MALDI-TOF-MS and UPLC-Q-TOF/MS analysis

The manufacturing of indigo naturalis requires prolonged leaf soaking and lime stirring; the resulting indigo purity is less than 3.00% and the yield of indigo (measured in stems and leaves weight) is less than 0.50%, making it unsuitable for use in industrial procedures like printing and dyeing. An enzymatic method of creating indigo without the requirement for lime was investigated in order to generate high purity indigo. Single factor tests were performed to optimize the enzymatic preparation conditions. The findings showed that 60 °C, pH 5.5, 200 mL of leaves extract containing 0.45 mg/mL indican, and a 4:1 ratio of the acidic cellulose (activity: 9000 U/mL, liquid) to indican were the ideal parameters for enzymatic preparation. The yield of indigo was 40.32%, and the contents of indigo and indirubin were 37.37% and 2.30%, respectively. MALDI-TOF-MS in positive ion mode and UPLC-Q-TOF-MS in both positive and negative ion modes were used to analyze indigo extracts from Baphicacanthus cusia(Nees) Bremek by enzymatic preparation. It has been discovered that 13 alkaloids, 5 organic acids, 3 terpenoids, 3 steroids, 2 flavones, and 7 other compounds are present in indigo extracts. The presence of the indigo, indirubin, isorhamnetin, tryptanthrin, indigodole B, and indigodole C determined by UPLC-Q-TOF-MS was verified by MALDI-TOF-MS analysis. The enzymatic preparation of indigo extracts kept the same chemical makeup as conventional indigo naturalis. Thermal analysis and SEM morphology were used to confirm that there was no lime in the indigo extract. During the enzymatic process, Baphicacanthus cusia (Nees) Bremek was employed more effectively, increasing the yield and purity of indigo.

Bifunctional MNPs@UIO-66-Arg core-shell-satellite nanocomposites for enrichment of phosphopeptides

A facile and mild method based on self-assembled lysozyme (LYZ) to fabricate bifunctional MNPs@UIO-66-Arg core-shell-satellite nanocomposites (CSSNCs) is reported for the high-efficiency enrichment of phosphopeptides. Under physiological conditions, LYZ rapidly self-assembled into a robust coating on Fe3O4@SiO2 magnetic nanoparticles (MNPs) with abundant surface functional groups, which effectively mediate heterogeneous nucleation and growth of UIO-66 nanocrystals. Well-defined MNPs@UIO-66 CSSNCs with stacked pores, showing high specific surface area (333.65 m2 g- 1) and low mass transfer resistance, were successfully fabricated by fine-tuning of the reaction conditions including reaction time and acetic acid content. Furthermore, the UIO-66 shells were further modified with arginine to obtain bifunctional MNPs@UIO-66-Arg CSSNCs. Thanks to the unique morphology and synergistic effect of Zr-O clusters and guanidine groups, the bifunctional MNPs@UIO-66-Arg CSSNCs exhibited outstanding enrichment performance for phosphopeptides, delivering a low limit of detection (0.1 fmol), high selectivity (β-casein/BSA, mass ratio 1:2000), and good capture capacity (120 mg g- 1). The mechanism for phosphopeptides capture may attribute to the hydrogen bonds, electrostatic interactions, and Zr-O-P bonds between phosphate groups in peptides and guanidyl/Zr-O clusters on bifunctional MNPs@UIO-66-Arg CSSNCs. In addition, the small stacking pores on the core-shell-satellite architecture may selectively capture phosphopeptides with low molecular weight, eliminating interference of other large molecular proteins in complex biological samples.

Description of new species of Mycobacterium terrae complex isolated from sewage at the São Paulo zoological park foundation in Brazil

Five mycobacterial isolates from sewage were classified as members of the genus Mycobacterium but presented inconclusive species assignments. Thus, the isolates (MYC017, MYC098, MYC101, MYC123 and MYC340) were analyzed by phenotypical, biochemical, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and genomic features to clarify their taxonomic position. Phenotypic analysis and biochemical tests did not distinguish these isolates from other non-pigmented mycobacteria. In contrast, MALDI-TOF MS analysis showed that isolates were not related to any previously described Mycobacterium species. Comparative genomic analysis showed values of ANI and dDDH between 81.59-85.56% and 24.4-28.8%, respectively, when compared to the genomes of species of this genus. In addition, two (MYC101 and MYC123) presented indistinguishable protein spectra from each other and values of ANI = 98.57% and dDDH = 97.3%, therefore being considered as belonging to the same species. Phylogenetic analysis grouped the five isolates within the Mycobacterium terrae complex (MTC) but in a specific subclade and separated from the species already described and supported by 100% bootstrap value, confirming that they are part of this complex but different from earlier described species. According to these data, we propose the description of four new species belonging to the Mycobacterium genus: (i) Mycobacterium defluvii sp. nov. strain MYC017T (= ATCC TSD-296T = JCM 35364T), (ii) Mycobacterium crassicus sp. nov. strain MYC098T (= ATCC TSD-297T = JCM 35365T), (iii) Mycobacterium zoologicum sp. nov. strain MYC101T (= ATCC TSD-298T = JCM 35366T) and MYC123 (= ATCC BAA-3216 = JCM 35367); and (iv) Mycobacterium nativiensis sp. nov. strain MYC340T (= ATCC TSD-299T = JCM 35368T).

Clinical impact of the combination of rapid species identification and antifungal stewardship intervention in adults with candidemia

BACKGROUND

Candidemia is associated with a high mortality rate. This study aimed to evaluate the clinical impact of a diagnostic intervention and antifungal stewardship in adults with candidemia, including effectiveness in facilitating appropriate antifungals and improving patient outcomes.

METHODS

A pre-post quasi-experimental study was conducted to analyze the impact of the integrated workflow of rapid species identification and antifungal stewardship intervention provided by infectious disease specialists for adults with candidemia at a medical center in southern Taiwan from March 1st, 2014 to February 29th, 2016. The primary endpoint was 30-day crude mortality, and secondary outcomes included the time to species identification, time to initial antifungal modification, and length of hospital stay.

RESULTS

Total 303 patients with candidemia were included, including 152 adults in the pre-intervention period (Mar. 1st, 2014-Feb. 28th, 2015; control group) and 151 in the intervention period (Mar. 1st, 2015-Feb. 29th, 2016; case group). Demographic and clinical characteristics of patients in two groups were similar. The case group had a shorter time to species identification (72 vs. 96 h, P < 0.001) and earlier receipt of antifungals (47 vs. 59 h, P < 0.001) than the control group. Of note, the 30-day mortality rate (27.2% vs. 39.5%, P = 0.028) was lower and the hospital stay (43.5 vs. 46.0 days, P = 0.006) was shorter in the case group.

CONCLUSION

Rapid diagnostic workflow and antifungal stewardship provided by infectious disease specialists can promote early initiation of antifungal therapy and improve outcome for adults with candidemia.

Three novel simple sequence repeats (SSRs) identified by MALDI-TOF-MS method were associated with backfat in pig

Backfat trait is an important economic trait and highly heritable, but difficult to evaluate. Thus, it is of great significance to explore optimal backfat thickness of pigs by using marker-assisted selection (MAS) to speed up its breeding process and improve economic efficiency. This study aimed to investigate the relationship between genetic variations (e.g., SSRs) and backfat of Qinghai Bamei pigs using MALDI-TOF Mass Spectrometry (MALDI-TOF-MS). Herein, five alternative SSR loci (namely V1, V2, V3, V4 and V5) were selected for subsequent detection. The results suggested that 3 (141-, 143- and 145-), 3 (128-, 130- and 132-), 2 (160- and 162-), 2 (136- and 139-) and 3 (170-, 184- and 192-) alleles of V1, V2, V3, V4 and V5 were found, respectively. Subsequent analysis showed that there was linkage equilibrium among five SSRs and Hap19 (13.1%) (141-/132-/160-/139-/192-) had the highest haplotype frequency. Among these five SSR loci, V1, V2 and V3 loci were significantly associated to the backfat of Qinghai Bamei sows. These findings enriched the study of SSRs in Qinghai Bamei pigs, and (AC)n (Chr15:85485851-85485995), (AC)n (Chr10:52724583-52724713) and (TG)n (Chr4:90732644-90732802) could be utilized as the candidate locus for MAS in pig industry.HIGHLIGHTSFive novel SSR loci was identified in pigs through MALDI-TOF MS.V1, V2 and V3 loci was were significantly associated to the backfat of pigs.

Identification and antibiogram of Enterobacterales from direct urine samples using matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) technology and disk-plate diffusion technique

Identification and antibiogram of uropathogenic microorganisms from direct urine samples present a great clinical impact. Here, we present a combined procedure to determine identification (IDd) of bacteria through MALDI-TOF-MS technology and antibiogram (ATBd) using disk-plate diffusion technique, of UTI-producing Enterobacterales against the most used antibiotics. Ninety-four urine samples with presence of pyuria and Gram-negative bacilli were selected. The IDd showed a high success rate (90%). ATBd procedure showed a high correlation for tested antibiotics. This simplified, low cost and reduced work time two-step procedure significantly reduces results turnaround time and benefit the clinical management of patients with UTI.

Isolation of Mycoplasma salivarium in the empyema of a diabetic patient with deep neck infection and necrotizing mediastinitis: A case report

Mycoplasma species (spp.) are predominantly found in the human oropharynx, and extracavity infections are rare. Conventional culture limitations hinder Mycoplasma spp. recovery, potentially causing overlooked infections. Molecular techniques reveal their roles in various infections. Mycoplasma pneumoniae causes pneumonia, while Mycoplasma salivarium (M. salivarium) in empyema is scarcely reported. We present a case of a 61-year-old man who suffered from tonsillitis, deep neck infection, necrotizing mediastinitis, and bilateral pleural infections. Mixed pathogens, mainly M. salivarium, were implicated.

Monitoring of low-molecular-weight protein aggregation by CE-SDS as a complementary method to SE-HPLC

Capillary electrophoresis with sodium dodecyl sulfate (CE-SDS) has long been proven to have excellent performance in the analysis and characterization of therapeutic proteins. However, it is rarely used for the detection of low-molecular-weight proteins or peptides. Our research has proved the ability of CE-SDS to characterize the purity of low-molecular-weight proteins (i.e., <10 kDa) and even polypeptides. In this article, insulin glargine was used as a model protein, and CE-SDS was used to analyze the samples damaged by heating and light exposure. The monomers, dimers, and trimers of insulin glargine were effectively separated, and the results of the mass spectrometry also confirmed the existence of two kinds of insulin aggregates. For comparison, the size-exclusion high-performance liquid chromatography (SE-HPLC) only showed a single aggregate peak. In addition, the denaturation conditions caused only the covalent aggregates to appear in the CE-SDS analysis. These advantages also make CE-SDS an excellent supplementary technology to the traditional SE-HPLC, providing biopharmaceutical analysts with more information.

Untying the anchor for the lipopolysaccharide: lipid A structural modification systems offer diagnostic and therapeutic options to tackle polymyxin resistance

Polymyxin antibiotics are the last resort for treating patients in intensive care units infected with multiple-resistant Gram-negative bacteria. Due to their polycationic structure, their mode of action is based on an ionic interaction with the negatively charged lipid A portion of the lipopolysaccharide (LPS). The most prevalent polymyxin resistance mechanisms involve covalent modifications of lipid A: addition of the cationic sugar 4-amino-L-arabinose (L-Ara4N) and/or phosphoethanolamine (pEtN). The modified structure of lipid A has a lower net negative charge, leading to the repulsion of polymyxins and bacterial resistance to membrane disruption. Genes encoding the enzymatic systems involved in these modifications can be transferred either through chromosomes or mobile genetic elements. Therefore, new approaches to resistance diagnostics have been developed. On another note, interfering with these enzymatic systems might offer new therapeutic targets for drug discovery. This literature review focuses on diagnostic approaches based on structural changes in lipid A and on the therapeutic potential of molecules interfering with these changes.

In-vitro Activity of Isepamicin against Gram-negative Bacteria in Comparison to Other Aminoglycosides Routinely used at a Teaching Hospital in Northern India

Background  Isepamicin is a 1-N-S-a-hydroxy-b-aminopropionyl derivative of gentamicin B and the spectrum of pathogenic microorganisms covered by it and its effectiveness is similar to that of amikacin except the action of aminoglycoside inhibitor enzymes is ineffectual on it. Material and Methods  We performed a prospective study in the Bacteriology section of the Department of Microbiology at a 1,600-bedded hospital in Northern India from Jan 2022 to March 2022. Isepamicin was tested for susceptibility against gram-negative bacteria, identified by routine biochemicals and matrix-assisted-desorption/ionization -time of flight-mass spectrometry (MALDI-TOF-MS) assay. The antibiotic susceptibility testing for each of the isolates was performed by Kirby Bauer's disc diffusion method, according to the CLSI 2019 guidelines. Results  The majority of isolates were obtained from blood samples (50, 39.1%). Among the non-inducible Enterobacteriaceae , Escherichia coli was least susceptible to amikacin (8/27, 29.63%) and most susceptible to isepamicin (18/27, 66.67%). Klebsiella pneumoniae followed the same pattern of susceptibility as E. coli and was least susceptible to Amikacin (20/46, 43.48%) and most susceptible to isepamicin (24/46, 52.17%). Enterobacter cloacae (6/7, 85.71%) was most susceptible to both amikacin and isepamicin, followed by 71.43% (5/7, 71.43%) susceptibility to gentamicin and tobramycin each. Enterobacter aerogenes was equally 53.33% (8/15) susceptible to all antibiotics. Pseudomonas aeruginosa was the most susceptible isolate to all antibiotics (18/21, 85.71%). Conclusion  Isepamicin is a potential antimicrobial agent for treating an array of gram-negative bacteria-associated infections and shows better in vitro activity than older aminoglycoside agents.

Clinical presentations and microbiological analysis of cerebrospinal fluid samples in cases of suspected bacterial meningitis patients attending a 1600 bedded teaching hospital from 2019 to 2022: A retrospective study

Background

Meningitis can be attributed to bacterial, fungal, or viral agents. In this study, we demonstrate the common bacterial agents causing meningitis along with their antibiotics susceptibility pattern in patients of all age groups.

Material and Methods

This retrospective, observational study was carried out in the Department of Microbiology with cerebrospinal fluid (CSF) samples collected from November 2019 to May 2022. We collected 1986 nonrepeat CSF samples from clinically suspected patients of bacterial meningitis, and clinical information about the patients was extracted from the hospital information system.

Results

Out of the 1986 CSF samples included in our study, 150 (7.55%) were found to be positive on bacterial culture. Most of our patients were in the age group of 0-20 years. Common clinical manifestations observed in our patients were: high-grade fever, 87 patients (58%); severe headache, 126 patients (84%); neck rigidity, 47 patients (31.3%); altered mental status, 76 patients (50.7%) and photophobia, 83 patients (55.3%). The most commonly isolated bacteria was Acinetobacter species (30%). The mean length of hospitalization (37.76 ± 25.30), the mean total cell count, high levels of protein (mg/dl) and low levels of glucose (mg/dl) of CSF were statistically significant in meningitis caused by multidrug-resistant bacteria.

Conclusion

We recognized the spectrum of pathogens causing meningitis at our center along with the antibiotic resistance pattern to guide and facilitate early treatment by primary health care professionals and family medicine practitioners.

Antimicrobial Resistance and Biofilm Formation of Escherichia coli Isolated from Pig Farms and Surroundings in Bulgaria

Escherichia coli (E. coli) is a ubiquitous microorganism with pathogenic and saprophytic clones. The objective of this study was to evaluate the presence, virulence, antibiotic resistance and biofilm formation of E. coli in three industrial farms in Bulgaria, as well as their adjacent sites related to the utilization of manure (feces, wastewater in a separator, lagoons, means of transport, and soils). The isolation of single bacterial cultures was performed via standard procedures with modifications, and E. coli isolates were identified via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and polymerase chain reaction (PCR). The disk diffusion method was used to assess antimicrobial resistance, and PCR was used to detect genes for antibiotic resistance (GAR) (qnr, aac(3), ampC, blaSHV/blaTEM and erm) and virulence genes (stx, stx2all, LT, STa, F4 and eae). The protocol of Stepanović was utilized to measure the biofilm formation of the isolates. A total of 84 isolates from different samples (n = 53) were identified as E. coli. Almost all demonstrated antimicrobial resistance, and most of them demonstrated resistance to multiple antibiotics from different classes. No virulence genes coding the Shiga toxin or enterotoxins or those associated with enteropathogenicity were detected. No GAR from those tested for quinolones, aminoglycosides and macrolides were found. However, all isolates that were resistant to a penicillin-class antibiotic (56) had β-lactamase-producing plasmid genes. All of them had ampC, and 34 of them had blaTEM. A total of 14 isolates formed strongly adherent biofilms. These results in a country where the use of antibiotics for growth promotion and prophylaxis in farms is highly restricted corroborate that the global implemented policy on antibiotics in human medicine and in animal husbandry needs revision.

Uptake, bioaccumulation, biodistribution and depuration of polystyrene nanoplastics in zebrafish (Danio rerio)

Plastic nanoparticles formed from both daily use of plastics and their wastes have emerged as a potential health and environmental hazard. It is necessary to study the biological process of nanoplastics in ecological risk assessment. To address this concern, we quantitatively investigated the accumulation and depuration of polystyrene nanoplastics (PSNs) in the tissues of zebrafish after the aquatic exposure using a quantitative method based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Via the PSNs-spiked freshwater, zebrafish were exposed to three different concentrations of PSNs for 30 days, followed by 16 days of depuration. The results showed that the amounts of PSNs accumulated in zebrafish tissues were in the following order: intestine > liver > gill > muscle > brain. The uptake and depuration of PSNs in zebrafish both followed pseudo-first-order kinetics. It was revealed that the bioaccumulation was concentration, tissue and time dependent. When the PSNs concentration is low, the steady state might take longer time (or not occur) than that of a high concentration. After 16 days of depuration, there were still some PSNs present in the tissues particularly in the brain, where it might take 70 days or more to remove 75 % of PSNs. Overall, this work offers important knowledge on the bioaccumulation of PSNs, which may be useful for future studies into the health hazards of PSNs in aquatic environments.

Site-Specific Fluorescent Labeling of Hemagglutinin-Specific Antigen Binding Fragment through Amine Chemistry Revealed by Mass Spectrometry

To capture the structure of assembled hemagglutinin (HA) nanoparticles at single-particle resolution, HA-specific antigen binding fragments (Fabs) were labeled by fluorescent (FLR) dyes as probes to highlight the HA trimers displayed on the assembled tetravalent HA nanoparticles for a qualitative localization microscopic study. The FLR dyes were conjugated to the Fabs through N-hydroxysuccinimide (NHS) ester mediated amine coupling chemistry. The labeling profile, including labeling ratio, distribution, and site-specific labeling occupancy, can affect the imaging results and introduce inconsistency. To evaluate the labeling profile so as to evaluate the labeling efficiency, a combination of intact mass measurement by MALDI-MS and peptide mapping through LC-MS/MS was implemented. At the intact molecular level, the labeling ratio and distribution were determined. Through peptide mapping, the labeled residues were identified and the corresponding site-specific labeling occupancy was measured. A systematic comparative investigation of four different FLR-labeled 1H01-Fabs (generated from H1 strain HA specific mAb 1H01) allowed accurate profiling of the labeling pattern. The data indicate that the labeling was site-specific and semiquantitative. This warrants the consistency of single-particle fluorescent imaging experiments and allows a further imaging characterization of the single nanoparticles.

Maldi-Tof-Ms Identified Rhodococcus Hoagie Bacteraemia In An Immunocompromised Patient

Rhodococcus hoagie, previously referred to as R. equi, is a Gram-positive intracellular coccobacillus that belongs to the Nocardiaceae family. This multi-host pathogen causes infections in farm animals, particularly foals, but also in immunosuppressed patients, mainly individuals treated with high doses of corticosteroids, subjected to organ transplant, or infected with human immunodeficiency virus Objectives of the study are to report a bloodstream infection in an immunocompromised patient. Immunocompromised patients with advanced HIV who presented bloodstream infection, residing in an urban setting and having undertaken no trips to the countryside or elsewhere during the COVID-19 pandemic. Blood culture by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was done in order to identify the bacteria. The immunocompromised female patient presented bloodstream infection by Rhodococcus hoagie, which was identified using MALDI-TOF-MS. R. hoagie can cause a severe infection with a high mortality rate if prompt treatment with a combination of antibiotics is not established. A high level of suspicion is required to establish the diagnosis, as it may be misdiagnosed as pulmonary tuberculosis. On gram stain, R. hoagie may appear as beaded to solid staining coccobacilli, which can be dismissed as a "diphtheroid" contaminant. The infection was identified using MALDI-TOF-MS.

Analysis of Immunogenic Galactose-α-1,3-galactose-Containing N-Glycans in Beef, Mutton, and Pork Tenderloin by Combining Matrix-Assisted Laser Desorption/Ionization-Mass Spectroscopy and Capillary Electrophoresis Hyphenated with Mass Spectrometry via Electrospray Ionization

Severe allergic reactions to certain types of meat following tick bites have been reported in geographic regions which are endemic with ticks. This immune response is directed to a carbohydrate antigen (galactose-α-1,3-galactose or α-Gal), which is present in glycoproteins of mammalian meats. At the moment, asparagine-linked complex carbohydrates (N-glycans) with α-Gal motifs in meat glycoproteins and in which cell types or tissue morphologies these α-Gal moieties are present in mammalian meats are still unclear. In this study, we analyzed α-Gal-containing N-glycans in beef, mutton, and pork tenderloin and provided for the first time the spatial distribution of these types of N-glycans in various meat samples. Terminal α-Gal-modified N-glycans were found to be highly abundant in all analyzed samples (55, 45, and 36% of N-glycome in beef, mutton, and pork, respectively). Visualizations of the N-glycans with α-Gal modification revealed that this motif was mainly present in the fibroconnective tissue. To conclude, this study contributes to a better understanding of the glycosylation biology of meat samples and provides guidance for processed meat products, in which only meat fibers are required as an ingredient (i.e., sausages or canned meat).

Integration of antimicrobial stewardship intervention with rapid organism identification improve outcomes in adult patients with bloodstream infections

BACKGROUND

Integration of antimicrobial stewardship intervention (ASI) with rapid organism identification has the potential for early customization of antimicrobial therapy and improved clinical outcomes. We aimed to evaluate the impact of this combined approach on antimicrobial therapy-related outcomes in patients with bloodstream infections (BSIs).

MATERIALS AND METHODS

A pre-post quasi-experimental study was conducted to analyze the impact of ASI with organism identification via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) among patients with BSIs. Outcomes were compared to a historic pre-intervention group. The 30-day mortality was the primary endpoint. Secondary outcomes included time to first antibiotic modification, length of hospital stay.

RESULTS

A total of 1004 adult patients with BSIs were included in the final analysis, 519 patients classified into the intervention group and 485 patients in the preintervention group. The patients in the intervention group were younger (66 vs. 70 years, P = 0.02). The 30-day crude mortality (14.6% vs. 29.9%, P < 0.001) was lower, the time to organism identification (72.25 vs. 83.6 h, P < 0.001) and length of hospital stay (12 days vs. 14 days, P < 0.001) were shorter in the intervention group. Acceptance of an ASI was associated with a trend toward a reduced 30-day mortality on multivariable analysis (odds ratio 0.33; 95% CI: 0.24-0.47; P < 0.001).

CONCLUSION

The ASI combined with MALDI-TOF-MS approach decreased time to organism identification and time to appropriate antimicrobial therapy would achieve a better clinical outcome in the patients with BSIs.

Elucidation of the Bridging Pattern of the Lantibiotic Pseudomycoicidin

Lantibiotics are post-translationally modified antibiotic peptides with lanthionine thioether bridges that represent potential alternatives to conventional antibiotics. The lantibiotic pseudomycoicidin is produced by Bacillus pseudomycoides DSM 12442 and is effective against many Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus. While prior work demonstrated that pseudomycoicidin possesses one disulfide bridge and four thioether bridges, the ring topology has so far remained unclear. Here, we analyzed several pseudomycoicidin analogues that are affected in ring formation via MALDI-TOF-MS and tandem mass spectrometry with regard to their dehydration and fragmentation patterns, respectively. As a result, we propose a bridging pattern involving Thr8 and Cys13, Thr10 and Cys16, Ser18 and Cys21, and Ser20 and Cys26, thus, forming two double ring systems. Additionally, we localized the disulfide bridge to connect Cys3 and Cys7 and, therefore, fully elucidated the bridging pattern of pseudomycoicidin.

[Salivary Peptide Profiling Analysis of Patients with Periodontitis and Chronic Obstructive Pulmonary Disease]

Objective

To analyze the salivary peptide profiles of patients with periodontitis (PD) and chronic obstructive pulmonary disease (COPD), to identify differentially expressed peptides that are associated with diseases, to explore for biomarkers with potential diagnostic significance, and to probe for new perspectives for the early prevention and treatment of COPD.

Methods

A total of 10 PD patients (the PD group), 10 PD patients with COPD (the PD plus COPD group), and 8 healthy controls (the Control group) were selected for the study. The clinical data and saliva samples of the subjects were collected. Salivary supernatant samples were separated and purified with weak-cation-exchange magnetic bead-based (WCX-MB). With matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), the biodata of the samples were obtained and differential salivary peptide profiling was conducted to screen for peptides exhibiting inter-group differences. In addition, all the differentially expressed peptides were examined and verified with liquid chromatography tandem mass spectrometry (LC-MS/MS).

Result

An average of 77 peptide mass peaks were detected among three groups, the peaks intensities differed significantly for 10 peptides between PD patients and PD patients with COPD. Among them, eight peptides (1193.5, 1836.2, 1735.1, 1321.3, 1356.8, 2086.8, 1863.6, and 2230.9) showed increased expression and two peptides (1067.3 and 1124.4) showed decreased expression in the PD plus COPD group, in comparison with the PD group. Among the 10 differential peptides, 1193.5 and 1356.8 were identified as histidine-rich protein-1, submaxillary gland androgen-regulated protein 3B, and salivary acidic proline-rich protein 1/2.

Conclusion

With WCX-MB and MALDI-TOF-MS, we have identified, from the saliva of patients with concomitant PD and COPD, differentially expressed salivary peptides that were associated with diseases. The differentially expressed peptides thus screened out show promises for being used as auxiliary biomarkers for early diagnosis of COPD.

MALDI-TOF-MS for rapid screening analysis of M-protein in serum

Monoclonal immunoglobin (M-protein) is a serum biomarker for the diagnosis of plasma cell dyscrasias. Despite limitation of analytical sensitivity and resolution, serum protein electrophoresis and immunofixation electrophoresis are still the front-line tests for the detection of M-proteins. Herein, we developed a MALDI-TOF Mass spectrometry-based method for the screening test of M-proteins in human serum. Based on the unique mass signature of different immunoglobin isotypes, M-Proteins could be rapidly identified and typed. The method demonstrated with high analytical performance and throughput, rapid and simple, which could be a new choice for the diagnosis of plasma cell dyscrasias.

Pathogenicity and virulence of bacterial strains associated with summer mortality in marine mussels (Perna canaliculus)

The occurrence of pathogenic bacteria has emerged as a plausible key component of summer mortalities in mussels. In the current research, four bacterial isolates retrieved from moribund Greenshell࣪ mussels, Perna canaliculus, from a previous summer mortality event, were tentatively identified as Vibrio and Photobacterium species using morpho-biochemical characterization and MALDI-TOF MS and confirmed as V. celticus, P. swingsii, P. rosenbergii, and P. proteolyticum using whole genome sequencing. These isolates were utilized in a laboratory challenge where mussels were injected with cell concentrations ranging from 105 to 109 CFU/mussel. Of the investigated isolates, P. swingsii induced the highest mortality. Additionally, results from quantitative polymerase chain reaction analysis, focusing on known virulence genes were detected in all isolates grown under laboratory conditions. Photobacterium rosenbergii and P. swingsii showed the highest expression levels of these virulence determinants. These results indicate that Photobacterium spp. could be a significant pathogen of P. canaliculus, with possible importance during summer mortality events. By implementing screening methods to detect and monitor Photobacterium concentrations in farmed mussel populations, a better understanding of the host-pathogen relationship can be obtained, aiding the development of a resilient industry in a changing environment.

Toolbox Accelerating Glycomics (TAG): Improving Large-Scale Serum Glycomics and Refinement to Identify SALSA-Modified and Rare Glycans

Glycans are involved in many fundamental cellular processes such as growth, differentiation, and morphogenesis. However, their broad structural diversity makes analysis difficult. Glycomics via mass spectrometry has focused on the composition of glycans, but informatics analysis has not kept pace with the development of instrumentation and measurement techniques. We developed Toolbox Accelerating Glycomics (TAG), in which glycans can be added manually to the glycan list that can be freely designed with labels and sialic acid modifications, and fast processing is possible. In the present work, we improved TAG for large-scale analysis such as cohort analysis of serum samples. The sialic acid linkage-specific alkylamidation (SALSA) method converts differences in linkages such as α2,3- and α2,6-linkages of sialic acids into differences in mass. Glycans modified by SALSA and several structures discovered in recent years were added to the glycan list. A routine to generate calibration curves has been implemented to explore quantitation. These improvements are based on redefinitions of residues and glycans in the TAG List to incorporate information on glycans that could not be attributed because it was not assumed in the previous version of TAG. These functions were verified through analysis of purchased sera and 74 spectra with linearity at the level of R2 > 0.8 with 81 estimated glycan structures obtained including some candidate of rare glycans such as those with the N,N’-diacetyllactosediamine structure, suggesting they can be applied to large-scale analyses.

Multimodal analysis of south-eastern Black Sea sediment bacterial population diversity

This study focused on marine sediments from the Black Sea, mainly due to bacterial diversity-induced public health / biotechnology application value. Sediment samples were gathered from 14 locations at differing depths across Turkish shores on a seasonal basis over 10 months, with bacterial identifications performed through using multimodal analytical platforms. Overall, 26 differing, predominantly Gram-positive (57.5 %) bacterial species were identified for this region, including Bacillaceae (50.0 %) and Pseudomonadaceae (15.0 %). The most dominant classes were identified as Bacilli (52.5 %) and Gammaproteobacteria (40.0 %). Ten isolates (25 %) to the species level and thirty-six isolates (90 %) to the genus level were identified using VITEK® MS and Bruker Microflex® LT/SH, in comparison to 16S rRNA sequencing results. Identified species - particularly, novel reported species - can contribute to the knowledge of microbial life dwelling upon sediments of the south-eastern regions of the Black Sea.

Development and application of a sensitive phosphonium-hydrazide oligosaccharide labelling reagent in capillary electrophoresis- electrospray ionization- mass spectrometry

Glycosylation is one of the most ubiquitous post-translational modifications (PTM) of proteins. Although the ionization efficiency of native glycans is fairly low, with the assistance of chemical derivation strategies, mass spectrometry (MS) has been extensively used in glycomics because of its high sensitivity, accuracy, and speed. In this study, a novel glycan labelling reagent, (4-hydrazidebutyl) triphenylphosphonium bromide (P₄HZD), with a permanent positive charge was developed. The comprehensive capabilities of P₄HZD for MS analysis of oligosaccharides were evaluated in detail using maltodextrin as a standard. This labelling reagent can be used in common biological MS techniques such as matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometry. The MS signal intensity of maltodextrin species could be enhanced up to 96-fold in MALDI-MS by labelling with P₄HZD, making P₄HZD favorable for MALDI-MS-based high-throughput screening of oligosaccharides. Moreover, P₄HZD-labelled oligosaccharides with a degree of polymerization (DP) from 1 to 18 could be separated and analysed by capillary electrophoresis (CE) combined with positive ion mode ESI-MS. In comparison with a commercialized oligosaccharide tag, Girard's reagent P (GirP), P₄HZD was more effective for enhancing the signal of oligosaccharides in the middle or higher mass range using both ESI and MALDI ion sources. Two biologics, immunoglobulin G 2 (IgG 2) and fusion protein (FP), were chosen as model complex biological samples to test the efficacy of detection and separation of oligosaccharides by MALDI-MS and CE-ESI-MS analysis with P₄HZD labelling. The results indicated that P₄HZD is a promising labelling reagent for the detection of oligosaccharides in complex biological samples. The tandem workflow combines the strengths of MALDI-MS and CE-ESI-MS to fulfil the analytical demands of high-throughput screening, while affording good separation.

Exploring polymerisation of methylglyoxal with NH3 or alanine to analyse the formation of typical polymers in melanoidins

To investigate the formation of typical melanoidin polymers, methylglyoxal (MGO) with NH₃ or alanine (Ala) was used to form coloured compounds, with glyoxal or acetone used as controls. The products were characterised using chromatography, mass spectrometry, and spectroscopy. Spectroscopic results showed that the coloured compounds formed were similar to melanoidins in food. GC-MS results showed that the MGO-based reaction generated similar volatile compounds using the Maillard reaction. Mass spectrometry showed that the molecular weights of structural units in the polymers were mainly 162, 169, and 176 Da, and these could be reassembled using the basic units derived from MGO alone or in combination with nitrogen. Hence, polymers recombined using basic structural units should be considered while determining melanoidin biomarkers. The preparation of coloured compounds using MGO with NH₃ can be used as a novel method to produce the control compounds for melanoidin after process optimization.

Nanocomposites of boronic acid-functionalized magnetic multi-walled carbon nanotubes with flexible branched polymers as a novel desorption/ionization matrix for the capture and direct detection of cis-diol-flavonoid compounds coupled with MALDI-TOF-MS

Novel boronic acid-functionalized magnetic multi-walled carbon nanotubes with flexible branched polymer (Fe₃O₄@MWCNTs@ε-PL@BA) nanocomposites were fabricated and applied as the desorption/ionization matrix for the MALDI-TOF-MS determination of low molecular weight flavonoids. The prepared nanocomposite was systematically characterized by various techniques. Compared to the traditional organic matrix, the proposed Fe₃O₄@MWCNTs@ε-PL@BA matrix has excellent ionization efficiency and low-background noise interference due to the MWCNTs unique electron-phonon interaction and the high introduction density of boronic acid functional groups. Good sensitivity and ultra-high salt tolerance of the Fe₃O₄@MWCNTs@ε-PL@BA-assisted MALDI-TOF-MS were permitted for the determination and quantification of flavonoids in actual samples. Noticeably, the limits of detection (LODs) for the target flavonoids were in the range 17-33 nM. The relative standard deviations (RSDs) of spot-to-spot and sample-to-sample (n = 10) were ≤ 9.8% and ≤ 10.1%, respectively. Furthermore, the wide linear ranges (0.1 - 500 µg/mL) and satisfactory calibration plot coefficients (R² > 0.99) of flavonoids were achieved by MALDI-TOF-MS with the Fe₃O₄@MWCNTs@ε-PL@BA matrix. Good recoveries (92-105.5%) were achieved for the target flavonoids in practical food samples. Hence, the prepared Fe₃O₄@MWCNTs@ε-PL@BA nanocomposites have applications in the selective and efficient capture of target flavonoids active biomolecules coupled with MALDI-TOF-MS determination in actual samples.

MALDI-TOF-MS integrated workflow for food authenticity investigations: An untargeted protein-based approach for rapid detection of PDO feta cheese adulteration

Advances in Matrix-assisted Laser Desorption/Ionization -Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS) have led to its supremacy for complex assessment of food authenticity studies, like dairy products fraud, holding promise for the discovery of potential authenticity (bio)markers. In this study, an integrated untargeted protein-based workflow in combination with advanced chemometrics is presented, to address authenticity challenges in PDO feta cheese which is legally manufactured by the mixture of sheep/goat milk. Potential markers attributed to specific animal origin were found from protein profiles acquired for authentic feta and white cheeses (prepared from cow milk), belonging to 4 kDa-18.5 kDa mass area. Rapid detection of feta cheese adulteration from cow milk was also achieved down to 1% adulteration level. The discriminative models showed high predictive ability for feta cheese authenticity (Q² = 0.920, RMSEE = 0.053) and its adulteration (Q² = 0.835, RMSEE = 0.121), introducing a reliable approach in routine analysis. The methodology was successfully applied in detection of cow milk in sheep yoghurt.

p38-MAPK recruits the proteolytic pathways in Caenorhabditis elegans during bacterial infection

In eukaryotic organisms, cell-signalling completely relies on Post Translational Modifications (PTMs) that can function as regulatory switches. Phosphorylation is a fundamental and frequently occurring PTM in almost all eukaryotes. Herein, we have studied the importance of protein phosphorylation using classical proteomic techniques in C. elegans upon bacterial infection. The differentially regulated proteins during bacterial infection were excised from SDS-PAGE (One-Dimensional) gel (TiO₂ column elutes) and subjected to MALDI-TOF-MS which ended up in identifying 220 proteins kinetically. KEGG pathway analysis of those proteins suggested that MAPK pathway was part of the innate immunity. Thus, we have characterized p38-MAPK (one of the crucial downstream MAPKs) using immunoblotting, subcellular fractionation, coimmunoprecipitation, LC-MS/MS, bioinformatics studies and qPCR. Meanwhile, KU25 strain (pmk-1 mutant) exhibited an earlier mortality during infection suggesting the crucial role of p38-MAPK during host-pathogen interaction. Interestingly, Reactome pathway analysis of p38 interactors (CoIP coupled to LC-MS/MS) revealed the involvement of various proteolytic pathway players (ubiquitination, SUMOylation and Neddylation) during bacterial infection. Further, the regulation of SUMOylation and Neddylation was identified and validated using immunoblotting and qPCR analyses, respectively. Concisely, our study indicated that bacterial infection triggers the MAPK cascade to elicit innate immunity which in turn recruits proteolytic pathways to counteract the invading pathogen.

Kappa/Lambda light-chain typing in Alzheimer's Disease

BACKGROUND

Alzheimer's disease is a progressive neurodegenerative disorder characterized by memory loss and cognitive impairment. The diagnosis of Alzheimer's disease according to symptomatic events is still a puzzling task. Developing a biomarker-based, low-cost, and high-throughput test, readily applicable in clinical laboratories, dramatically impacts the rapid and reliable detection of the disease.

OBJECTIVE

This study aimed to develop an accurate, sensitive, and reliable screening tool for diagnosing Alzheimer's disease, which can significantly reduce the cost and time of existing methods.

METHODS

We have employed a MALDI-TOF-MS-based methodology combined with a microaffinity chromatogra Results: We observed a statistically significant difference in the kappa light chain over lambda light chain (κLC/LC) ratios between patients with AD and controls (% 95 CI: -0.547 to -0.269, p<0.001). Our method demonstrated higher sensitivity (100.00%) and specificity (71.43%) for discrimination between AD and controls.

CONCLUSION

We have developed a high-throughput screening test with a novel sample enrichment method for determining κLC/LC ratios associated with AD diagnosis. Following further validation, we believe our test has a potential for clinical laboratories.

Growth conditions affect biofilms of Staphylococcus aureus producing mastitis: Contribution of MALDI-TOF-MS to strain characterization

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S. aureus native strains formed in vitro high biofilm in milk.

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Milk whey and free iron medium significantly decreased the biofilms of S. aureus.

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MALDI-TOF-MS was a useful tool to categorize different levels of biofilm formation.

Bovine mastitis is a disease of dairy cattle prevalent throughout the world that causes alterations in the quality and composition of milk, compromising technological performance. Staphylococcus aureus is one of the most important pathogens that produce clinical, subclinical, and chronic mastitis. Biofilms are considered a virulence factor necessary for the survival of S. aureus in the mammary gland. Its zoonotic potential is important not only for the dairy industry sector but also for public health. This study aimed to evaluate the effect of different growing culture conditions on the biofilm formation of S. aureus isolated from mastitis and to test the MALDI-TOF-MS's ability to discriminate among different biofilm formation levels. Fluids commonly found in the dairy environment were incorporated to approach the pathogen's behavior in natural surroundings. PIA production was also evaluated. All strains were able to form high biofilms in TSB, TSBg, and milk. Milk changed the behavior of some strains which formed more biofilms in this medium than in TSBg. The free iron medium CTSBg and milk whey inhibited the biofilm formation of the most strains. MALDI-TOF-MS performance was an excellent tool to discriminate between high, moderate, and low biofilm producers strains of S. aureus in each media, confirming the results of crystal violet assay. PIA production was variable among the strains and showed a media-dependent behavior. Our data highlights the importance of considering the growing conditions that mimic the natural ones to the study of biofilm formation in vitro.

Bacteroides pyogenes isolated from appendiceal abscess in a patient without animal contact

Bacteroides pyogenes is a member of the oral flora of cats and dogs. We report a case of B. pyogenes isolated from an appendiceal abscess in a patient without a history of animal contact. This species was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and sequencing of 16S rRNA, rpoB, gyrB and hsp60 genes.

A proteomic analysis of Pseudevernia furfuracea after exposure to Cr+6 by MALDI-TOF mass spectrometry

The problem of heavy metal pollution in nature has increased rapidly in recent years. Hexavalent chromium (Cr⁺⁶) is one of the most toxic heavy metals that cause environmental pollution. Although many studies in the literature that illuminate the stress response mechanisms of biological organisms such as bacteria, algae, and plants against heavy metals, there is limited information about revealing the protein level changes of lichen species in response to heavy metal stress. Here, we used a MALDI-TOF-based proteomic assay to determine protein level changes in Pseudevernia furfuracea after exposure to Cr⁺⁶ heavy metal stress at 6, 18 and 24 h. It was determined that expression levels of 26, 149 and 66 proteins changed in P. furfuracea. 6, 18 and 24 h after Cr⁺⁶ application compared to the control sample, respectively. We identified 9 common proteins expressed at three different time levels (6, 18, 24 h) and evaluated their protein-protein interaction profiles with the STRING tool. According to the results of the study, it was determined that the expression level of six proteins was up-regulated (OP4, KIP3, BNI5, VSP64, HSP 60, BCK1) and three proteins were down-regulated (MNS1, ABZ2, ATG4) from the expression level of nine proteins in total with Cr⁺⁶ exposure. It was determined that nine proteins were also found to be effective in biological processes such as stress signaling, transcription regulation and cellular detoxification metabolisms. To confirm the protein expression level, we analyzed the HSP60 protein by western blot assay. It has been shown that exposure to Cr⁺⁶ exposure in P. furfuracea caused an increase in HSP60 protein level compared to the control sample (non-exposed Cr⁺⁶). In this study, new knowledge are presented for the use of P. furfuracea as a biosorption agent in the removal of industrial wastes in biotechnological applications.

Virulence and Antimicrobial Resistance Pattern of Aeromonas spp. Colonizing European Pond Turtles Emys orbicularis and Their Natural Environment. First Study from Poland

The aim of the study was to isolate and identify species belonging to the Aeromonas genus and evaluate the antimicrobial resistance and virulence patterns of isolates colonizing European pond turtles (Emys orbicularis) from natural environment of Eastern Poland. In total, 74 turtles and 15 samples of water from their natural environment were examined. More than 40 strains were isolated and identified: A. bestiarum (n = 1), A. hydrophila (n = 13), A. allosaccharophila (n = 2), A. salmonicida (n = 3), and A. veronii (n = 23). The highest incidence of resistance was noted for ampicillin (100%) and sulfamethoxazole (62.0%), followed by erythromycin and colistin (both 40.5%). Moreover, eight strains were intermediately resistant to meropenem (19%). Most Aeromonas isolates were found to possess more than one virulence gene among fla, aer, hlyA, act, ela, alt, and ast. We showed that the population of free-living European pond turtles was highly colonized by Aeromonas spp. Such strains may be an infectious agent not only for the population of turtles but also for other species of animals inhabiting their natural environment. Moreover, the undesirable properties of water quality caused by the presence of drug-resistant aeromonads could have a negative impact on human health.

Looking at time dependent differentiation of mesenchymal stem cells by culture media using MALDI-TOF-MS

Mesenchymal stem cells (MSCs) are multipotent cells which are popular in human regenerative medicine. These cells can renew themselves and differentiate into several specialized cell types including osteoblasts, adipocytes, and chondrocytes under physiological and experimental conditions. MSCs can secret a lot of components including proteins and metabolites. These components have significant effects on their surrounding cells and also can be used to characterize them. This characterization of multipotent MSCs plays a critical role in their therapeutic potential. The metabolic profile of culture media verified by applying matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF-MS) techniques. Also, the differentiation and development of MSCs have monitored through culture media metabolome or secretome (secreted metabolites). Totally, 24 potential metabolites were identified. Between them 12 metabolites are unique to BM-MSCs and 5 metabolites are unique to AD-MSCs. Trilineage differentiation including chondrocytes, osteoblasts, and adipocytes, as well as metabolites that are being differentiated, have been shown in different weeks. In the present study, the therapeutic effects of MSCs analyzed by decoding the metabolome for MSCs secretome via metabolic profiling using MALDI-TOF-MS techniques.

Using surfactants as matrix for the matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) of amino acids: Sodium dodecyl sulfate (SDS) and sodium octyl sulfate (SOS)

In the present study, the applicability of two surfactants including sodium dodecyl sulfate (SDS) and sodium octyl sulfate (SOS) as the matrix for the Matrix-Assisted Laser Desorption/Ionization (MALDI) of several amino acids (phenylalanine (Phe), valine (Val), proline (Pro), alanine (Ala), and tyrosine (Tyr)) is investigated. Also, the effect of the material of the repeller plate of the ionization part of the used time of flight (TOF) mass spectrometer on the spectral patterns of the amino acids is studied. Furthermore, the recorded MALDI spectra of amino acids are compared with their corresponding direct laser desorption/ionization (direct-LDI) TOF mass spectra. It is observed that the SDS is an appropriate matrix for the Na⁺ transfer to the Phe and Val amino acids, especially, when the Ag metal is selected as the material of the repeller plate. In this case, the peaks of the [M + Na]⁺ and [M-H + 2Na]⁺ species are considerably more intense compared to when the NaF salt is used as a Na⁺ source in the LDI of these amino acids. Unlike Phe and Val, the SDS is not a good matrix for the other selected amino acids. The decrease of the carbonic chain length of the surfactant on the MALDI spectrum of Phe is investigated and it is seen that the mentioned important peaks disappeared in the presence of SOS as the matrix. The density functional theory (DFT) calculation is employed to characterize the structure of [M + Na]⁺ and [M-H + 2Na]⁺ species and determine the interaction sites of amino acids for the Na⁺ attachment. Also, the change in standard Gibbs free energy (∆G^°) of the M + Na⁺ → [M + Na]⁺ and [M + Na]⁺ + Na⁺ → [M-H + 2Na]⁺ + H⁺ reactions are calculated. Based on the values of ∆G^°, the attachment of the first Na⁺ to the amino acid takes place in the gas phase while the attachment of the second one to [M + Na]⁺ is not a favorable process in the gas phase.

Novel mannosylerythritol lipid biosurfactant structures from castor oil revealed by advanced structure analysis

Mannosylerythritol lipids (MEL) are glycolipid biosurfactants that are produced by fungi of the Ustilaginaceae family in the presence of hydrophobic carbon sources like plant oils. In the present study, we investigated the structural composition of mannosylerythritol lipids produced from castor oil using seven different microorganisms and compared them to the structures resulting from other plant oils. Castor oil is an industrially relevant plant oil that is used neither for human consumption nor as a feedstock for animal feed and is therefore presenting an interesting alternative to currently employed edible plant oils like rapeseed or soybean oil. The main fatty acid in castor oil is the mono-hydroxylated ricinoleic acid, providing the possibility to produce novel MEL structures with interesting features. Analysis of the produced MELs from castor oil by different chromatographic and mass spectrometry techniques revealed that all seven microorganisms were generally able to integrate hydroxylated fatty acids into the MEL molecule, although at varying degrees. These novel MELs containing a hydroxy fatty acid (4-O-(2'-O-alka(e)noyl-3'-O-hydroxyalka(e)noyl-4'/6'-O-acetyl-β-D-mannopyranosyl)-erythritol) were more hydrophilic than conventional MEL and therefore showed a different elution behavior in chromatography. Large shares of novel hydroxy MELs in the mixture (around 50 % of total MELs) were found for the two MEL-B/C producing species Ustilago siamensis and Ustilago shanxiensis, but also for the MEL-A/B/C producer Moesziomyces aphidis (around 25 %). In addition, tri-acylated hydroxylated MELs with a third long-chain fatty acid esterified to the free hydroxyl group of the hydroxy fatty acid were identified for some species. Overall, the production of MEL from castor oil with the investigated organisms provided a complex mixture of various novel MEL structures that can be exploited for further research.

First Chinese case report of Helcococcus kunzii in a patient with diabetic foot

BACKGROUND

Infection of Helcococcus kunzii(H. kunzii) from diabetic foot wound is rarely reported. This case report describes the infection of H.kunzii and highlights the therapeutic effect on H.kunzii from a diabetic foot wound.

CASE PRESENTATION

In this study, one H. kunzii strain was isolated from a patient with diabetic foot, which was confirmed by 16S rRNA gene analysis and MALDI-TOF-MS. It is the first Chinese case of H. kunzii in a patient with diabetic foot. As a result of the lack of antibiotic sensitivity data and multiple comorbidities, antibiotics were used cautiously, and those administered during the first 3 months were ineffective. Then, vacuum sealing drainage (VSD) was applied during hospitalization; no antibiotics were used and the wound healed well.

CONCLUSIONS

VSD alone may be more effective in treating diabetic feet infected with H. kunzii, which may provide reference for clinical treatment of H. kunzii infection from diabetic foot.

A Novel Reversibly Glycosylated Polypeptide-2 of Bee Pollen from Rape (Brassica napus L.): Purification and Characterization

BACKGROUND

Reversibly glycosylated polypeptide (RGP), a kind of hydrosoluble and plasmodesmal-associated protein found in plants, plays a crucial role in the development of pollen.

OBJECTIVE

A novel RGP 2 was isolated and identified from rape (Brassica napus L.) bee pollen.

METHODS

RGP2 was isolated and purified by ion-exchange column and gel filtration chromatography, and characterized by MALDI-TOF-MS, LC-MS, immunological histological chemistry, and transmission electron microscope.

RESULTS

Our results indicated that the RGP2 is an acidic protein (pI=5.46) with the molecular weight 42388 Da. It contained 17 kinds of amino acids, among which aspartic acid had the highest amount (71.56 mg/g). Homologous alignment of amino acid sequence results showed that RGP2 was 80.33%, 85.02%, 86.06%, and 88.93% identical to Arabidopsis thaliana RGP2 (AtRGP2), Oryza sativa RGP (OsRGP), Triticum aestivum RGP (TaRGP), and Zea maize RGP (ZmRGP), respectively. The localization results showed that RGP2 in rape anther existed in exine and intine of anther cells of rape flower by immunological histological chemistry and the subcellular localization identified that RGP2 appeared around the Golgi apparatus in cytoplasm by transmission electron microscope.

CONCLUSION

RGP2 has a highly conserved sequence of amino acid residues and potential glycosylation sites.

Microbiota dynamics and volatile compounds in lupine based Moromi fermented at different salt concentrations

Fermented soy sauces are used as food seasonings in Eastern countries and all over the world. Depending on their cultural origins, their production differs in parameters such as wheat addition, temperature, and salt concentration. The fermentation of lupine seeds presents an alternative to the use of soybeans; however, the microbiota and influencing factors are currently unknown. In this study, we analyse the microbiota of lupine Moromi (mash) fermentations for a period of six months and determine the influence of different salt concentrations on the microbiota dynamics and the volatile compound composition. Cultured microorganisms were identified by protein profiling using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS), and 16S rRNA gene amplicon sequencing provided an overview of the microbiota including non-cultured bacteria. The volatile compounds were determined by gas chromatography-mass spectrometry (GC-MS). At all salt concentrations, we found that Tetragenococcus halophilus (up to 1.4 × 10⁹ colony forming units (CFU)/mL on day 21) and Chromohalobacter japonicus (1.9 × 10⁹ CFU/mL, day 28) were the dominating bacteria during Moromi fermentation. Debaryomyces hansenii (3.6 × 10⁸ CFU/mL, day 42) and Candida guilliermondii (2.2 × 10⁸ CFU/mL, day 2) were found to be the most prevalent yeast species. Interestingly, Zygosaccharomyces rouxii and other yeasts described as typical for soy Moromi were not found. With increasing salinity, we found lower diversity in the microbiota, the prevalence-gain of typical species was delayed, and ratios differed depending on their halo- or acid tolerance. GC-MS analysis revealed aroma-active compounds, such as pyrazines, acids, and some furanones, which were mostly different from the aroma compounds found in soy sauce. The absence of wheat may have caused a change in yeast microbiota, and the use of lupine seeds may have led to the differing aromatic composition. Salt reduction resulted in a more complex microbiome, higher cell counts, and did not show any spoiling organisms. With these findings, we show that seasoning sauce that uses lupine seeds as the sole substrate is a suitable gluten-free, soy-free and salt reduced alternative to common soy sauces with a unique flavour.

MALDI-TOF-MS analysis of hydrolysis products of beechwood and birchwood xylans catalyzed by xylanase from Bacillus subtilis

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was used to analyze the polymerization distribution of xylo-oligosaccharides from birchwood and beechwood xylans following hydrolysis by the xylanase (XynA) from Bacillus subtilis, which was obtained by recombinant expression and purified by Ni2+ affinity column chromatography. The hydrolysis products of birchwood and beechwood xylans were analyzed by thin layer chromatography (TLC) and MALDI-TOF-MS. In the birchwood hydrolysate, the main neutral xylo-oligosaccharides were xylobiose (X2 ) and xylotriose (X3 ), and the acidic xylo-oligosaccharides (polymerization degree 4-12) were attached via a single methyl-glucuronic acid sidechain (MeG). Both X2 and X3 were identified in the beechwood xylan hydrolysate and acidic xylo-oligosaccharides (polymerization degree 4-16), which were structurally similar to those in the birchwood xylan hydrolysate. Therefore, the recombinant xylanase, XynA, has the potential to produce xylobiose (X2 ) and xylotriose (X3 ) as well as acidic xylo-oligosaccharides (MeGXn ) that would be applied in food industry. PRACTICAL APPLICATIONS: Xylo-oligosaccharides are a novel functional food additive, which has great potential in improving the quality of food. Xylo-oligosaccharides with methyl-glucuronic acid sidechains (MeG) are acidic xylo-oligosaccharides (MeGXn), which can be applied in the preparation of drugs for the treatment of cystitis and mucopolysaccharidosis. In this study, xylanase XynA was first obtained by gene cloning and expression and then used to hydrolyze the birchwood and beechwood xylans. The polymerization distribution of xylo-oligosaccharides generated during the enzymatic digestion was then determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Through enzyme hydrolysis, we are able to produce xylobiose and xylotriose for food additives.

One-step preparation of carbonaceous spheres rich in phosphate groups via hydrothermal carbonization for effective phosphopeptides enrichment

A green strategy was developed to prepare carbonaceous spheres rich in phosphoric acid groups on the surface with D-Glucose 6-phosphate sodium salt (called G6PNa₂) as a sole carbon source through one-step hydrothermal carbonization method. The method is simple and facile and meets the standards of green chemistry as water is the sole solvent employed. Following the hydrothermal carbonization synthesis, the carbonaceous spheres were further functionalized with Ti⁴⁺. The main factors including reaction temperature, reaction time, and concentration of G6PNa₂ were systematically studied in order to obtain the desirable morphology and the optimum phosphopeptides enrichment, for the resulting Ti⁴⁺ functionalized carbonaceous spheres (CS-Ti⁴⁺). The performance evaluation of the CS-Ti⁴⁺ prepared under the optimum conditions demonstrated excellent selectivity (1:1000), low detection limit (1 fmol) and high recovery rate (85%) towards phosphopeptides. Furthermore, 24 low-abundance phosphopeptides were captured from human saliva using CS-Ti⁴⁺, indicating its great potential in mass spectrometry-based phosphoproteome studies.

MALDI-TOF Mass Spectrometry and 16S rRNA Gene Sequence Analysis for the Identification of Foodborne Clostridium Spp

BACKGROUND

Clostridium is a genus of Gram-positive, spore-forming, anaerobic bacteria comprising approximately 100 species. Some Clostridium spp. (C. botulinum, C. perfringens, C. tetani and C. difficile) were recognized to cause acute food poisoning, botulism, tetanus, and diarrheal illness in humans. Thus, rapid identification of Clostridium spp. is critical for source tracking of contaminated food and to understand the transmission dynamics of these foodborne pathogens.

OBJECTIVE

This study was carried out to rapidly identify Clostridium-like isolates by MALDI-TOF MS and rRNA sequencing methods.

METHODS

Thirty-three Clostridium-like isolates were recovered from various baby food and surveillance samples. Species identification of these isolates was accomplished using VITEK MS system. Sequence characterization of the 16S rRNA region was done on an ABI 3500XL Genetic Analyzer.

RESULTS

The VITEK MS system identified 28 of the 33 Clostridium-like isolates with a high confidence value (99.9%); no ID was observed for the rest of the five isolates. Nucleotide sequencing of 16S rRNA region identified all 33 Clostridium-like isolates. Furthermore, while characterizing the 16S rRNA gene, eleven distinct Clostridium spp. (Clostridium aciditolerans, Clostridium aerotolerans, Clostridium argentinense, Clostridium beijerinckii, Clostridium bifermentans, Clostridium butyricum, Clostridium cochlearium, Clostridium difficile, Clostridium perfringens, Clostridium sporogenes, and Clostridium subterminale) were recognized among the 33 Clostridium-like isolates. One of the Clostridium-like isolate was identified as the Citrobacter amalonaticus by both diagnostic methods. The generated 16S rRNA sequences matched completely (100%) with sequences available in GenBank for Clostridium and Citrobacter species. Species identification attained by the VITEK MS for the Clostridium-like isolates was comparable to the 16S rRNA sequencing based data.

HIGHLIGHTS

MALDI-TOF mass spectrometry and 16S rRNA sequencing can be used in the species identification of Clostridium species.

Mining the Royal Jelly Proteins: Combinatorial Hexapeptide Ligand Library Significantly Improves the MS-Based Proteomic Identification in Complex Biological Samples

Royal jelly (RJ) is a complex, creamy secretion produced by the glands of worker bees. Due to its health-promoting properties, it is used by humans as a dietary supplement. However, RJ compounds are not fully characterized yet. Hence, in this research, we aimed to broaden the knowledge of the proteomic composition of fresh RJ. Water extracts of the samples were pre-treated using combinatorial hexapeptide ligand libraries (ProteoMiner^TM kit), trypsin-digested, and analyzed by a nanoLC-MALDI-TOF/TOF MS system. To check the ProteoMiner^TM performance in the MS-based protein identification, we also examined RJ extracts that were not prepared with the ProteoMiner^TM kit. We identified a total of 86 proteins taxonomically classified to Apis spp. (bees). Among them, 74 proteins were detected in RJ extracts pre-treated with ProteoMiner^TM kit, and only 50 proteins were found in extracts non-enriched with this technique. Ten of the identified features were hypothetical proteins whose existence has been predicted, but any experimental evidence proves their in vivo expression. Additionally, we detected four uncharacterized proteins of unknown functions. The results of this research indicate that the ProteoMiner^TM strategy improves proteomic identification in complex biological samples. Broadening the knowledge of RJ composition may contribute to the development of standards and regulations, enhancing the quality of RJ, and consequently, the safety of its supplementation.

Identification of Microorganisms from Several Surfaces by MALDI-TOF MS: P. aeruginosa Is Leading in Biofilm Formation

New ecological trends and changes in consumer behavior are known to favor biofilm formation in household appliances, increasing the need for new antimicrobial materials and surfaces. Their development requires laboratory-cultivated biofilms, or biofilm model systems (BMS), which allow for accelerated growth and offer better understanding of the underlying formation mechanisms. Here, we identified bacterial strains in wildtype biofilms from a variety of materials from domestic appliances using matrix-assisted laser desorption/ionization-time of flight mass spectroscopy (MALDI-TOF-MS). Staphylococci and pseudomonads were identified by MALDI-TOF-MS as the main genera in the habitats and were analyzed for biofilm formation using various in vitro methods. Standard quantitative biofilm assays were combined with scanning electron microscopy (SEM) to characterize biofilm formation. While Pseudomonas putida, a published lead germ, was not identified in any of the collected samples, Pseudomonas aeruginosa was found to be the most dominant biofilm producer. Water-born Pseudomonads were dominantly found in compartments with water contact only, such as in detergent compartment and detergent enemata. Furthermore, materials in contact with the washing load are predominantly colonized with bacteria from the human.

First pediatric case of osteomyelitis caused by Robinsoniella peoriensis

Robinsoniella peoriensis is a gram-positive, spore-forming, anaerobic rod. In our study, we isolated R. peoriensis from an open fracture of the left distal tibia of a three-year-old male patient. Tissue anaerobic culture was positive for R. peoriensis. It was identified with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry and confirmed via 16S rRNA gene sequencing. The patient responded to ampicillin-sulbactam and amikacin antibiotic therapy. Antimicrobial susceptibility testing should be performed to guide the choice of treatment. To the best of our knowledge, this is the first report of R. peoriensis osteomyelitis in a pediatric patient and first report from Turkey.

Formation mechanisms and characterisation of the typical polymers in melanoidins from vinegar, coffee and model experiments

Melanoidins, are of increasing interest for their potential biological activities. However, little knowledge is available on their structure. In the present study, vinegar, coffee and model melanoidins were degraded by NaBH₄, and the resultant reaction products were characterised by chromatography, mass spectrometry and spectrometry methods to elucidate the mechanism of formation of melanoidin skeleton molecules. The study identified a typical polymer with a molecular weight (MW) interval of 74 Da, which was polymerised by aldol condensation and reduced by NaBH₄, followed by intermolecular dehydration. MW of the theoretically derived typical polymers matched the detected polymers, validating the speculated pathway involved in the formation of melanoidins skeleton molecules. The study also revealed that melanoidins from different sources contain polymers with the same MW and different binding preferences, contributing to the heterogeneity of melanoidins. Overall, these findings indicated that the identified polymers could be used as potential candidate biomarkers for melanoidins.

Establishing Classification Tree Models in Rheumatoid Arthritis Using Combination of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry and Magnetic Beads

Background: There is no simple method for early diagnosis and evaluation of rheumatoid arthritis (RA). This study aimed to determine potential biomarkers and establish diagnostic patterns for RA using proteomic fingerprint technology combined with magnetic beads.

Methods: The serum protein profiles of 97 RA patients and 76 healthy controls (HCs) were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) with weak cationic exchange (WCX) magnetic beads. Samples were randomly divided into training (83 RA patients and 56 HCs) and test sets (14 RA patients and 20 HCs). Patients were classified according to their Disease Activity Score: in remission, n = 28; with low disease activity, n = 17; with moderate disease activity, n = 21; with high disease activity, n = 31. There are 44 RA patients alone, 22 RA patients with interstitial lung disease (RA-ILD), 18 RA patients with secondary Sjögren's syndrome (RA-sSS), 6 RA patients with osteonecrosis of the femoral head (RA-ONFH), and 7 RA patients with other complications. Eleven patients were treated with etanercept only for half a year, after which their serum protein profiles were detected. The proteomic pattern was identified by Biomarker Patterns Software, and the potential biomarkers for RA diagnosis were further identified and quantified by enzyme-linked immunosorbent assay.

Results: The diagnostic pattern with four potential protein biomarkers, mass-to-charge (m/z) 3,448.85, 4,716.71, 8,214.29, and 10,645.10, could accurately recognize RA patients from HCs (specificity, 91.57%; sensitivity, 92.86%). The test set were correctly classified by this model (sensitivity, 95%; specificity, 100%). The components containing the four biomarkers were preliminarily retrieved through the ExPasy database, including the C-C motif chemokine 24 (CCL24), putative metallothionein (MT1DP), sarcolipin (SLN), and C-X-C motif chemokine 11 (CCXL11). Only the CCL24 level was detected to have a significant decrease in the serum of RA patients as compared with HCs (p < 0.05). No significant difference was found in others, but a decreasing trend consistent with the down-regulation of the four biomarkers detected by MALDI-TOF-MS was observed. The diagnostic models could effectively discriminate between RA alone and RA with complications (RA-ILD: m/z 10,645.10 and 12,595.86; RA-sSS: m/z 6,635.62 and 33,897.72; RA-ONFH: m/z 2,071.689). The classification model, including m/z 1,130.776, 1,501.065, 2,091.198, and 11,381.87, could distinguish between RA patients with disease activity and those in remission. RA with low disease activity could be efficiently discriminated from other disease activity patients by specific protein biomarkers (m/z 2,032.31, 2,506.214, and Z9286.495). Two biomarkers (m/z 2,032.31 and 4,716.71) were applied to build the classification model for RA patients with moderate and high disease activities. Biological markers for etanercept (m/z 2,671.604064, 5,801.840579, 8,130.195641, and 9,286.49499) were observed between the responder (n = 7) and non-responder groups (n = 4) (p < 0.05).

Conclusion: We successfully established a series of diagnostic models involving RA and RA with complications as well as assessed disease activity. Furthermore, we found that CCL24 may be a valuable auxiliary diagnostic indicator for RA. These results provide reference values for clinical practice in the future.

The Algal Polysaccharide Ulvan Induces Resistance in Wheat Against Zymoseptoria tritici Without Major Alteration of Leaf Metabolome

This study aimed to examine the ability of ulvan, a water-soluble polysaccharide from the green seaweed Ulva fasciata, to provide protection and induce resistance in wheat against the hemibiotrophic fungus Zymoseptoria tritici. Matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF-MS) analysis indicated that ulvan is mainly composed of unsaturated monosaccharides (rhamnose, rhamnose-3-sulfate, and xylose) and numerous uronic acid residues. In the greenhouse, foliar application of ulvan at 10 mg.ml^-1 2 days before fungal inoculation reduced disease severity and pycnidium density by 45 and 50%, respectively. Ulvan did not exhibit any direct antifungal activity toward Z. tritici, neither in vitro nor in planta. However, ulvan treatment significantly reduced substomatal colonization and pycnidium formation within the mesophyll of treated leaves. Molecular assays revealed that ulvan spraying elicits, but does not prime, the expression of genes involved in several wheat defense pathways, including pathogenesis-related proteins (β-1,3-endoglucanase and chitinase), reactive oxygen species metabolism (oxalate oxidase), and the octadecanoid pathway (lipoxygenase and allene oxide synthase), while no upregulation was recorded for gene markers of the phenylpropanoid pathway (phenylalanine ammonia-lyase and chalcone synthase). Interestingly, the quantification of 83 metabolites from major chemical families using ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) in both non-infectious and infectious conditions showed no substantial changes in wheat metabolome upon ulvan treatment, suggesting a low metabolic cost associated with ulvan-induced resistance. Our findings provide evidence that ulvan confers protection and triggers defense mechanisms in wheat against Z. tritici without major modification of the plant physiology.

On the standardization of ZooMS nomenclature

Zooarchaeology by Mass Spectrometry (ZooMS) is rapidly becoming a staple in archaeological and cultural heritage science. Developed a decade ago, this peptide mass fingerprinting technique is expanding from a small group of researchers mainly involved in method development to a broader group of scientists using it as another tool in their toolboxes. With new researchers beginning to use the method, it is imperative that a user-friendly, standardized approach be established. A major barrier has been the often haphazard and changing nomenclature used to label peptide markers necessary for taxonomic identification. Consistent, reliable, and easy-to-understand nomenclature is key to the growth of ZooMS, particularly as the reference library continues to expand. We propose a new set of standardized guidelines for peptide markers based on their position in the type I collagen sequence from the beginning of the highly conserved, helical region. Since this region has no insertions or deletions over a wide range of taxonomic groups, the proposed nomenclature system can be used reliably and consistently across all vertebrate taxa. We propose to label ZooMS peptide markers with the gene, followed by the position of the first and last amino acid of the marker from the start of the helical region. SIGNIFICANCE STATEMENT: We propose a standardized nomenclature system for ZooMS peptide markers that provides consistent labels across multiple, broad taxonomic groups. This system unambiguously locates the marker peptides in the type I collagen sequence, avoids duplication of marker names, and facilitates the creation of large ZooMS databases which can include all vertebrates.