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Lemna sect. Uninerves Hegelm. consists of three species, Lemna minuta Kunth (synonym L. minuscula), L. valdiviana Phil. and L. yungensis Landolt. Lemna yungensis was discovered growing on rocks in the Yungas in Bolivia by E. Landolt and was described just 20 years ago. In the original description, Landolt reported that this species is closely related to L. valdiviana and that it is difficult to distinguish the three species on a morphological basis. Therefore, the taxonomic position and status of L. yungensis remained controversial. Here, we carried out a detailed taxonomic study, integrating approaches that include quantitative morphometry, metabolomic profiling by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) as well as molecular genetic analysis using amplified fragment length polymorphism (AFLP), and barcoding of plastidic sequences. We also investigated genome sizes of clones of the three species. Whereas L. minuta can easily be differentiated from L. valdiviana and L. yungensis, it was not possible to distinguish L. valdiviana from L. yungensis with any of the methods used. These data imply that L. yungensis is identical to L. valdiviana. Thus, the name L. yungensis should be synonymised with the name L. valdiviana, since this is the older name.

The accurate identification and proper typing of basidiomycetes are required in medical, sanitary maintenance, agriculture, and biotechnology fields. A diagnostic method based on information from whole-cell proteins acquired by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was investigated to identify wood-rotting fungi, a group of filamentous fungi. In this study, mass spectra of intracellular peptides obtained from cultured mycelia of 50 strains of 10 wood-rotting fungal species were obtained multiple times and mass spectral patterns (MSPs) consisting of peaks that characterized the fungal species or strain was created to construct an in-house database. The species identification was conducted by comparing the newly obtained raw mass spectra with the MSPs in the database using the MALDI Biotyper. The results showed that the peak patterns of the mass spectra were reproducible and matched at the strain level. A cluster analysis based on the MSPs was also conducted to examine inter-and intraspecific diversity among the tested wood-rotting basidiomycetes. Most of the fungal strains examined in this study could be identified to a species level; however, the strains belonging to Pleurotus could only be identified to a genus level. This was due to an intraspecific variation, so the identification accuracy could be amendable with a more enhanced database.

The varied ways in which mutations in presenilins (PSEN1 and PSEN2) affect amyloid b precursor protein (APP) processing in causing early‐onset familial Alzheimer disease (FAD) are complex and not yet properly understood. Nonetheless, one useful diagnostic marker is an increased ratio of Ab42 to Ab40 (Ab42/Ab40) in patients' brain and biological fluids as well as in transgenic mice and cells. We studied Ab and APP processing for a set of nine clinical PSEN mutations on a novel and highly reproducible enzyme‐linked immunosorbent assay (ELISA)‐based in vitro method and also sought correlation with brain Ab analyzed by image densitometry and mass spectrometry. All mutations significantly increased Ab42/Ab40 in vitro by significantly decreasing Ab40 with accumulation of APP C‐terminal fragments, a sign of decreased PSEN activity. A significant increase in absolute levels of Ab42 was observed for only half of the mutations tested. We also showed that age‐of‐onset of PSEN1‐linked FAD correlated inversely with Ab42/Ab40 (r=–0.89; P=0.001) and absolute levels of Ab42 (r=–0.83; P=0.006), but directly with Ab40 levels (r=0.69; P=0.035). These changes also partly correlated with brain Ab42 and Ab40 levels. Together, our data suggested that Ab40 might be protective by perhaps sequestering the more toxic Ab42 and facilitating its clearance. Also, the in vitro method we describe here is a valid tool for assaying the pathogenic potential of clinical PSEN mutations in a molecular diagnostic setting. Hum Mutat 27(7), 686–695, 2006. Published 2006 Wiley‐Liss, Inc.

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.

Phylogeographic analyses have advanced our understanding of evolutionary processes in the deep sea, yet patterns of genetic variation and population divergence at abyssal depths remain poorly understood. The bivalve Ledella ultima is one of the most abundant protobranchs in the abyssal Atlantic, making it a valuable model organism for studying phylogeographic patterns and population connectivity. However, evidence for sex‐specific heteroplasmic mtDNA challenges the assessment of genetic structure using mitochondrial markers alone. To address this, we used mtDNA (COI, 16S), single‐nucleotide polymorphisms (SNPs) from 2b‐RAD, and proteomic profiles to examine the population structure of L. ultima across seven Atlantic basins spanning over 10,000 km in latitude. Five mitochondrial lineages with a lack of geographic structure were consistently identified by COI and 16S. Conversely, SNP and proteomic data did not mirror these findings, denoting that heteroplasmic mtDNA inflates intraspecific genetic divergence in this gonochoric species. Despite the SNP data revealing overall low genetic divergence, subtle genetic structure was detected by admixture analyses supporting two source populations: one in the north and central Atlantic, and a second in the south Atlantic, with moderate admixture in the Brazil and Cape basins. Proteomic fingerprinting revealed two basin‐separated groups with patterns distinct from the nuclear data, suggesting environmentally driven shifts in protein expression. Our findings underscore the value of integrating nuclear genomic and proteomic tools to decipher population connectivity at abyssal depths, where minimal genetic differentiation necessitates fine‐scale analyses.

Sophorolipids are carbohydrate-based, amphiphilic biosurfactants that are of increasing interest for use in environmentally benign cleaning agents. Sophorolipid production was tested for 26 strains representing 19 species of the Starmerella yeast clade, including Starmerella bombicola and Candida apicola, which were previously reported to produce sophorolipids. Five of the 19 species tested showed significant production of sophorolipids: S. bombicola, C. apicola, Candida riodocensis, Candida stellata and a new species, Candida sp. NRRL Y-27208. A high-throughput matrix-assisted laser desorption/ionization-time of flight MS assay was developed that showed S. bombicola and C. apicola to produce a lactone form of sophorolipid, whereas C. riodocensis, C. stellata and Candida sp. NRRL Y-27208 produced predominantly free acid sophorolipids. Phylogenetic analysis of sequences for the D1/D2 domains of the nuclear large subunit rRNA gene placed all sophorolipid-producing species in the S. bombicola subclade of the Starmerella clade.

Use matrix‐assisted laser desorption ionisation time‐of‐flight mass spectrometry (MALDI‐TOF MS) to screen the specific mass peaks of carbapenem‐resistant Klebsiella pneumoniae (CRKP), compare the differences in spectrum peaks between intestinal and bloodstream screening of CRKP, and assess the utility of MALDI‐TOF MS in quickly identifying various CRKP sources. From 2014 to 2023, a total of 267 Klebsiella pneumoniae strains were collected at Quzhou People's Hospital, including 60 intestinal screening isolates from ICU patients and 207 bloodstream infection isolates. MALDI‐TOF MS was used to profile peptides in CRKP and carbapenem‐sensitive Klebsiella pneumoniae (CSKP), followed by analysis with flexAnalysis and ClinProTools 3.0. Statistically significant protein peaks were selected to build classification models, which were verified using non‐duplicate strains. MALDI‐TOF MS achieved > 99.9% accuracy in identifying Klebsiella pneumoniae. Characteristic peaks (2523.43, 3041.62, 4520.11, 10,079.18 Da) were used to develop resistance analysis models, with the optimal model (SNN) showing 90.08% sensitivity, 95.80% specificity and identification accuracies of 90% for CSKP and 89.66% for CRKP. Another model using peaks (8876, 8993, 9139 Da) differentiated CRKP origins, with the ideal model (QC) achieving 86.85% sensitivity, 88.46% specificity, and accuracies of 81.82% for bloodstream and 95.00% for intestinal CRKP. Matrix‐assisted laser desorption ionisation time‐of‐flight mass spectrometry combined with machine learning algorithms, such as Genetic Algorithm, Supervised Neural Network and Quick Classifier, is used to screen for characteristic mass peaks associated with carbapenem‐resistant Klebsiella pneumoniae (CRKP). The integration of MALDI‐TOF MS with machine learning provides a faster and more efficient alternative to traditional antibiotic resistance detection methods in the laboratory, supporting improved diagnostic workflows and infection control strategies (Created in BioRender).

Adulteration of extra virgin olive oil (EVOO) by addition of other vegetable oils or lower-grade olive oils is a common problem of the oil market worldwide. Therefore, we developed a fast protocol for detection of EVOO adulteration by mass spectrometry fingerprinting of triacylglycerol (TAG) profiles based on MALDI-TOF/MS. For that purpose, EVOO TAG profiles were compared with those of edible sunflower oil and olive oil composed of refined olive oil and virgin olive oils. Adulteration of EVOO was simulated by addition of sunflower and mixture of refined olive oil and virgin olive oils at 1, 10 and 20% w/w. Results of mass spectrometry TAG profiling were compared with routinely assessed K values for identification of adulteration. MALDI-TOF/MS technology coupled with statistical analysis was proven as useful for detection of adulteration in EVOO at a rate down to 1%. In contrast, standard spectrophotometric methods failed to identify minor adulterations. In addition, the ability of MALDI-TOF/MS in detection of adulteration was tested on EVOO samples from different geographical regions. Results demonstrated that MALDI-TOF/MS technology coupled with statistical analysis is able to distinguish adulterated oils from other EVOO.

This study aims to investigate the resistance of potential probiotic Bacillus species to various conditions in the gastrointestinal (GI) tract and their safety characteristics. MALDI‐TOF MS identified all tested strains with a good safety score of ≥ 2.0; the strains demonstrated the capacity to pass through the Gl tract, exhibiting a reduction of > 6 log/CFU live cells. Furthermore, they exhibited varying survival rates in an acidic environment (pH 2.0–3.0) and the presence of Ox‐Bile (1% w/v) (p < 0.05). Following exposure to pH 3.0 and Ox‐Bile, the survival rate of Bacillus spp. ranged between 85.94% and 91.24% and 87.30% and 91.54%, respectively. The results of the in vitro experiments showed that the six Bacillus strains had comparable characteristics (e.g., tolerance to GI track enzyme, auto‐aggregation ability) to the reference probiotic strain Lactiplantibacillus plantarum LA15. The auto‐aggregation results of the B. clausii BA8 strain, which has demonstrated resistance to GI tract conditions, were also noteworthy. This strain showed 72.32% after 2 h and 74.55% at the end of 5 h. Most suitable for use as probiotic strains B. clausii BA8 and B. subtilis BA11, sequenced via Illumina NovaSeq, showed average nucleotide identity (ANI) values of 98.1% and 97.8%, respectively. The genome annotation of B. clausii and B. subtilis with Prokka revealed 4,498,248‐4,215,606 bp genome length, 44%–43% GC content, and 110–26 contigs, respectively. B. clausii BA8 has been comprehensively characterized, is of low risk for human consumption, and has been recommended as a potential probiotic strain. However, further in vivo experimentation is required to confirm these findings. Bacillus clausii BA8 and Bacillus subtilis BA11 strains can be used as alternatives to LABs. Identifying key genetic features of B. subtilis BA8 and B. clausii BA11 strains with whole genome sequencing. The strains robust resistance to harsh gastrointestinal tract (GIT) conditions and strong aggregation abilities.

This study explored the microbial diversity in two underexplored natural springs, Arincho Chumik and Chutron, located in the Shigar Valley, Gilgit Baltistan, utilizing a culture‐centered method combined with Matrix‐Assisted Laser Desorption Ionization‐Time of Flight Mass Spectrometry (MALDI‐TOF MS). The outcomes revealed a diverse microbial landscape, with a total of 18 unique bacterial strains isolated, comprising nine from each spring. From the total 18 isolated strains, 7 (39%) were noticed to be gram‐positive, while 11 (61%) were gram‐negative. Interestingly, species like Brevundimonas and Acinetobacter were present in Arincho and Chutron springs, respectively, highlighting the unique physicochemical environments and their impact on microbial populations. The examination also uncovers the existence of pigment‐producing bacteria, suggesting potential biotechnological applications. The chilly freshwater spring of Arincho possessed certain opportunistic bacteria, including Bacillus cereus, Dietzia cinnamea, and Microbacterium species. Likewise, human‐related microorganisms like Micrococcus leuteus were also identified in samples from the Chutron thermal spring. Additionally, the recognition of opportunistic pathogens among the strains underlines the health effects for the local communities, especially for the elderly and immune‐deficient individuals. The quality of these water resources ought to be supervised by regulatory authorities to decrease public health risks and pathogen transmission. MALDI‐TOF MS reveals diverse bacterial populations in Shigar Valley's natural springs, including opportunistic pathogens and pigment‐producing species. This study highlights the need for monitoring water quality to mitigate public health risks and explores potential biotechnological applications.