Explore the vast range of titles available.

Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here, we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven image analysis of cellular phenotypes with automated single-cell or single-nucleus laser microdissection and ultra-high-sensitivity mass spectrometry. DVP links protein abundance to complex cellular or subcellular phenotypes while preserving spatial context. By individually excising nuclei from cell culture, we classified distinct cell states with proteomic profiles defined by known and uncharacterized proteins. In an archived primary melanoma tissue, DVP identified spatially resolved proteome changes as normal melanocytes transition to fully invasive melanoma, revealing pathways that change in a spatial manner as cancer progresses, such as mRNA splicing dysregulation in metastatic vertical growth that coincides with reduced interferon signaling and antigen presentation. The ability of DVP to retain precise spatial proteomic information in the tissue context has implications for the molecular profiling of clinical samples. Deep Visual Proteomics combines machine learning, automated image analysis and single-cell proteomics.

Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein profiling methods as a major pillar for cellular atlas building of complex samples, from tissues to full organisms. Emerging methods yield omics measurements at resolutions covering the nano- to microscale, enabling the charting of cellular heterogeneity, complex tissue architectures and dynamic changes during development and disease. We present an overview of the developing landscape of in situ spatial genome, transcriptome and proteome technologies, exemplify their impact on cell biology and translational research, and discuss current challenges for their community-wide adoption. Among many transformative applications, we envision that spatial methods will map entire organs and enable next-generation pathology.Spatial omics methods enable the charting of cellular heterogeneity, complex tissue architectures and dynamic changes during development and disease. The authors review the developing landscape of in situ spatial transcriptome, genome and proteome technologies and highlight their impact on basic and translational research.

Conspecific brood parasitism occurs in many birds and some insects, fishes, and amphibians. Here, we develop and test a novel molecular technique for ecological analysis, protein fingerprinting (PF), based on isoelectric focusing electrophoresis (IEF) in immobilized pH gradients. It is applied here to albumen from birds' eggs and permits accurate identification of eggs laid by different females. This technique greatly clarifies female alternative reproductive tactics and laying patterns in brood-parasitic Common Goldeneye ducks Bucephala clangula. A small, nondestructive sample of albumen is taken through a hole drilled through the eggshell, which is then sealed with superglue, preserving egg hatchability. IEF yields a rich pattern of albumen bands with extensive variation among females. Observation and video recording of egg-laying by 21 color-marked females showed that they had unique band patterns, which were fully repeatable within and between years. Brood parasitism occurred in two-thirds (13 of 19) of the video-recorded nests of color-ringed females, with up to five parasitic females per nest. Of 234 eggs, 36% were laid by females other than the incubating host. These results suggest that intraspecific brood parasitism is more common and important than suggested by earlier studies using traditional methods. Protein fingerprinting yields individual resolution similar to that of a DNA multilocus fingerprinting probe, and has several advantages. The albumen band pattern represents only the laying female, not her mate(s), making it easy to determine the maternity of eggs, and to identify a parasite that spreads her eggs among a number of nests. Albumen can be sampled as soon as the egg is laid, before predation or other losses occur, maximizing sample size and minimizing bias. Protein fingerprinting is relatively inexpensive and easy. It is also useful for several purposes other than maternity determination, such as relatedness estimation for categories of individuals.

Brood parasitism can be costly to host fitness, which in turn may favour host strategies that decrease these costs. Duck (Anatinae) nests are often parasitized by eggs of other ducks, and one way that hosts can respond to potentially costly brood parasitism is to move parasitic eggs to the clutch periphery, where egg incubation temperatures can be suboptimal relative to the clutch centre. We explored whether red‐breasted mergansers Mergus serrator use discriminatory egg incubation against parasitic eggs laid by conspecifics in a population where conspecific brood parasitism (CBP) is common. We used isoelectric focusing electrophoresis of egg albumen from entire clutches of 12 parasitized nests to identify parasitic eggs. A randomization test pooling identified parasitic eggs (n = 50) across nests revealed that hosts did not position parasitic eggs along the periphery of clutches or out of the central region more than was expected by chance, and this was the case for parasitic eggs laid both before and after the onset of incubation. Similarly, nest‐level analyses showed that parasitic eggs were random in all but the smallest clutch, which contained one identified parasitic egg. Thus, parasitic eggs were not moved to the periphery of heavily parasitized clutches, where egg temperature gradients between central and peripheral regions of nests are expected to be greatest. Only four eggs (< 0.5% of 1276 eggs) were found buried within nest bowls. Eggs that were removed from nests consisted of parasite and host eggs and were more likely along the periphery of clutches prior to their removal than was expected by chance. Our results indicate that discriminatory egg incubation of parasitic eggs is not a well‐developed tactic for defending against CBP in red‐breasted mergansers, though hosts may rely on certain cues to decide which eggs are to be removed from nests (e.g. addled eggs).

Aeromonas is recognized as a human pathogen following ingestion of contaminated food and water. One major problem in Aeromonas identification is that certain species are phenotypically very similar. The antimicrobial resistance is another significant challenge worldwide. We therefore aimed to use mass spectrometry technology for identification and discrimination of Aeromonas species and to screen the antimicrobial resistance of Aeromonas hydrophila (A. hydrophila). A total of 150 chicken meat and water samples were cultured, and then, the isolates were identified biochemically by the Vitek® 2 Compact system. Proteomic identification was performed by MALDI‐TOF MS and confirmed by a microchannel fluidics electrophoresis assay. Principal component analysis (PCA) and single‐peak analysis created by MALDI were also used to discriminate the Aeromonas species. The antimicrobial resistance of the A. hydrophila isolates was determined by Vitek® 2 AST cards. In total, 43 samples were positive for Aeromonas and comprised 22 A. hydrophila, 12 Aeromonas caviae (A. caviae), and 9 Aeromonas sobria (A. sobria) isolates. Thirty‐nine out of 43 (90.69%) Aeromonas isolates were identified by the Vitek® 2 Compact system, whereas 100% of the Aeromonas isolates were correctly identified by MALDI‐TOF MS with a score value ≥2.00. PCA successfully separated A. hydrophila, A. caviae and A. sobria isolates into two groups. Single‐peak analysis revealed four discriminating peaks that separated A. hydrophila from A. caviae and A. sobria isolates. The resistance of A. hydrophila to antibiotics was 95.46% for ampicillin, 50% for cefotaxime, 45.45% for norfloxacin and pefloxacin, 36.36% for ceftazidime and ciprofloxacin, 31.81% for ofloxacin and 27.27% for nalidixic acid and tobramycin. In conclusion, chicken meat and water were tainted with Aeromonas spp., with a high occurrence of A. hydrophila. MALDI‐TOF MS is a powerful technique for characterizing aeromonads at the genus and species levels. Future studies should investigate the resistance of A. hydrophila to various antimicrobial agents. The sequencing results indicated that A. hydrophila is the most prevalent Aeromonas spp. isolated from food and water. MALDI‐TOF MS is a powerful technique used for identification of Aeromonas at the genus and species‐level. Principal component analysis (PCA) and single‐peak analysis are successful tools to discriminate the Aeromonas spp. VITEK® 2 AST Cards can also use as a detective method of antimicrobial resistance.

Proteins in a proteome can be identified from a sequence of K integers equal to the digitized volumes of subsequences with L residues from the primary sequence of a stretched protein.Exhaustive computations on the proteins of Helicobacter pylori (UniProt id UP000000210) with L and K in the range 4–8 show that ~90% of the proteins can be identified uniquely in this manner. This computational result can be translated into practice with a nanopore, an emerging technology that does not require analyte immobilization, proteolysis or labeling. Unlike other methods, most of which focus on a specific target protein, nanopore-based methods enable the identification of multiple proteins from a sample in a single run. Recent work by Kennedy, Kolmogorov and associates shows that the blockade current due to a protein molecule translocating through a nanopore is roughly proportional to one or more contiguous residues. The present study points to a modified version in which the volumes of subsequences (rather than of single residues) may be obtained by integrating the blockade current due to L contiguous residues. The advantages arising from this include lower detector bandwidth, elimination of the homopolymer problem and reduced noise. Because an identifier is based on near as well as distant (up to 2KL-L) residues, this approach uses more global information than an approach based on single residues and short-range correlations. The results of the study, which are available in a data supplement, are discussed in detail. Potential implementation issues are addressed.

Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.

Familial Mediterranean fever (FMF) is the most prevalent autoinflammatory disease. Typical findings are recurrent fever attacks with serositis, skin rash, and synovitis. FMF is caused by mutations in the MEFV gene, encoding pyrin protein. Pyrin functions in innate immunity and triggers inflammation via inflammatory mediators’ production and acts as the primary regulatory component of the inflammasome. On the other hand, various miRNAs play crucial roles in the pathogenesis of different types of cancers and immune-related and neurodegenerative diseases. However, their association with FMF is still unclear. Therefore, in this study, we assessed the roles of selected thirteen miRNAs associated with immune functions. We recruited genetically diagnosed 28 FMF patients and 28 healthy individuals. The expression profiling of the miRNAs was determined by qRT-PCR and normalized to SNORD61. Our analysis revealed that miR-34a-5p, miR-142-3p, miR-216a-5p, miR-340-5p, miR-429, and miR-582-5p were upregulated, whereas miR-107, miR-569, and miR-1304-5p were downregulated in the FMF patients. Among them, miR-107 was found to be the most remarkable in M694V homozygous mutants compared to other homozygous mutants. During clinical follow-up of the patients with M694V mutation, which is closely related to amyloidosis, evaluation of mir-107 expression might be crucial and suggestive. Our results showed that miRNAs might serve a function in the pathogenesis of FMF. Further studies may provide novel and effective diagnostic and therapeutic agents that target examined miRNAs. Targeting miRNAs in FMF seems to be promising and may yield a new generation of rational therapeutics and diagnostic or monitoring tools enabling FMF treatment.

Peptide microarrays have become increasingly accessible in recent years and as a result, more widely applied. Beyond its initial utility in substrate profiling, researchers are adopting peptide microarrays for the comparative screening of many different classes of enzymes, proteins/ proteomes and even living cells. Understanding the basis of peptide interactions at these diverse levels provides an unprecedented window into dissecting the complex cellular circuitries and molecular architectures of living systems. The peptides on the arrays may serve to sense protein activity (like substrates) or act as small molecule ligands (for potential therapeutic leads) in profiling, detection or diagnostic applications. This review will chart the progress made in peptide microarrays, with a focus on the recent advances that could impact how the field will be shaped in the coming years. These developments, along with the diminishing costs of library synthesis and growing commercial support, recognize that peptide microarrays will no longer remain just a vital research tool, but also a platform that could now be harnessed for wider drug discovery and point-of-care applications.

ATP2, a putative type 4 P-type ATPase, is a phosphatidylinositol-4-phosphate (PI4P)-regulated phospholipid transporter with an interesting potential as an antimalarial drug target due to its conservation across Plasmodium species and its essential role in the life cycle of Plasmodium falciparum. Despite its importance, the exact mechanism of its action and regulation is still not fully understood. In this study we used coarse-grained molecular dynamics (CG-MD) to elucidate the lipid–protein interactions between a heterogeneous lipid membrane containing phosphatidylinositol and Plasmodium chabaudi ATP2 (PcATP2), an ortholog of P. falciparum ATP2. Our study reveals structural information of the lipid fingerprint of ATP2, and provides structural information on the potential phosphatidylinositol allosteric binding site. Moreover, we identified a set of evolutionary conserved residues that may play a key role in the binding and stabilization of lipids in the binding pocket.