Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry

Plasmonic Nanogap-Enhanced Tunable Three-Dimensional Nanoframes in Application to Clinical Diagnosis of Alzheimer's Disease

Advancements in nanotechnology led to significant improvements in synthesizing plasmon-enhanced nanoarchitectures for biosensor applications, and high-yield productivity at low cost is vital to step further into medical commerce. Metal nanoframes via wet chemistry are gaining attention for their homogeneous structure and outstanding catalytic and optical properties. However, nanoframe morphology should be considered delicately when brought to biosensors to utilize its superior characteristics thoroughly, and the need to prove its clinical applicability still remains. Herein, we controlled the frameworks of double-walled nanoframes (DWFs) precisely via wet chemistry to construct a homogeneous plasmon-enhanced nanotransducer for localized surface plasmon resonance biosensors. By tuning the physical properties considering the finite-difference time-domain simulation results, biomolecular interactions were feasible in the electromagnetic field-enhanced nanospace. As a result, DWF10 exhibited a 10-fold lower detection limit of 2.21 fM compared to DWF14 for tau detection. Further application into blood-based clinical and Alzheimer's disease (AD) diagnostics, notable improvement in classifying mild cognitive impairment patients against healthy controls and AD patients, was demonstrated along with impressive AUC values. Thus, in response to diverse detection methods, optimizing nanoframe dimensions such as nanogap and frame thickness to maximize sensor performance is critical to realize future POCT diagnosis.

In Vivo Synthetic Anticancer Approach by Resourcing Mouse Blood Albumin as a Biocompatible Artificial Metalloenzyme

Methods for producing drugs directly at the cancer site, particularly using bioorthogonal metal catalysts, are being explored to mitigate the side effects of therapy. Albumin-based artificial metalloenzymes (ArMs) catalyze reactions in living mice while protecting the catalyst in the hydrophobic pocket. Here, we describe the in situ preparation and application of biocompatible tumor-targeting ArMs using circulating albumin, which is abundant in the bloodstream. The ArM was formed using blood albumin through the intravenous injection of ruthenium conjugated with an albumin-binding ligand; the tumor-targeting unit was conjugated to the ArM using its catalytic activity, and the ArM was transported to the cancer site. The delivered ArM catalyzed a second tagging reaction of the proapoptotic peptide on the cancer surface, successfully suppressing cancer proliferation. This approach, which efficiently leveraged the persisting reactivity twice in vivo, holds promise for future in vivo metal-catalyzed drug synthesis utilizing endogenous albumin.

Micro Scale Chromatography of Human Plasma Proteins for Nano LC-ESI-MS/MS

Organic precipitation of proteins with acetonitrile demonstrated complete protein recovery and improved chromatography of human plasma proteins. The separation of 25 μL of human plasma into 22 fractions on a QA SAX resin facilitated more effective protein discovery despite the limited sample size. Micro chromatography of plasma proteins over quaternary amine (QA) strong anion exchange (SAX) resins performed best, followed by diethylaminoethyl (DEAE), heparin (HEP), carboxymethyl cellulose (CMC), and propyl sulfate (PS) resins. Two independent statistical methods, Monte Carlo comparison with random MS/MS spectra and the rigorous X!TANDEM goodness of fit algorithm protein p-values corrected to false discovery rate q-values (q≤ 0.01) that agreed on at least 12,000 plasma proteins, each represented by at least three fully tryptic corrected peptide observations. There was qualitative agreement on 9,393 protein/gene symbols between the linear quadrupole versus orbital ion trap but also quantitative agreement with a highly significant linear regression relationship between log observation frequency (F value 4,173, p-value 2.2e-16). The use of a QA resin showed nearly perfect replication of all the proteins that were also found using DEAE-, HEP-, CMC-, and PS-based chromatographic methods combined and together estimated the size of the size of the plasma proteome as ≥12,000 gene symbols.

Extraction of naturally occurring peptides versus the tryptic digestion of proteins from fetal versus adult bovine serum for LC-ESI-MS/MS

The naturally occurring peptides and digested proteins of fetal versus adult bovine serum were compared by LC-ESI-MS/MS after correction against noise from blank injections and random MS/MS spectra as statistical controls. Serum peptides were extracted by differential precipitation with mixtures of acetonitrile and water. Serum proteins were separated by partition chromatography over quaternary amine resin followed by tryptic digestion. The rigorous X!TANDEM goodness of fit algorithm that has a low error rate as demonstrated by low FDR q-values (q ≤ 0.01) showed qualitative and quantitative agreement with the SEQUEST cross correlation algorithm on 12,052 protein gene symbols. Tryptic digestion provided a quantitative identification of the serum proteins where observation frequency reflected known high abundance. In contrast, the naturally occurring peptides reflected the cleavage of common serum proteins such as C4A, C3, FGB, HPX, A2M but also proteins in lower concentration such as F13A1, IK, collagens and protocadherins. Proteins associated with cellular growth and development such as actins (ACT), ribosomal proteins like Ribosomal protein S6 (RPS6), synthetic enzymes and extracellular matrix factors were enriched in fetal calf serum. In contrast to the large literature from cord blood, IgG light chains were absent from fetal serum as observed by LC-ESI-MS/MS and confirmed by ELISA.

Exploring affinity chromatography in proteomics: A comprehensive review

Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.

Precursor carboxy-silica for functionalization with interactive ligands. IV. Carbodiimide assisted preparation of immobilized antibody stationary phases for high performance immuno-affinity chromatography of human serum

In this Part IV of the article series dealing with the functionalization of the precursor carboxy silica with various chromatographic ligands, immuno affinity (IA) columns were prepared with immobilized anti-apolipoprotein B (AAP B) and anti-haptoglobin (AHP) antibodies for use in immuno affinity chromatography (IAC) in the aim of selectivily capturing their corresponding antigens from healthy and cancer human sera. Diseased human serum with adenocarcinoma cancer was selected as a typical diseased biological fluid. Besides preferentially capturing their corresponding antigens, the AAP B column captured from disease-free and cancer sera, 34 proteins and 33 proteins, respectively, while the AHP column enriched 38 and 47 proteins, respectively. This nonspecific binding can be attributed to the many proteins human serum have, which could mediate protein-protein interactions thus leading to the so-called "sponge effect". This kind of behavior can be exploited positively in the determination of differentially expressed proteins (DEPs) for diseased serum with respect to healthy serum and in turn allow the identification of an array of potential biomarkers for cancer. In fact, For AHP column, 13 upregulated and 22 downregulated proteins were identified whereas for AAP B column the numbers were 23 and 10, respectively. The DEPs identified with both columns match those reported in the literature for other types of cancers. The different expression of proteins in each IAC column can be related to the variability of protein-protein interactions. In addition, an array of a few biomarkers is more indicative of a certain disease than a single biomarker.

Sample-to-answer lateral flow assay with integrated plasma separation and NT-proBNP detection

Through enabling whole blood detection in point-of-care testing (POCT), sedimentation-based plasma separation promises to enhance the functionality and extend the application range of lateral flow assays (LFAs). To streamline the entire process from the introduction of the blood sample to the generation of quantitative immune-fluorescence results, we combined a simple plasma separation technique, an immunoreaction, and a micropump-driven external suction control system in a polymer channel-based LFA. Our primary objective was to eliminate the reliance on sample-absorbing separation membranes, the use of active separation forces commonly found in POCT, and ultimately allowing finger prick testing. Combining the principle of agglutination of red blood cells with an on-device sedimentation-based separation, our device allows for the efficient and fast separation of plasma from a 25-µL blood volume within a mere 10 min and overcomes limitations such as clogging, analyte adsorption, and blood pre-dilution. To simplify this process, we stored the agglutination agent in a dried state on the test and incorporated a filter trench to initiate sedimentation-based separation. The separated plasma was then moved to the integrated mixing area, initiating the immunoreaction by rehydration of probe-specific fluorophore-conjugated antibodies. The biotinylated immune complex was subsequently trapped in the streptavidin-rich detection zone and quantitatively analyzed using a fluorescence microscope. Normalized to the centrifugation-based separation, our device demonstrated high separation efficiency of 96% and a yield of 7.23 µL (= 72%). Furthermore, we elaborate on its user-friendly nature and demonstrate its proof-of-concept through an all-dried ready-to-go NT-proBNP lateral flow immunoassay with clinical blood samples.

Differential Protease Specificity by Collagenase as a Novel Approach to Serum Proteomics That Includes Identification of Extracellular Matrix Proteins without Enrichment

Circulating extracellular matrix (ECM) proteins are serological biomarkers of interest due to their association with pathologies involving disease processes such as fibrosis and cancers. In this study, we investigate the potential for serum biomarker research using differential protease specificity (DPS), leveraging alternate protease specificity as a targeting mechanism to selectively digest circulating ECM protein serum proteins. A proof-of-concept study is presented using serum from patients with cirrhotic liver or hepatocellular carcinoma. The approach uses collagenase DPS for digestion of deglycosylated serum and liquid-chromatography-trapped ion mobility-tandem mass spectrometry (LC-TIMS-MS/MS) to enhance the detection of ECM proteins in serum. It requires no sample enrichment and minimizes the albumin average precursor intensity readout to less than 1.2%. We further demonstrate the capabilities for using the method as a high-throughput matrix-assisted laser/desorption ionization mass spectrometry (MALDI-MS) assay coupled with reference library searching. A goal is to improve the depth and breadth of biofluid proteomics for noninvasive assays.

Chicken muscle antibody array reveals the regulations of LDHA on myoblast differentiation through energy metabolism

Myoblast proliferation and differentiation are highly dynamic and regulated processes in skeletal muscle development. Given that proteins serve as the executors for the majority of biological processes, exploring key regulatory factors and mechanisms at the protein level offers substantial opportunities for understanding the skeletal muscle development. In this study, a total of 607 differentially expressed proteins between proliferation and differentiation in myoblasts were screened out using our chicken muscle antibody array. Biological function analysis revealed the importance of energy production processes and compound metabolic processes in myogenesis. Our antibody array specifically identified an upregulation of LDHA during differentiation, which was associated with the energy metabolism. Subsequent investigation demonstrated that LDHA promoted the glycolysis and TCA cycle, thereby enhancing myoblasts differentiation. Mechanistically, LDHA promotes the glycolysis and TCA cycle but inhibits the ETC oxidative phosphorylation through enhancing the NADH cycle, providing the intermediate metabolites that improve the myoblasts differentiation. Additionally, increased glycolytic ATP by LDHA induces Akt phosphorylation and activate the PI3K-Akt pathway, which might also contribute to the promotion of myoblasts differentiation. Our studies not only present a powerful tool for exploring myogenic regulatory factors in chicken muscle, but also identify a novel role for LDHA in modulating myoblast differentiation through its regulation of cellular NAD+ levels and subsequent downstream effects on mitochondrial function.

Perspectives of Proteomics in Respiratory Allergic Diseases

Proteomics in respiratory allergic diseases has such a battery of techniques and programs that one would almost think there is nothing impossible to find, invent or mold. All the resources that we document here are involved in solving problems in allergic diseases, both diagnostic and prognostic treatment, and immunotherapy development. The main perspectives, according to this version, are in three strands and/or a lockout immunological system: (1) Blocking the diapedesis of the cells involved, (2) Modifications and blocking of paratopes and epitopes being understood by modifications to antibodies, antagonisms, or blocking them, and (3) Blocking FcεRI high-affinity receptors to prevent specific IgEs from sticking to mast cells and basophils. These tools and targets in the allergic landscape are, in our view, the prospects in the field. However, there are still many allergens to identify, including some homologies between allergens and cross-reactions, through the identification of structures and epitopes. The current vision of using proteomics for this purpose remains a constant; this is also true for the basis of diagnostic and controlled systems for immunotherapy. Ours is an open proposal to use this vision for treatment.

Serum proteome profiles in patients treated with targeted temperature management after out-of-hospital cardiac arrest

BACKGROUND

Definition of temporal serum proteome profiles after out-of-hospital cardiac arrest may identify biological processes associated with severe hypoxia-ischaemia and reperfusion. It may further explore intervention effects for new mechanistic insights, identify candidate prognostic protein biomarkers and potential therapeutic targets. This pilot study aimed to investigate serum proteome profiles from unconscious patients admitted to hospital after out-of-hospital cardiac arrest according to temperature treatment and neurological outcome.

METHODS

Serum samples at 24, 48, and 72 h after cardiac arrest at three centres included in the Target Temperature Management after out-of-hospital cardiac arrest trial underwent data-independent acquisition mass spectrometry analysis (DIA-MS) to find changes in serum protein concentrations associated with neurological outcome at 6-month follow-up and targeted temperature management (TTM) at 33 °C as compared to 36 °C. Neurological outcome was defined according to Cerebral Performance Category (CPC) scale as "good" (CPC 1-2, good cerebral performance or moderate disability) or "poor" (CPC 3-5, severe disability, unresponsive wakefulness syndrome, or death).

RESULTS

Of 78 included patients [mean age 66 ± 12 years, 62 (80.0%) male], 37 (47.4%) were randomised to TTM at 36 °C. Six-month outcome was poor in 47 (60.3%) patients. The DIA-MS analysis identified and quantified 403 unique human proteins. Differential protein abundance testing comparing poor to good outcome showed 19 elevated proteins in patients with poor outcome (log₂-fold change (FC) range 0.28-1.17) and 16 reduced proteins (log₂(FC) between - 0.22 and - 0.68), involved in inflammatory/immune responses and apoptotic signalling pathways for poor outcome and proteolysis for good outcome. Analysis according to level of TTM showed a significant protein abundance difference for six proteins [five elevated proteins in TTM 36 °C (log₂(FC) between 0.33 and 0.88), one reduced protein (log₂(FC) - 0.6)] mainly involved in inflammatory/immune responses only at 48 h after cardiac arrest.

CONCLUSIONS

Serum proteome profiling revealed an increase in inflammatory/immune responses and apoptosis in patients with poor outcome. In patients with good outcome, an increase in proteolysis was observed, whereas TTM-level only had a modest effect on the proteome profiles. Further validation of the differentially abundant proteins in response to neurological outcome is necessary to validate novel biomarker candidates that may predict prognosis after cardiac arrest.

Investigating centrifugal filtration of serum-based FTIR spectroscopy for the stratification of brain tumours

Discrimination of brain cancer versus non-cancer patients using serum-based attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy diagnostics was first developed by Hands et al with a reported sensitivity of 92.8% and specificity of 91.5%. Cameron et al. then went on to stratifying between specific brain tumour types: glioblastoma multiforme (GBM) vs. primary cerebral lymphoma with a sensitivity of 90.1% and specificity of 86.3%. Expanding on these studies, 30 GBM, 30 lymphoma and 30 non-cancer patients were selected to investigate the influence on test performance by focusing on specific molecular weight regions of the patient serum. Membrane filters with molecular weight cut offs of 100 kDa, 50 kDa, 30 kDa, 10 kDa and 3 kDa were purchased in order to remove the most abundant high molecular weight components. Three groups were classified using both partial least squares-discriminate analysis (PLS-DA) and random forest (RF) machine learning algorithms; GBM versus non-cancer, lymphoma versus non-cancer and GBM versus lymphoma. For all groups, once the serum was filtered the sensitivity, specificity and overall balanced accuracies decreased. This illustrates that the high molecular weight components are required for discrimination between cancer and non-cancer as well as between tumour types. From a clinical application point of view, this is preferable as less sample preparation is required.

Immunoprecipitation: Variations, Considerations, and Applications

Immunoprecipitation (IP) refers to methods of affinity chromatography that enrich and/or purify a specific protein from a complex mixture using a specific antibody immobilized on a solid support. Several operations and processes that are dependent on the isolation, concentration, and modification of proteins have seen improvement in their selectivity and separation based on the integration of IP-specific reactions into their workflows. This relatively simple principle has contributed significantly to our understanding of proteins and their behaviors and has become increasingly fundamental to most protein characterization studies today. In this chapter, we review the basic principles of IP and the several factors that influence each stage, and subsequently the success, of an IP experiment. Moreover, variations in application of the IP principle are discussed, and the adaptability of the techniques based on such is highlighted in the provision of two IP workflows to purify a particular protein from an entire cellular proteosome. These workflows cover the preparation and fractionation of crude cellular lysate into individual subcellular fractions, through to both "batch" and "column"-based extractions of the target protein of interest. Protocols for determining the validity of the workflows, and the presence/abundance of the protein of interest, are also briefly described.

The Surface Charge of Polymer-Coated Upconversion Nanoparticles Determines Protein Corona Properties and Cell Recognition in Serum Solutions

Applications of nanoparticles (NPs) in the life sciences require control over their properties in protein-rich biological fluids, as an NP quickly acquires a layer of proteins on the surface, forming the so-called "protein corona" (PC). Understanding the composition and kinetics of the PC at the molecular level is of considerable importance for controlling NP interaction with cells. Here, we present a systematic study of hard PC formation on the surface of upconversion nanoparticles (UCNPs) coated with positively-charged polyethyleneimine (PEI) and negatively-charged poly (acrylic acid) (PAA) polymers in serum-supplemented cell culture medium. The rationale behind the choice of UCNP is two-fold: UCNP represents a convenient model of NP with a size ranging from 5 nm to >200 nm, while the unique photoluminescent properties of UCNP enable direct observation of the PC formation, which may provide new insight into this complex process. The non-linear optical properties of UCNP were utilised for direct observation of PC formation by means of fluorescence correlation spectroscopy. Our findings indicated that the charge of the surface polymer coating was the key factor for the formation of PC on UCNPs, with an ensuing effect on the NP-cell interactions.

LEDGF is a new growth factor in fetal serum

Fetal serum supports the immortal growth of mammalian cell lines in culture while adult serum leads to the terminal differentiation and death of cells in culture. Many of the proteins in fetal serum that support the indefinite division and growth of cancerous cell lines remain obscure. The peptides and proteins of fetal versus adult serum were analyzed by liquid chromatography, nano electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS). Three batches of fetal serum contained the Alpha Fetoprotein marker while adult serum batches did not. Insulin (INS), and insulin-like growth factor (ILGF), fibroblast growth factor (FGF), epidermal growth factor (EGF) and platelet derived growth factor (PDGF) were increased in fetal serum. New fetal growth factors including MEGF, HDGFRP and PSIP1 and soluble growth receptors such as TNFR, EGFR, NTRK2 and THRA were discovered. Addition of insulin or the homeotic transcription factor PSIP1, also referred to as Lens Epithelium Derived Growth Factor (LEDGF), partially restored the rounded phenotype of rapidly dividing cells but was not as effective as fetal serum. Thus, a new growth factor in fetal serum, LEDGF/PSIP1, was directly observed by tandem mass spectrometry and confirmed by add back experiments to cell culture media alongside insulin.

A Combined Near-Infrared and Mid-Infrared Spectroscopic Approach for the Detection and Quantification of Glycine in Human Serum

Serum is an important candidate in proteomics analysis as it potentially carries key markers on health status and disease progression. However, several important diagnostic markers found in the circulatory proteome and the low-molecular-weight (LMW) peptidome have become analytically challenging due to the high dynamic concentration range of the constituent protein/peptide species in serum. Herein, we propose a novel approach to improve the limit of detection (LoD) of LMW amino acids by combining mid-IR (MIR) and near-IR spectroscopic data using glycine as a model LMW analyte. This is the first example of near-IR spectroscopy applied to elucidate the detection limit of LMW components in serum; moreover, it is the first study of its kind to combine mid-infrared (25-2.5 μm) and near-infrared (2500-800 nm) to detect an analyte in serum. First, we evaluated the prediction model performance individually with MIR (ATR-FTIR) and NIR spectroscopic methods using partial least squares regression (PLS-R) analysis. The LoD was found to be 0.26 mg/mL with ATR spectroscopy and 0.22 mg/mL with NIR spectroscopy. Secondly, we examined the ability of combined spectral regions to enhance the detection limit of serum-based LMW amino acids. Supervised extended wavelength PLS-R resulted in a root mean square error of prediction (RMSEP) value of 0.303 mg/mL and R² value of 0.999 over a concentration range of 0-50 mg/mL for glycine spiked in whole serum. The LoD improved to 0.17 mg/mL from 0.26 mg/mL. Thus, the combination of NIR and mid-IR spectroscopy can improve the limit of detection for an LMW compound in a complex serum matrix.

Proteomics Studies in Gestational Diabetes Mellitus: A Systematic Review and Meta-Analysis

Gestational Diabetes Mellitus (GDM) is the most common metabolic complication during pregnancy and is associated with serious maternal and fetal complications such as pre-eclampsia and stillbirth. Further, women with GDM have approximately 10 times higher risk of diabetes later in life. Children born to mothers with GDM also face a higher risk of childhood obesity and diabetes later in life. Early prediction/diagnosis of GDM leads to early interventions such as diet and lifestyle, which could mitigate the maternal and fetal complications associated with GDM. However, no biomarkers identified to date have been proven to be effective in the prediction/diagnosis of GDM. Proteomic approaches based on mass spectrometry have been applied in various fields of biomedical research to identify novel biomarkers. Although a number of proteomic studies in GDM now exist, a lack of a comprehensive and up-to-date meta-analysis makes it difficult for researchers to interpret the data in the existing literature. Thus, we undertook a systematic review and meta-analysis on proteomic studies and GDM. We searched MEDLINE, EMBASE, Web of Science and Scopus from inception to January 2022. We searched Medline, Embase, CINHAL and the Cochrane Library, which were searched from inception to February 2021. We included cohort, case-control and observational studies reporting original data investigating the development of GDM compared to a control group. Two independent reviewers selected eligible studies for meta-analysis. Data collection and analyses were performed by two independent reviewers. The PROSPERO registration number is CRD42020185951. Of 120 articles retrieved, 24 studies met the eligibility criteria, comparing a total of 1779 pregnant women (904 GDM and 875 controls). A total of 262 GDM candidate biomarkers (CBs) were identified, with 49 CBs reported in at least two studies. We found 22 highly replicable CBs that were significantly different (nine CBs were upregulated and 12 CBs downregulated) between women with GDM and controls across various proteomic platforms, sample types, blood fractions and time of blood collection and continents. We performed further analyses on blood (plasma/serum) CBs in early pregnancy (first and/or early second trimester) and included studies with more than nine samples (nine studies in total). We found that 11 CBs were significantly upregulated, and 13 CBs significantly downregulated in women with GDM compared to controls. Subsequent pathway analysis using Database for Annotation, Visualization and Integrated Discovery (DAVID) bioinformatics resources found that these CBs were most strongly linked to pathways related to complement and coagulation cascades. Our findings provide important insights and form a strong foundation for future validation studies to establish reliable biomarkers for GDM.

Separation of Serum and Plasma Proteins for In-Depth Proteomic Analysis

There are probably no biological samples that did more to spur interest in proteomics than serum and plasma. The belief was that comparing the proteomes of these samples obtained from healthy and disease-affected individuals would lead to biomarkers that could be used to diagnose conditions such as cancer. While the continuing development of mass spectrometers with greater sensitivity and resolution has been invaluable, the invention of strategic strategies to separate circulatory proteins has been just as critical. Novel and creative separation techniques were required because serum and plasma probably have the greatest dynamic range of protein concentration of any biological sample. The concentrations of circulating proteins can range over twelve orders of magnitude, making it a challenge to identify low-abundance proteins where the bulk of the useful biomarkers are believed to exist. The major goals of this article are to (i) provide an historical perspective on the rapid development of serum and plasma proteomics; (ii) describe various separation techniques that have made obtaining an in-depth view of the proteome of these biological samples possible; and (iii) describe applications where serum and plasma proteomics have been employed to discover potential biomarkers for pathological conditions.

Total protein assay by PCA-based RGB-spectrum conversion methods with smartphone-acquired digital images

Total protein concentrations in the aqueous solutions were determined from the absorption spectra reproduced from smartphone-captured digital color images. We employed two different procedures for protein determination: the pyrogallol red molybdate method and Bradford's method. The principal-component-analysis-based reproduction process, which was previously reported by our research group, enabled the conversion of RGB values to score values for a linear combination of loading vectors to generate reproduced absorption spectra. The reproduced spectra were identical to those measured using a commercially available spectrophotometer. The total protein assays of commercial soymilk and human serum samples were carried out with both coloration reagents, and the obtained results were in good agreement with those attained using a conventional spectrophotometer. These results show that the proposed method enables smartphone-based ratiometric analysis of real samples without requiring any monochromating equipment.

Nanoparticle protein corona evolution: from biological impact to biomarker discovery

Nanoparticles exposed to biological fluids such as blood, quickly interact with their surrounding milieu resulting in a biological coating that results in large part as a function of the physicochemical properties of the nanomaterial. The large nanoparticle surface area-to-volume ratio further augments binding of biological molecules and the resulting biomolecular or protein corona, once thought of as problematic biofouling, is now viewed as a rich source of biological information that can guide the development of nanomedicines. This review gives an overview of the utility of the protein corona in proteomic profiling and discusses how a better understanding of nano-bio interactions can accelerate the clinical translation of nanomedicines and facilitate the identification of disease-specific biomarkers. With the FDA requirement of the protein corona analysis of nanoparticles in place, it is envisaged that analyzing the protein corona of nanoparticles on a case-by-case basis can provide highly valuable nano-bio interface information that can aid and improve their clinical translation.

Human Blood and Bird Egg Proteins Identified in Red Paint Covering a 1000-Year-Old Gold Mask from Peru

We analyzed a red paint sample from the surface of a gold mask excavated from a Middle Sicán elite tomb in Peru. The mask covered the face of the principal male and dates from ca. 1000 AD, a period when many painted precious metal objects were produced. The paint's inorganic pigment was identified more than 30 years ago as cinnabar (a mercuric sulfide scarlet-red to brown-red mineral), but the identity of the effective organic binder remained a mystery. Fourier transform infrared (FTIR) analysis of the sample indicated a proteinaceous composition, and no lipids were recovered from an N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) derivatized extract of the sample analyzed by gas chromatography-mass spectrometry (GC-MS). Proteomics analysis by nanoLC-MS/MS identified unique peptides in the sample, which were matched to human blood and bird egg proteins via Uniprot database searches. These included immunoglobulin heavy chain, immunoglobulin G, serum albumin, and ovomucoid. Cinnabar-based paints were typically used in the context of social elites and ritually important items. The presence of human blood would support previous ideas that red cinnabar paint may represent "life force" intended to support "rebirth". As the red paint sample came from the first scientifically excavated Sicán gold mask, the results suggest a method to authenticate similar unprovenanced masks now in private and museum collections. Proteomics data set identifier https://doi.org/10.5287/bodleian:1ajYbBgQP.

Butyrylcholinesterase-Protein Interactions in Human Serum

Measuring various biochemical and cellular components in the blood is a routine procedure in clinical practice. Human serum contains hundreds of diverse proteins secreted from all cells and tissues in healthy and diseased states. Moreover, some serum proteins have specific strong interactions with other blood components, but most interactions are probably weak and transient. One of the serum proteins is butyrylcholinesterase (BChE), an enzyme existing mainly as a glycosylated soluble tetramer that plays an important role in the metabolism of many drugs. Our results suggest that BChE interacts with plasma proteins and forms much larger complexes than predicted from the molecular weight of the BChE tetramer. To investigate and isolate such complexes, we developed a two-step strategy to find specific protein–protein interactions by combining native size-exclusion chromatography (SEC) with affinity chromatography with the resin that specifically binds BChE. Second, to confirm protein complexes′ specificity, we fractionated blood serum proteins by density gradient ultracentrifugation followed by co-immunoprecipitation with anti-BChE monoclonal antibodies. The proteins coisolated in complexes with BChE were identified by mass spectroscopy. These binding studies revealed that BChE interacts with a number of proteins in the human serum. Some of these interactions seem to be more stable than transient. BChE copurification with ApoA-I and the density of some fractions containing BChE corresponding to high-density lipoprotein cholesterol (HDL) during ultracentrifugation suggest its interactions with HDL. Moreover, we observed lower BChE plasma activity in individuals with severely reduced HDL levels (≤20 mg/dL). The presented two-step methodology for determination of the BChE interactions can facilitate further analysis of such complexes, especially from the brain tissue, where BChE could be involved in the pathogenesis and progression of AD.

Proteomics: Concepts and applications in human medicine

Proteomics is the complete evaluation of the function and structure of proteins to understand an organism’s nature. Mass spectrometry is an essential tool that is used for profiling proteins in the cell. However, biomarker discovery remains the major challenge of proteomics because of their complexity and dynamicity. Therefore, combining the proteomics approach with genomics and bioinformatics will provide an understanding of the information of biological systems and their disease alteration. However, most studies have investigated a small part of the proteins in the blood. This review highlights the types of proteomics, the available proteomic techniques, and their applications in different research fields.

Human blood serum proteome changes after 6 hours of sleep deprivation at night

Background

The aim of this study was to discover significantly changed proteins in human blood serum after loss of 6 h sleep at night. Furthermore, to reveal affected biological process- and molecular function categories that might be clinically relevant, by exploring systems biological databases.

Methods

Eight females were recruited by volunteer request. Peripheral venous whole blood was sampled at 04:00 am, after 6 h of sleep and after 6 h of sleep deprivation. We used within-subjects design (all subjects were their own control). Blood serum from each subject was depleted before protein digestion by trypsin and iTRAQ labeling. Labled peptides were analyzed by mass spectrometry (LTQ OritrapVelos Elite) connected to a LC system (Dionex Ultimate NCR-3000RS).

Results

We identified 725 proteins in human blood serum. 34 proteins were significantly differentially expressed after 6 h of sleep deprivation at night. Out of 34 proteins, 14 proteins were up-regulated, and 20 proteins were down-regulated. We emphasized the functionality of the 16 proteins commonly differentiated in all 8 subjects and the relation to pathological conditions. In addition, we discussed Histone H4 (H4) and protein S100-A6/Calcyclin (S10A6) that were upregulated more than 1.5-fold. Finally, we discussed affected biological process- and molecular function categories.

Conclusions

Overall, our study suggest that acute sleep deprivation, at least in females, affects several known biological processes- and molecular function categories and associates to proteins that also are changed under pathological conditions like impaired coagulation, oxidative stress, immune suppression, neurodegenerative related disorder, and cancer. Data are available via ProteomeXchange with identifier PXD021004.

Human blood microRNA hsa-miR-21-5p induces vitellogenin in the mosquito Aedes aegypti

Mosquito vectors transmit various diseases through blood feeding, required for their egg development. Hence, blood feeding is a major physiological event in their life cycle, during which hundreds of genes are tightly regulated. Blood is a rich source of proteins for mosquitoes, but also contains many other molecules including microRNAs (miRNAs). Here, we found that human blood miRNAs are transported abundantly into the fat body tissue of Aedes aegypti, a key metabolic center in post-blood feeding reproductive events, where they target and regulate mosquito genes. Using an artificial diet spiked with the mimic of an abundant and stable human blood miRNA, hsa-miR-21-5p, and proteomics analysis, we found over 40 proteins showing differential expression in female Ae. aegypti mosquitoes after feeding. Of interest, we found that the miRNA positively regulates the vitellogenin gene, coding for a yolk protein produced in the mosquito fat body and then transported to the ovaries as a protein source for egg production. Inhibition of hsa-miR-21-5p followed by human blood feeding led to a statistically insignificant reduction in progeny production. The results provide another example of the involvement of small regulatory molecules in the interaction of taxonomically vastly different taxa.

The IgGFc-binding protein FCGBP is secreted with all GDPH sequences cleaved but maintained by interfragment disulfide bonds

Mucus forms an important protective barrier that minimizes bacterial contact with the colonic epithelium. Intestinal mucus is organized in a complex network with several specific proteins, including the mucin-2 (MUC2) and the abundant IgGFc-binding protein, FCGBP. FCGBP is expressed in all intestinal goblet cells and is secreted into the mucus. It is comprised of repeated von Willebrand D (vWD) domain assemblies, most of which have a GDPH amino acid sequence that can be autocatalytically cleaved, as previously observed in the mucins MUC2 and mucin-5AC. However, the functions of FCGBP in the mucus are not understood. We show that all vWD domains of FCGBP with a GDPH sequence are cleaved and that these cleavages occur early during biosynthesis in the endoplasmic reticulum. All cleaved fragments, however, remain connected via a disulfide bond within each vWD domain. This cleavage generates a C-terminal-reactive Asp-anhydride that could react with other molecules, such as MUC2, but this was not observed. Quantitative analyses by MS showed that FCGBP was mainly soluble in chaotropic solutions, whereas MUC2 was insoluble, and most of the secreted FCGBP was not covalently bound to MUC2. Although FCGBP has been suggested to bind immunoglobulin G, we were unable to reproduce this binding in vitro using purified proteins. In conclusion, while the function of FCGBP is still unknown, our results suggest that it does not contribute to covalent crosslinking in the mucus, nor incorporate immunoglobulin G into mucus, instead the single disulfide bond linking each fragment could mediate controlled dissociation.

Thermal neutron cross sections of amino acids from average contributions of functional groups

The experimental thermal neutron cross sections of the 20 proteinogenic amino acids have been measured over the incident-neutron energy range spanning from 1 meV to 10 keV and data have been interpreted using the multi-phonon expansion based on first-principles calculations. The scattering cross section, dominated by the incoherent inelastic contribution from the hydrogen atoms, can be rationalised in terms of the average contributions of different functional groups, thus neglecting their correlation. These results can be used for modelling the total neutron cross sections of complex organic systems like proteins, muscles, or human tissues from a limited number of starting input functions. This simplification is of crucial importance for fine-tuning of transport simulations used in medical applications, including boron neutron capture therapy as well as secondary neutrons-emission induced during proton therapy. Moreover, the parametrized neutron cross sections allow a better treatment of neutron scattering experiments, providing detailed sample self-attenuation corrections for a variety of biological and soft-matter systems.

The differences of the impact of a lipid and protein corona on the colloidal stability, toxicity, and degradation behavior of iron oxide nanoparticles

AIM

In this study, the influence of a serum albumin (SA) and human plasma (HP) derived protein- and lipid molecule corona on the toxicity and biodegradability of different iron oxide nanoparticles (IONP) was investigated.

METHODS

IONP were synthesized and physicochemically characterized regarding size, charge, and colloidal stability. The adsorbed proteins were quantified and separated by gel electrophoresis. Adsorbed lipids were profiled by ultraperformance liquid chromatography-ESI-tandem mass spectrometry. The biocompatibility was investigated using isolated erythrocytes and a shell-less hen's egg model. The biodegradability was assessed by iron release studies in artificial body fluids.

RESULTS

The adsorption patterns of proteins and lipids varied depending on the surface characteristics of the IONP like charge and hydrophobicity. The biomolecule corona modified IONP displayed favorable colloidal stability and toxicological profile compared to IONP without biomolecule coronas, reducing erythrocyte aggregation and hemolysis in vitro as well as the corresponding effects ex ovo/in vivo. The coronas decreased the degradation speed of all tested IONP compared to bare particles, but, whereas all IONP degraded at the same rate for the SA corona, substantial differences were evident for IONP with HP-derived corona depending on the lipid adsorption profile.

CONCLUSION

In this study the impact of the proteins and lipids in the biomolecule corona on the entire IONP application cycle from the injection process to the degradation was demonstrated.

Assessment of Antibody Stability in a Novel Protein-Free Serum Model

Therapeutic proteins can degrade upon administration as they are subjected to a variety of stresses in human body compartments. In vivo degradation may cause undesirable pharmacokinetic/pharmacodynamic profiles. Pre-clinical in vitro models have gained scientific interest as they enable one to evaluate the in vivo stability of monoclonal antibodies (mAbs) and ultimately can improve patient safety. We used a novel approach by stripping serum of endogenous proteins, which interfere with analytical test methods. This enabled the direct analysis of the target protein without laborious sample work-up procedures. The developed model retained the osmolality, conductivity, temperature, and pH of serum. We compared the impact of human, bovine, and artificial serum to accelerated stability conditions in histidine buffer. Target mAbs were assessed in regard to visible and sub-visible particles, as well as protein aggregation and fragmentation. Both mAbs degraded to a higher extent under physiological conditions compared to accelerated stability conditions. No relevant stability differences between the tested mAbs were observed. Our results reinforced the importance of monitoring protein stability in biological fluids or fluids emulating these conditions closely. Models enabling analysis in fluids directly allow high throughput testing in early pre-clinical stages and help in selecting molecules with increased in vivo stability.

Biomolecular interactions of ultrasmall metallic nanoparticles and nanoclusters

The use of nanoparticles (NPs) in biomedicine has made a gradual transition from proof-of-concept to clinical applications, with several NP types meeting regulatory approval or undergoing clinical trials. A new type of metallic nanostructures called ultrasmall nanoparticles (usNPs) and nanoclusters (NCs), while retaining essential properties of the larger (classical) NPs, have features common to bioactive proteins. This combination expands the potential use of usNPs and NCs to areas of diagnosis and therapy traditionally reserved for small-molecule medicine. Their distinctive physicochemical properties can lead to unique in vivo behaviors, including improved renal clearance and tumor distribution. Both the beneficial and potentially deleterious outcomes (cytotoxicity, inflammation) can, in principle, be controlled through a judicious choice of the nanocore shape and size, as well as the chemical ligands attached to the surface. At present, the ability to control the behavior of usNPs is limited, partly because advances are still needed in nanoengineering and chemical synthesis to manufacture and characterize ultrasmall nanostructures and partly because our understanding of their interactions in biological environments is incomplete. This review addresses the second limitation. We review experimental and computational methods currently available to understand molecular mechanisms, with particular attention to usNP-protein complexation, and highlight areas where further progress is needed. We discuss approaches that we find most promising to provide relevant molecular-level insight for designing usNPs with specific behaviors and pave the way to translational applications.

Machine Learning-Assisted Array-Based Detection of Proteins in Serum Using Functionalized MoS2 Nanosheets and Green Fluorescent Protein Conjugates

Abnormal concentrations of a specific protein or the presence of some biomarker proteins may indicate life-threatening diseases. Pattern-based detection of specific analytes using affinity-regulated receptors is one of the potential alternatives to specific antigen-antibody-based detection. In this report, we have schemed a sensor array by using various functionalized two-dimensional (2D)-MoS2 nanosheets and green fluorescent protein (GFP) as the receptor and the signal transducer, respectively. Two-dimensional MoS2 has been used as a promising candidate for recognition of the bioanalytes because of its high surface-to-volume ratio compared to those of other nanomaterials. Easy surface tunability of this material provides additional advantages to analyze the target of interest. The optimized 2D-MoS2-GFP conjugates are able to discriminate 15 different proteins at 50 nM concentration with a detection limit of 1 nM. Moreover, proteins in the binary mixture and in the presence of serum were discriminated successfully. Ten different proteins in serum media at relevant concentrations were classified successfully with 100% jackknifed classification accuracy, which proves the potentiality of the above system. We have also implemented and discussed the implication of using different machine learning models on the pattern recognition problem associated with array-based sensing.

Monitoring deep-tissue oxygenation with a millimeter-scale ultrasonic implant

Vascular complications following solid organ transplantation may lead to graft ischemia, dysfunction or loss. Imaging approaches can provide intermittent assessments of graft perfusion, but require highly skilled practitioners and do not directly assess graft oxygenation. Existing systems for monitoring tissue oxygenation are limited by the need for wired connections, the inability to provide real-time data or operation restricted to surface tissues. Here, we present a minimally invasive system to monitor deep-tissue O₂ that reports continuous real-time data from centimeter-scale depths in sheep and up to a 10-cm depth in ex vivo porcine tissue. The system is composed of a millimeter-sized, wireless, ultrasound-powered implantable luminescence O₂ sensor and an external transceiver for bidirectional data transfer, enabling deep-tissue oxygenation monitoring for surgical or critical care indications.

Whole blood and blood components from vertebrates differentially affect egg formation in three species of anautogenous mosquitoes

Background

Most female mosquitoes are anautogenous and must blood feed on a vertebrate host to produce eggs. Prior studies show that the number of eggs females lay per clutch correlates with the volume of blood ingested and that protein is the most important macronutrient for egg formation. In contrast, how whole blood, blood fractions and specific blood proteins from different vertebrates affect egg formation is less clear. Since egg formation is best understood in Aedes aegypti, we examined how blood and blood components from different vertebrates affect this species and two others: the malaria vector Anopheles gambiae and arbovirus vector Culex quinquefasciatus.

Methods

Adult female mosquitoes were fed blood, blood fractions and purified major blood proteins from different vertebrate hosts. Markers of reproductive response including ovary ecdysteroidogenesis, yolk deposition into oocytes and number of mature eggs produced were measured.

Results

Ae. aegypti, An. gambiae and C. quinquefasciatus responded differently to meals of whole blood, plasma or blood cells from human, rat, chicken and turkey hosts. We observed more similarities between the anthropophiles Ae. aegypti and An. gambiae than the ornithophile C. quinquefasciatus. Focusing on Ae. aegypti, the major plasma-derived proteins (serum albumin, fibrinogen and globulins) differentially stimulated egg formation as a function of vertebrate host source. The major blood cell protein, hemoglobin, stimulated yolk deposition when from pigs but not humans, cows or sheep. Serum albumins from different vertebrates also variably affected egg formation. Bovine serum albumin (BSA) stimulated ovary ecdysteroidogenesis, but more weakly induced digestive enzyme activities than whole blood. In contrast, BSA-derived peptides and free amino acids had no stimulatory effects on ecdysteroidogenesis or yolk deposition into oocytes.

Conclusions

Whole blood, blood fractions and specific blood proteins supported egg formation in three species of anautogenous mosquitoes but specific responses varied with the vertebrate source of the blood components tested.

Detection of Glycine as a Model Protein in Blood Serum Using 2D-IR Spectroscopy

Glycine (Gly) is used as a model system to evaluate the ability of ultrafast two-dimensional infrared (2D-IR) spectroscopy to detect and quantify the low-molecular-weight proteinaceous components of blood serum. Combining data acquisition schemes to suppress absorption bands of H₂O that overlap with the protein amide I band with analysis of peak patterns appearing in the off-diagonal region of the 2D-IR spectrum allows separation of the Gly spectral signature from that of the dominant protein fraction of serum in a transmission-mode 2D-IR measurement without any sample manipulation, e.g., filtration or drying. 2D-IR spectra of blood serum samples supplemented with varying concentrations of Gly were obtained, and a range of data analysis methods compared, leading to a detection limit of ∼3 mg/mL for Gly. The reported methodology provides a platform for a critical assessment of the sensitivity of 2D-IR for measuring the concentrations of amino acids, peptides, and low-molecular-weight proteins present in serum samples. We conclude that, in the case of several clinically relevant diagnostic molecules and their combinations, the potential exists for 2D-IR to complement IR absorption methods as the benefits of the second frequency dimension offered by 2D-IR spectroscopy outweigh the added technical complexity of the measurement.

Human body-fluid proteome: quantitative profiling and computational prediction

Empowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers and therapeutic drugs. In the meantime, a tremendous progress in disclosing the body-fluid proteomes was made, resulting in a collection of over 15 000 different proteins detected in major human body fluids. However, common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational effort utilizing statistical and machine-learning approaches has shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first summarized the experimental progresses using a combination of conventional and high-throughput technologies, along with the major discoveries, and focused on current research status of 16 types of body-fluid proteins. Next, the emerging computational work on protein prediction based on support vector machine, ranking algorithm, and protein-protein interaction network were also surveyed, followed by algorithm and application discussion. At last, we discuss additional critical concerns about these topics and close the review by providing future perspectives especially toward the realization of clinical disease biomarker discovery.

Omics in Systems Biology: Current Progress and Future Outlook

Biological research has undergone tremendous changes over the past three decades. Research used to almost exclusively focus on a single aspect of a single molecule per experiment. Modern technologies have enabled thousands of molecules to be simultaneously analyzed and the way that these molecules influence each other to be discerned. The change is so dramatic that it has given rise to a whole new descriptive suffix (i.e., omics) to describe these fields of study. While genomics was arguably the initial driver of this new trend, it quickly spread to other biological entities resulting in the creation of transcriptomics, proteomics, metabolomics, etc. The development of these "big four omics" created a wave of other omic fields, such as epigenomics, glycomics, lipidomics, microbiomics, and even foodomics; all with the purpose of comprehensively studying all the molecular entities or processes within their respective domain. The large number of omic fields that are invented even led to the term "panomics" as a way to classify them all under one category. Ultimately, all of these omic fields are setting the foundation for developing systems biology; in which the focus will be on determining the complex interactions that occur within biological systems.

Physicochemical Property Correlations with Ionization Efficiency in Capillary Vibrating Sharp-Edge Spray Ionization (cVSSI)

The relative contributions to ionization efficiency by three molecular chemical properties have been examined for field-free and field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) using mass spectrometry (MS) analysis. Ion intensities have been recorded for model compounds under each operational ionization mode as well as for aqueous and nonaqueous (methanol) solvent systems. Multiple regression analysis suggests that for field-free cVSSI, ion intensity is mostly associated with the log of the base dissociation constant (pK_b) and proton affinity (PA) for both aqueous and methanol solutions. Comparatively, for field-enabled cVSSI using aqueous solutions, the dominant factor correlated with ion intensity is the log of the partition coefficient (log P). To a lesser degree, this is observed for methanol solutions as well. For ESI, pK_b is the dominant factor associated with ion signal levels from methanol and aqueous solutions. These results are supported by studies conducted on two different mass spectrometers employing different cVSSI emitter tips. The relationship of ion intensity and pK_b in ESI is supported by multiple studies; however, the shift to other chemical properties with the addition of cVSSI suggests the possibility that a different (or combinations of) ionization mechanism(s) may be operative for these ionization modes. These results are briefly considered in light of the different ESI mechanisms.

A Fluorescent Probe for Selective Facile Detection of H2S in Serum Based on an Albumin-Binding Fluorophore and Effective Masking Reagent

A fluorescent probe (4-(2-(4-(diethylamino)phenyl)-4-methyl-5-oxo-4,5-dihydrothieno[3,2-b]pyridin-7-yl)phenyl 2,4-dinitrobenzenesulfonate, KF-DNBS) for facile detection of H₂S in serum was developed based on the combination of an environment-sensitive fluorophore (2-(4-(diethylamino)phenyl)-7-(4-hydroxyphenyl)-4-methylthieno[3,2-b]pyridin-5(4H)-one, KF) with albumin and the 2,4-dinitrobenzene sulfonyl (DNBS) group as a recognition unit for H₂S. KF-DNBS showed remarkable fluorescence enhancement due to H₂S-triggered thiolysis followed by the formation of a fluorescent fluorophore (KF)-albumin complex. The H₂S detection limit of KF-DNBS was estimated to be 3.2 μM, and KF-DNBS achieves a high selectivity to H₂S over biothiols by employing 2-formyl benzene boronic acid (2-FBBA) as an effective masking reagent. Furthermore, under optimized sensing conditions, KF-DNBS could be applied to accurately determine spiked H₂S in human serum without the need for any further procedure for the removal of serum proteins.

Comprehensive Analysis of Low Molecular Weight Serum Proteome Enrichment for Mass Spectrometric Studies

RATIONALE

The low molecular weight (LMW) proteins present in circulating body fluids, such as serum and plasma, hold biological significance as possible biomarkers. A major obstacle in mass spectrometry-based proteomics of serum is the presence of abundant high molecular weight proteins which mask the identification and quantitation of lower molecular weight proteins. Traditional methods involve the use of affinity resins to remove high molecular weight proteins, such as albumin and immunoglobulin G, with concomitant loss of lower molecular weight proteins. Considering the importance of depleting high molecular proteins, this paper compares an affinity resin, a gel-filter, and an acetonitrile (ACN) precipitation method to achieve successful removal of high molecular weight proteins and recovery of lower molecular weight proteins.

METHODS

Serum enrichment was carried out by multiple methods such as with the commercially available serum protein mini kit, ACN precipitation, and a gel filter method. Mass spectrometric runs were carried out on an AB SCIEX ESI QTOF 5600 mass spectrometer. Mass spectrometry analysis of the enriched serum obtained by ACN precipitation and gel filter method was performed for global proteome profiling. Quantitative mass spectrometry using isobaric tags for relative and absolute quantitation (iTRAQ) for ACN-precipitated enriched serum was also carried out.

RESULTS

The gel filter method, though allowing for the resolution and identification of LMW proteins, was better suited for global proteome analysis and not preferred for quantitative proteomic experiments. In contrast, enrichment by the ACN precipitation method allowed for the reproducible identification and quantitation of LMW proteins having molecular weight ≥4 kDa.

CONCLUSIONS

Using only chilled ACN and centrifugation, most of the highly abundant proteins were successfully removed from the serum, while recovering a significant portion of the LMW proteome. A more rapid protocol, which is compatible with iTRAQ labeling, to achieve improved results has been elucidated, thus allowing for better screening and identification of potential biomarkers.

Mass spectrometry profiling of low molecular weight proteins and peptides isolated by acetone precipitation

Solvent-based protein precipitation provides exceptional recovery, particularly when the ionic strength of the solution is controlled. While precipitation is ideally suited for intact protein purification ahead of mass-spectrometry, low molecular weight (LMW) proteins and peptides are considered less susceptible to aggregation in organic solvent. As the combination of salt and organic solvent (i.e. acetone) has yet to be exploited to precipitate LMW proteins, we herein determine the low mass limit for solvent-based protein precipitation. We establish optimized conditions for high recovery precipitation of LMW proteins and peptides. Our results demonstrate a strong dependence on the type of salt to recover LMW components from complex mixtures. Inclusion of 100 mM ZnSO₄ with 97% acetone provides near quantitative recovery of all peptides down to 2 kDa, and continues to exceed 90% yield for peptides at a molecular weight of 1 kDa. A detailed characterization of the precipitated peptides resulting from trypsin and pepsin digestion of complex systems is provided by bottom-up mass spectrometry.

Neuroinflammation and fibrosis in stroke: The good, the bad and the ugly

Stroke is the leading cause of death and the main cause of disability in surviving patients. The detrimental interaction between immune cells, glial cells, and matrix components in stroke pathology results in persistent inflammation that progresses to fibrosis. A substantial effort is being directed toward understanding the exact neuroinflammatory events that take place as a result of stroke. The initiation of a potent cytokine response, along with immune cell activation and infiltration in the ischemic core, has massive acute deleterious effects, generally exacerbated by comorbid inflammatory conditions. There is secondary neuroinflammation that promotes further injury, resulting in cell death, but conversely plays a beneficial role, by promoting recovery. This highlights the need for a better understanding of the neuroinflammatory and fibrotic processes, as well as the need to identify new mechanisms and potential modulators. In this review, we summarize several aspects of stroke-induced inflammation, fibrosis, and include a discussion of cytokine inhibitors/inducers, immune cells, and fibro-inflammation signaling inhibitors in order to identify new pharmacological means of intervention.

GDF5 induces TBX3 in a concentration dependent manner - on a gold nanoparticle gradient

Organs and tissues, such as cartilage and limbs, are formed during development through an orchestration of growth factors that function as morphogens. Examples of growth factors include growth differentiation factor 5 (GDF5) and transforming growth factors beta 1 and 3 (TGFβ-1 and TGFβ-3) which can specify creation of more than one cell type after forming a concentration gradient in vivo. Here, we studied the impact of morphogen gradients during differentiation of induced pluripotent stem cells (iPSCs) into the chondrocyte lineage. Cell budding zones, consisting of condensed cell aggregates, were observed only in gradients of GDF5. T-box transcription factor 3 (TBX3) was detected specifically in the budding zones (ranging from 500-1,500 particles/μm2) of nuclei and cell vesicles. A homogenous density of GDF5 of 900 particles/μm2 on a surface induced budding and expression of TBX3 after five days in iPSCs. Therefore, we conclude that a gradient of GDF5, as well as the specific homogenous density of GDF5, support the induction of TBX3 in iPCSs. Moreover, differentiation of iPSCs first on GDF5 gradient or homogenous surfaces for five days and then in a three-dimensional structure for five weeks resulted in pellets that expressed TBX3.

Cloning, purification and characterization of a recombinant protease with novel thrombolytic activity in human plasma and rat thrombosis models

BACKGROUND

There is a need to identify and develop novel thrombolytic agents that can directly digest fibrin clots from various biological resources.

OBJECTIVE

To clone, express, purify, and characterize a recombinant protease named rvFMP capable of cleaving fibrinogen, fibrin polymer, and cross-linked fibrin in human plasma milieu and rat thrombosis model systems.

RESULTS

We cloned a vFMP-encoding gene from the genomic DNA of V. furnissii KCCM41679 using polymerase chain reaction (PCR), expressed in Escherichia coli, and purified rvFMP (stands for recombinant vibrio furnissii metalloprotease). The proteolytic activity of purified rvFMP enzyme could be clearly inhibited by 1,10-phenanthroline and ethylene glycol tetraacetic acid, but not by diisopropyl fluorophosphate, suggesting that it can be a typical metalloprotease. rvFMP showed an effective proteolytic activity in cleaving cross-linked fibrins in human plasma milieu. Remarkably, rvFMP exhibited a clear thrombolytic activity in rat thrombosis models such as ferric chloride-exposed rat carotid artery and carrageenan-treated rat tail. However, rvFMP (1.5 mg/kg) evoked no internal bleeding and also showed no lethal effect in mice. The recombinant enzyme also showed no cytotoxicity and had an inability to induce tumour necrosis factor-α (TNF-α) in Raw264.7 cells.

CONCLUSION

rvFMP can be a candidate enzyme capable of being developed as a novel direct-acting thrombolytic agent.

Utilizing Experimental Mouse Model to Identify Effectors of Hepatocellular Carcinoma Induced by HBx Antigen

Hepatocellular carcinoma (HCC) is among the ten most commonly diagnosed cancers and the fourth leading cause of cancer-related death. Patients with hepatitis B virus (HBV) infection are prone to developing chronic liver diseases (i.e., fibrosis and cirrhosis), and the HBV X antigen plays an important role in the development of HCC. The difficulty in detecting HCC at the early stages is one of the main reasons that the death rate approximates the incidence rate. The regulators controlling the downstream liver protein expression from HBV infection are unclear. Mass spectrometric techniques and customized programs were used to identify differentially expressed proteins which may be involved in the development of liver fibrosis and HCC progression in hepatitis B virus X protein transgenic mice (HBx mice). FSTL1, CTSB, and TGF-β enhanced the signaling pathway proteins during the pathogenesis of HBx. Missing proteins can be essential in cell growth, differentiation, apoptosis, migration, metastasis or angiogenesis. We found that LHX2, BMP-5 and GDF11 had complex interactions with other missing proteins and BMP-5 had both tumor suppressing and tumorigenic roles. BMP-5 may be involved in fibrosis and tumorigenic processes in the liver. These results provide us an understanding of the mechanism of HBx-induced disorders, and may serve as molecular targets for liver treatment.

Myoglobin molecule charging in electrolyte solutions

The compensated charge of myoglobin molecule in electrolyte solution is considerably smaller than the nominal charge.