Comparative proteomic analysis of seed germination between allotetraploid cotton Gossypium hirsutum and Gossypium barbadense

Seed germination, a key initial event in the plant life cycle, directly affects cotton yield and quality. Gossypium barbadense and Gossypium hirsutum gradually evolved through polyploidization, resulting in different characteristics, and this interspecific variation lacks genetic and molecular explanation. This work aimed to compare the proteomes between G. barbadense and G. hirsutum during seed germination. Here, we identified 2740 proteins for G. barbadense and 3758 for G. hirsutum. In the initial state, proteins in two cotton involved similar bioprocess, such as sugar metabolism, DNA repairing, and ABA signaling pathway. However, in the post-germination stage, G. hirsutum expressed more protein related to redox homeostasis, peroxidase activity, and pathogen interactions. Analyzing the different expression patterns of 915 single-copy orthogroups between the two kinds of cotton indicated that most of the differentially expressed proteins in G. barbadense were related to carbon metabolism. In contrast, most proteins in G. hirsutum were associated with stress response. Besides that, by proteogenomic analysis, we found 349 putative non-canonical peptides, which may be involved in plant development. These results will help to understand the different characteristics of these two kinds of cotton, such as fiber quality, yield, and adaptability. SIGNIFICANCE STATEMENT: Cotton is the predominant natural fiber crop worldwide; Gossypium barbadense and Gossypium hirsutum have evolved through polyploidization to produce differing traits. However, given their specific features, the divergence of mechanisms underlying seed germination between G. hirsutum and G. barbadense has not been discussed. Here, we explore what protein contributes to interspecific differences between G. barbadense and G. hirsutum during the seed germination period. This study helps to elucidate the evolution and domestication history of cotton polyploids and may allow breeders to understand their domestication history better and improve fiber quality and adaptability.

sOCP: a framework predicting smORF coding potential based on TIS and in-frame features and effectively applied in the human genome

Small open reading frames (smORFs) have been acknowledged to play various roles on essential biological pathways and affect human beings from diabetes to tumorigenesis. Predicting smORFs in silico is quite a prerequisite for processing the omics data. Here, we proposed the smORF-coding-potential-predicting framework, sOCP, which provides functions to construct a model for predicting novel smORFs in some species. The sOCP model constructed in human was based on in-frame features and the nucleotide bias around the start codon, and the small feature subset was proved to be competent enough and avoid overfitting problems for complicated models. It showed more advanced prediction metrics than previous methods and could correlate closely with experimental evidence in a heterogeneous dataset. The model was applied to Rattus norvegicus and exhibited satisfactory performance. We then scanned smORFs with ATG and non-ATG start codons from the human genome and generated a database containing about a million novel smORFs with coding potential. Around 72 000 smORFs are located on the lncRNA regions of the genome. The smORF-encoded peptides may be involved in biological pathways rare for canonical proteins, including glucocorticoid catabolic process and the prokaryotic defense system. Our work provides a model and database for human smORF investigation and a convenient tool for further smORF prediction in other species.

Identified Small Open Reading Frame-Encoded Peptides in Human Serum with Nanoparticle Protein Coronas

The low-molecular-weight proteins (LMWP) in serum and plasma are related to various human diseases and can be valuable biomarkers. A small open reading frame-encoded peptide (SEP) is one kind of LMWP, which has been found to function in many bioprocesses and has also been found in human blood, making it a potential biomarker. The detection of LMWP by a mass spectrometry (MS)-based proteomic assay is often inhibited by the wide dynamic range of serum/plasma protein abundance. Nanoparticle protein coronas are a newly emerging protein enrichment method. To analyze SEPs in human serum, we have developed a protocol integrated with nanoparticle protein coronas and liquid chromatography (LC)/MS/MS. With three nanoparticles, TiO2, Fe3O4@SiO2, and Fe3O4@SiO2@TiO2, we identified 164 new SEPs in the human serum sample. Fe3O4@SiO2 and a nanoparticle mixture obtained the maximum number and the largest proportion of identified SEPs, respectively. Compared with acetonitrile-based extraction, nanoparticle protein coronas can cover more small proteins and SEPs. The magnetic nanoparticle is also fit for high-throughput parallel protein separation before LC/MS. This method is fast, efficient, reproducible, and easy to operate in 96-well plates and centrifuge tubes, which will benefit the research on SEPs and biomarkers.

Systematic Proteomics Study on the Embryonic Development of Danio rerio

The early development of zebrafish (Danio rerio) is a complex and dynamic physiological process involving cell division, differentiation, and movement. Currently, the genome and transcriptome techniques have been widely used to study the embryonic development of zebrafish. However, the research of proteomics based on proteins that directly execute functions is relatively vacant. In this work, we apply label-free quantitative proteomics to explore protein profiling during zebrafish's embryogenesis, and a total of 5961 proteins were identified at 10 stages of zebrafish's early development. The identified proteins were divided into 11 modules according to weighted gene coexpression network analysis (WGCNA), and the characteristics between modules were significantly different. For example, mitochondria-related functions enriched the early development of zebrafish. Primordial germ cell-related proteins were identified at the 4-cell stage, while the eye development event is dominated at 5 days post fertilization (dpf). By combining with published transcriptomics data, we discovered some proteins that may be involved in activating zygotic genes. Meanwhile, 137 novel proteins were identified. This study comprehensively analyzed the dynamic processes in the embryonic development of zebrafish from the perspective of proteomics. It provided solid data support for further understanding of the molecular mechanism of its development.

Identification of novel smORFs and microprotein acting in response to rehydration of Nostoc flagelliforme

Nostoc flagelliforme, a terrestrial cyanobacterium spread throughout arid and semi-arid areas, has been long known for its outstanding adaptability to extremely dry conditions. This microorganism is able to recover biological activities within hours after months of anhydrobiosis state, attracting investigation through proteomic analysis. Except for canonical proteome, microproteins encoded by small ORFs (smORFs) have recently been regarded as indispensable participants in metabolic processes. However, the involvement of smORFs in Nostoc flagelliforme remains unknown. Here we first constructed a smORF database in Nostoc flagelliforme using bioinformatic prediction, resulting in 6072 novel smORFs. Then LS-MS/MS analysis was applied to identify expression patterns of microproteins and seek smORFs and their encoded microprotein playing a role during rehydration. In total, 18 novel microproteins were mined based on a smORF searching strategy combined with three proteomic assays, of which five were annotated as ribosomal proteins, one as RNA polymerase subunit, and one as acetohydroxy acid isomeroreductase. We also suggested the possible functions of smORFs according to their expression pattern and discovered two neighboring and homologous smORFs. All these results will expand our knowledge of smORFs-encoded microproteins and their relation to the stress response of extremophilic microorganisms. This article is protected by copyright. All rights reserved.

CyanoMapDB: a database integrating experimentally validated protein-protein interactions in cyanobacteria

As one of the essential life forms in the biosphere, research on cyanobacteria has been growing remarkably for decades. Biological functions in organisms are often accomplished through protein-protein interactions (PPIs), which help to regulate interacting proteins or organize them into an integral machine. However, the study of PPIs in cyanobacteria falls far behind that in mammals and has not been integrated for ease of use. Thus, we built CyanoMapDB (http://www.cyanomapdb.msbio.pro/), a database providing cyanobacterial PPIs with experimental evidence, consisting of 52,304 PPIs among 6,789 proteins from 23 cyanobacterial species. We collected available data in UniProt, STRING, and IntAct, and mined numerous PPIs from co-fractionation MS data in cyanobacteria. The integrated data are accessible in CyanoMapDB (http://www.cyanomapdb.msbio.pro/), enabling users to easily query proteins of interest, investigate interacting proteins with evidence from different sources, and acquire a visual network of the target protein. We believe that CyanoMapDB will promote research involved with cyanobacteria and plants.

Microprotein Dysregulation in the Serum of Patients with Atrial Fibrillation

The incidence rate of atrial fibrillation (AF) has stayed at a high level in recent years. Despite the intensive efforts to study the pathologic changes of AF, the molecular mechanism of disease development remains unclarified. Microproteins are ribosomally translated gene products from small open reading frames (sORFs) and are found to play crucial biological functions, while remain rare attention and indistinct in AF study. In this work, we recruited 65 AF patients and 65 healthy subjects for microproteomic profiling. By differential analysis and cross-validation between independent datasets, a total of 4 microproteins were identified as significantly different, including 3 annotated ones and 1 novel one. Additionally, we established a diagnostic model with either microproteins or global proteins by machine learning methods and found the model with microproteins achieved comparable and excellent performance as that with global proteins. Our results confirmed the abnormal expression of microproteins in AF and may provide new perspectives on the mechanism study of AF.

Identification and analysis of short open reading frame encoded peptides in different regions of mouse brain

Short open reading frame-encoded peptides (SEPs) are generally 2-100 amino acids in length and participate in various biological processes of the organism. The brain is the central hub of life activities, where different regions perform distinct functions. To characterize SEPs in brain regions, we analyzed SEPs in five mouse brain areas, including hippocampus, frontal cortex, temporal cortex, occipital cortex, and parietal cortex, with mass spectrometry-based proteomics. We obtained 1,095 proteins with less than 100 amino acids and identified 373 SEPs. Approximately 83% of these SEPs are reported for the first time. Half of them are encoded by ncRNA, and nearly one-third can find orthology across species. Specific SEPs were identified in each brain region. For example, IP_1018875 was identified in the frontal cortex, possibly related to autophagy and neuronal signaling. These results enrich the proteome of the mouse brain and help facilitate subsequent studies on the function of SEPs.

[Etiological diagnostic value of metagenomic next-generation sequencing in peritoneal dialysis-related peritonitis]

Objective: To explore the etiological diagnostic value of metagenomic next-generation sequencing (mNGS) in peritoneal dialysis (PD)-related peritonitis. Methods: The study was a retrospective cohort study. The clinical data of patients with PD-related peritonitis who were treated and underwent microbial cultivation and mNGS test at the same time from June 2020 to July 2021 in the Affiliated Drum Tower Hospital, Medical School of Nanjing University were analyzed. The positive rate, detection time and consistency between mNGS test and traditional microbial culture were compared. Results: A total of 18 patients with age of (50.4±15.4) years old and median dialysis time of 34.0 (12.4, 62.0) months were enrolled in the study, including 11 males and 7 females. Pathogenic microorganisms were isolated in 17 patients by mNGS test, with a positive rate of 17/18, which was higher than 13/18 of microbial culture, but the difference was not statistically significant (P=0.219). Both mNGS test and microbial culture isolated positive pathogenic bacteria in 12 patients, and mNGS test isolated the same types of pathogenic bacteria as microbial cultivation did in 11 patients. In five patients with negative microbial culture, mNGS test also isolated pathogenic microorganisms, including 3 cases of Staphylococcus epidermidis, 1 case of Mycobacterium tuberculosis and 1 case of Ureaplasma urealyticum. In 1 patient, microbial culture isolated pathogenic bacteria (Escherichia coli) whereas mNGS test did not. The detection time of mNGS was 25.0 (24.0, 27.0) h, which was significantly shorter than 89.0 (72.8, 122.0) h of microbial culture (Z=3.726, P<0.001). Conclusions: mNGS test can improve the detection rate of pathogenic microorganisms in PD-related peritonitis and greatly shorten the detection time, and has good consistency with microbial culture. mNGS may provide a new approach for pathogen identification of PD-related peritonitis, especially refractory peritonitis.

Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803

Synechocystis sp. PCC 6803 (hereafter: Synechocystis) is a model organism for studying photosynthesis, energy metabolism, and environmental stress. Although known as the first fully sequenced phototrophic organism, Synechocystis still has almost half of its proteome without functional annotations. In this study, by using co-fractionation coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS), we define 291 multi-protein complexes, encompassing 24,092 protein-protein interactions (PPIs) among 2062 distinct gene products. This information not only reveals the roles of photosynthesis in metabolism, cell motility, DNA repair, cell division, and other physiological processes, but also shows how protein functions vary from bacteria to higher plants due to changes in interaction partners. It also allows us to uncover the functions of hypothetical proteins, such as Sll0445, Sll0446, and Sll0447 involved in photosynthesis and cell motility, and Sll1334 involved in regulation of fatty acid biogenesis. Here we present the most extensive PPI data for Synechocystis so far, which provide critical insights into fundamental molecular mechanisms in cyanobacteria.

Identification of Microproteins in Saccharomyces cerevisiae under Different Stress Conditions

Small open reading frame-encoded peptides (SEPs) are microproteins with a length of 100 amino acids or less, which may play a critical role in maintaining cell homeostasis under stress. Therefore, we used mass spectrometry-based proteomics to explore microproteins potentially involved in cellular stress responses in Saccharomyces cerevisiae. A total of 225 microproteins with 1920 unique peptides were identified under six culture conditions: normal, oxidation, starvation, ultraviolet radiation, heat shock, and heat shock with starvation. Among these microproteins, we found 70 SEPs with 75 unique peptides. The annotated microproteins are involved in stress-related processes, such as cell redox reactions, cell wall modification, protein folding and degradation, and DNA damage repair. It suggests that SEPs may also play similar functions under stress conditions. For example, SEP IP_008057, translated from a short coding sequence of YJL159W, may play a role in heat shock. This study identified stress-responsive SEPs in S. cerevisiae and provided valuable information to determine the functions of these proteins, which enrich the genome and proteome of S. cerevisiae and show clues to improving the stress tolerance of S. cerevisiae.

Proteome-wide analysis of stress response to temperature in Sulfolobus islandicus

Sulfolobus islandicus is thermophilic archaea that live in an extreme environment of 75 °C-80 °C and pH 2-3. Currently, the molecular mechanism of archaeal adaptation to high temperatures and the stability of proteins at high temperatures are still unclear. This study utilizes proteomics to analyze the differential expression of S. islandicus proteins at different temperatures. We found that ribosomes, glycolysis, nucleotide metabolism, RNA metabolism, transport system, and sulfur metabolism are all affected by temperature. Methylation modification of some proteins changed with temperature. Thermal proteome profiling (TPP) was used to analyze the thermal stability of proteins under 65 °C-85 °C growth conditions. It is suggested that the T_m values of proteins are mainly distributed around the optimum growth temperature (OGT). The proteins in the glycolysis pathway had high thermal stability. Meanwhile, proteins related to DNA replication and translation showed low thermal stability. The protein thermal stability of S. islandicus cultured under 65 °C and 85 °C was higher than that of 75 °C. Our study reveals that S. islandicus may adapt to temperature changes by regulating protein synthesis and carbon metabolism pathways, changing post-translational modifications, and improving protein stability at the same time. SIGNIFICANCE: The molecular mechanism of archaeal adaptation to high temperatures and the stability of proteins at high temperatures are still unclear. Our proteomics study identified 477 differentially expressed proteins of S. islandicus at different temperatures, suggesting that ribosomes, glycolysis, nucleotide metabolism, RNA metabolism, transport system, and sulfur metabolism are affected by temperature. Meanwhile, we found that methylation modification of some proteins changed with temperature. To evaluate the thermal stability of the proteome, we performed thermal proteome profiling to analyze the Tm of proteins under 65 °C-85 °C growth conditions. T_m values of proteins are mainly distributed around the optimum growth temperature. The proteins in the glycolysis pathway had high thermal stability. Meanwhile, proteins related to DNA replication and translation showed low thermal stability. Our study reveals that S. islandicus may adapt to temperature changes by regulating protein synthesis and carbon metabolism pathways, changing post-translational modifications, and improving protein stability at the same time.

Proteomic-driven identification of short open reading frame-encoded peptides

Accumulating evidence has shown that a large number of short open reading frames (sORFs) also have the ability to encode proteins. The discovery of sORFs opens up a new research area, leading to the identification and functional study of sORF encoded peptides (SEPs) at the omics level. Besides bioinformatics prediction and ribosomal profiling, mass spectrometry (MS) has become a significant tool as it directly detects the sequence of SEPs. Though MS-based proteomics methods have proved to be effective for qualitative and quantitative analysis of SEPs, the detection of SEPs is still a great challenge due to their low abundance and short sequence. To illustrate the progress in method development, we described and discussed the main steps of large-scale proteomics identification of SEPs, including SEP extraction and enrichment, MS detection, data processing and quality control, quantification, and function prediction and validation methods. This article is protected by copyright. All rights reserved.

Comparative Network Biology Discovers Protein Complexes That Underline Cellular Differentiation in Anabaena sp

The filamentous cyanobacterium Anabaena sp. PCC 7120 can differentiate into heterocysts to fix atmospheric nitrogen. During cell differentiation, cellular morphology and gene expression undergo a series of significant changes. To uncover the mechanisms responsible for these alterations, we built protein–protein interaction (PPI) networks for these two cell types by cofractionation coupled with mass spectrometry. We predicted 280 and 215 protein complexes, with 6322 and 2791 high-confidence PPIs in vegetative cells and heterocysts, respectively. Most of the proteins in both types of cells presented similar elution profiles, whereas the elution peaks of 438 proteins showed significant changes. We observed that some well-known complexes recruited new members in heterocysts, such as ribosomes, diflavin flavoprotein, and cytochrome c oxidase. Photosynthetic complexes, including photosystem I, photosystem II, and phycobilisome, remained in both vegetative cells and heterocysts for electron transfer and energy generation. Besides that, PPI data also reveal new functions of proteins. For example, the hypothetical protein Alr4359 was found to interact with FraH and Alr4119 in heterocysts and was located on heterocyst poles, thereby influencing the diazotrophic growth of filaments. The overexpression of Alr4359 suspended heterocyst formation and altered the pigment composition and filament length. This work demonstrates the differences in protein assemblies and provides insight into physiological regulation during cell differentiation.

•

PPIs in two types of cells of Anabaena sp. 7120 were systematically identified.

•

10,302 and 8557 high-confidence PPIs were obtained and over 80% were novel.

•

About 438 proteins showed significant changes in vegetative cells and heterocysts.

•

Protein Alr4359 was found to influence the diazotrophic growth of filaments.

Systematic Identification of Microproteins during the Development of Drosophila melanogaster

Short open reading frame-encoded peptides (SEPs) are microproteins with less than 100 amino acids that play an essential role in the growth and development of organisms. There are plenty of short open reading frames in Drosophila melanogaster that potentially code polypeptides. We chose 11 time points during the life cycle of Drosophila to investigate microproteins, particularly those related to development. Finally, we identified a total of 410 microproteins, of which 27 were noncoding RNA-encoded proteins. Of the 410 microproteins, 74 were expressed in all stages from embryo to adults, whereas 300 microproteins were only found in one or two time points. Approximately, one-third of the microproteins were not reported previously and 44 were obtained from de novo sequencing, validated by synthetic peptides. These microproteins are related to the main bioprocesses of growth and development, such as multicellular organism reproduction, postmating behavior, and oviposition. Over half of the microproteins have predicted functional domains and are conserved across species, suggesting that these microproteins have critical functions in fly development. This work enriches the D. melanogaster proteome and provides a significant data resource for growth and development research.

[Effect of Echinococcus granulosus hydatid cyst fluid protein on allergic rhinitis induced by ovalbumin in mice]

OBJECTIVE

To investigate the protective effect of Echinococcus granulosus hydatid cyst fluid protein (HCFP) on ovalbumin (OVA)-induced allergic rhinitis (AR) in mice.

METHODS

Twenty-four BALB/c mice at ages of 8 to 10 weeks, each weighing approximately 20 g, were randomly divided into four groups, including groups A (blank control group), B (blank intervention group), C (AR model group) and D (AR+HCFP intervention group), with 6 mice in each group. On days 0, 2, 4, 6, 8, 10 and 12, mice in groups A, B, C and D were injected with 200 μL sterile phosphate buffered saline (PBS), 200 μL sterile PBS containing 20 μg HCFP, 200 μL sterile PBS containing 50 μg OVA and 5 mg Al(OH)₃ gel, and 200 μL sterile PBS containing 50 μg OVA, 5 mg Al(OH)₃ gel and 20 μg HCFP, respectively. On days 14 to 20, mice in groups A, B, C and D were administered with 40 μL sterile PBS, 40 μL sterile PBS containing 20 μg HCFP, 40 μL sterile PBS containing 2 mg OVA and 40 μL sterile PBS containing 2 mg OVA and 20 μL HCFP by nasal drop, respectively. Mouse behavioral changes were observed and behavioral scores were estimated. The serum levels of interferon-γ (IFN-γ), interleukin-4 (IL-4), IL-5, IL-10, transforming growth factor-β (TGF-β) and OVA-specific IgE antibody (OVA-sIgE) were measured using enzyme-linked immunosorbent assay (ELISA), and the pathological changes of mouse nasal mucosa were observed by hematoxylin and eosin (HE) staining.

RESULTS

The mean behavioral score was significantly greater in Group C (6.83 ± 0.50) than in groups A (1.17 ± 0.52) and B (1.33 ± 0.52) (P < 0.05), while a lower mean behavioral score was estimated in Group D (3.50 ± 0.50) than in Group C (P < 0.05). There were significant differences among the groups in terms of serum IFN-γ (F = 4.08, P < 0.05), IL-4 (F = 275.90, P < 0.05), IL-5 (F = 96.82, P < 0.05), IL-10 (F = 77.67, P < 0.05), TGF-β (F = 9.98, P < 0.05) and OVA-sIgE levels (F = 44.69, P < 0.05). The serum IFN-γ level was significantly lower in Group C than in groups A, B and C (P < 0.05), and the serum levels of IL-4, IL-5 and OVA-sIgE were significantly higher in Group C than in groups A, B and C (P < 0.05), while the serum IL-10 and TGF-β levels were significantly greater in Group D than in Group C (P < 0.05). Microscopy showed apparent loss of nasal mucosa cilia, increased number and enlargement of goblet cells, interstitial edema and submucous vascular dilation in Group C, while the pathological changes of nasal mucosa were alleviated in Group D relative to Group C.

CONCLUSIONS

E. granulosus HCFP has a protective activity against OVA-induced allergic rhinitis in mice.

Identification of Microproteins in Hep3B Cells at Different Cell Cycle Stages

Microproteins are generated from small open reading frames and turn out to play various vital biological functions. As an essential biological event of eukaryotic cells, the cell cycle is involved in cell replication and division. For such a highly regulated event, microproteins associated with cell cycle regulation remained unclarified. Utilizing a combination of bottom-up and top-down proteomics, we analyzed microproteins at specific cell cycle stages of Hep3B cells. A total of 657 microproteins were identified under three cell cycle stages, including 151 in the G0/G1 stage, 163 in the S stage, and 132 in the G2/M stage. The annotation of these microproteins showed their cell cycle-specific functions, such as translation, nuclear assembly, chromatin organization, and the G2/M transition of the mitotic cell cycle. Meanwhile, more than 50% of identified microproteins were ncRNA-encoded. These nonannotated novel microproteins contain several function domains, such as the nucleoside diphosphate kinase domain, the high mobility group domain, and the DNA-binding domain. This suggested the potential functions of these novel microproteins in specific cell cycle stages. This study presented a large-scale profile of microproteins at different cell cycle stages from Hep3B and may provide new perspectives on the regulation mechanism of the cell cycle. Liquid chromatography-mass spectrometry data were deposited to ProteomeXchange using the identifier PXD030286.

Ginseng berry concentrate prevents colon cancer via cell cycle, apoptosis regulation, and inflammation-linked Th17 cell differentiation

The Asian ginseng root (Panax ginseng C.A. Meyer) is a very commonly used herbal medicine worldwide. Ginseng fruit, including the berry (or pulp) and seed, is also valuable for several health conditions including immunostimulation and cancer chemoprevention. In this study, the anticancer and anti-proliferative effects of the extracts of ginseng berry and seed were evaluated. The ginsenosides in the ginseng berry concentrate (GBC) and ginseng seed extract (GSE) were analyzed. We then evaluated their anti-colorectal cancer potentials, including antiproliferation, cell cycle arrest, and apoptotic induction. Further investigation consisted of the berry's adaptive immune responses, such as the actions on the differentiation of T helper cells Treg, Th1, and Th17. The major constituents in GBC were ginsenosides Re and Rd, which can be compared to those in the root. The GBC significantly inhibited colon cancer cell growth, and its anti-proliferative effect involved mechanisms including G2/M cell cycle arrest via upregulation of cyclin A and induction of apoptosis via regulation of apoptotic related gene expressions. GBC also downregulated the expressions of pro-inflammatory cytokine genes. For the adaptive immune responses, GBC did not influence Th1 and Treg cell differentiation but significantly inhibited Th17 cell differentiation and thus regulated the balance of Th17/Treg for adaptive immunity. Although no ginsenoside was detected in the GSE, interestingly, it obviously enhanced colon cancer cell proliferation with the underlined details to be determined. Our results suggested that GBC is a promising dietary supplement for cancer chemoprevention and immunomodulation.

Mapping Microproteins and ncRNA-Encoded Polypeptides in Different Mouse Tissues

Small open reading frame encoded peptides (SEPs), also called microproteins, play a vital role in biological processes. Plenty of their open reading frames are located within the non-coding RNA (ncRNA) range. Recent research has demonstrated that ncRNA-encoded polypeptides have essential functions and exist ubiquitously in various tissues. To better understand the role of microproteins, especially ncRNA-encoded proteins, expressed in different tissues, we profiled the proteomic characterization of five mouse tissues by mass spectrometry, including bottom-up, top-down, and de novo sequencing strategies. Bottom-up and top-down with database-dependent searches identified 811 microproteins in the OpenProt database. De novo sequencing identified 290 microproteins, including 12 ncRNA-encoded microproteins that were not found in current databases. In this study, we discovered 1,074 microproteins in total, including 270 ncRNA-encoded microproteins. From the annotation of these microproteins, we found that the brain contains the largest number of neuropeptides, while the spleen contains the most immunoassociated microproteins. This suggests that microproteins in different tissues have tissue-specific functions. These unannotated ncRNA-coded microproteins have predicted domains, such as the macrophage migration inhibitory factor domain and the Prefoldin domain. These results expand the mouse proteome and provide insight into the molecular biology of mouse tissues.

Effective Model of Food Allergy in Mice Sensitized with Ovalbumin and Freud's Adjuvant

To better explore the pathophysiology of FA and its therapy, we aimed to establish a simple and practicable FA model with Freund's adjuvant and introduce an easy and reliable laboratory evaluation method for assessment of inflammation in intestinal segments at different anatomical locations. BALB/c mice were sensitized with ovalbumin combined with Freund's adjuvant. Complete Freund's adjuvant was chosen for the first sensitization and two weeks later incomplete Freund's adjuvant was used for a second sensitization. Two weeks later, the sensitized mice were challenged with 50 mg ovalbumin every other day. After the 6 challenge, all mice were assessed for systemic anaphylaxis, and then sacrificed for sample collection. All sensitized mice showed anaphylactic symptoms and markedly increased levels of serum ovalbumin-specific IgE and IgG1. The activity of mast cell protease-1 (mMCPT-1) was significantly increased in the serum and interstitial fluid of the duodenum, jejunum, ileum, and colon. A successful FA model was established, of which inflammation occurred in the duodenum, jejunum, ileum, and colon. This model provides a reliable and simple tool for analysis of the mechanism of FA and methods of immunotherapy. Moreover, combined detection of ovalbumin-specific antibody and local mMCPT-1 levels could potentially be used as the major indicator for assessment of food allergy.

Improved Identification of Small Open Reading Frames Encoded Peptides by Top-Down Proteomic Approaches and De Novo Sequencing

Small open reading frames (sORFs) have translational potential to produce peptides that play essential roles in various biological processes. Nevertheless, many sORF-encoded peptides (SEPs) are still on the prediction level. Here, we construct a strategy to analyze SEPs by combining top-down and de novo sequencing to improve SEP identification and sequence coverage. With de novo sequencing, we identified 1682 peptides mapping to 2544 human sORFs, which were all first characterized in this work. Two-thirds of these new sORFs have reading frame shifts and use a non-ATG start codon. The top-down approach identified 241 human SEPs, with high sequence coverage. The average length of the peptides from the bottom-up database search was 19 amino acids (AA); from de novo sequencing, it was 9 AA; and from the top-down approach, it was 25 AA. The longer peptide positively boosts the sequence coverage, more efficiently distinguishing SEPs from the known gene coding sequence. Top-down has the advantage of identifying peptides with sequential K/R or high K/R content, which is unfavorable in the bottom-up approach. Our method can explore new coding sORFs and obtain highly accurate sequences of their SEPs, which can also benefit future function research.

Identification and analysis of small proteins and short open reading frame encoded peptides in Hep3B cell

The small proteins and short open reading frames encoded peptides (SEPs) are of fundamental importance because of their essential roles in biological processes. However, the annotation or identification of them is challenging, in part owing to the limitation of the traditional genome annotation pipeline and their inherent characteristics of low abundance and low molecular weight. To discover and characterize SEPs in Hep3B cell line, we developed an optimized peptidomic assay by combining different peptide extraction and separation methods. The organic solvent precipitation method in peptidomic showed promotion in the enrichment of low molecular proteins or peptides, and the data clearly showed a beneficial effect from the reduction of sample complexity, resulting in high-quality MS/MS spectra. Furthermore, different strategies exhibited good complementarity in improving the total amount of small proteins and their sequence coverage. In total, 1192 proteins within less than 100 amino acids were identified, including 271 newly discovered SEPs that been annotated in the OpenProt database and 147 SEPs of them encoded from ncRNA or lincRNA. Results in this work provide robust evidence to date that the human proteome is more complicated than previously appreciated, and this will be a benefit to discoveries of proteins without function annotation. SIGNIFICANCE: In this work, methods were optimized to identify SEPs in Hep3B. The organic solvent precipitation presents promotion in enrichment of low molecular proteins or peptides, and the data clearly showed a beneficial effect from the reduction of sample complexity, resulting in high quality MS/MS spectra. Different strategies exhibited good complementarity in improving total amount of small proteins and their sequence coverage. In total, 1192 proteins within less than 100 amino acids were identified, including 271 newly discovered SEPs that been annotated in the OpenProt database and 147 SEPs of them encoded from ncRNA or lincRNA. Furthermore, 22 SEPs generated from the uORF may has potential effect in translation control, and 149 newly identified SEPs have known functional domains or cross-species conservation. Results in this work present robust evidence for the coding potential of the ignored region of human genomes and may provide additional insights into tumor biology.

Archaeal Chromatin Proteins Cren7 and Sul7d Compact DNA by Bending and Bridging

Archaeal chromatin proteins Cren7 and Sul7d from Sulfolobus are DNA benders. To better understand their architectural roles in chromosomal DNA organization, we analyzed DNA compaction by Cren7 and Sis7d, a Sul7d family member, from Sulfolobus islandicus at the single-molecule (SM) level by total single-molecule internal reflection fluorescence microscopy (SM-TIRFM) and atomic force microscopy (AFM). We show that both Cren7 and Sis7d were able to compact singly tethered λ DNA into a highly condensed structure in a three-step process and that Cren7 was over an order of magnitude more efficient than Sis7d in DNA compaction. The two proteins were similar in DNA bending kinetics but different in DNA condensation patterns. At saturating concentrations, Sis7d formed randomly distributed clusters whereas Cren7 generated a single and highly condensed core on plasmid DNA. This observation is consistent with the greater ability of Cren7 than of Sis7d to bridge DNA. Our results offer significant insights into the mechanism and kinetics of chromosomal DNA organization in Crenarchaea.IMPORTANCE A long-standing question is how chromosomal DNA is packaged in Crenarchaeota, a major group of archaea, which synthesize large amounts of unique small DNA-binding proteins but in general contain no archaeal histones. In the present work, we tested our hypothesis that the two well-studied crenarchaeal chromatin proteins Cren7 and Sul7d compact DNA by both DNA bending and bridging. We show that the two proteins are capable of compacting DNA, albeit with different efficiencies and in different manners, at the single molecule level. We demonstrate for the first time that the two proteins, which have long been regarded as DNA binders and benders, are able to mediate DNA bridging, and this previously unknown property of the proteins allows DNA to be packaged into highly condensed structures. Therefore, our results provide significant insights into the mechanism and kinetics of chromosomal DNA organization in Crenarchaeota.

A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies

Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes.

EPIC: software toolkit for elution profile-based inference of protein complexes

Protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We and others previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to precision mass spectrometry analysis (chromatographic fractionation-mass spectrometry, CF-MS), but the resulting data are challenging to process and interpret. Here, we describe EPIC (elution profile-based inference of complexes), a software toolkit for automated scoring of large-scale CF-MS data to define high-confidence multi-component macromolecules from diverse biological specimens. As a case study, we used EPIC to map the global interactome of Caenorhabditis elegans, defining 612 putative worm protein complexes linked to diverse biological processes. These included novel subunits and assemblies unique to nematodes that we validated using orthogonal methods. The open source EPIC software is freely available as a Jupyter notebook packaged in a Docker container (https://hub.docker.com/r/baderlab/bio-epic/).

Evaluating the treatment effectiveness of copper-based algaecides on toxic algae Microcystis aeruginosa using single cell-inductively coupled plasma-mass spectrometry

Single cell-inductively coupled plasma-mass spectrometry (SC-ICP-MS) is an emerging technology. In this work, we have developed a novel SC-ICP-MS method to quantify metal ions in individual cells of a toxic cyanobacterial species, Microcystis aeruginosa (M. aeruginosa), without complicated post-dosing sample preparation, and applied this method to study the treatment effectiveness of copper-based algaecides (cupric sulfate and EarthTec®) on the toxic algae M. aeruginosa. The developed SC-ICP-MS method uses new intrinsic metal element magnesium to determine real transport efficiency and cell concentration. The cell viability and microcystin-LR release by algaecide treatment were studied by flow cytometry and ultra-fast liquid chromatography-tandem mass spectrometry, respectively. The results showed that this novel method was very rapid, highly sensitive (detection limits of intracellular copper and magnesium were 65 ag/cell and 98 ag/cell, respectively), and reproducible (relative standard deviation within 12%). The algaecide effectiveness study further demonstrated that copper in the forms of cupric sulfate and copper-based algaecide EarthTec® successfully diminished M. aeruginosa populations. The higher the copper concentration used to treat the cells, the faster the speeds of copper uptake and cell lysis in the copper concentrations ranged from 0 to 200 μg/L of copper-based algaecide. The cells exhibit obvious heterogeneity in copper uptake. The result suggests that M. aeruginosa cells uptake and cumulate copper followed by cellular lysis and microcystin-LR release. These novel results indicated that though the copper-based algaecides could control this type of harmful algal bloom, further treatment to remove the released algal toxin from the treated water would be needed.

Serum fatty acid patterns in patients with schizophrenia: a targeted metabonomics study

Previous studies have indicated that schizophrenia is linked to abnormal lipid metabolism. Free fatty acids (FFAs) in peripheral blood can reflect the status of lipid metabolism in human body. The purpose of this study was to scan the FFA pattern and elucidate the characteristics of lipid metabolic abnormality in schizophrenia patients. One hundred and ten patients with schizophrenia (SCZs) and 109 healthy controls (HCs) were included in the study and divided into a discovery set and a validation set. Forty-seven serum FFAs were detected by UPLC-QTOF-MS and 39 of them were absolutely quantified by establishing standard curves. Monounsaturated fatty acids (MUFAs) and ω-6 polyunsaturated fatty acids (ω-6 PUFAs) were significantly increased in SCZs compared with HCs. Desaturation from saturated fatty acids to MUFAs and β-oxidation were enhanced, as estimated by the ratios of products to precursors. These results suggest that lipolysis and β-oxidation are upregulated in SCZ, presumably resulting from insufficient brain energy supply.

Adverse impact of intermittent portal clamping on long-term postoperative outcomes in hepatocellular carcinoma

Introduction To evaluate the impact of intermittent portal clamping (IPC) on long-term postoperative outcomes in patients with hepatocellular carcinoma (HCC). Methods Clinical records of 355 patients underwent curative liver resection for HCC in January 2007 to December 2010 were retrospectively reviewed. According to how portal clamping was performed, patients were grouped as: IPC, n=113; other portal clamping (OPC), n=190; and no portal clamping (NPC), n=52. Results Median recurrence-free survival (RFS) was statistically significantly shorter in the IPC (39.4 months) than OPC (47.3 months, p=0.010) and NPC groups (51.4 months, p=0.008). Median overall survival (OS) was also significantly shorter with IPC (46.3 months), versus 52.9 months with OPC (p=0.022) and 56.2 months with NPC (p=0.015). Kaplan-Meier survival analysis revealed that 5-year cumulative RFS was much lower in the IPC (42.5%) than OPC (50.9%, p=0.014) and NPC groups (49.6%, p=0.013). Five-year cumulative OS was also much lower in the IPC (44.9%) than OPC (58.0%, p=0.020) and NPC groups (57.7%, p=0.025). On univariate analysis, tumour grade, size and number, TNM stage, blood transfusion, vascular invasion and IPC were significantly inversely correlated with RFS and OS. On multivariate analysis, tumour size and number, blood transfusion, vascular invasion and IPC remained significant. Conclusions Our study suggests that IPC is an independent risk factor for poor long-term postoperative outcomes in patients with HCC.

Study of the Role of Transforming Growth Factor β-1 in Organ Damage Protection in Porcine Model of Brain Death

BACKGROUND

From the medical and ethical points of view, donation after brain death is a more acceptable organ source than that from a living donor because it has the advantage of providing multiple organs from a single donor source. Hence, it has become a more promising field of research which focuses on the protection of organs at brain death Here we investigated the role of transforming growth factor (TGF)-β1 in a porcine model of brain death.

METHODS

A porcine model of brain death was established by increasing the intracranial pressure (ICP) after which TGF-β1 was monitored by immunofluorescence at the following time points: before ICP was performed (t1), at brain death (t2), and at 3 (t3), 6 (t4), 9 (t5), and 18 (t6) hours after brain death. The data were analyzed using the fixed effect regression method and the correlation between the results was determined by Pearson analysis.

RESULTS

Our results showed that there was a significant increase in the levels of TGF-β1 (P < .05), urea (P < .01), creatinine (P < .01), and aspartate aminotransferase (AST; P < .01) during the 18-hour brain death process. There were negative correlations between TGF-β1 and urea, creatinine, alanine aminotransferase, AST, and total bilirubin. The negative correlations between TGF-β1 and creatinine and AST achieved statistical significance (P < .05).

CONCLUSIONS

These findings taken together confirm that significant damages are caused to the myocardial fiber cell and kidney glomerulus during brain death process, and that TGF-β1 is associated with the protection of these organs.

Computed tomography-guided percutaneous microwave ablation treatment for lung metastases from nasopharyngeal carcinoma

BACKGROUND

The objective of this retrospective study was to evaluate the safety and efficacy of percutaneous microwave ablation (MWA) for treating lung metastases from nasopharyngeal carcinoma (NPC).

PATIENTS AND METHODS

From December 2012 to November 2014, 17 patients (15 males, and two females, averaged 45.7 years old) with lung metastases from NPC accepted computed tomography (CT)-guided percutaneous MWA. The average number of lung metastases was 1.7 (range: 1-4), and the biggest tumor diameter was 4.2 cm (range: 0.8-4.2 cm). Nineteen nodules located in the right lung and 10 nodules located in the left lung. A total of 29 ablation sites were performed to 29 lung metastases in 22 MWA sessions. Postoperative assessments of complete tumor necrosis rate, safety, local tumor progression, and survival period were carried out.

RESULTS

Of the 29 lesions, complete response was achieved for 27 lesions; residual tumor was found in one lesion 3 months postoperatively; and another lesion was found enlarged 3-month postoperatively with obvious enhancement. Four patients had a small amount of postoperative parenchyma bleeding and two patients had a small amount of pneumothorax. Six months after MWA treatment, new metastatic lesions appeared in six patients, five patients had new metastatic lesions inside the lung, and the other patient had metastatic lesions in the thoracic vertebra. The time for the appearance of new pulmonary metastases for the five patients was 4-20 months, averaged 7.2 months.

CONCLUSION

CT-guided MWA is a promising treatment alternative for local tumor control in selected patients with lung metastases from NPC.

An Unbiased Chemical Proteomics Method Identifies FabI as the Primary Target of 6-OH-BDE-47

Determination of the physical interactions of environmental chemicals with cellular proteins is important for characterizing biological and toxic mechanism of action. Yet despite the discovery of numerous bioactive natural brominated compounds, such as hydroxylated polybrominated diphenyl ethers (OH-PBDEs), their corresponding protein targets remain largely unclear. Here, we reported a systematic and unbiased chemical proteomics assay (Target Identification by Ligand Stabilization, TILS) for target identification of bioactive molecules based on monitoring ligand-induced thermal stabilization. We first validated the broad applicability of this approach by identifying both known and unexpected proteins bound by diverse compounds (anticancer drugs, antibiotics). We then applied TILS to identify the bacterial target of 6-OH-BDE-47 as enoyl-acyl carrier protein reductase (FabI), an essential and widely conserved enzyme. Using affinity pull-down and in vitro enzymatic assays, we confirmed the potent antibacterial activity of 6-OH-BDE-47 occurs via direct binding and inhibition of FabI. Conversely, overexpression of FabI rescued the growth inhibition of Escherichia coli by 6-OH-BDE-47, validating it as the primary in vivo target. This study documents a chemical proteomics strategy for identifying the physical and functional targets of small molecules, and its potential high-throughput application to investigate the modes-of-action of environmental compounds.

Free Nano-Object Ramsey Interferometry for Large Quantum Superpositions

We propose an interferometric scheme based on an untrapped nano-object subjected to gravity. The motion of the center of mass (c.m.) of the free object is coupled to its internal spin system magnetically, and a free flight scheme is developed based on coherent spin control. The wave packet of the test object, under a spin-dependent force, may then be delocalized to a macroscopic scale. A gravity induced dynamical phase (accrued solely on the spin state, and measured through a Ramsey scheme) is used to reveal the above spatially delocalized superposition of the spin-nano-object composite system that arises during our scheme. We find a remarkable immunity to the motional noise in the c.m. (initially in a thermal state with moderate cooling), and also a dynamical decoupling nature of the scheme itself. Together they secure a high visibility of the resulting Ramsey fringes. The mass independence of our scheme makes it viable for a nano-object selected from an ensemble with a high mass variability. Given these advantages, a quantum superposition with a 100 nm spatial separation for a massive object of 10^{9}  amu is achievable experimentally, providing a route to test postulated modifications of quantum theory such as continuous spontaneous localization.

The Role of miR-124 in Drosophila Alzheimer's Disease Model by Targeting Delta in Notch Signaling Pathway

Alzheimer's disease (AD) is a neurodegenerative disorder which mainly affects elderly population. MicroRNAs (miRNA) are small RNA molecules that fine-tune gene expression at posttranscriptional level and exert important functions in AD. MicroRNA-124 (miR-124) is a kind of miRNA abundantly expressed in the central nervous system. It is highly conserved from Caenorhabditis elegans to humans. However, its function in AD is still elusive. In this study, we found miR-124 was significantly down-regulated in AD flies. miR-124 mutant flies showed impaired climbing ability and shortened lifespan. In contrast, miR-124 expression rescued locomotive defects of AD flies. Using microarray analysis to test gene expression profiles of miR-124 mutant flies, we found that Notch signaling pathway was potentially targeted by miR-124. Further experiments showed that miR-124 regulated Notch ligand Delta expression by acting on specific site of Delta 3`UTR. In addition, reduced Delta expression by RNA interference extended lifespan and ameliorated learning defects of AD Drosophila. Notch inhibitor DAPT could also alleviate AD phenotypes, which confirmed our findings. In conclusion, our study indicates that miR-124 plays neuroprotective roles in AD Drosophila by targeting Delta in Notch signaling pathway, which helps further our understanding of miRNAs in the molecular pathology of AD.

Measurement of Shear Viscosity and Solubility of Polystyrene Melts Containing Various Blowing Agents

This article presents measured data on shear viscosity and solubility of HCFC-142b and HFC-134a/ethanol blowing agent laden polystyrene melts at different temperatures. This study establishes the baseline for more novel and innovative blowing agent systems to replace HCFC-142b. The shear viscosity is measured using a helical barrel rheometer. Apparent solubility is determined by observing the onset of gas bubble presence or absence in a specially designed optical cell with sapphire windows using a microscope–CCD camera–monitor/recorder system. The article presents a selection of viscosity and solubility data and, where possible, compares them with measurements carried out by others. The dynamic methods of measuring solubility and viscosity of gas laden polymer melts used in this study are closer to the polymer foam manufacturing practice.

Minimally Invasive Cardiac Output Monitoring: Agreement of Oesophageal Doppler, LiDCOrapid™ and Vigileo FloTrac™ Monitors in Non-Cardiac Surgery

There is lack of data about the agreement of minimally invasive cardiac output monitors, which make it impossible to determine if they are interchangeable or differ objectively in tracking physiological trends. We studied three commonly used devices: the oesophageal Doppler and two arterial pressure–based devices, the Vigileo FloTrac™ and LiDCOrapid™. The aim of this study was to compare the agreement of these three monitors in adult patients undergoing elective non-cardiac surgery. Measurements were taken at baseline and after predefined clinical interventions of fluid, metaraminol or ephedrine bolus. From 24 patients, 131 events, averaging 5.2 events per patient, were analysed. The cardiac index of LiDCOrapid versus FloTrac had a mean bias of −6.0% (limits of agreement from −51% to 39%) and concordance of over 80% to the three clinical interventions. The cardiac index of Doppler versus LiDCOrapid and Doppler versus FloTrac, had an increasing negative bias at higher mean cardiac outputs and there was significantly poorer concordance to all interventions. Of the preload-responsive parameters, Doppler stroke volume index, Doppler systolic flow time and FloTrac stroke volume variation were fair at predicting fluid responsiveness while other parameters were poor. While there is reasonable agreement between the two arterial pressure–derived cardiac output devices (LiDCOrapid and Vigileo FloTrac), these two devices differ significantly to the oesophageal Doppler technology in response to common clinical intraoperative interventions, representing a limitation to how interchangeable these technologies are in measuring cardiac output.

Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes

Our analysis examines the conservation of multiprotein complexes among metazoa through use of high resolution biochemical fractionation and precision mass spectrometry applied to soluble cell extracts from 5 representative model organisms Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Strongylocentrotus purpuratus, and Homo sapiens. The interaction network obtained from the data was validated globally in 4 distant species (Xenopus laevis, Nematostella vectensis, Dictyostelium discoideum, Saccharomyces cerevisiae) and locally by targeted affinity-purification experiments. Here we provide details of our massive set of supporting biochemical fractionation data available via ProteomeXchange (PXD002319-PXD002328), PPIs via BioGRID (185267); and interaction network projections via (http://metazoa.med.utoronto.ca) made fully accessible to allow further exploration. The datasets here are related to the research article on metazoan macromolecular complexes in Nature [1].