Differentially Abundant Proteins Research Articles

Effects of Liquid Nitrogen Freezing, Immersion Freezing, and Air Freezing on Properties of Perca fluviatilis Fillets and Analysis of Potential Protein Markers Based on Label-Free Proteomics

The effects of liquid nitrogen freezing (LNF), immersion freezing (IF), and air freezing (AF) combined with thawing in running water at 20°C on the quality of Perca fluviatilis fillets were investigated using label-free proteomics technology. The ice crystal equivalent diameter (12.30±0.33 μm) and ice crystal area ratio (7.61±2.81%) of LNF were significantly lower than IF and AF (P < 0.05). The ice crystals of LNF were small and evenly distributed, and the mechanical damage to the cell structure is small. LNF samples were closer to fresh samples regarding texture. Proteomic analysis identified a total of 11 differentially abundant proteins (DAPs) associated with LNF, IF, and AF. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these DAPs were primarily catalytic proteins, metabolic enzymes, and structural proteins involved in metabolic pathways such as pyruvate metabolism, glycolysis, and arginine and proline metabolism. Among them, tubulin beta chain (A0A8C3G6F1), carbonic anhydrase (A0A2P1JP97), immunoglobulin-like and fibronectin type III domain-containing protein 1 (A0A484DE91), and tubulin are predicted to serve as potential protein markers for freezing, thawing loss, hardness, and springiness of Perca fluviatilis fillets post-thawing. These findings provide a basis for further research into the quality change induced by protein degradation of frozen Perca fluviatilis.

Phosphorylation of 399S at CsHsp70 of Cymbidium sinense is essential to maintain chlorophyll stability

The Chinese orchids symbolise nobility and gentility in China, and the variation of leaf color makes Cymbidium sinense more diversified and valuable. However, its color variations especially at the protein level still remain largely unexplored. In this study, the proteomics and phosphoproteomics of Cymbidium sinense leaf color variation mutants were studied. A total of 1059 differentially abundant proteins (DAPs) and 1127 differentially abundant phosphorylation sites belonging to 644 phosphoproteins (DAPPs) were identified in the yellow section of leaf variegation mutant of Cymbidium sinense (MY) compared with the green section (MG). Moreover, 349 co-expressing proteins were found in both omics’ datasets, while only 26 proteins showed the same expression patterns in the two omics. The interaction network analysis of kinases and phosphatases showed that DAPs and DAPPs in photosynthesis, response to hormones, pigment metabolic process, phosphorylation, glucose metabolic process, and dephosphorylation might contribute to leaf color variation. The abundance of 28 Hsps and 28 phosphorylation sites belonging to 10 Hsps showed significant differences between MG and MY. CsHsp70 was selected to explore the function in Cymbidium sinense leaf variegation. The results showed CsHsp70 is essential for maintaining photosynthetic pigment content and the 399S phosphorylation site is crucial to the function of CsHsp70. Collectively, our findings construct a comprehensive coverage of protein and protein phosphorylation in leaf variegation of C. sinense, providing valuable insights into its formation mechanisms.

Proteomics profiling reveals the detoxification and tolerance behavior of two bread wheat (Triticum aestivum L.) varieties under arsenate stress

Arsenic (As) contaminated irrigation water caused a significant buildup of its level in the agricultural soil and edible tissues of wheat. High levels of As negatively impact grain quality, wheat yield, and human health consequently. It is still unknown how wheat varieties respond to As stress at the proteomic level. Therefore, the present study aimed to deliver mechanistic details regarding the role of proteins in tolerance mechanism against As stress. Two wheat varieties (BARANI-70 and NARC-2009) were exposed to arsenate treatment (200µM) in a hydroponic experiment to evaluate the impacts of arsenic stress using proteomics. Roots of both varieties were used for protein extraction, digestion, and LC-MS/MS analysis to identify differentially abundant proteins (DAPs). Furthermore, various bioinformatic tools were used to study subcellular localization, functional categories, and pathway analysis. The findings identified 67 DAPs in BARANI-70 (up-regulated=56; down-regulated=11) and 89 DAPs in NARC-2009 (up-regulated=34; down-regulated=55). Subcellular localization revealed significant up-regulation of DAPs in mitochondria and chloroplast for BARANI-70 but down-regulation in NARC-2009 under As stress. Functional analysis revealed significant upregulation of DAPs for glutathione, peroxidase, glutathione peroxidase, lactoylglutathione lyase, and glutathione-s-transferase in BARANI-70. Pathway analysis showed regulation of DAPs involved in tetrapyrrole biosynthesis and glycolysis-TCA particularly in BARANI-70 compared to NARC-2009. Furthermore, BARANI-70 showed better growth response under As stress compared to NARC-2009. Thus, better synthesis of stress-responsive DAPs and important pathways in BARANI-70 contributed towards its tolerance against As stress. The present research supports the use of tolerant varieties and identified protein biomarkers to enhance crop resilience against As stress.

Physiological and Proteomic Analyses of mtn1 Mutant Reveal Key Players in Centipedegrass Tiller Development.

Tillering directly determines the seed production and propagation capacity of clonal plants. However, the molecular mechanisms involved in the tiller development of clonal plants are still not fully understood. In this study, we conducted a proteome comparison between the tiller buds and stem node of a multiple-tiller mutant mtn1 (more tillering number 1) and a wild type of centipedegrass. The results showed significant increases of 29.03% and 27.89% in the first and secondary tiller numbers, respectively, in the mtn1 mutant compared to the wild type. The photosynthetic rate increased by 31.44%, while the starch, soluble sugar, and sucrose contents in the tiller buds and stem node showed increases of 13.79%, 39.10%, 97.64%, 37.97%, 55.64%, and 7.68%, respectively, compared to the wild type. Two groups comprising 438 and 589 protein species, respectively, were differentially accumulated in the tiller buds and stem node in the mtn1 mutant. Consistent with the physiological characteristics, sucrose and starch metabolism as well as plant hormone signaling were found to be enriched with differentially abundant proteins (DAPs) in the mtn1 mutant. These results revealed that sugars and plant hormones may play important regulatory roles in the tiller development in centipedegrass. These results expanded our understanding of tiller development in clonal plants.

Steam cooking drives alterations of proteomics, protein structural and functional properties in rice (Oryza sativa l.)

Rice, as an important staple food consumed by people, is gradually becoming a concern for many consumers in terms of its eating quality. Many studies have found that protein is an important factor to determine the edible quality of rice. However, the protein changes during rice cooking have not been compared and studied in detail. In this study, the structural and functional characteristics of rice proteins before and after steaming were comprehensively compared. Meanwhile, proteomic strategies were also applied to analyze changes in protein composition and expression. Steaming promoted the aggregation of cooked rice proteins, resulting in a more compact structure and a significant increase in particle size (raw rice, 304.33 nm; cooked rice, 565.17 nm). Compared with raw rice protein (43.33%; 133.91%), the solubility (22.29%) and foaming capacity (119.53%) of cooked rice protein were significantly reduced, while emulsion activity was slightly improved. The differential abundance proteins were found to be predominantly down-regulated after steaming (238 proteins) and mostly enriched in metabolic pathways. The steaming process of rice mainly involves oxidative phosphorylation, thiamine metabolism, ether lipid metabolism, glycerophospholipid metabolism, multiple amino acid metabolism and other metabolic pathways, and they are closely related to each other. This study deepens the understanding of proteomic changes and structural/functional properties of rice proteins during steaming.

Dietary xylo-oligosaccharides and arabinoxylans improved growth efficiency by reducing gut epithelial cell turnover in broiler chickens

BackgroundOne of the main roles of the intestinal mucosa is to protect against environmental hazards. Supplementation of xylo-oligosaccharides (XOS) is known to selectively stimulate the growth of beneficial intestinal bacteria and improve gut health and function in chickens. XOS may have an impact on the integrity of the intestinal epithelia where cell turnover is critical to maintain the compatibility between the digestive and barrier functions. The aim of the study was to evaluate the effect of XOS and an arabinoxylan-rich fraction (AXRF) supplementation on gut function and epithelial integrity in broiler chickens.MethodsA total of 128 broiler chickens (Ross 308) were assigned into one of two different dietary treatments for a period of 42 d: 1) control diet consisting of a corn/soybean meal-based diet; or 2) a control diet supplemented with 0.5% XOS and 1% AXRF. Each treatment was randomly distributed across 8 pens (n = 8) with 8 chickens each. Feed intake and body weight were recorded weekly. On d 42, one male chicken per pen was selected based on average weight and euthanized, jejunum samples were collected for proteomics analysis.ResultsDietary XOS/AXRF supplementation improved feed efficiency (P < 0.05) from d 1 to 42 compared to the control group. Proteomic analysis was used to understand the mechanism of improved efficiency uncovering 346 differentially abundant proteins (DAP) (Padj < 0.00001) in supplemented chickens compared to the non-supplemented group. In the jejunum, the DAP translated into decreased ATP production indicating lower energy expenditure by the tissue (e.g., inhibition of glycolysis and tricarboxylic acid cycle pathways). In addition, DAP were associated with decreased epithelial cell differentiation, and migration by reducing the actin polymerization pathway. Putting the two main pathways together, XOS/AXRF supplementation may decrease around 19% the energy required for the maintenance of the gastrointestinal tract.ConclusionsDietary XOS/AXRF supplementation improved growth efficiency by reducing epithelial cell migration and differentiation (hence, turnover), actin polymerization, and consequently energy requirement for maintenance of the jejunum of broiler chickens.

DIA-Based Proteomic Analysis Reveals MYOZ2 as a Key Protein Affecting Muscle Growth and Development in Hybrid Sheep.

Hybridization of livestock can be used to improve varieties, and different hybrid combinations produce unique breeding effects. In this study, male Southdown and Suffolk sheep were selected to hybridize with female Hu sheep to explore the effects of male parentage on muscle growth and the development of offspring. Using data-independent acquisition technology, we identified 119, 187, and 26 differentially abundant proteins (DAPs) between Hu × Hu (HH) versus Southdown × Hu (NH), HH versus Suffolk × Hu (SH), and NH versus SH crosses. Two DAPs, MYOZ2 and MYOM3, were common to the three hybrid groups and were mainly enriched in muscle growth and development-related pathways. At the myoblast proliferation stage, MYOZ2 expression decreased cell viability and inhibited proliferation. At the myoblast differentiation stage, MYOZ2 expression promoted myoblast fusion and enhanced the level of cell fusion. These findings provide new insights into the key proteins and metabolic pathways involved in the effect of male parentage on muscle growth and the development of hybrid offspring in sheep.

Proteomic Analysis of a Rat Streptozotocin Model Shows Dysregulated Biological Pathways Implicated in Alzheimer's Disease.

Alzheimer's Disease (AD) is an age-related neurodegenerative disorder characterized by progressive memory loss and cognitive impairment, affecting 35 million individuals worldwide. Intracerebroventricular (ICV) injection of low to moderate doses of streptozotocin (STZ) in adult male Wistar rats can reproduce classical physiopathological hallmarks of AD. This biological model is known as ICV-STZ. Most studies are focused on the description of behavioral and morphological aspects of the ICV-STZ model. However, knowledge regarding the molecular aspects of the ICV-STZ model is still incipient. Therefore, this work is a first attempt to provide a wide proteome description of the ICV-STZ model based on mass spectrometry (MS). To achieve that, samples from the pre-frontal cortex (PFC) and hippocampus (HPC) of the ICV-STZ model and control (wild-type) were used. Differential protein abundance, pathway, and network analysis were performed based on the protein identification and quantification of the samples. Our analysis revealed dysregulated biological pathways implicated in the early stages of late-onset Alzheimer's disease (LOAD), based on differentially abundant proteins (DAPs). Some of these DAPs had their mRNA expression further investigated through qRT-PCR. Our results shed light on the AD onset and demonstrate the ICV-STZ as a valid model for LOAD proteome description.

Proteomics analysis of differentially abundant proteins in the rohu kidney infected with Edwardsiella tarda

Edwardsiella tarda (Et) is a zoonotic gram-negative pathogen with a diverse host range, including fish. However, the in-depth molecular mechanisms underlying the response of Labeo rohita (rohu) kidney to Et are poorly understood. A proteomic and histopathological analysis was performed for the rohu kidney after Et infection. The histopathology of the infected rohu kidney showed vacuolation and necrosis. After LC-MS/MS analysis, ~1240 proteins were identified with ≥2 unique peptides. A total of 96 differentially abundant proteins (DAPs) were observed between the control and Et infected group (ET). Metascape and STRING analysis were used for the gene ontology (GO), and protein-protein interaction network (PPI) for the significant pathways of DAPs. In PPI, low-abundant proteins were mapped to metabolic pathways and oxidative phosphorylation (cox5ab, uqcrfs1). High-abundance proteins were mapped to ribosomes (rplp2), protein process in the ER (hspa8), and immune system (ptgdsb.1, muc2). Our label-free proteomic approach in the rohu kidney revealed abundant enriched proteins involved in vesicle coat (ehd4), complement activation (c3a.1, c9, c7a), phagosome (thbs4, mapk1), metabolic reprogramming (hao1, glud1a), wound healing (vim, alox5), and the immune system (psap) after Et infection. A targeted proteomics approach of multiple reaction monitoring (MRM) validated the DAPs (nprl3, ambp, vmo1a, hspg2, muc2, hao1 and glud1a) between control and ET. Overall, the current analysis of histology and proteome in the rohu kidney provides comprehensive data on pathogenicity and the potential immune proteins against Et.

Decoding the influence of semen collection processes on goat sperm quality from a perspective of seminal plasma proteomics

This study aims to assess the impact of semen collection methods on goat semen quality and seminal plasma (SP) proteomes. Semen was collected by artificial vagina (AV) or electro-ejaculator (EE) and semen parameters were evaluated. Tandem mass tag coupled with liquid chromatography–tandem mass spectrometry was used to screen SP differentially abundant proteins (DAPs) between EE and AV. PRM was used to confirm the reliability of the data. In contrast to EE, a lower volume, higher progressive motility and concentration were observed in AV. No differences were found in total motility, membrane integrity, acrosome integrity, and ROS production between EE and AV. In total, 1692 proteins were identified in SP, including 210 DAPs. Among them, 120 and 90 proteins were down-regulated and up-regulated in AV compared to EE, respectively. The GO annotation showed that DAPs are mainly localized in the membrane, involved in deference responses to bacterium, RNA processing, and related to oxidoreductase activity. KEGG demonstrated tight associations of DAPs with specific amino acids, carbon metabolism, citrate cycle, and propanoate metabolism. In conclusion, this study provides valuable insights into the effects of semen collection on goat semen quality and explores the potential action mechanism based on the modification of SP proteomes. Significance of the studyThe quality of fresh semen directly influences the results of artificial insemination and semen cryopreservation in livestock. This study represents the first attempt to evaluate the impact of semen collection methods including electroejaculation and artificial vagina on sperm quality and seminal plasma proteomes in goat. The results of this study demonstrated that semen collection methods directly impacted the quality of goat semen. Then, the proteomic strategy was used to explore the potential action mechanism of semen collection methods on sperm. Some differentially abundant proteins that potentially influence semen quality were identified. Furthermore, this study suggests the possibility of utilizing specific proteins as predictive markers for goat semen quality.

Multiomics Approach Reveals Serum Biomarker Candidates for Congenital Zika Syndrome.

The Zika virus (ZIKV) can be vertically transmitted, causing congenital Zika syndrome (CZS) in fetuses. ZIKV infection in early gestational trimesters increases the chances of developing CZS. This syndrome involves several pathologies with a complex diagnosis. In this work, we aim to identify biological processes and molecular pathways related to CZS and propose a series of putative protein and metabolite biomarkers for CZS prognosis in early pregnancy trimesters. We analyzed serum samples of healthy pregnant women and ZIKV-infected pregnant women bearing nonmicrocephalic and microcephalic fetuses. A total of 1090 proteins and 512 metabolites were identified by bottom-up proteomics and untargeted metabolomics, respectively. Univariate and multivariate statistical approaches were applied to find CZS differentially abundant proteins (DAP) and metabolites (DAM). Enrichment analysis (i.e., biological processes and molecular pathways) of the DAP and the DAM allowed us to identify the ECM organization and proteoglycans, amino acid metabolism, and arachidonic acid metabolism as CZS signatures. Five proteins and four metabolites were selected as CZS biomarker candidates. Serum multiomics analysis led us to propose nine putative biomarkers for CZS prognosis with high sensitivity and specificity.

A260 ADVANCING INFLAMMATORY BOWEL DISEASE DIAGNOSIS THROUGH STOOL PROTEOMIC SIGNATURES OBTAINED VIA DIA-MASS SPECTROMETRY AND MACHINE LEARNING

Abstract Background Resembling symptoms between flare-up Inflammatory bowel disease (IBD) and other gastrointestinal diseases and conditions, make the initial diagnosis and accurate treatment of this disease challenging. Currently, the most common clinical methods used for diagnosing and monitoring IBD are colonoscopy and biopsy, which are invasive and uncomfortable procedures, and the fecal calprotectin test, which is not sufficiently accurate. Therefore, it is necessary to develop an alternative method. Aims In this study, our aim was to develop a robust predictive model for a noninvasive and accurate test to distinguish active IBD from non-IBD controls. Methods A total of 120 samples were collected, with 78 samples separated for retrospective analysis and model training, while 42 samples were set aside for prospective validation. We employed SWATH mass spectrometry for the identification and quantification of the stool proteome. The obtained data underwent multiple stages, including data preprocessing, feature selection, model training, and performance evaluation. We optimized data processing procedures through advanced bioinformatics, selecting an appropriate pipeline that included data normalization, batch effect correction, and missing value imputation. Subsequently, we assessed various machine learning algorithms to determine the most effective classifier for predicting IBD based on the selected proteins. Results After data preprocessing, we identified 48 differentially abundant proteins (DAPs). To eliminate redundant proteins, we employed Correlation-based Feature Selection (CFS), resulting in selecting 7 proteins. To identify the most suitable predictive model for our dataset, we assessed five popular machine learning methods: Support Vector Machines (SVM), Random Forests, Logistic Regression, k-nearest neighbors (KNN), and Naive Bayes. Among these, SVM exhibited the highest performance. Finally, we evaluated the model's performance by applying the selected algorithm to 42 prospective blind samples. The results revealed a sensitivity of 96% and a specificity of 76%, highlighting its strength and effectiveness. Conclusions In conclusion, this study offers a proof of concept for the application of SWATH for precise IBD diagnosis using stool proteomics and showcases the effectiveness of our data processing and machine learning approach. Additionally, it highlights the potential of this method for classifying Crohn's Disease (CD) vs. Ulcerative Colitis (UC) and distinguishing active IBD from remission. Workflow of study Funding Agencies CIHRCrohn's and Colitis Canada , Studentship from CRMUS,

Effects of Quality Enhancement of Frozen Tuna Fillets Using Ultrasound-Assisted Salting: Physicochemical Properties, Histology, and Proteomics.

Salting pretreatment is an effective method to improve the quality of frozen fish. This study investigated the quality changes and proteomic profile differences of frozen yellowfin tuna fillets pretreated with ultrasound-assisted salting (UAS) and static salting (SS). This study was centered on three aspects: physicochemical indicators' determination, histological observation, and proteomic analysis. The results showed that UAS significantly increased yield, salt content, and water-holding capacity (WHC), decreased total volatile base nitrogen (TVBN) compared to SS (p < 0.05), and significantly increased water in the protein matrix within myofibrils. Histological observations showed that the tissue cells in the UAS group were less affected by frozen damage, with a more swollen structure and rougher surface of myofibrils observed. Furthermore, 4D label-free proteomics revealed 56 differentially abundant proteins (DAPs) in UAS vs. NT comparison, mainly structural proteins, metabolic enzymes, proteasomes, and their subunits, which are associated with metabolic pathways such as calcium signaling pathway, gap junction, actin cytoskeletal regulation, and necroptosis, which are intimately associated with quality changes in freeze-stored tuna fillets. In brief, UAS enhances the potential for the application of salting pretreatment to improve frozen meat quality, and 4D label-free proteomics provides knowledge to reveal the potential links between quality and molecular changes in processed frozen meat to optimize future UAS meat processing.

Studying Antifatigue Mechanism of Tyr-Pro-Leu-Pro in Exercise Mice Using Label-Free Proteomics.

In our previous study, yeast-derived peptide Tyr-Pro-Leu-Pro (YPLP) was found to prolong treadmill time and relieve muscle fatigue in ICR mice. The present study aimed to further investigate the antifatigue mechanism of YPLP. Three doses of YPLP (10, 25, and 50 mg/kg·d) were given to exercise mice for 4 weeks. Results showed that YPLP reduced the oxidative response via the nuclear factor erythroid-2-related factor 2 (Nrf2) pathway and promoted energy metabolism through the AMP-activated protein kinase (AMPK) pathway. Label-free proteomics results showed that 81 differential abundance proteins (DAPs) were regulated by high-dose YPLP. These DAPs belonged to proteasome, mitochondrial, and muscle proteins. YPLP was mainly involved in proteasome, aminoacyl-tRNA biosynthesis, focal adhesion, and MAPK signal pathways to enhance muscle endurance. Furthermore, real-time quantitative PCR and Western blotting results proved that YPLP upregulated Psmd14 expression and downregulated p38 MAPK expression. Overall, this study revealed the mechanism behind YPLP to alleviate exercise fatigue.

Comparative physiological, biochemical and proteomic analyses reveal key proteins and crucial regulatory pathways related to drought stress tolerance in faba bean (Vicia faba L.) leaves

Drought is one of the important abiotic factors that affect faba bean growth and productivity in the Mediterranean region. In order to study the response of faba bean plant to water-deficit stress, a physiological and proteomic analysis was carried out in leaf tissue. All physiological parameters were affected by drought. The physiological mechanism underlying the response of faba bean leaves to water-deficit was therefore attributed to the alleviation of oxidative stress via the accumulation of proline and to the synergistic action of the antioxidant enzyme system (CAT, SOD, APX and GPOX). Proteomic analysis identified 2000 proteins from faba bean leaves, of which were 81 differentially expressed. Of those, 36 were downregulated and 45 were upregulated under water-deficit treatment. KEGG and GO enrichments indicated differentially abundant proteins (DAPs) related to photosynthesis, antioxidants and ROS detoxifying enzymes, biosynthesis of amino acids and secondary metabolites, molecular chaperones, signal transduction, energy and carbohydrate metabolism and metabolic enzymes. The current results provide evidence for a complex synergetic pathway, in which ROS detoxification mechanisms and photoprotection constituted the major aspect of water-deficit tolerance in faba bean leaves. These results offer a foundational basis regarding the molecular mechanism involved in drought resistance within the faba bean species.

Exogenous Melatonin Promotes Glucoraphanin Biosynthesis by Mediating Glutathione in Hairy Roots of Broccoli (Brassica oleracea L. var. italica Planch).

To investigate the mechanism of melatonin (MT)-mediated glutathione (GSH) in promoting glucoraphanin (GRA) and sulforaphane (SF) synthesis, the gene expression pattern and protein content of hairy broccoli roots under MT treatment were analyzed by a combination of RNA-seq and tandem mass spectrometry tagging (TMT) techniques in this study. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that both proteins and mRNAs with the same expression trend were enriched in the "Glutathione metabolism (ko00480)" and "Proteasome (ko03050)" pathways, and most of the differentially expressed genes (DEGs) and differentially abundant proteins (DAPs) regulating the two pathways were downregulated. The results showed that endogenous GSH concentration and GR activity were increased in hairy roots after MT treatment. Exogenous GSH could promote the biosynthesis of GRA and SF, and both exogenous MT and GSH could upregulate the expression of the GSTF11 gene related to the sulfur transport gene, thus promoting the biosynthesis of GRA. Taken together, this study provides a new perspective to explore the complex molecular mechanisms of improving GRA and SF synthesis levels by MT and GSH regulation.

Proteomic Analysis Revealed the Antagonistic Effect of Decapitation and Strigolactones on the Tillering Control in Rice.

Removing the panicle encourages the growth of buds on the elongated node by getting rid of apical dominance. Strigolactones (SLs) are plant hormones that suppress tillering in rice. The present study employed panicle removal (RP) and external application of synthesized strigolactones (GR) to modulate rice bud growth at node 2. We focused on the full-heading stage to investigate proteomic changes related to bud germination (RP-Co) and suppression (GR-RP). A total of 434 represented differentially abundant proteins (DAPs) were detected, with 272 DAPs explicitly specified in the bud germination process, 106 in the bud suppression process, and 28 in both. DAPs in the germination process were most associated with protein processing in the endoplasmic reticulum and ribosome biogenesis. DAPs were most associated with metabolic pathways and glycolysis/gluconeogenesis in the bud suppression process. Sucrose content and two enzymes of sucrose degradation in buds were also determined. Comparisons of DAPs between the two reversed processes revealed that sucrose metabolism might be a key to modulating rice bud growth. Moreover, sucrose or its metabolites should be a signal downstream of the SLs signal transduction that modulates rice bud outgrowth. Contemplating the result so far, it is possible to open new vistas of research to reveal the interaction between SLs and sucrose signaling in the control of tillering in rice.

DIA-based quantitative proteomic analysis of porcine endometrium in the peri-implantation phase

The 12th day of gestation is a critical period for embryo loss and the beginning of imminent implantation in sows. Data independent acquisition (DIA) technology is one of the high-throughput, high-resolution and reproducible proteomics technologies for large-scale digital qualitative and quantitative research. The aim of this study was to identify and characterize the protein abundance landscape of Yorkshire pig endometrium on the 12th day of pregnancy (P12) and estrous cycle (C12) using DIA proteomics. A total of 1251 differentially abundant proteins (DAPs) were identified, of which 882 were up-regulated and 369 were down-regulated at P12. Functional enrichment analysis showed that the identified proteins were related to metabolism, biosynthesis and signaling pathways. Three proteins were selected for Western blot (WB) validation and the results were consistent with the DIA data. Further combined with transcriptome data, fibrinogen like 2 (FGL2) and S100 calcium binding protein A8 (S100A8) were verified to be highly abundant in the P12 endometrial epithelium. In summary, there were significantly different abundance of proteome profiles in C12 and P12 endometrium, suggesting that DAPs are associated with changes in endometrial receptivity, which laid the foundation for further research on related regulatory mechanisms. SignificanceThe 12th day of gestation is an important point in the peri-implantation period of pigs, when the endometrium presents a receptive state under the stimulation of estrogen. DIA proteomics technology is an emerging protein identification technology in recent years, which can obtain protein information through comprehensive and unbiased scanning. In this study, DIA technology was used to characterize endometrial proteins in pigs during the peri-implantation period. The results showed that higher protein abundance was detected using the DIA technique, and some of these DAPs may be involved in regulating embryo implantation. This study will help to better reveal the related proteins involved in embryo implantation, and lay a foundation for further research on the mechanism of endometrial regulation of embryo implantation. Significance of the studyThe 12th day of gestation is an important point in the peri-implantation period of pigs, when the endometrium presents a receptive state under the stimulation of estrogen. DIA proteomics technology is an emerging protein identification technology in recent years, which can obtain protein information through comprehensive and unbiased scanning. In this study, DIA technology was used to characterize endometrial proteins in pigs during the peri-implantation period. The results showed that higher protein abundance was detected using the DIA technique, and some of these DAPs may be involved in regulating embryo implantation. This study will help to better reveal the related proteins involved in embryo implantation, and lay a foundation for further research on the mechanism of endometrial regulation of embryo implantation.

Proteomic Analysis Identifies Distinct Protein Patterns for High Ovulation in FecB Mutant Small Tail Han Sheep Granulosa Cells.

The Booroola fecundity (FecB) mutation in the bone morphogenetic protein receptor type 1B (BMPR1B) gene increases ovulation in sheep. However, its effect on follicular maturation is not fully understood. Therefore, we collected granulosa cells (GCs) at a critical stage of follicle maturation from nine wild-type (WW), nine heterozygous FecB mutant (WB), and nine homozygous FecB mutant (BB) Small Tail Han sheep. The GCs of three ewes were selected at random from each genotype and consolidated into a single group, yielding a total of nine groups (three groups per genotype) for proteomic analysis. The tandem mass tag technique was utilized to ascertain the specific proteins linked to multiple ovulation in the various FecB genotypes. Using a general linear model, we identified 199 proteins significantly affected by the FecB mutation with the LIMMA package (p < 0.05). The differential abundance of proteins was enriched in pathways related to cholesterol metabolism, carbohydrate metabolism, amino acid biosynthesis, and glutathione metabolism. These pathways are involved in important processes for GC-regulated 'conservation' of oocyte maturation. Further, the sparse partial least-squares discriminant analysis and the Fuzzy-C-mean clustering method were combined to estimate weights and cluster differential abundance proteins according to ovulation to screen important ovulation-related proteins. Among them, ZP2 and ZP3 were found to be enriched in the cellular component catalog term "egg coat", as well as some apolipoproteins, such as APOA1, APOA2, and APOA4, enriched in several Gene Ontology terms related to cholesterol metabolism and lipoprotein transport. A higher abundance of these essential proteins for oocyte maturation was observed in BB and WB genotypes compared with WW ewes. These proteins had a high weight in the model for discriminating sheep with different FecB genotypes. These findings provide new insight that the FecB mutant in GCs improves nutrient metabolism, leading to better oocyte maturation by altering the abundance of important proteins (ZP2, ZP3, and APOA1) in favor of increased ovulation or better oocyte quality.

Activation of estrogen receptor induces differential proteomic responses mainly involving migration, invasion, and tumor development pathways in human testicular embryonal carcinoma NT2/D1 cells

The aims of the present study were to investigate the global changes on proteome of human testicular embryonal carcinoma NT2/D1 cells treated with 17β-estradiol (E2), and the effects of this hormone on migration, invasion, and colony formation of these cells. A quantitative proteomic analysis identified the presence of 1230 proteins in both E2-treated and control cells. The analysis revealed 75 differentially abundant proteins (DAPs), out of which 43 proteins displayed a higher abundance and, 30 proteins showed a lower abundance in E2-treated NT2/D1 cancer cells. Functional analysis using IPA highlighted some activation processes such as migration, invasion, metastasis, and tumor growth. Interestingly, the treatment with E2 and ERβ-selective agonist DPN increased the migration of NT2/D1 cells. On the other hand, ERα-selective agonist PPT did not modify cell migration, indicating that ERβ is the upstream receptor involved in this process. The activation of ERβ increased the invasion and anchorage‑independent growth of NT2/D1 cells more intensely than ERα. ERα and ERβ may play overlapping roles on invasion and colony formation of these cells. Further studies are required to clarify the mechanism underlying these effects. The molecular mechanisms revealed by proteomic and functional studies might also guide the development of potential targets for a better understanding of the biology of these cells and novel treatments for non-seminoma in the future.