scholarly journals Comparative proteomic analysis of pepper (Capsicum annuum L.) seedlings under selenium stress

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8020
Author(s):  
Chenghao Zhang ◽  
Baoyu Xu ◽  
Wei Geng ◽  
Yunde Shen ◽  
Dongji Xuan ◽  
...  
Keyword(s):  
High Performance ◽  
Animal Health ◽  
Enrichment Analysis ◽  
Integrated Approach ◽  
Quantitative Information ◽  
Protein Levels ◽  
Treatment Comparison ◽  
Tandem Mass Tag ◽  
Mock Treatment ◽  
Shock Proteins

Selenium (Se) is an essential trace element for human and animal health. Se fertilizer has been used to increase the Se content in crops to meet the Se requirements in humans and animals. To address the challenge of Se poisoning in plants, the mechanisms underlying Se-induced stress in plants must be understood. Here, to elucidate the effects of Se stress on the protein levels in pepper, we used an integrated approach involving tandem mass tag labeling, high performance liquid chromatography fractionation, and mass spectrometry-based analysis. A total of 4,693 proteins were identified, 3,938 of which yielded quantitative information. Among them, the expression of 172 proteins was up-regulated, and the expression of 28 proteins was down-regulated in the Se/mock treatment comparison. According to the above data, we performed a systematic bioinformatics analysis of all identified proteins and differentially expressed proteins (DEPs). The DEPs were most strongly associated with the terms “metabolic process,” “posttranslational modification, protein turnover, chaperones,” and “protein processing in endoplasmic reticulum” according to Gene Ontology, eukaryotic orthologous groups classification, and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, respectively. Furthermore, several heat shock proteins were identified as DEPs. These results provide insights that may facilitate further studies on the pepper proteome expressed downstream of the Se stress response. Our data revealed that the responses of pepper to Se stress involve various pathways.

Phosphoproteome Reveals the Lactation Mechanism in Caprine Mammary Gland Tissues in Peak and Late Lactation Stages

2020 ◽  
Author(s):  
Chao Zhu ◽  
Hao Yin ◽  
Quyu Duan ◽  
Fu Li ◽  
Yue Jiang ◽  
...  
Keyword(s):  
Protein Phosphorylation ◽  
Calcium Signalling ◽  
Enrichment Analysis ◽  
Protein Translation ◽  
Integrated Approach ◽  
Rna Degradation ◽  
Signalling Pathway ◽  
Tandem Mass ◽  
Mapk Signalling Pathway ◽  
Tandem Mass Tag

Abstract Background: Protein phosphorylation plays an important role in lactation. Differentially modified modification sites between peak lactation (PL, 90 days postpartum) and late lactation (LL, 280 days postpartum) were investigated using an integrated approach, namely, liquid chromatography with tandem mass spectrometry (LC-MS/MS) and tandem mass tag (TMT) labelling, to understand the molecular biological mechanisms in goat breast tissues.Results: A total of 1,938 (1,111 up-regulated, 827 down-regulated) differentially modified modification sites of 1,172 proteins were identified (P values < 0.05 and fold change of phosphorylation ratios > 1.5). In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that ribosome (chx03010), RNA transport (chx03013), protein export (chx03060), calcium signalling pathway (chx04020), oxytocin signalling pathway (chx04921), RNA degradation (chx03018) and MAPK signalling pathway (chx04010) were enriched in relation to energy metabolism and protein translation. The results of western blot showed phosphorylation levels of ACACA, EIF4EBP1 and IRS1 increased and JUN decreased in PL compared with LL. The result was consistent with phosphoproteome. Conclusions: Overall, these data indicate that protein phosphorylation is closely related to lactation and differentially modified modification sites might have potential research value in the regulation of goat lactation.

scholarly journals Quantitative proteomic analysis of aberrant expressed lysine acetylation in gastrointestinal stromal tumors

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Bo Wang ◽  
Long Zhao ◽  
Zhidong Gao ◽  
Jianyuan Luo ◽  
Haoran Zhang ◽  
...  
Keyword(s):  
Risk Group ◽  
Risk Groups ◽  
Quantitative Information ◽  
Differentially Expressed ◽  
High Rate ◽  
Lysine Acetylation ◽  
Kegg Pathways ◽  
Tandem Mass Tag ◽  
Cell Components ◽  
Nih Classification

Abstract Background Gastrointestinal stromal tumor (GIST) is a common digestive tract tumor with high rate of metastasis and recurrence. Currently, we understand the genome, transcriptome and proteome in GIST. However, posttranscriptional modification features in GIST remain unclear. In the present study, we aimed to construct a complete profile of acetylome in GIST. Methods Five common protein modifications, including acetylation, succinylation, crotonylation, 2-hydroxyisobutyrylation, and malonylation were tested among GIST subgroups and significantly differentially- expressed lysine acetylation was found. The acetylated peptides labeled with Tandem Mass Tag (TMT)under high sensitive mass spectrometry, and some proteins with acetylation sites were identified. Subsequently, these proteins and peptides were classified into high/moderate (H/M) risk and low (L) risk groups according to the modified NIH classification standard. Furthermore, cell components, molecular function, biological processes, KEGG pathways and protein interaction networks were analyzed. Results A total of 2904 acetylation sites from 1319 proteins were identified, of which quantitative information of 2548 sites from 1169 proteins was obtained. Finally, the differentially-expressed lysine acetylation sites were assessed and we found that 42 acetylated sites of 38 proteins were upregulated in the H/M risk group compared with the L risk group, while 48 acetylated sites of 44 proteins were downregulated, of which Ki67 K1063Ac and FCHSD2 K24Ac were the two acetylated proteins that were most changed. Conclusions Our novel findings provide further understanding of acetylome in GIST and might demonstrate the possibility in the acetylation targeted diagnosis and therapy of GIST.

scholarly journals N-protein presents early in blood, dried blood and saliva during asymptomatic and symptomatic SARS-CoV-2 infection

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dandan Shan ◽  
Joseph M. Johnson ◽  
Syrena C. Fernandes ◽  
Hannah Suib ◽  
Soyoon Hwang ◽  
...  
Keyword(s):  
Single Molecule ◽  
High Performance ◽  
Point Of Care ◽  
Capillary Blood ◽  
Molecular Testing ◽  
Sample Collection ◽  
Protein Assay ◽  
N Protein ◽  
Protein Levels ◽  
Percent Agreement

AbstractThe COVID-19 pandemic continues to have an unprecedented impact on societies and economies worldwide. There remains an ongoing need for high-performance SARS-CoV-2 tests which may be broadly deployed for infection monitoring. Here we report a highly sensitive single molecule array (Simoa) immunoassay in development for detection of SARS-CoV-2 nucleocapsid protein (N-protein) in venous and capillary blood and saliva. In all matrices in the studies conducted to date we observe >98% negative percent agreement and >90% positive percent agreement with molecular testing for days 1–7 in symptomatic, asymptomatic, and pre-symptomatic PCR+ individuals. N-protein load decreases as anti-SARS-CoV-2 spike-IgG increases, and N-protein levels correlate with RT-PCR Ct-values in saliva, and between matched saliva and capillary blood samples. This Simoa SARS-CoV-2 N-protein assay effectively detects SARS-CoV-2 infection via measurement of antigen levels in blood or saliva, using non-invasive, swab-independent collection methods, offering potential for at home and point of care sample collection.

scholarly journals Identification of Hub Genes Associated With Melanoma Development by Comprehensive Bioinformatics Analysis

2021 ◽  
Vol 11 ◽  
Author(s):  
Jie Jiang ◽  
Chong Liu ◽  
Guoyong Xu ◽  
Tuo Liang ◽  
Chaojie Yu ◽  
...  
Keyword(s):  
Target Gene ◽  
Enrichment Analysis ◽  
High Expression ◽  
Expression Data ◽  
Hub Genes ◽  
Gene Therapies ◽  
Protein Levels ◽  
Melanoma Diagnosis ◽  
Melanoma Patients ◽  
Core Genes

IntroductionThis study aimed to identify important genes associated with melanoma to further develop new target gene therapies and analyze their significance concerning prognosis.Materials and methodsGene expression data for melanoma and normal tissue were downloaded from three databases. Differentially co-expressed genes were identified by WGCNA and DEGs analysis. These genes were subjected to GO, and KEGG enrichment analysis and construction of the PPI visualized with Cytoscape and screened for the top 10 Hub genes using CytoHubba. We validated the Hub gene’s protein levels with an immunohistochemical assay to confirm the accuracy of our analysis.ResultsA total of 435 differentially co-expressed genes were obtained. Survival curves showed that high expression of FOXM1,\ EXO1, KIF20A, TPX2, and CDC20 in melanoma patients with 5 of the top 10 hub genes was associated with reduced overall survival (OS). Immunohistochemistry showed that all five genes were expressed at higher protein levels in melanoma than in paracancerous tissues.ConclusionFOXM1, EXO1, KIF20A, TPX2, and CDC20 are prognosis-associated core genes of melanoma, and their high expression correlates with the low prognosis of melanoma patients and can be used as biomarkers for melanoma diagnosis, treatment, and prognosis prediction.

scholarly journals Commercial practice of out-wintering dairy heifers in Great Britain

2020 ◽  
Vol 82 ◽  
pp. 161-169
Author(s):  
Norton E. Atkins ◽  
Keith E. Walley ◽  
Liam A. Sinclair
Keyword(s):  
Great Britain ◽  
High Performance ◽  
Animal Health ◽  
Live Weight ◽  
Herd Size ◽  
Dairy Farmers ◽  
Commercial Practice ◽  
Dairy Heifers ◽  
Supplementary Feed ◽  
Strip Grazing

The majority of dairy cattle in Great Britain (GB) are housed during winter but replacement heifers are out-wintered on some farms, a practice that may reduce the need for high capital-cost housing and facilitate herd expansion. Dairy farmers that were out-wintering replacement heifers in GB in 2012 were surveyed to determine current practice and attitudes. A typical system involved heifers strip grazing pasture or a crop, with baled grass silage as supplementary feed; strongly resembling outdoor wintering systems in New Zealand. Many used more than one grazed forage; predominantly, pasture on 68%, kale on 53% and fodder beet on 33% of farms. Supplementary feed was 44% of the diet in younger, and 35% in older heifers. Although farms were approximately three times larger than the national average and 60% were expanding, expanding herd size was not the primary reason for out-wintering, with the main reasons being to reduce cost and improve animal health and welfare. Farmers that out-wintered heifers typically reported good animal average dairy gain of 0.6 kg/d and high body condition, however, this contrasts with some measured performance in GB. Farmers may benefit from accurate feed allocation and monitoring heifer live weight during winter to ensure high performance.  

scholarly journals Identification of Urine Metabolic Biomarkers for Vogt-Koyanagi-Harada Disease

2021 ◽  
Vol 9 ◽  
Author(s):  
Rui Chang ◽  
Ying Zhu ◽  
Jing Xu ◽  
Lin Chen ◽  
Guannan Su ◽  
...  
Keyword(s):  
High Performance ◽  
Area Under The Curve ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Healthy Controls ◽  
Roc Curve Analysis ◽  
Multivariate Statistical ◽  
Flight Mass Spectrometry ◽  
Laboratory Biomarkers ◽  
Vkh Disease

The diagnosis of Vogt-Koyanagi-Harada (VKH) disease is mainly based on a complex clinical manifestation while it lacks objective laboratory biomarkers. To explore the potential molecular biomarkers for diagnosis and disease activity in VKH, we performed an untargeted urine metabolomics analysis by ultra-high-performance liquid chromatography equipped with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF/MS). Through univariate and multivariate statistical analysis, we found 9 differential metabolites when comparing VKH patients with healthy controls, and 26 differential metabolites were identified when comparing active VKH patients with inactive VKH patients. Pathway enrichment analysis showed that glycine, serine and threonine metabolism, and arginine and proline metabolism were significantly altered in VKH versus healthy controls. Lysine degradation and biotin metabolism pathways were significantly altered in active VKH versus inactive VKH. Furthermore, the receiver operating characteristic (ROC) curve analysis revealed that the combination of acetylglycine and gamma-glutamylalanine could differentiate VKH from healthy controls with an area under the curve (AUC) of 0.808. A combination of ureidopropionic acid and 5′-phosphoribosyl-5-amino-4-imidazolecarboxamide (AICAR) had an excellent AUC of 0.958 for distinguishing active VKH from inactive VKH. In summary, this study identified abnormal metabolites in urine of patients with VKH disease. Further studies are needed to confirm whether these metabolites are specific for this disease.

scholarly journals Splenic Nodules: Canine Visceral leishmaniasis?

2021 ◽  
Vol 49 ◽  
Author(s):  
Gilsan Aparecida De Oliveira ◽  
Vitória Aline Santos Sarmento ◽  
Isabelle Vanderlei Martins Bastos ◽  
Alberon Ribeiro De Araújo ◽  
Lígia Buzzá Roo De Mendonça ◽  
...  
Keyword(s):  
Differential Diagnosis ◽  
Visceral Leishmaniasis ◽  
Animal Health ◽  
Rapid Test ◽  
Good Alternative ◽  
Canine Visceral Leishmaniasis ◽  
Biochemical Alterations ◽  
University Center ◽  
Protein Levels ◽  
Endemic Areas

Background: Canine visceral leishmaniasis (CVL) is a parasitic disease of high lethality caused by the protozoan Leishmania infantum in Brazil and is often related to splenomegaly. However, splenic nodules in dogs, although frequent, have not previously been reported as associated with CVL, but with neoplastic diseases. Considering that most dogs infected are oligosymptomatic or asymptomatic and that splenic nodules are common to other diseases, it is prudent to differentially diagnose CVL in view of its high zoonotic potential and lethality. The objective of the study was to describe a case of splenomegaly with splenic nodules associated with CVL in an asymptomatic dog treated with 2% miltefosina.                                             Case: A 5-year-old male Rottweiler with 41 kg, with a history of inappetence, apathy and weight loss was referred to the Veterinary Medicine School Clinic of the Cesmac University Center, Maceió, AL, Brazil. However, during palpation a slight increase in the spleen was noted. Hematological, hemoparasite, biochemical and abdominal ultrasonographic examinations were requested to clarify the clinical suspicion of hemoparasitosis. The hematological and biochemical results respectively showed the following: normocytic normochromic anemia, hyperproteinemia and thrombocytopenia, in addition to hypoalbuminemia, with elevated total protein levels. The test for hemoparasites was negative. Ultrasonography showed mixed echogenicity suggestive of nodules. The rapid test for Ehrlichia, Anaplasma and L. infantum was performed. It was positive only for L. infantum. ELISA, IFAT and qPCR tests were performed to confirm the result. The test showed a cut-off result of 0.371 for ELISA, positive for RIFI at a cut-off of 1:40 and qPCR with less than 1 fg and with amplification above 36 cycles. In view of these results, treatment with 2% miltefosine at a dose of 1 mL/ 10 kg was started once a day, after feeding, for 28 days. The animal was monitored throughout treatment and re-evaluated every 10 days for 30 days, showing signs of clinical development, presenting satisfactory results.Discussion: Canine splenomegaly can be associated with a variety of disease possibilities. In asymptomatic canine visceral leishmaniasis (CanL), the slight increase in spleen and the presence of splenic nodules may lead to a false diagnosis. Splenic nodules may be associated with dogs of advanced age and may be due to lymphoid nodular hyperplasia, which causes nodules with echogenicity, hyperechoic regions with well demarcated irregularity, with centralized hypoechoic areas and an absence of hematological and biochemical alterations. The cause of splenomegaly associated with nodules may be difficult to diagnose and require much time and effort. Therefore, diseases such as visceral leishmaniasis of high lethality must be the priority in differential diagnosis in endemic areas in order to minimize the risk of transmission. In addition to allowing an early intervention aiming at good animal health results and preventive measures, such as the use of repellent collars that reduce the risk of phlebotomo infection. The differential diagnosis of CVL is necessary in endemic areas, even in asymptomatic dogs that may present splenic alterations suggestive of other diseases. Treatment with 2% miltefosine was shown to be, in this case, effective at reducing the splenic nodules and a good alternative for the quality of life of the animal.

scholarly journals High expression of MCM10 is predictive of poor outcomes in lung adenocarcinoma

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10560
Author(s):  
Mingrui Shao ◽  
Shize Yang ◽  
Siyuan Dong
Keyword(s):  
Lung Adenocarcinoma ◽  
Complex Disease ◽  
Enrichment Analysis ◽  
Integrated Approach ◽  
Replication Initiation ◽  
Prognostic Biomarkers ◽  
Normal Lung ◽  
Pathway Enrichment Analysis ◽  
Therapeutic Value

Backgrounds Lung adenocarcinoma is a complex disease that results in over 1.8 million deaths a year. Recent advancements in treating and managing lung adenocarcinoma have led to modest decreases in associated mortality rates, owing in part to the multifactorial etiology of the disease. Novel prognostic biomarkers are needed to accurately stage the disease and act as the basis of adjuvant treatments. Material and Methods The microarray datasets GSE75037, GSE31210 and GSE32863 were downloaded from the Gene Expression Omnibus (GEO) database to identify prognostic biomarkers for lung adenocarcinoma and therapy. The differentially expressed genes (DEGs) were identified by GEO2R. Functional and pathway enrichment analysis were performed by Kyoto Encyclopedia of Genes and Genomes and Gene Ontology (GO). Validation was performed based on 72 pairs of lung adenocarcinoma and adjacent normal lung tissues. Results Results showed that the DEGs were mainly focused on cell cycle and DNA replication initiation. Forty-one hub genes were identified and further analyzed by CytoScape. Here, we provide evidence which suggests MCM10 is a potential target with prognostic, diagnostic and therapeutic value. We base this on an integrated approach of comprehensive bioinformatics analysis and in vitro validation using the A549 lung adenocarcinoma cell line. We show that MCM10 overexpression correlates with a poor prognosis, while silencing of this gene decreases aberrant growth by 2-fold. Finally, evaluation of 72 clinical biopsy samples suggests that overexpression of MCM10 in the lung adenocarcinoma highly correlates with larger tumor size. Together, this work suggests that MCM10 may be a clinically relevant gene with both predictive and therapeutic value in lung adenocarcinoma.

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