scholarly journals SBP-SITA: A sequence-based prediction tools for S-itaconation

2021 ◽  
Author(s):  
Laizhi Zhang ◽  
Xuanwen Wang ◽  
Lin Zhang ◽  
Yanzheng Meng ◽  
Yu Chen ◽  
...  

As a recently-reported post-translational modification, S-itaconation plays an important role in inflammation suppression. In order to understand its regulatory mechanism in many life activities, the essential step is the recognition of S-itaconation. However, it is difficult to identify S-itaconation in the proteome for the high cost, which limits further investigation. In this study, we constructed an ensemble algorithm based on Soft Voting Classifier. The area under the ROC curve (AUC) value 0.73 for ensemble model. Accordingly, we constructed the on-line prediction tool dubbed SBP-SITA for easily identifying Cystine sites. SBP-SITA is available at http://www.bioinfogo.org/sbp-sita.

2020 ◽  
Author(s):  
Abraham Más ◽  
Laura Castaño-Miquel ◽  
Lorenzo Carretero-Paulet ◽  
Núria Colomé ◽  
Francesc Canals ◽  
...  

AbstractPost-translational modification by Small Ubiquitin-related Modifier (SUMO) is an essential regulatory mechanism in eukaryotes. In the cell, SUMO conjugates are highly enriched in the nucleus and, consistently, SUMOylation machinery components are mainly nuclear. Nonetheless, cytosolic SUMO targets also exist and the mechanisms that facilitate SUMO conjugation in the cytosol are unknown. Here, we show that the nuclear localization of the Arabidopsis SUMO activating enzyme large subunit SAE2 is dependent on two nuclear localization signals, the canonical NLS1 and the non-canonical NLS2 identified and validated here. NLS2 is proteolytic processed from SAE2 during seed development, facilitating SAE2 enrichment in the cytosol. Results obtained using transgenic plants expressing different SAE2 proteoforms suggest that SAE2 cytosolic enrichment could constitute a rapid signal for growth arrest. Phylogenetic studies indicated that the Arabidopsis NLS1-NLS2 structural organization is conserved only in seed plants, providing a potential evolutionary role of cytosolic SUMOylation in seed appearance.


2017 ◽  
Vol 112 ◽  
pp. 188-189
Author(s):  
Alex Harrison ◽  
Audray Fortin ◽  
Natalia Zamorano ◽  
Stefany Chartier ◽  
Elise Caron ◽  
...  

2020 ◽  
pp. jbc.RA120.016116
Author(s):  
Ravin Seepersaud ◽  
Alexander C. Anderson ◽  
Barbara A. Bensing ◽  
Biswa P Choudhury ◽  
Anthony J. Clarke ◽  
...  

The serine-rich repeat (SRR) glycoproteins of Gram-positive bacteria are a family of adhesins that bind to a wide range of host ligands, and expression of SRR glycoproteins is linked with enhanced bacterial virulence. The biogenesis of these surface glycoproteins involves their intracellular glycosylation and export via the accessory Sec (aSec) system. While all aSec components are required for SRR glycoprotein export, Asp2 of Streptococcus gordonii also functions as an O-acetyltransferase that modifies GlcNAc residues on the SRR adhesin GspB. Since these GlcNAc residues can also be modified by the glycosyltransferases Nss and Gly, it has been unclear whether the post-translational modification of GspB is coordinated. We now report that acetylation modulates the glycosylation of exported GspB. Loss of O-acetylation due to aps2 mutagenesis led to the export of GspB glycoforms with increased glucosylation of the GlcNAc moieties. Linkage analysis of the GspB glycan revealed that both O-acetylation and glucosylation occurred at the same C6 position on GlcNAc residues, and that O-acetylation prevented Glc deposition. Whereas streptococci expressing non-acetylated GspB with increased glucosylation were significantly reduced in their ability to bind human platelets in vitro, deletion of the glycosyltransferases nss and gly in the asp2 mutant restored platelet binding to wild-type levels. These findings demonstrate that GlcNAc O-acetylation controls GspB glycosylation, such that binding via this adhesin is optimized. Moreover, since O-acetylation has comparable effects on the glycosylation of other SRR adhesins, acetylation may represent a conserved regulatory mechanism for the post-translational modification of the SRR glycoprotein family.


2020 ◽  
Vol 9 (2) ◽  
pp. 40-46
Author(s):  
Sachin Punatar ◽  
Lingaraj Nayak ◽  
Avinash Bonda ◽  
Anant Gokarn ◽  
Aniket Mohite ◽  
...  

Engraftment fever (EF) is a common complication of autologous HSCT (AHSCT). It is difficult to discern it from infectious fever (IF). We studied the significance of total blood leucocyte count (TLC) to C-reactive protein (CRP) ratio in differentiating EF from IF. 109 consecutive AHSCT patients were retrospectively analysed between March 2011 and August 2013. Breakthrough fever (BF) was defined as new-onset fever preceded by an afebrile period of at least 48 hours. The BF episodes were classified as IF or EF. Infectious fever was diagnosed in case of blood culture positivity, radiological signs of infection, or fever subsiding within 48 hours of changing the antibiotics. Engraftment fever was defined in cases associated with rising leucocyte counts without identifiable infective focus. EF responded well to steroid therapy. Daily TLC and CRP values were obtained from patients’ records. Optimal cut-off value of ratio on day of BF was obtained by plotting ROC curve. Sensitivity and specificity were calculated at this value. Among 109 cases, the breakthrough fever manifested in seventy patients. The median term for BF was day +9. Sixty-two patients had the EF. Median value of TLC/CRP ratio on the day of BF was significantly higher in patients with EF than with IF (0.139 vs 0.038, p=0.013). With ROC analysis, the AUC value was 0.78 (95%CI – 0.66-0.89, p<0.0001). The ROC curve provided the optimal TLC/CRP value of 0.056. Using a ratio >0.056 for EF, the sensitivity and specificity were 63% (95%CI 50-75%) and 100% (95%CI 63-100%) respectively. TLC/CRP ratio >0.056 is highly specific for EF. Prospective studies are warranted to confirm these findings.


2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 1592-1592 ◽  
Author(s):  
Alyson L. Mahar ◽  
Susan Halabi ◽  
Lisa M. McShane ◽  
Patricia A. Groome ◽  
Carolyn C. Compton ◽  
...  

1592 Background: Clinical prediction in cancer depends on a myriad of prognostic factors, and relies on sound methodology for model building and validation. Increased understanding of complex tumour biology allows for simultaneous consideration of biological markers and standard clinical and pathological factors for prediction. We evaluated published studies supporting existing prediction tools in three cancers. Methods: Scientific literature and online resources were searched for clinical prediction tools for survival in three cancers: colorectal, lung, and melanoma. A priori criteria determined by the Molecular Modellers Working Group of the AJCC were evaluated and included: defined patient population, consideration of standard prognostic variables, model development approaches, validation strategies, performance metrics, presentation form of prediction tool, and intended clinical use. Results: Seventy-eight tools intended for prediction of survival were identified for the three cancers: 41 in colorectal, 23 in lung, and 14 in melanoma. Clinical presentations varied within each: 23 of the colorectal cancer tools focused on advanced disease with liver metastases and the remaining varied by stage; 16 lung cancer tools focused on NSCLC and 7 on SCLC. Even in narrowly defined situations, there was no consensus on key variables; for example, no variables were common to all 8 prediction tools for metastatic lung cancer. Variable definitions were missing or vague and the form of the model was often not provided, hampering independent validation and usability. Only 32/78 tools were supported by appropriate internal validity statistics and 21/78 with external validation. Often the development of risk scores did not create groups for whom treatment decisions would be similar. Conclusions: The quality of the literature supporting clinical prediction tools is variable, and the accuracy and utility of many existing tools is undetermined. Methodological guidelines for prediction tool development and validation should be adopted and adhered to. Studies developing and validating clinical prediction tools in cancer must be reported in complete and transparent fashion to facilitate proper interpretation and judgment of utility.


2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Chuandong Song ◽  
Bin Yang

Lysine malonylation is a novel-type protein post-translational modification and plays essential roles in many biological activities. Having a good knowledge of malonylation sites can provide guidance in many issues, including disease prevention and drug discovery and other related fields. There are several experimental approaches to identify modification sites in the field of biology. However, these methods seem to be expensive. In this study, we proposed malNet, which employed neural network and utilized several novel and effective feature description methods. It was pointed that ANN’s performance is better than other models. Furthermore, we trained the classifiers according to an original crossvalidation method named Split to Equal validation (SEV). The results achieved AUC value of 0.6684, accuracy of 54.93%, and MCC of 0.1045, which showed great improvement than before.


Diagnostics ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 896
Author(s):  
Carlos E. Galván-Tejada ◽  
Karen E. Villagrana-Bañuelos ◽  
Laura A. Zanella-Calzada ◽  
Arturo Moreno-Báez ◽  
Huizilopoztli Luna-García ◽  
...  

Sudden infant death syndrome (SIDS) is defined as the death of a child under one year of age, during sleep, without apparent cause, after exhaustive investigation, so it is a diagnosis of exclusion. SIDS is the principal cause of death in industrialized countries. Inborn errors of metabolism (IEM) have been related to SIDS. These errors are a group of conditions characterized by the accumulation of toxic substances usually produced by an enzyme defect and there are thousands of them and included are the disorders of the β-oxidation cycle, similarly to what can affect the metabolism of different types of fatty acid chain (within these, short chain fatty acids (SCFAs)). In this work, an analysis of postmortem SCFAs profiles of children who died due to SIDS is proposed. Initially, a set of features containing SCFAs information, obtained from the NIH Common Fund’s National Metabolomics Data Repository (NMDR) is submitted to an univariate analysis, developing a model based on the relationship between each feature and the binary output (death due to SIDS or not), obtaining 11 univariate models. Then, each model is validated, calculating their receiver operating characteristic curve (ROC curve) and area under the ROC curve (AUC) value. For those features whose models presented an AUC value higher than 0.650, a new multivariate model is constructed, in order to validate its behavior in comparison to the univariate models. In addition, a comparison between this multivariate model and a model developed based on the whole set of features is finally performed. From the results, it can be observed that each SCFA which comprises of the SFCAs profile, has a relationship with SIDS and could help in risk identification.


2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Mehdi Mirsaeidi ◽  
Hesham R. Omar ◽  
Golnaz Ebrahimi ◽  
Micheal Campos

Introduction.The association between the level of systemic inflammation and systemic hypertension (sHTN) among subjects with sarcoidosis has not been previously explored.Methods.A retrospective study was conducted to investigate the relation between the level of systemic inflammation in sarcoidosis, measured by various serum inflammatory markers, and sHTN.Results.Among a total of 108 cases with sarcoidosis (mean age: 53.4 years, 76.9% females), 55 (50.9%) had sHTN and 53 (49.1%) were normotensive. ESR was highly associated with sHTN. The patients with sHTN had higher mean ESR levels compared with normotensives (48.8 ± 35 versus 23.2 ± 27 mm/hr, resp.;P=0.001). ROC curve analysis for ESR revealed an AUC value of 0.795 (95% CI: 0.692–0.897;P=0.0001). With regard to CRP, there was a trend towards higher mean values in sHTN group (3.4 versus 1.7 mg/L;P=0.067) and significantly higher prevalence of sHTN in the highest CRP quartile compared to the lowest one (69.6% versus 30%; OR 4.95;P=0.017). ROC curve analysis for CRP revealed an AUC value of 0.644 (95% CI: 0.518–0.769;P=0.03). On multivariate analysis, ESR and the CRP remained independent predictors for sHTN among subjects with sarcoidosis.Conclusion.Systemic inflammation is associated with the presence of sHTN in sarcoidosis.


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