Bioinformatic approaches to improve the identification of peptides from proteomics experiments

2006 ◽  
Author(s):  
King Wai Lau ◽  
J. Siepen
Keyword(s):  
Bioinformatic Approaches

Identification of a lncRNA prognostic signature-related to stem cell index and its significance in colorectal cancer

2021 ◽  
Author(s):  
Xiao-Cheng Wang ◽  
Ya Liu ◽  
Fei-Wu Long ◽  
Liang-Ren Liu ◽  
Chuan-Wen Fan
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Prognostic Markers ◽  
The Cancer Genome Atlas ◽  
Prognostic Signature ◽  
Free Survival ◽  
Cancer Genome Atlas ◽  
Bioinformatic Approaches ◽  
Cell Phenotypes ◽  
The Relationship

Background: The relationship between long noncoding RNAs (lncRNAs) and the mRNA stemness index (mRNAsi) in colorectal cancer (CRC) is still unclear. Materials & methods: The mRNAsi, mRNAsi-related lncRNAs and their clinical significance were analyzed by bioinformatic approaches in The Cancer Genome Atlas (TCGA)-COREAD dataset. Results: mRNAsi was negatively related to pathological features but positively related to overall survival and recurrence-free survival in CRC. A five mRNAsi-related lncRNAs prognostic signature was further developed and showed independent prognostic factors related to overall survival in CRC patients, due to the five mRNAsi-related lncRNAs involved in several pathways of the cancer stem cells and malignant cancer cell phenotypes. Conclusion: The present study highlights the potential roles of mRNAsi-related lncRNAs as alternative prognostic markers.

scholarly journals Apoptosis resistance of senescent cells is an intrinsic barrier for senolysis induced by cardiac glycosides

2021 ◽  
Author(s):  
Pavel I. Deryabin ◽  
Alla N. Shatrova ◽  
Aleksandra V. Borodkina
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Broad Spectrum ◽  
General Feature ◽  
Cardiac Glycosides ◽  
Human Mesenchymal Stem Cells ◽  
Apoptosis Resistance ◽  
The Core ◽  
Bioinformatic Approaches

AbstractTargeted elimination of senescent cells, senolysis, is one of the core trends in the anti-aging therapy. Cardiac glycosides were recently proved to be a broad-spectrum senolytics. Here we tested senolytic properties of cardiac glycosides towards human mesenchymal stem cells (hMSCs). Cardiac glycosides had no senolytic ability towards senescent hMSCs of various origins. Using biological and bioinformatic approaches we compared senescence development in ‘cardiac glycosides-sensitive’ A549 and ‘-insensitive’ hMSCs. The absence of senolysis was found to be mediated by the effective potassium import and increased apoptosis resistance in senescent hMSCs. Weakening “antiapoptotic defense” predisposes hMSCs to senolysis. We revealed that apoptosis resistance, previously recognized as a common characteristic of senescence, in fact, is not a general feature of senescent cells. Moreover, only apoptosis-prone senescent cells are sensitive to cardiac glycosides-induced senolysis. Thus, we can speculate that the effectiveness of senolysis might depend on whether senescent cells indeed become apoptosis-resistant as compared to their proliferating counterparts. Graphic abstract

scholarly journals Bioinformatic approaches for the structure and function of membrane proteins

BMB Reports ◽  
2009 ◽  
Vol 42 (11) ◽  
pp. 697-704 ◽  
Author(s):  
Hyun-Jun Nam ◽  
Jou-Hyun Jeon ◽  
Sang-Uk Kim
Keyword(s):  
Membrane Proteins ◽  
Structure And Function ◽  
Bioinformatic Approaches ◽  
And Function

scholarly journals Genome-wide analysis of BURP genes and identification of a BURP-V gene RcBURP4 in Rosachienesis

2021 ◽  
Author(s):  
Lufeng Fu ◽  
Zhujun Zhang ◽  
Hai Wang ◽  
Xiaojuan Zhao ◽  
Lin Su ◽  
...  
Keyword(s):  
Stress Responses ◽  
Light Response ◽  
Regulatory Elements ◽  
Vital Role ◽  
Severe Drought ◽  
Comprehensive Overview ◽  
Genome Database ◽  
Genome Wide ◽  
Bioinformatic Approaches ◽  
The Rose

Abstract BURP proteins are unique to plants and may contribute greatly to growth, development, and stress responses of plants. Despite the vital role of BURP proteins, little is known about these proteins in rose (Rosa spp.). In the present study, nine genes belonging to the BURP family in R. chienesis were identified by using multiple bioinformatic approaches against the rose genome database. The nine RcBURPs, with diverse structures, were located on all chromosomes of the rose genome, except for Chr2 and Chr3. Phylogenic analysis revealed that these RcBURPs can be classified into eight subfamilies, including BNM2-like, PG1β-like, USP-like, RD22-like, BURP-V, BURP-VI, BURP-VII, and BURP-VIII. Conserved motif and exon-intron analyses indicated a conserved pattern within the same subfamily. The presumed cis-regulatory elements (CREs) within the promoter region of each RcBURP were analyzed and the results showed that all RcBURPs contained different types of CREs, including abiotic stress-, light response-, phytohormones response-, and plant growth and development-related CREs. Transcriptomic analysis revealed that a BURP-V member, RcBURP4, was induced in rose leaves and roots under mild and severe drought treatments. We then overexpressed RcBURP4 in Arabidopsis and examined its role under abscisic acid (ABA), NaCl, polyethylene glycol (PEG), and drought treatments. Furthermore, RcBURP4-silenced rose plants exhibited decreased tolerance to dehydration. The results obtained from this study provide the first comprehensive overview of RcBURPs and highlight the importance of RcBURP4 in rose plant.

scholarly journals The fungal gene cluster for biosynthesis of the antibacterial agent viriditoxin

2019 ◽  
Author(s):  
Andrew S. Urquhart ◽  
Jinyu Hu ◽  
Yit-Heng Chooi ◽  
Alexander Idnurm
Keyword(s):  
Secondary Metabolites ◽  
Gene Cluster ◽  
Gene Disruption ◽  
Biosynthetic Pathway ◽  
Fluorescent Protein ◽  
Model Species ◽  
Paecilomyces Variotii ◽  
Bioinformatic Approaches ◽  
Green Fluorescent ◽  
Fungal Gene

AbstractBackgroundViriditoxin is one of the ‘classical’ secondary metabolites produced by fungi and that has antibacterial and other activities; however, the mechanism of its biosynthesis has remained unknown.ResultsHere, a gene cluster responsible for its synthesis was identified, using bioinformatic approaches from two species that produce viriditoxin and then through gene disruption and metabolite profiling. All eight genes in the cluster inPaecilomyces variotiiwere mutated, revealing their roles in the synthesis of this molecule and establishing its biosynthetic pathway which includes an interesting Baeyer-Villiger monooxygenase catalyzed reaction. Additionally, a candidate catalytically-inactive hydrolase was identified as being required for the stereoselective biosynthesis of (M)-viriditoxin. The localization of two proteins were assessed by fusing these proteins to green fluorescent protein, revealing that at least two intracellular structures are involved in the compartmentalization of the synthesis steps of this metabolite.ConclusionsThe full pathway for synthesis of viriditoxin was established by a combination of genomics, bioinformatics, gene disruption and chemical analysis processes. Hence, this work reveals the basis for the synthesis of an understudied class of fungal secondary metabolites and provides a new model species for understanding the synthesis of biaryl compounds with a chiral axis.

Innovative bioinformatic approaches for developing peptide‐based vaccines against hypervariable viruses

2010 ◽  
Vol 89 (1) ◽  
pp. 81-89 ◽  
Author(s):  
Danylo Sirskyj ◽  
Francisco Diaz‐Mitoma ◽  
Ashkan Golshani ◽  
Ashok Kumar ◽  
Ali Azizi
Keyword(s):  
Bioinformatic Approaches
Sign in / Sign up

Export Citation Format

Share Document