scholarly journals Automated Quantitative Assessment of Proteins' Biological Function in Protein Knowledge Bases

2008 ◽  
Vol 2008 ◽  
pp. 1-7
Author(s):  
Gabriele Mayr ◽  
Günter Lepperdinger ◽  
Peter Lackner
Keyword(s):  
Functional Data ◽  
Biological Function ◽  
Sequence Data ◽  
Knowledge Bases ◽  
Computer Assisted ◽  
Biological Functions ◽  
Comprehensive Collection ◽  
Quantitative Score ◽  
Protein Sequence Data

Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

scholarly journals Gigantea: Uncovering New Functions in Flower Development

2020 ◽  
Author(s):  
Claudio Brandoli ◽  
Cesar Petri ◽  
Marcos Egea-Cortines ◽  
Julia Weiss
Keyword(s):  
Circadian Rhythm ◽  
Flower Development ◽  
Biological Function ◽  
Genome Structure ◽  
Floral Initiation ◽  
Biological Functions ◽  
Photoperiodic Flowering ◽  
Volatile Production ◽  
Hormone Signalling

GIGANTEA (GI) is a gene involved in multiple biological functions, which were analysed and are partially conserved in a series of mono- and dicotyledonous plant species. The identified biological functions include control over the circadian rhythm, light signalling, cold tolerance, hormone signalling and photoperiodic flowering. The latter function is a central role of GI, as it involves a multitude of pathways, both dependent and independent of the gene CONSTANS(CO) as well as on the basis of interaction with miRNA. The complexity of gene function of GI increases due to the existence of paralogs showing changes in genome structure as well as incidences of sub- and neofunctionalization. We present an updated report of the biological function of GI, integrating late insights into its role in floral initiation, flower development and flower volatile production.

scholarly journals Targeting Mitochondrial Proteases for Therapy of Acute Myeloid Leukemia

2021 ◽  
Author(s):  
Xinrong Xiang ◽  
Rui Bao ◽  
Yu Wu ◽  
Youfu Luo
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Cancer Metabolism ◽  
Biological Function ◽  
Biological Functions ◽  
Acute Myeloid

Targeting cancer metabolism has emerged as an attractive approach to improve therapeutic regimens in acute myeloid leukemia (AML). Mitochondrial proteases are closely related to cancer metabolism, but their biological functions have not been well characterized in AML. According to different catogory, we comprehensively reviewed the role of mitochondrial proteases in AML. This review highlights some ‘powerful’ mitochondrial protease targets, including their biological function, chemical modulators, and applicative prospect in AML.

scholarly journals Gigantea: Uncovering New Functions in Flower Development

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1142
Author(s):  
Claudio Brandoli ◽  
Cesar Petri ◽  
Marcos Egea-Cortines ◽  
Julia Weiss
Keyword(s):  
Circadian Rhythm ◽  
Flower Development ◽  
Biological Function ◽  
Genome Structure ◽  
Floral Initiation ◽  
Biological Functions ◽  
Flower Production ◽  
Photoperiodic Flowering ◽  
Hormone Signalling

GIGANTEA (GI) is a gene involved in multiple biological functions, which have been analysed and are partially conserved in a series of mono- and dicotyledonous plant species. The identified biological functions include control over the circadian rhythm, light signalling, cold tolerance, hormone signalling and photoperiodic flowering. The latter function is a central role of GI, as it involves a multitude of pathways, both dependent and independent of the gene CONSTANS(CO), as well as on the basis of interaction with miRNA. The complexity of the gene function of GI increases due to the existence of paralogs showing changes in genome structure as well as incidences of sub- and neofunctionalization. We present an updated report of the biological function of GI, integrating late insights into its role in floral initiation, flower development and volatile flower production.

Hegel's Organizational Account of Biological Functions

2020 ◽  
pp. 1-19
Author(s):  
Edgar Maraguat
Keyword(s):  
Natural Selection ◽  
Biological Function ◽  
The Other ◽  
Proper Function ◽  
Biological Functions ◽  
Real Work ◽  
Organizational Account ◽  
Philosophical Debates ◽  
Self Production

Abstract Two concepts have polarized the philosophical debates on functions since the 1970s. One is Millikan's concept of ‘proper function’, meant to capture the aetiology of biological organs and artefacts. The other is Cummins's concept of ‘dispositional function’, designed to account for the real work that functional devices perform within a system. In this paper I locate Hegel's concept of biological function in the context of those debates. Admittedly, Hegel's concept is ‘etiological’, since in his account the existence of purposive organs is explained by appeal to their purpose, yet, against Millikan's concept, Hegel's does not presuppose the phenomenon of natural selection nor derives the function of tokens from the function of types. So, my aim is, first, to present Hegel's approach to biological functions as one neither purely etiological nor purely dispositional. It will appear rather as an example of an organizational account (as those advocated today by McLaughlin, Mossio and others), that attributes function according to present performances (unlike etiological accounts) and emphasizes the role of functional parts in their self-production within the system they belong to (unlike dispositional accounts). Finally, I briefly discuss how Hegel's concept performs against common objections to organizational accounts.

Collection of Ego-Centered Network Data with Computer-Assisted Interviews

Methodology ◽  
2006 ◽  
Vol 2 (1) ◽  
pp. 7-15 ◽  
Author(s):  
Joachim Gerich ◽  
Roland Lehner
Keyword(s):  
Survey Methods ◽  
A Priori ◽  
Dynamic Structure ◽  
Computer Assisted ◽  
Network Data ◽  
Great Effort ◽  
Self Administration ◽  
Face To Face ◽  
Full Network

Although ego-centered network data provide information that is limited in various ways as compared with full network data, an ego-centered design can be used without the need for a priori and researcher-defined network borders. Moreover, ego-centered network data can be obtained with traditional survey methods. However, due to the dynamic structure of the questionnaires involved, a great effort is required on the part of either respondents (with self-administration) or interviewers (with face-to-face interviews). As an alternative, we will show the advantages of using CASI (computer-assisted self-administered interview) methods for the collection of ego-centered network data as applied in a study on the role of social networks in substance use among college students.

Aurora Kinase Inhibitors in Head and Neck Cancer

2018 ◽  
Vol 18 (3) ◽  
pp. 199-213
Author(s):  
Guangying Qi ◽  
Jing Liu ◽  
Sisi Mi ◽  
Takaaki Tsunematsu ◽  
Shengjian Jin ◽  
...  
Keyword(s):  
Head And Neck Cancer ◽  
Cancer Therapy ◽  
Kinase Inhibitors ◽  
Biological Function ◽  
Aurora Kinase ◽  
Aurora Kinases ◽  
Related Research ◽  
Chemotherapy Drugs ◽  
Aurora Kinase Inhibitors

Aurora kinases are a group of serine/threonine kinases responsible for the regulation of mitosis. In recent years, with the increase in Aurora kinase-related research, the important role of Aurora kinases in tumorigenesis has been gradually recognized. Aurora kinases have been regarded as a new target for cancer therapy, resulting in the development of Aurora kinase inhibitors. The study and application of these small-molecule inhibitors, especially in combination with chemotherapy drugs, represent a new direction in cancer treatment. This paper reviews studies on Aurora kinases from recent years, including studies of their biological function, their relationship with tumor progression, and their inhibitors.

scholarly journals Overexpressed pseudogene MT1L associated with tumor immune infiltrates and indicates a worse prognosis in BLCA

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Yanpeng Ding ◽  
Nuomin Liu ◽  
Mengge Chen ◽  
Yulian Xu ◽  
Sha Fang ◽  
...  
Keyword(s):  
Immune Cells ◽  
Biological Function ◽  
Prognostic Biomarker ◽  
Poor Survival ◽  
Common Cancer ◽  
Kaplan Meier ◽  
Cox Analysis ◽  
Kaplan Meier Plotter ◽  
Worse Prognosis

Abstract Background BLCA is a common cancer worldwide, and it is both aggressive and fatal. Immunotherapy (ICT) has achieved an excellent curative effect in BLCA; however, only some BLCA patients can benefit from ICT. MT1L is a pseudogene, and a previous study suggested that MT1L can be used as an indicator of prognosis in colorectal cancer. However, the role of MT1L in BLCA has not yet been determined. Methods Data were collected from TCGA, and logistic regression, Kaplan-Meier plotter, and multivariate Cox analysis were performed to demonstrate the correlation between the pseudogene MT1L and the prognosis of BLCA. To identify the association of MT1L with tumor-infiltrating immune cells, TIMER and TISIDB were utilized. Additionally, GSEA was performed to elucidate the potential biological function. Results The expression of MT1L was decreased in BLCA. Additionally, MT1L was positively correlated with immune cells, such as Tregs (ρ = 0.708) and MDSCs (ρ = 0.664). We also confirmed that MT1L is related to typical markers of immune cells, such as PD-1 and CTLA-4. In addition, a high MT1L expression level was associated with the advanced T and N and high grade in BLCA. Increased expression of MT1L was significantly associated with shorter OS times of BLCA patients (p < 0.05). Multivariate Cox analysis revealed that MT1L expression could be an independent prognostic factor in BLCA. Conclusion Collectively, our findings demonstrated that the pseudogene MT1L regulates the immune microenvironment, correlates with poor survival, and is an independent prognostic biomarker in BLCA.

scholarly journals Regulatory Role of microRNAs Targeting the Transcription Co-Factor ZNF521 in Normal Tissues and Cancers

2021 ◽  
Vol 22 (16) ◽  
pp. 8461
Author(s):  
Emanuela Chiarella ◽  
Annamaria Aloisio ◽  
Stefania Scicchitano ◽  
Heather Mandy Bond ◽  
Maria Mesuraca
Keyword(s):  
Transcription Factor ◽  
Molecular Mechanisms ◽  
Transitional Cell ◽  
Biological Functions ◽  
Aberrant Expression ◽  
Normal Tissues ◽  
Novel Mirna ◽  
Mirna Expression Profiling ◽  
Mirna Deregulation

Powerful bioinformatics tools have provided a wealth of novel miRNA–transcription factor networks crucial in controlling gene regulation. In this review, we focus on the biological functions of miRNAs targeting ZNF521, explaining the molecular mechanisms by which the dysregulation of this axis contributes to malignancy. ZNF521 is a stem cell-associated co-transcription factor implicated in the regulation of hematopoietic, neural, and mesenchymal stem cells. The aberrant expression of ZNF521 transcripts, frequently associated with miRNA deregulation, has been detected in several tumors including pancreatic, hepatocellular, gastric, bladder transitional cell carcinomas as well as in breast and ovarian cancers. miRNA expression profiling tools are currently identifying a multitude of miRNAs, involved together with oncogenes and TFs in the regulation of oncogenesis, including ZNF521, which may be candidates for diagnostic and prognostic biomarkers of cancer.

scholarly journals The dynamic behavior of lipid droplets in the pre-metastatic niche

2020 ◽  
Vol 11 (11) ◽  
Author(s):  
Chunliang Shang ◽  
Jie Qiao ◽  
Hongyan Guo
Keyword(s):  
Tumor Cells ◽  
Immune Cells ◽  
Stromal Cells ◽  
Lipid Droplets ◽  
Metastatic Tumor ◽  
Current Evidence ◽  
Biological Functions ◽  
Metastatic Niche ◽  
Niche Formation

AbstractThe pre-metastatic niche is a favorable microenvironment for the colonization of metastatic tumor cells in specific distant organs. Lipid droplets (LDs, also known as lipid bodies or adiposomes) have increasingly been recognized as lipid-rich, functionally dynamic organelles within tumor cells, immune cells, and other stromal cells that are linked to diverse biological functions and human diseases. Moreover, in recent years, several studies have described the indispensable role of LDs in the development of pre-metastatic niches. This review discusses current evidence related to the biogenesis, composition, and functions of LDs related to the following characteristics of the pre-metastatic niche: immunosuppression, inflammation, angiogenesis/vascular permeability, lymphangiogenesis, organotropism, reprogramming. We also address the function of LDs in mediating pre-metastatic niche formation. The potential of LDs as markers and targets for novel antimetastatic therapies will be discussed.

scholarly journals The role of m6A modification in the biological functions and diseases

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Xiulin Jiang ◽  
Baiyang Liu ◽  
Zhi Nie ◽  
Lincan Duan ◽  
Qiuxia Xiong ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Rna Modification ◽  
Biological Functions ◽  
Rna Methylation ◽  
Downstream Target ◽  
Different Types ◽  
M6a Rna Methylation

AbstractN6-methyladenosine (m6A) is the most prevalent, abundant and conserved internal cotranscriptional modification in eukaryotic RNAs, especially within higher eukaryotic cells. m6A modification is modified by the m6A methyltransferases, or writers, such as METTL3/14/16, RBM15/15B, ZC3H3, VIRMA, CBLL1, WTAP, and KIAA1429, and, removed by the demethylases, or erasers, including FTO and ALKBH5. It is recognized by m6A-binding proteins YTHDF1/2/3, YTHDC1/2 IGF2BP1/2/3 and HNRNPA2B1, also known as “readers”. Recent studies have shown that m6A RNA modification plays essential role in both physiological and pathological conditions, especially in the initiation and progression of different types of human cancers. In this review, we discuss how m6A RNA methylation influences both the physiological and pathological progressions of hematopoietic, central nervous and reproductive systems. We will mainly focus on recent progress in identifying the biological functions and the underlying molecular mechanisms of m6A RNA methylation, its regulators and downstream target genes, during cancer progression in above systems. We propose that m6A RNA methylation process offer potential targets for cancer therapy in the future.

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