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Cellular Structures

Cellular Structures: Discover the diverse array of structures that form the building blocks of cells.
From organelles and membranes to the extracellular matrix, explore the intricate components that enable cellular function and facilitate communication within living organisms.
Understand the importance of cellular structures in biological procesess, and learn how researchers can optimize experimental protocols to enhnace reproducibility and accuracy when studying these fundamental elements of life.

Most cited protocols related to «Cellular Structures»

By default, the GeneMANIA prediction server uses one of two different adaptive network weighting methods. For longer gene lists, GeneMANIA uses the basic weighting method [called GeneMANIAEntry-1 in (10 (link)) and called ‘assigned based on query genes’ on the web site] and weights each network so that after the networks are combined, the query genes interact as much as possible with each other while interacting as little as possible with genes not in the list. GeneMANIA learns from longer gene lists, allowing a gene list-specific network weighting to be calculated. Shorter gene lists do not contain enough information for GeneMANIA to learn which networks mediate the underlying functional relationship among the genes. For short gene lists, GeneMANIA uses a similar principle to weight networks, but tries to reproduce Gene Ontology (GO) biological process co-annotation patterns rather than the gene list. This method is described in detail in (11 ). The user may choose other adaptive and non-adaptive weighting methods in the advanced options panel, found directly under the gene query text box. The two non-adaptive methods are the most conservative options and work well on small gene lists (10 (link)). These methods allow users to choose either to weight every individual network equally, or weight each class (e.g. co-expression and protein interaction) of network equally. Network weights can also be assigned based on how well they reproduce GO co-annotation patterns for that organism in the molecular function, biological process or cellular component hierarchies. Note that the annotation-based weighting may slightly inflate weights for networks on which current annotations are based or for networks that were derived based on co-annotation patterns of genes. The networks most affected by this inflation are the older, smaller scale protein and genetic interaction studies and networks classified as ‘predicted’. However, this inflation does not seem to have a large impact on weights and may be largely avoided by only using networks derived from high-throughput assays with the annotation-based schemes.
Publication 2010
Acclimatization Biological Processes Biopharmaceuticals Cellular Structures Gene Annotation Gene Regulatory Networks Genes High-Throughput Screening Proteins Reproduction
Statistical enrichment of ontology terms is dependent upon the genome-wide gene set used in the analysis. GREAT currently supports testing of human (Homo sapiens NCBI Build 36.1, or UCSC hg18) and mouse (Mus musculus NCBI Build 37, or UCSC mm9). To limit the gene sets to only high-confidence genes and gene predictions, we use only the subset of the UCSC Known Genes45 that are protein coding, are on assembled chromosomes and possess at least one meaningful GO annotation14 (link). GO is an ontological representation of information related to the biological processes, cellular components and molecular functions of genes. We rely on the idea that if a gene has been annotated for function it should be included in the gene set, and if no function has been ascribed to a gene its status may be unclear and thus it is best omitted from the gene set. In GREAT version 1.1.3, we use GO data downloaded on 5 March 2009 for human and 23 March 2009 for mouse, leading to gene sets of 17,217 and 17,506 genes for human and mouse, respectively.
A single gene may have multiple splice variants. As annotations are generally given at the gene level, GREAT uses a single transcription start site (TSS) to specify the location of each gene. The TSS used is that of the ‘canonical isoform’ of the gene as defined by the UCSC Known Genes track45 .
Publication 2010
Biological Processes Cellular Structures Chromosomes Genes Genome Homo sapiens Mice, House Mice, Laboratory Operator, Genetic Protein Isoforms Proteins Transcription Initiation Site
DIANA-miRPath v3.0 database has been extended to support features such as microRNA nomenclature history (18 ), a novel miRNA/gene name suggestion mechanism, as well as analysis support for seven species (H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, G. gallus and D. rerio). The new database schema incorporates KEGG pathways, as well as GO and GOSlim annotations, enabling functional annotation of miRNAs and miRNA combinations using all datasets, or their subsets (GO cellular component, biological processes or molecular function). Gene and miRNA annotations are derived from Ensembl (19 (link)) and miRBase (20 (link)), respectively. Single nucleotide polymorphism locations and pathogenicity are derived from dbSNP (21 (link)).
miRNA:gene interactions are derived from the in silico miRNA target prediction algorithms: DIANA-microT-CDS and TargetScan 6.2, the latter in both Context+ and Conservation modes. DIANA-microT-CDS is the fifth version of the microT algorithm (3 (link)). It is a highly accurate target prediction algorithm trained against CLIP-Seq datasets, enabling target prediction in 3′ UTR and CDS mRNA regions. The user of DIANA-miRPath v3.0 can also utilize experimentally supported interactions from DIANA-TarBase v.7.0. TarBase v7.0 incorporates more than half a million experimentally supported miRNA:gene interactions derived from hundreds of publications and more than 150 CLIP-Seq libraries (17 (link)). The number of indexed interactions is 9–250-fold higher compared to any other manually curated database. The user of miRPath v3.0 can harness this wealth of information and substitute or combine in silico predicted targets with high quality experimentally validated interactions. Currently, this functionality is supported for H. sapiens and M. musculus and C. elegans, since most relevant wet-lab experiments correspond to these species. As more experimental data become available for other organisms in DIANA-TarBase, the experimentally supported functional analysis module will be further extended.
Publication 2015
Biological Processes Caenorhabditis elegans Cellular Structures Cross-Linking and Immunoprecipitation Followed by Deep Sequencing Drosophila melanogaster Genes MicroRNAs Muscle Tissue Pathogenicity RNA, Messenger Single Nucleotide Polymorphism Zebrafish
To account for proteins targeted to some of the common bacterial hyperstructures and host-destined SCLs, new subcategory localizations have been introduced in PSORTb 3.0, as listed in Table 1. This represents, to our knowledge, the first implementation of subcategories for primary SCL localizations, for an SCL predictor. These subcategory localizations for a protein were identified using the SCL-BLAST module, which infers localization by homology using criteria that are of measured high precision (Nair and Rost, 2002 (link)). Proteins detected to have a secondary localization are also predicted as one of the four main categories for Gram-positive bacteria or one of five main compartments for Gram-negative bacteria (or similarly for those bacteria with atypical cell structures). Any protein exported past the outer-most layer of the bacterial cell is considered as extracellular, whereas proteins localized to one of the membranes that are part of a hyperstructure (such as the flagellum) are identified both as an inner or outer membrane protein as well as a protein of that hyperstructure. The basal components of the flagellum are not annotated as such, since they are often homologous to proteins that are not part of the flagellar apparatus (for example, a general ATPase).

New subcategory SCLs predicted by PSORTb 3.0

SCL subcategoriesDescription
Host-associatedAny proteins destined to the host cell cytoplasm, cell membrane or nucleus by any of the bacterial secretion systems
Type III secretionComponents of the Type III secretion apparatus
FimbrialComponents of a bacterial or archaeal fimbrium or pilus
FlagellarComponents of a bacterial or archaeal flagellum
SporeComponents of a spore
Publication 2010
Adenosine Triphosphatases Archaea Bacteria Bacterial Fimbria Cell Nucleus Cells Cellular Structures Cytoplasm Flagella Gram-Positive Bacteria Gram Negative Bacteria Membrane Proteins Plasma Membrane Proteins secretion Spores Staphylococcal Protein A Tissue, Membrane

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Publication 2019
Biological Processes Bone Marrow CD8-Positive T-Lymphocytes Cells Cellular Structures Gene Expression Genes Genes, vif Population Group Single-Cell RNA-Seq Tissue Donors

Most recents protocols related to «Cellular Structures»

Example 3

SLMs were first subjected to X-ray diffraction (XRD) to decipher any order arising due to self-assembly of cellular components. XRD spectra shown in FIG. 10A indicate that both EC-SLM and LR-SLM have a main diffraction peak corresponding to a d-spacing value of 0.44 nm, while EC-SLM has two additional ordering of 0.88 nm and 0.23 nm (FIG. 10A). Although, it is difficult to assign the identity of these peaks, XRD spectra do establish that SLMs are amorphous materials. Thermal gravimetric analysis (TGA) of SLMs showed that the material degrades above 130° C., while the earlier weight loss could be attributed to loss of water (FIG. 11). Differential scanning calorimetry (DSC) investigation of EC-SLM showed a glass-transition-like second-order transition (50-60° C.) during the first cycle of the heating curve (FIG. 12). However, the successive second and third cycles of DSC did not reveal the presence of such transitions, which can be attributed to the probable role of water acting as a plasticizer. Similar features were also observed for the DSC traces of LR-SLM and SC-SLM (FIG. 13). EC-SLM appeared to be transparent but the absorption spectra recorded in the visible range clearly showed that SLMs have less than 10% transparency (FIG. 15).

Patent 2024
Calorimetry, Differential Scanning Cellular Structures Physical Examination Plasticizers Sirolimus Vitrification X-Ray Diffraction
The participants in these
activities were 60 fourth-year university-level
students from Chemistry and Chemistry & Material Sciences areas.
They were separated into two groups that followed the same activities.
During the sessions, the 30 subjects shared the same classroom and
were instructed by the same teacher. A survey conducted at the beginning
of the semester showed that none of them had any prior experience
with PDB or PyMOL.
The activities were divided into three 2
h class sessions.

Session
1
. The students were instructed
in the basic skills of PDB and PyMOL software required to visualize
and manipulate macromolecular structures. As an example for training,
the spike protein of SARS-CoV-2 was employed.

Session 2. PyMOL was used to manipulate
and explain the structure of the ACE2 receptor cell, along with its
complexes with the SARS-CoV-2 spike protein.

Session 3. Structural analysis of several
antibodies in complex with the spike protein were studied. Finally,
students were able to answer the question: how is it explained
chemically that vaccines save lives?

At the end of this session, an anonymous survey was carried
out
in which the students were requested to assess different aspects of
their experience.
Publication 2023
ACE2 protein, human Cellular Structures Molecular Structure M protein, multiple myeloma spike protein, SARS-CoV-2 Student Vaccines
The protein–protein interaction (PPI) network was built and downloaded with the STRING database [11 (link)], and the top 10 hub genes were obtained using the CytoHubba [12 (link)] method after visualization with Cytoscape.
The mRNA groups with functional significance in cancer were clustered with the MCODE plug-in, according to the following criteria: MCODE score > 5, degree cut-off = 2, node score cut-off = 0.2, maximum depth = 100, and K-core = 2. We studied the biological functions and signaling mechanisms of the top three DEM clusters. Gene Ontology (GO) annotation included three aspects: BP, molecular function, and cellular component. The Kyoto Encyclopedia of Genes and Genomes (KEGG) was used to identify the possible pathways in which the molecule was involved, and the screening criterion was set at p < 0.05.
Publication 2023
Biological Processes Cellular Structures Gene Annotation Genes Genome Malignant Neoplasms RNA, Messenger
All the SNPs in SZ-PRS under a certain p value threshold were extracted and mapped to the corresponding genes where they were located based on dbSNP database. A gene list was obtained and uploaded to the online tool DAVID Bioinformatics Resources v6.8 (https://david.ncifcrf.gov/,) [34 (link), 35 (link)] for the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) [36 (link)] pathway analyses. The functions of genes were annotated with three GO terms: biological process (BP), cellular component (CC) and molecular function (MF). Multiple testing corrections were performed with Benjamini method (significance level at 0.05).
Publication 2023
Biological Processes Cellular Structures Genes Genome Operator, Genetic Single Nucleotide Polymorphism
The GO database describes our knowledge of the biological domain regarding molecular functions, cellular components, and biological processes. According to the relationship of pathways in the KEGG database, the interaction network of a significant pathway was constructed to find the core pathway that plays a key role [12 (link)–14 ]. Fisher’s exact test was used to select significant GO categories and KEGG pathways, and the significance threshold was defined as P values < 0.05.
Publication 2023
Biological Processes Biopharmaceuticals Cellular Structures

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More about "Cellular Structures"

Cellular structures are the diverse array of components that make up the building blocks of cells.
These include organelles, membranes, the extracellular matrix, and other fundamental elements that enable cellular function and communication within living organisms.
Understanding the importance of cellular structures is crucial for biological processes and researchers can optimize experimental protocols to enhance reproducibility and accuracy when studying these essential elements of life.
Cellular structures include a wide range of components, such as the nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes, peroxisomes, and the cytoskeleton.
These structures play crucial roles in cellular activities like energy production, protein synthesis, and intracellular transport.
Additionally, the extracellular matrix provides structural support and facilitates cell-to-cell communication.
Researchers can utilize a variety of techniques and reagents to study cellular structures, such as fluorescence microscopy with DAPI staining, Triton X-100 for membrane permeabilization, and TRIzol reagent for RNA extraction.
Bioinformatics tools like Ingenuity Pathway Analysis (IPA) can also help researchers analyze the complex pathways and interactions involving cellular structures.
To enhance the reproducibility and accuracy of their experiments, researchers can optimize their protocols by comparing different methods and products, such as those found in the comprehensive database of PubCompare.ai.
This AI-driven platform enables researchers to identify the best protocols and products for their specific research needs, improving the efficiency and reliability of their experiments.
Whether you're studying organelle function, extracellular matrix dynamics, or any other aspect of cellular structures, understanding the key components and utilizing the right experimental tools and techniques can be a game-changer in your research.
Stay up-to-date with the latest advancements in this field and leverage the power of AI-driven platforms like PubCompare.ai to enhance the quality and impact of your work.