scholarly journals Spectrum of protein localization in proteomes captures evolutionary relation between species

2019 ◽  
Author(s):  
Valérie Marot-Lassauzaie ◽  
Tatyana Goldberg ◽  
Burkhard Rost
Keyword(s):  
Protein Function ◽  
Homo Sapiens ◽  
Protein Localization ◽  
Model Organisms ◽  
Prediction Methods ◽  
Systematic Bias ◽  
Human Protein Atlas ◽  
Species Comparisons ◽  
The One ◽  
Evolutionary Comparisons

AbstractThe native subcellular localization or cellular compartment of a protein is the one in which it acts most often; it is one aspect of protein function. Do ten eukaryotic model organisms differ in their location spectrum, i.e. the fraction of its proteome in each of its seven major compartments? As experimental annotations of locations remain biased and incomplete, we need prediction methods to answer this question. To gauge the bias of prediction methods, we merged all available experimental annotations for the human proteome. In doing so, we found important values in both Swiss-Prot and the Human Protein Atlas (HPA). After systematic bias corrections, the complete but faulty prediction methods appeared to be more appropriate to compare location spectra between species than the incomplete more accurate experimental data. This work compared the location spectra for ten eukaryotes: Homo sapiens, Gorilla gorilla, Pan troglodytes, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Anopheles gambiae, Caenorhabitis elegans, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Overall, the predicted location spectra were similar. However, the detailed differences were significant enough to plot trees and 2D (PCA) maps relating the ten organisms using a simple Euclidean distance in seven states, corresponding to the seven studied localization classes. The relations based on the simple predicted location spectra captured aspects of cross-species comparisons usually revealed only by much more detailed evolutionary comparisons.

scholarly journals Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species

2021 ◽  
Author(s):  
Valérie Marot-Lassauzaie ◽  
Tatyana Goldberg ◽  
Jose Juan Almagro Armenteros ◽  
Henrik Nielsen ◽  
Burkhard Rost
Keyword(s):  
Protein Function ◽  
Homo Sapiens ◽  
Evolutionary Relationship ◽  
Subcellular Location ◽  
Model Organisms ◽  
Prediction Methods ◽  
Systematic Bias ◽  
Phylogenetic Relations ◽  
The One ◽  
Cellular Compartments

AbstractThe native subcellular location (also referred to as localization or cellular compartment) of a protein is the one in which it acts most frequently; it is one aspect of protein function. Do ten eukaryotic model organisms differ in their location spectrum, i.e., the fraction of its proteome in each of seven major cellular compartments? As experimental annotations of locations remain biased and incomplete, we need prediction methods to answer this question. After systematic bias corrections, the complete but faulty prediction methods appeared to be more appropriate to compare location spectra between species than the incomplete more accurate experimental data. This work compared the location spectra for ten eukaryotes: Homo sapiens (human), Gorilla gorilla (gorilla), Pan troglodytes (chimpanzee), Mus musculus (mouse), Rattus norvegicus (rat), Drosophila melanogaster (fruit/vinegar fly), Anopheles gambiae (African malaria mosquito), Caenorhabitis elegans (nematode), Saccharomyces cerevisiae (baker’s yeast), and Schizosaccharomyces pombe (fission yeast). The two largest classes were predicted to be the nucleus and the cytoplasm together accounting for 47–62% of all proteins, while 7–21% of the proteins were predicted in the plasma membrane and 4–15% to be secreted. Overall, the predicted location spectra were largely similar. However, in detail, the differences sufficed to plot trees (UPGMA) and 2D (PCA) maps relating the ten organisms using a simple Euclidean distance in seven states (location classes). The relations based on the simple predicted location spectra captured aspects of cross-species comparisons usually revealed only by much more detailed evolutionary comparisons. Most interestingly, known phylogenetic relations were reproduced better by paralog-only than by ortholog-only trees.

scholarly journals Convolutional Neural Network-Based Artificial Intelligence for Classification of Protein Localization Patterns

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 264
Author(s):  
Kaisa Liimatainen ◽  
Riku Huttunen ◽  
Leena Latonen ◽  
Pekka Ruusuvuori
Keyword(s):  
Neural Network ◽  
Artificial Intelligence ◽  
Convolutional Neural Network ◽  
High Throughput ◽  
Protein Function ◽  
Protein Localization ◽  
Convolutional Network ◽  
High Throughput Analysis ◽  
Fully Convolutional Network

Identifying localization of proteins and their specific subpopulations associated with certain cellular compartments is crucial for understanding protein function and interactions with other macromolecules. Fluorescence microscopy is a powerful method to assess protein localizations, with increasing demand of automated high throughput analysis methods to supplement the technical advancements in high throughput imaging. Here, we study the applicability of deep neural network-based artificial intelligence in classification of protein localization in 13 cellular subcompartments. We use deep learning-based on convolutional neural network and fully convolutional network with similar architectures for the classification task, aiming at achieving accurate classification, but importantly, also comparison of the networks. Our results show that both types of convolutional neural networks perform well in protein localization classification tasks for major cellular organelles. Yet, in this study, the fully convolutional network outperforms the convolutional neural network in classification of images with multiple simultaneous protein localizations. We find that the fully convolutional network, using output visualizing the identified localizations, is a very useful tool for systematic protein localization assessment.

scholarly journals Myosinome: A Database of Myosins from Select Eukaryotic Genomes to Facilitate Analysis of Sequence-Structure-Function Relationships

2012 ◽  
Vol 6 ◽  
pp. BBI.S9902 ◽  
Author(s):  
Divya P. Syamaladevi ◽  
Margaret S Sunitha ◽  
S. Kalaimathy ◽  
Chandrashekar C. Reddy ◽  
Mohammed Iftekhar ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Atp Hydrolysis ◽  
Homo Sapiens ◽  
Relevant Literature ◽  
Myosin Ii ◽  
Coiled Coil ◽  
Structural Features ◽  
Model Organisms ◽  
Congenital Diseases ◽  
C Elegans

Myosins are one of the largest protein superfamilies with 24 classes. They have conserved structural features and catalytic domains yet show huge variation at different domains resulting in a variety of functions. Myosins are molecules driving various kinds of cellular processes and motility until the level of organisms. These are ATPases that utilize the chemical energy released by ATP hydrolysis to bring about conformational changes leading to a motor function. Myosins are important as they are involved in almost all cellular activities ranging from cell division to transcriptional regulation. They are crucial due to their involvement in many congenital diseases symptomatized by muscular malfunctions, cardiac diseases, deafness, neural and immunological dysfunction, and so on, many of which lead to death at an early age. We present Myosinome, a database of selected myosin classes (myosin II, V, and VI) from five model organisms. This knowledge base provides the sequences, phylogenetic clustering, domain architectures of myosins and molecular models, structural analyses, and relevant literature of their coiled-coil domains. In the current version of Myosinome, information about 71 myosin sequences belonging to three myosin classes (myosin II, V, and VI) in five model organisms ( Homo Sapiens, Mus musculus, D. melanogaster, C. elegans and S. cereviseae) identified using bioinformatics surveys are presented, and several of them are yet to be functionally characterized. As these proteins are involved in congenital diseases, such a database would be useful in short-listing candidates for gene therapy and drug development. The database can be accessed from http://caps.ncbs.res.in/myosinome .

scholarly journals Identification of high-efficiency 3′GG gRNA motifs in indexed FASTA files with ngg2

2015 ◽  
Vol 1 ◽  
pp. e33 ◽  
Author(s):  
Elisha D. Roberson
Keyword(s):  
High Efficiency ◽  
Homo Sapiens ◽  
Model Organisms ◽  
Proof Of Concept ◽  
Protein Coding ◽  
C Elegans ◽  
Protein Coding Genes ◽  
Starting Point ◽  
Command Line Tool ◽  
Reference Genomes

CRISPR/Cas9 is emerging as one of the most-used methods of genome modification in organisms ranging from bacteria to human cells. However, the efficiency of editing varies tremendously site-to-site. A recent report identified a novel motif, called the 3′GG motif, which substantially increases the efficiency of editing at all sites tested inC. elegans. Furthermore, they highlighted that previously published gRNAs with high editing efficiency also had this motif. I designed a Python command-line tool, ngg2, to identify 3′GG gRNA sites from indexed FASTA files. As a proof-of-concept, I screened for these motifs in six model genomes:Saccharomyces cerevisiae,Caenorhabditis elegans,Drosophila melanogaster,Danio rerio,Mus musculus, andHomo sapiens. I also scanned the genomes of pig (Sus scrofa) and African elephant (Loxodonta africana) to demonstrate the utility in non-model organisms. I identified more than 60 million single match 3′GG motifs in these genomes. Greater than 61% of all protein coding genes in the reference genomes had at least one unique 3′GG gRNA site overlapping an exon. In particular, more than 96% of mouse and 93% of human protein coding genes have at least one unique, overlapping 3′GG gRNA. These identified sites can be used as a starting point in gRNA selection, and the ngg2 tool provides an important ability to identify 3′GG editing sites in any species with an available genome sequence.

scholarly journals iProteinDB: an integrative database of Drosophila post-translational modifications

2018 ◽  
Author(s):  
Yanhui Hu ◽  
Richelle Sopko ◽  
Verena Chung ◽  
Romain A. Studer ◽  
Sean D. Landry ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Function ◽  
Large Scale ◽  
Model Organisms ◽  
General Strategy ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Functional Sites ◽  
Evolutionarily Conserved ◽  
And Function

AbstractPost-translational modification (PTM) serves as a regulatory mechanism for protein function, influencing stability, protein interactions, activity and localization, and is critical in many signaling pathways. The best characterized PTM is phosphorylation, whereby a phosphate is added to an acceptor residue, commonly serine, threonine and tyrosine. As proteins are often phosphorylated at multiple sites, identifying those sites that are important for function is a challenging problem. Considering that many phosphorylation sites may be non-functional, prioritizing evolutionarily conserved phosphosites provides a general strategy to identify the putative functional sites with regards to regulation and function. To facilitate the identification of conserved phosphosites, we generated a large-scale phosphoproteomics dataset from Drosophila embryos collected from six closely-related species. We built iProteinDB (https://www.flyrnai.org/tools/iproteindb/), a resource integrating these data with other high-throughput PTM datasets, including vertebrates, and manually curated information for Drosophila. At iProteinDB, scientists can view the PTM landscape for any Drosophila protein and identify predicted functional phosphosites based on a comparative analysis of data from closely-related Drosophila species. Further, iProteinDB enables comparison of PTM data from Drosophila to that of orthologous proteins from other model organisms, including human, mouse, rat, Xenopus laevis, Danio rerio, and Caenorhabditis elegans.

scholarly journals From holism to compositionality: memes and the evolution of segmentation, syntax, and signification in music and language

2015 ◽  
Vol 8 (4) ◽  
pp. 463-500 ◽  
Author(s):  
STEVEN JAN
Keyword(s):  
Homo Sapiens ◽  
Logical Form ◽  
Semantic Content ◽  
Information Encoding ◽  
Modern Language ◽  
Conceptual Structures ◽  
Music And Language ◽  
Initial Support ◽  
The One ◽  
Universal Darwinism

abstractSteven Mithen argues that language evolved from an antecedent he terms “Hmmmmm, [meaning it was] Holistic, manipulative, multi-modal, musical and mimetic”. Owing to certain innate and learned factors, a capacity for segmentation and cross-stream mapping in early Homo sapiens broke the continuous line of Hmmmmm, creating discrete replicated units which, with the initial support of Hmmmmm, eventually became the semantically freighted words of modern language. That which remained after what was a bifurcation of Hmmmmm arguably survived as music, existing as a sound stream segmented into discrete units, although one without the explicit and relatively fixed semantic content of language. All three types of utterance – the parent Hmmmmm, language, and music – are amenable to a memetic interpretation which applies Universal Darwinism to what are understood as language and musical memes. On the basis of Peter Carruthers’ distinction between ‘cognitivism’ and ‘communicativism’ in language, and William Calvin’s theories of cortical information encoding, a framework is hypothesized for the semantic and syntactic associations between, on the one hand, the sonic patterns of language memes (‘lexemes’) and of musical memes (‘musemes’) and, on the other hand, ‘mentalese’ conceptual structures, in Chomsky’s ‘Logical Form’ (LF).

scholarly journals Innovative technologies and living spaces; Updated living standards according to the evolution of homo sapiens

2020 ◽  
pp. 91-108
Author(s):  
Alp Karaca
Keyword(s):  
French Revolution ◽  
Social Life ◽  
New Technologies ◽  
Homo Sapiens ◽  
Study Data ◽  
Living Standards ◽  
Innovative Technology ◽  
Human Beings ◽  
Social Lives ◽  
The One

Homosapiens is the common family name for contemporary human beings. There are different kinds of homo species but the most recent one with the most improved abilities are human beings of the present era, who have adapted themselves to the new technologies and life conditions by improving themselves. The substantial improvements in technology started with the French Revolution in 1799. Initially, technology helped human beings in the production and industry sectors. Thereafter, in the 1990s, technology penetrated living spaces, firstly helping with household duties and then impacting social life, first with the radio and later with the television. Living spaces started to change through the organisation of spaces, and most houses were organised according to location reserved for the television. This is the biggest change brought about by technology in living spaces. The expectations of human beings were on the rise simultaneously with economic welfare and consumption-based demands. In the 2000s, phyisical limitations occurred, while expectations increased even more. These were constraints over time, materials and economy, and the solution came from technology via virtual reality and generated cyber spaces, which were without limits, economical and surpassed the built environments. Due to the lack of physical conditions, built envionments ceded their place to virtual living spaces and virtual cities. In the present study, data collection was undertaken via a study of innovations within living spaces and also via an observation of social lives within living spaces. The present article aims to present what can be foreseen, on the basis of cause and effect, concerning the impacts of the current evolution on the one hand and massive outbreaks of viruses on the other hand, the impacts on the physical spaces of the homosapiens species that have succeeded in adapting to all the changes that they have come across from their beginnings until the present era, the impacts that both phenomena will have on the current living standards and living spaces of humans and what changes human living spaces will undergo in the ongoing process of evolution. Human beings will continue renewing themselves throughout the said phenomena before concluding their process of evolution.   Keywords: Innovative, technology, living spaces, living standards, homosapiens.

Substance and Cognition of Biological Phenomena

1970 ◽  
Vol 4 (1) ◽  
pp. 55-71
Author(s):  
Piotr Lenartowicz
Keyword(s):  
Homo Sapiens ◽  
Chemical Substance ◽  
The Other ◽  
Natural Behavior ◽  
Other Hand ◽  
Biological Phenomena ◽  
The One ◽  
Living Being

Biologists are not used to the term „substance". They prefer to say „a living being", „an organism", a „specimen of species Homo sapiens'' - for instance. Chemists, on the other hand, when they say „this is a new substance" they usually mean the same Aristotle would mean - I think. The chemical meaning of the term „substance" is closest to the one I am going to discuss in this paper. To know a substance, one has to accumulate and store a multitude of different forms of evidence concerning this „natural behavior". So that concept of the „nature" of a given chemical substance is necessarily very complex and it cannot result from a single sensation, or a momentary observation

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