scholarly journals The non-power model of the genetic code: a paradigm for interpreting genomic information

2016 ◽  
Vol 374 (2063) ◽  
pp. 20150062 ◽  
Author(s):  
Diego Luis Gonzalez ◽  
Simone Giannerini ◽  
Rodolfo Rosa
Keyword(s):  
Genetic Code ◽  
Power Model ◽  
Mathematical Framework ◽  
Genomic Information ◽  
Unified Framework ◽  
Hidden Symmetries ◽  
Protein Coding ◽  
The Core ◽  
Domains Of Life ◽  
Mitochondrial Code

In this article, we present a mathematical framework based on redundant (non-power) representations of integer numbers as a paradigm for the interpretation of genomic information. The core of the approach relies on modelling the degeneracy of the genetic code. The model allows one to explain many features and symmetries of the genetic code and to uncover hidden symmetries. Also, it provides us with new tools for the analysis of genomic sequences. We review briefly three main areas: (i) the Euplotid nuclear code, (ii) the vertebrate mitochondrial code, and (iii) the main coding/decoding strategies used in the three domains of life. In every case, we show how the non-power model is a natural unified framework for describing degeneracy and deriving sound biological hypotheses on protein coding. The approach is rooted on number theory and group theory; nevertheless, we have kept the technical level to a minimum by focusing on key concepts and on the biological implications.

scholarly journals Identification and characterization of cis-regulatory elements for photoreceptor type-specific transcription in zebrafish

2019 ◽  
Author(s):  
Wei Fang ◽  
Yi Wen ◽  
Xiangyun Wei
Keyword(s):  
Core Promoter ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Protein Coding ◽  
Core Promoters ◽  
Protein Coding Genes ◽  
The Core ◽  
Cell Type Specific ◽  
Identification And Characterization

AbstractTissue-specific or cell type-specific transcription of protein-coding genes is controlled by both trans-regulatory elements (TREs) and cis-regulatory elements (CREs). However, it is challenging to identify TREs and CREs, which are unknown for most genes. Here, we describe a protocol for identifying two types of transcription-activating CREs—core promoters and enhancers—of zebrafish photoreceptor type-specific genes. This protocol is composed of three phases: bioinformatic prediction, experimental validation, and characterization of the CREs. To better illustrate the principles and logic of this protocol, we exemplify it with the discovery of the core promoter and enhancer of the mpp5b apical polarity gene (also known as ponli), whose red, green, and blue (RGB) cone-specific transcription requires its enhancer, a member of the rainbow enhancer family. While exemplified with an RGB cone-specific gene, this protocol is general and can be used to identify the core promoters and enhancers of other protein-coding genes.

scholarly journals Widespread use of the “ascidian” mitochondrial genetic code in tunicates

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 2072
Author(s):  
Julien Pichon ◽  
Nicholas M. Luscombe ◽  
Charles Plessy
Keyword(s):  
Genetic Code ◽  
Stop Codon ◽  
Mitochondrial Protein ◽  
Sequence Alignments ◽  
Additional Species ◽  
Multiple Sequence ◽  
Oikopleura Dioica ◽  
Mitochondrial Genetic Code ◽  
Mitochondrial Sequences ◽  
Mitochondrial Code

Background: Ascidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBI GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences. Methods: We collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes. Results: All tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile → Met) and TGA (Trp → Arg) codons. Conclusions: We recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional species-specific differences.

Scholastická logika „vědění“ I.

2018 ◽  
Vol 15 (5) ◽  
pp. 127-205
Author(s):  
Miroslav Hanke ◽  
Keyword(s):  
Middle Ages ◽  
Epistemic Logic ◽  
Unified Framework ◽  
Founding Father ◽  
The Core ◽  
Cognitive Operations ◽  
Conceptual Background ◽  
John Wyclif ◽  
Negative Introspection ◽  
Positive Introspection

Fourteenth-century logic gave rise, among others, to the genre De scire et dubitare, which offered a unified framework for discussing different forms of epistemic sophisms by utilising the underlying systems of epistemic logic. One of the problems introduced in this context already by the founding father of this genre, William Heytesbury, was the so-called axiom of positive introspection, i.e., the principle that an agent who knows that something is the case, knows that she knows that it is the case. Owing to Heytesbury’s enormous popularity in the subsequent centuries, discussion of this problem became relatively widespread. This debate was addressed already in Boh’s seminal Epistemic Logic in the Later Middle Ages, which, despite its limitations acknowledged by its author, is a standard source. The present study elaborates on Boh by extending the corpus of his works (both in the sense of including new authors and of utilising manuscripts along with printed editions) and drawing new connections based on that. The core of the survey consists of an analysis of the positions of William Heytesbury and John Wyclif (both pertaining to the context of Merton College), their Italian reception by Peter of Mantua, and the “continental” reception of Heytesbury by John of Holland. The main goals of this study are to formalise the key arguments, which makes it possible to address the underlying systems of epistemic logic and their respective “strength”, and to articulate the conceptual background of those arguments and systems (the concepts of evidence, attention, and order of cognitive operations). The gist of the debate is, on one of the sides, an attempt to prove that it is impossible to doubt whether one knows that something is the case by employing whether the principles of positive introspection and of distribution of knowledge over implication, or the principles of positive and negative introspection combined.

scholarly journals Resource conservation manifests in the genetic code

Science ◽  
2020 ◽  
Vol 370 (6517) ◽  
pp. 683-687
Author(s):  
Liat Shenhav ◽  
David Zeevi
Keyword(s):  
Genetic Code ◽  
Nutrient Limitation ◽  
Nitrogen Availability ◽  
Resource Conservation ◽  
Marine Microbes ◽  
Carbon And Nitrogen ◽  
Selective Pressures ◽  
Domains Of Life ◽  
Cell Data ◽  
Competition For Resources

Nutrient limitation drives competition for resources across organisms. However, much is unknown about how selective pressures resulting from nutrient limitation shape microbial coding sequences. Here, we study this “resource-driven selection” by using metagenomic and single-cell data of marine microbes, alongside environmental measurements. We show that a significant portion of the selection exerted on microbes is explained by the environment and is associated with nitrogen availability. Notably, this resource conservation optimization is encoded in the structure of the standard genetic code, providing robustness against mutations that increase carbon and nitrogen incorporation into protein sequences. This robustness generalizes to codon choices from multiple taxa across all domains of life, including the human genome.

scholarly journals Recursive subtyping revealed

2002 ◽  
Vol 12 (6) ◽  
pp. 511-548 ◽  
Author(s):  
VLADIMIR GAPEYEV ◽  
MICHAEL Y. LEVIN ◽  
BENJAMIN C. PIERCE
Keyword(s):  
Programming Language ◽  
Efficient Implementation ◽  
Basic Theory ◽  
Mathematical Framework ◽  
Fundamental Theory ◽  
The Core ◽  
End To End ◽  
Declarative Specifications

Algorithms for checking subtyping between recursive types lie at the core of many programming language implementations. But the fundamental theory of these algorithms and how they relate to simpler declarative specifications is not widely understood, due in part to the difficulty of the available introductions to the area. This tutorial paper offers an ‘end-to-end’ introduction to recursive types and subtyping algorithms, from basic theory to efficient implementation, set in the unifying mathematical framework of coinduction.

scholarly journals Tracing the evolution of the plastome and mitogenome in the Chloropicophyceae uncovered convergent tRNA gene losses and a variant plastid genetic code

2019 ◽  
Author(s):  
Monique Turmel ◽  
Adriana Lopes dos Santos ◽  
Christian Otis ◽  
Roxanne Sergerie ◽  
Claude Lemieux
Keyword(s):  
Genetic Code ◽  
Trna Gene ◽  
Marine Phytoplankton ◽  
Trna Genes ◽  
Protein Coding ◽  
Organelle Genomes ◽  
Phytoplankton Communities ◽  
Plastid Protein ◽  
Intergenic Regions ◽  
Phylogenetic Affinities

AbstractThe tiny green algae belonging to the Chloropicophyceae play a key role in marine phytoplankton communities; this newly erected class of prasinophytes comprises two genera (Chloropicon and Chloroparvula) containing each several species. We sequenced the plastomes and mitogenomes of eight Chloropicon and five Chloroparvula species to better delineate the phylogenetic affinities of these taxa and to infer the suite of changes that their organelle genomes sustained during evolution. The relationships resolved in organelle-based phylogenomic trees were essentially congruent with previously reported rRNA trees, and similar evolutionary trends but distinct dynamics were identified for the plastome and mitogenome. Although the plastome sustained considerable changes in gene content and order at the time the two genera split, subsequently it remained stable and maintained a very small size. The mitogenome, however, was remodeled more gradually and showed more fluctuation in size, mainly as a result of expansions/contractions of intergenic regions. Remarkably, the plastome and mitogenome lost a common set of three tRNA genes, with the trnI(cau) and trnL(uaa) losses being accompanied with important variations in codon usage. Unexpectedly, despite the disappearance of trnI(cau) from the plastome in the Chloroparvula lineage, AUA codons (the codons recognized by this gene product) were detected in certain plastid genes. By comparing the sequences of plastid protein-coding genes from chloropicophycean and phylogenetically diverse chlorophyte algae with those of the corresponding predicted proteins, we discovered that the AUA codon was reassigned from isoleucine to methionine in Chloroparvula. This noncanonical genetic code has not previously been uncovered in plastids.

scholarly journals A unified framework for dissecting the effects of common signals on functional and effective connectivity analyses: power, coherence, and Granger causality

2017 ◽  
Author(s):  
Dror Cohen ◽  
Naotsugu Tsuchiya
Keyword(s):  
Granger Causality ◽  
Effective Connectivity ◽  
Reference Electrode ◽  
Mathematical Framework ◽  
Connectivity Analysis ◽  
Unified Framework ◽  
Special Cases ◽  
Recorded Data ◽  
The Common ◽  
Common Signal

AbstractWhen analyzing neural data it is important to consider the limitations of the particular experimental setup. An enduring issue in the context of electrophysiology is the presence of common signals. For example a non-silent reference electrode adds a common signal across all recorded data and this adversely affects functional and effective connectivity analysis. To address the common signals problem, a number of methods have been proposed, but relatively few detailed investigations have been carried out. We address this gap by analyzing local field potentials recorded from the small brains of fruit flies. We conduct our analysis following a solid mathematical framework that allows us to make precise predictions regarding the nature of the common signals. We demonstrate how a framework that jointly analyzes power, coherence and quantities from the Granger causality framework allows us to detect and assess the nature of the common signals. Our analysis revealed substantial common signals in our data, in part due to a non-silent reference electrode. We further show that subtracting spatially adjacent signals (bipolar rereferencing) largely removes the effects of the common signals. However, in some special cases this operation itself introduces a common signal. The mathematical framework and analysis pipeline we present can readily be used by others to detect and assess the nature of the common signals in their data, thereby reducing the chance of misinterpreting the results of functional and effective connectivity analysis.

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