Nearly maximal information gain due to time integration in central dogma reactions

Living cells process information about their environment through the central dogma processes of transcription and translation, which drive the cellular response to stimuli. Here, we study the transfer of information from environmental input to the transcript and protein expression levels. Evaluation of both experimental and analogous simulation data reveals that transcription and translation are not two simple information channels connected in series. Instead, we show that the central dogma reactions often create a time-integrating information channel, where the translation channel receives and integrates multiple outputs from the transcription channel. This information channel model of the central dogma provides new information-theoretic selection criteria for the central dogma rate constants. Using the data for four well-studied species we show that their central dogma rate constants achieve information gain due to time integration while also keeping the loss due to stochasticity in translation relatively low (< 0.5 bits).

Reimagining the Power of Nucleic Acids as Therapeutic and Diagnostic Agents

The central dogma of molecular biology proposes that in a typical cell, the flow of genetic information proceeds from DNA to RNA to polypeptide [...]

Environmental Water and Sediment Microbial Communities Shape Intestine Microbiota for Host Health: The Central Dogma in an Anthropogenic Aquaculture Ecosystem

From increasing evidence has emerged a tight link among the environment, intestine microbiota, and host health status; moreover, the microbial interaction in different habitats is crucial for ecosystems. However, how the environmental microbial community assembly governs the intestinal microbiota and microbial communities of multiple habitats contribute to the metacommunity remain elusive. Here, we designed two delicate experiments from temporal and spatial scales in a shrimp culture pond ecosystem (SCPE). Of the SCPE metacommunity, the microbial diversity was mainly contributed to by the diversity of–βIntraHabitats and βInterHabitats, and water and sediment communities had a large contribution to the shrimp intestine community as shown by SourceTracker and Sloan neutral community model analyses. Also, phylogenetic bin-based null model results show that microbial assembly of three habitats in the SCPE appeared to be largely driven by stochastic processes. These results enrich our understanding of the environment–intestinal microbiota–host health closely linked relationship, making it possible to be the central dogma for an anthropogenic aquaculture ecosystem. Our findings enhance the mechanistic understanding of microbial assembly in the SCPE for further analyzing metacommunities, which has important implications for microbial ecology and animal health.

On the assumptions leading to the information loss paradox

The information loss paradox is usually stated as an incompatibility between general relativity and quantum mechanics. However, the assumptions leading to the problem are often overlooked and, in fact, a careful inspection of the main hypothesises suggests a radical reformulation of the problem. Indeed, we present a thought experiment involving a black hole that emits radiation and, independently of the nature of the radiation, we show the existence of an incompatibility between (i) the validity of the laws of general relativity to describe infalling matter far from the Planckian regime, and (ii) the so-called central dogma which states that as seen from an outside observer a black hole behaves like a quantum system whose number of degrees of freedom is proportional to the horizon area. We critically revise the standard arguments in support of the central dogma, and argue that they cannot hold true unless some new physics is invoked even before reaching Planck scales. This suggests that the information loss problem, in its current formulation, is not necessarily related to any loss of information or lack of unitarity. Therefore, in principle, semiclassical general relativity and quantum mechanics can be perfectly compatible before reaching the final stage of the black hole evaporation where, instead, a consistent theory of quantum gravity is needed to make any prediction.

Caspases Switch off the m 6 A RNA Modification Pathway to Foster the Replication of a Ubiquitous Human Tumor Virus

The discovery of an N 6 -methyladenosine (m 6 A) RNA modification pathway has fundamentally altered our understanding of the central dogma of molecular biology. This pathway is controlled by methyltransferases (writers), demethylases (erasers), and specific m 6 A binding proteins (readers).

4. Nucleic acids

This chapter focuses on nucleic acids. It begins by describing the central dogma of molecular biology. Fundamentally, the central dogma consists of DNA replication—the straightforward copying of information; transcription—the process of creating RNA from a DNA template; and translation—the creation of a protein sequence from an RNA template. The chapter then looks at the nucleic acid molecule’s secondary structures, their form and function, and how these underpin the three trunk data flows of the central dogma. The chapter also explores the idea of a primordial world without DNA or proteins, where RNA played the role of both cellular machinery and storage medium for genetic information.

Oxidative Stress in Bacteria and the Central Dogma of Molecular Biology

Ever since the “great oxidation event,” Earth’s cellular life forms had to cope with the danger of reactive oxygen species (ROS) affecting the integrity of biomolecules and hampering cellular metabolism circuits. Consequently, increasing ROS levels in the biosphere represented growing stress levels and thus shaped the evolution of species. Whether the ROS were produced endogenously or exogenously, different systems evolved to remove the ROS and repair the damage they inflicted. If ROS outweigh the cell’s capacity to remove the threat, we speak of oxidative stress. The injuries through oxidative stress in cells are diverse. This article reviews the damage oxidative stress imposes on the different steps of the central dogma of molecular biology in bacteria, focusing in particular on the RNA machines involved in transcription and translation.