Search results for: artificial gene regulatory networks
-
Evolving gene regulatory networks controlling foraging strategies of prey and predators in an artificial ecosystem
PublicationCo-evolution of predators and prey is an example of an evolutionary arms race, leading in nature to selective pressures in positive feedback. We introduce here an artificial life ecosystem in which such positive feedback can emerge. This ecosystem consists of a 2-dimensional liquid environment and animats controlled by evolving artificial gene regulatory networks encoded in linear genomes. The genes in the genome encode chemical...
-
Evolution of Animats Following a Moving Target in an Artificial Ecosystem
PublicationMany biological animals, even microscopically small, are able to track moving sources of food. In this paper, we investigate the emergence of such behavior in artificial animals (animats) in a 2-dimensional simulated liquid environment. These "predators" are controlled by evolving artificial gene regulatory networks encoded in linear genomes. The fate of the predators is determined only by their ability to gather food and reproduce—no...
-
Evolution of artificial single-cell organisms foraging for resources in a 3-dimensional environment
PublicationForaging for resources is a simple cognitive task that even one-celled biological organisms can ac- complish. We present an Artificial Life system in which artificial unicellular organisms (animats) forage for food in a 3-dimensional simulated liquid environment. The movement of animats is controlled by evolving artificial gene regulatory networks encoded in linear genomes. When an animat consumes enough food, it produces offspring...
-
Evolution of chemotaxis in single-cell artificial organisms
PublicationThe model of a liquid two-dimensional environment, which is based on physics of diffusion, allows us to simulate the diffusion of morphogenes. Artificial organisms move using a chemotaxis reacting to concentration difference. Organisms are controlled by a gene regulatory network coded in a linear genome and reproduce by division. We made a lot of experiments presenting organisms’ behaviour in various environment conditions. We...
-
Small regulatory bacterial RNAs regulating the envelope stress response
PublicationMost bacteria encode a large repertoire of RNA-based regulatory mechanisms. Recent discoveries have revealed that the expression of many genes is controlled by a plethora of base-pairing noncoding small regulatory RNAs (sRNAs), regulatory RNA-binding proteins and RNA-degrading enzymes. Some of these RNA-based regulated processes respond to stress conditions and are involved in the maintenance of cellular homeostasis. They achieve...
-
I, Robot: between angel and evil
PublicationThe boosting of most digital innovations within recent technology progress by artificial intelligence (AI) constitutes a growing topic of interest. Besides its technical aspects, increasing research activity may be observed in the domain of security challenges, and therefore of responsibility related to the controlled or hypothetically uncontrolled or autonomous emergence of AI solutions. Consequently, responsibility and ethics...
-
Molecular and structural basis of inner core lipopolysaccharide alterations in Escherichia coli: incorporation of glucuronic acid and phosphoethanolamine in the heptose region.
PublicationIt is well established that lipopolysaccharide (LPS) often carries nonstoichiometric substitutions in lipid A and in the inner core. In this work, the molecular basis of inner core alterations and their physiological significance are addressed. A new inner core modification of LPS is described, which arises due to the addition of glucuronic acid on the third heptose with a concomitant loss of phosphate on the second heptose. This...
-
Data governance: Organizing data for trustworthy Artificial Intelligence
PublicationThe rise of Big, Open and Linked Data (BOLD) enables Big Data Algorithmic Systems (BDAS) which are often based on machine learning, neural networks and other forms of Artificial Intelligence (AI). As such systems are increasingly requested to make decisions that are consequential to individuals, communities and society at large, their failures cannot be tolerated, and they are subject to stringent regulatory and ethical requirements....
-
A mechanistically approached review upon assorted cell lines stimulated by athermal electromagnetic irradiation
PublicationThe probable influence of electromagnetic irradiation on cancer treatment has been deduced from the interaction of artificial electromagnetic emissions with biological organisms. Nonetheless, the suspected health effects induced by electromagnetic-based technology imply that such a treatment may contaminate the adjacent healthy cells. Thus, gaining mechanistic insights into the problem is required to avoid athermal health hazards....
-
An Impact Analysis of Artificial Light at Night (ALAN) on Bats. A Case Study of the Historic Monument and Natura 2000 Wisłoujście Fortress in Gdansk, Poland
PublicationThe artificial light at night (ALAN) present in many cities and towns has a negative impact on numerous organisms that live alongside humans, including bats. Therefore, we investigated if the artificial illumination of the historic Wisłoujście Fortress in Gdańsk, Poland (part of the Natura 2000 network), during nighttime events, which included an outdoor electronic dance music (EDM) festival, might be responsible for increased...
-
Transcriptome profiling reveals distinctive traits of retinol metabolism and neonatal parallels in the MRL/MpJ mouse
PublicationBackground: The MRL/MpJ mouse is a laboratory inbred strain known for regenerative abilities which are manifested by scarless closure of ear pinna punch holes. Enhanced healing responses have been reported in other organs. A remarkable feature of the strain is that the adult MRL/MpJ mouse retains several embryonic biochemical characteristics, including increased expression of stem cell markers. Results: We explored the transcriptome...
-
Loop-mediated isothermal amplification (LAMP) as a diagnostic tool in detection of infectious diseases
PublicationLoop-mediated isothermal amplification (LAMP) is a gene amplification method which amplifies DNA with high specificity and efficiency under isothermal conditions. Because of its rapidity and simplicity, it is a valuable diagnostic tool in the early detection and identification of infectious diseases. LAMP method is based on the use of a set of four to six specially designed primers spanning six to eight distinct sequences on the...
-
Pregnane X receptor dependent up-regulation of CYP2C9 and CYP3A4 in tumor cells by antitumor acridine agents, C-1748 and C-1305, selectively diminished under hypoxia
PublicationInduction of proteins involved in drug metabolism and in drug delivery has a significant impact on drug-drug interactions and on the final therapeutic effects. Two antitumor acridine derivatives selected for present studies, C-1748 (9-(2’-hydroxyethylamino)-4-methyl-1-nitroacridine) and C-1305 (5-dimethylaminopropylamino-8-hydroxy-triazoloacridinone), expressed high and low susceptibility to metabolic transformations with liver...
-
DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis
PublicationThe human leukocyte antigen (HLA) haplotype DRB1*15:01 is the major risk factor for multiple sclerosis (MS). Here, we find that DRB1*15:01 is hypomethylated and predominantly expressed in monocytes among carriers of DRB1*15:01. A differentially methylated region (DMR) encompassing HLA-DRB1 exon 2 is particularly affected and displays methylation-sensitive regulatory properties in vitro. Causal inference and Mendelian randomization...
-
A MODEL FOR FORECASTING PM10 LEVELS WITH THE USE OF ARTIFICIAL NEURAL NETWORKS
PublicationThis work presents a method of forecasting the level of PM10 with the use of artificial neural networks. Current level of particulate matter and meteorological data was taken into account in the construction of the model (checked the correlation of each variable and the future level of PM10), and unidirectional networks were used to implement it due to their ease of learning. Then, the configuration of the network (built on the...
-
Digital Innovations and Smart Solutions for Society And Economy: Pros and Cons
PublicationRecent developments in artificial intelligence (AI) may involve significant potential threats to personal data privacy, national security, and social and economic stability. AI-based solutions are often promoted as “intelligent” or “smart” because they are autonomous in optimizing various processes. Be-cause they can modify their behavior without human supervision by analyzing data from the environ-ment, AI-based systems may be...
-
Regulation of LPS assembly via controlled proteolysis and sensing of LPS stress in Escherichia coli
PublicationLipopolysaccharide (LPS) is a complex glycolipid, essential for the bacterial viability and along with phospholipids, it constitutes the major amphiphilic component of outer membrane (OM) in most of the Gram-negative bacteria, including Escherichia coli. LPS molecules confer an effective permeability barrier to the OM and play a crucial role in bacteria-environment and -host interactions. The synthesis and accumulation of this...
-
Regulated assembly of lipopolysaccharide and sensing of its alterations in Escherichia coli
PublicationThis thesis describes mechanism of the regulation of the transcription of the rpoE gene encoding an essential RNA polymerase subunit in Escherichia coli. The RpoE regulates extracytoplasmic stress response regulon and is required to initiate transcription of genes, whose products are involvedin the folding of periplasmic proteins and synthesis and transport of outer membrane components. The transcriptional regulation of the rpoE...
-
USING ARTIFICIAL NEURAL NETWORKS FOR PREDICTING SHIP FUEL CONSUMPTION
PublicationIn marine vessel operations, fuel costs are major operating costs which affect the overall profitability of the maritime transport industry. The effective enhancement of using ship fuel will increase ship operation efficiency. Since ship fuel consumption depends on different factors, such as weather, cruising condition, cargo load, and engine condition, it is difficult to assess the fuel consumption pattern for various types...
-
Genome-Wide DNA Methylation and Gene Expression in Patients with Indolent Systemic Mastocytosis
PublicationMastocytosis is a clinically heterogenous, usually acquired disease of the mast cells with a survival time that depends on the time of onset. It ranges from skin-limited to systemic disease, including indolent and more aggressive variants. The presence of the oncogenic KIT p. D816V gene somatic mutation is a crucial element in the pathogenesis. However, further epigenetic regulation may also affect the expression of genes that...