scholarly journals Learning Processes in Hierarchical Pairs Regulate Entire Gene Expression in Cells

2021 ◽  
Author(s):  
Tomoyuki Yamaguchi
Keyword(s):  
Gene Expression ◽  
Learning Process ◽  
Expression Patterns ◽  
Two Factors ◽  
Regulatory Cascades ◽  
Target Ratio ◽  
A Cell ◽  
The Difference ◽  
Genetically Determined ◽  
Entire Gene

Abstract Expression of numerous genes is precisely controlled in a cell in various contexts. While genetic and epigenetic mechanisms contribute to this regulation, how each mechanism cooperates to ensure the proper expression patterns of whole gene remains unclear. Here, I theoretically show that the repetition of simple biological processes makes appropriate whole-gene expression only if the appropriateness of current pattern is roughly detectable. A learning pair model is developed, in which two factors autonomously approach the target ratio by repeating two stochastic processes; competitive amplification with a small addition term and decay depending on the difference between the current and target ratios. Furthermore, thousands of factors are self-regulated in a hierarchical-pair architecture, in which the activation degrees competitively amplify, while transducing the activation signal, and decay at four different probabilities. Changes in whole-gene expression during human early embryogenesis and hematopoiesis are reproduced in simulation using this epigenetic learning process in a single genetically-determined hierarchical-pair architecture of gene regulatory cascades. On the background of this learning process, I propose the law of biological inertia which means that a living cell basically maintains the expression pattern while renewing the contents.

scholarly journals RNA-seq: primary cells, cell lines and heat stress

2015 ◽  
Author(s):  
Carl J Schmdt ◽  
Elizabeth M Pritchett ◽  
Liang Sun ◽  
Richard V.N. Davis ◽  
Allen Hubbard ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Sequence Data ◽  
Expression Patterns ◽  
Effective Means ◽  
Cost Effective ◽  
Rna Seq ◽  
Individual Gene ◽  
Examine Gene Expression ◽  
A Cell

Transcriptome analysis by RNA-seq has emerged as a high-throughput, cost-effective means to evaluate the expression pattern of genes in organisms. Unlike other methods, such as microarrays or quantitative PCR, RNA-seq is a target free method that permits analysis of essentially any RNA that can be amplified from a cell or tissue. At its most basic, RNA-seq can determine individual gene expression levels by counting the number of times a particular transcript was found in the sequence data. Transcript levels can be compared across multiple samples to identify differentially expressed genes and infer differences in biological states between the samples. We have used this approach to examine gene expression patterns in chicken and human cells, with particular interest in determining response to heat stress.

scholarly journals Evidence from oyster suggests an ancient role for Pdx in regulating insulin gene expression in animals

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fei Xu ◽  
Ferdinand Marlétaz ◽  
Daria Gavriouchkina ◽  
Xiao Liu ◽  
Tatjana Sauka-Spengler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulatory Element ◽  
Expression Patterns ◽  
Homeobox Gene ◽  
Gene Interaction ◽  
Binding Interaction ◽  
Upstream Regulatory Element ◽  
A Cell ◽  
Insulin Gene Expression ◽  
Cell Culture Assay

AbstractHox and ParaHox genes encode transcription factors with similar expression patterns in divergent animals. The Pdx (Xlox) homeobox gene, for example, is expressed in a sharp spatial domain in the endodermal cell layer of the gut in chordates, echinoderms, annelids and molluscs. The significance of comparable gene expression patterns is unclear because it is not known if downstream transcriptional targets are also conserved. Here, we report evidence indicating that a classic transcriptional target of Pdx1 in vertebrates, the insulin gene, is a likely direct target of Pdx in Pacific oyster adults. We show that one insulin-related gene, cgILP, is co-expressed with cgPdx in oyster digestive tissue. Transcriptomic comparison suggests that this tissue plays a similar role to the vertebrate pancreas. Using ATAC-seq and ChIP, we identify an upstream regulatory element of the cgILP gene which shows binding interaction with cgPdx protein in oyster hepatopancreas and demonstrate, using a cell culture assay, that the oyster Pdx can act as a transcriptional activator through this site, possibly in synergy with NeuroD. These data argue that a classic homeodomain-target gene interaction dates back to the origin of Bilateria.

scholarly journals The Drosophila melanogaster Levodopa-Induced Depression Model Exhibits Negative Geotaxis Deficits and Differential Gene Expression in Males and Females

2021 ◽  
Vol 15 ◽  
Author(s):  
Thiago C. Moulin ◽  
Federico Ferro ◽  
Angela Hoyer ◽  
Pierre Cheung ◽  
Michael J. Williams ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Psychosocial Functioning ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Mating Frequency ◽  
Negative Geotaxis ◽  
Specific Effects ◽  
Males And Females ◽  
The Difference

More than 320 million people live with depression in the world, a disorder that severely limits psychosocial functioning and diminishes quality of life. The prevalence of major depression is almost two times higher in women than in men. However, the molecular mechanisms of its sex-specific pathophysiology are still poorly understood. Drosophila melanogaster is an established model for neurobiological research of depression-like states, as well as for the study of molecular and genetic sex differences in the brain. Here, we investigated sex-specific effects on forced-climbing locomotion (negative geotaxis) and gene expression of a fly model of depression-like phenotypes induced by levodopa administration, which was previously shown to impair normal food intake, mating frequency, and serotonin concentration. We observed that both males and females show deficits in the forced-climbing paradigm; however, modulated by distinct gene expression patterns after levodopa administration. Our results suggest that Drosophila models can be a valuable tool for identifying the molecular mechanisms underlying the difference of depressive disorder prevalence between men and women.

Laser Capture Microdissection, Amplified Antisense Rna, and Highdensity Microarrays: The New Frontier for Gene Expression Profiling From Limited Amounts of Tissue

2000 ◽  
Vol 6 (S2) ◽  
pp. 840-841
Author(s):  
Roger D. Madison, Ph.D.
Keyword(s):  
Gene Expression ◽  
Laser Capture Microdissection ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Mrna Levels ◽  
Functional Protein ◽  
Protein Levels ◽  
Degradation Rates ◽  
A Cell ◽  
Laser Capture

Because the genes in all somatic cells of an individual are identical, it is the differential expression of the proteins encoded by particular genes that determines a cell's phenotype. There is now increasing interest in relating the simultaneous expression patterns of multiple proteins to complex biological processes. The goal is to develop ‘expression profiles’ of the proteins that are active within a cell or tissue during a particular condition. The ultimate control of functional protein expression is quite complex and may involve transcriptional, combinatorial, and postranslational mechanisms, as well as differences in protein degradation rates that vary under different conditions. Although mRNA levels do not always predict functional protein levels, they are a useful first step in determining the expression profile.The evolution of three key technologies offers the promise of obtaining quantitative analysis of gene expression from restricted amounts of nervous system tissue. Laser capture microdissection can accomplish harvesting of identified cell populations from histologically processed tissue.

scholarly journals The dehydrins gene expression differs across ecotypes in Norway spruce and relates to weather fluctuations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jaroslav Čepl ◽  
Jan Stejskal ◽  
Jiří Korecký ◽  
Jakub Hejtmánek ◽  
Zuzana Faltinová ◽  
...  
Keyword(s):  
Gene Expression ◽  
Norway Spruce ◽  
Expression Patterns ◽  
Plant Stress ◽  
Genotyping By Sequencing ◽  
Day Length ◽  
Sequencing Platform ◽  
Individual Gene ◽  
Genetically Determined ◽  
Dehydrin Gene

AbstractNorway spruce has a broad natural distribution range, which results in a substantial variety of its physiological and genetic variation. There are three distinct altitudinal ecotypes described in this tree species. The physiological optimum of each ecotype may be shifted due to ongoing climate change, especially in traits associated with water demand that might be crucial for adaptation. Dehydrins are proteins that help to mitigate the adverse effects of dehydration. Dehydrin gene expression patterns appeared to be a suitable marker for plant stress assessment. Genetically determined differences in response between individuals and populations were formerly studied, however, mainly in controlled conditions. We evaluated ecotypic variation in dehydrin gene expression in a clonal bank comprised of all three ecotypes. A genetic relationship among targeted trees was uncovered utilizing GBS (Genotyping by Sequencing) platform. We sampled 4–6 trees of each ecotype throughout 15 months period. Subsequently, we assessed the RNA expression of dehydrin genes by qRT-PCR. For this study, we deliberately selected dehydrins from different categories. Our findings detected significant differences among ecotypes in dehydrin expression. The association of recorded climatic variables and individual gene expression across the study period was evaluated and revealed, for certain genes, a correlation between dehydrin gene expression and precipitation, temperature, and day-length.

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

Slow Down You’re Moving Too Fast

2015 ◽  
Vol 27 (2) ◽  
pp. 53-63 ◽  
Author(s):  
Annie Lang ◽  
Nancy Schwartz ◽  
Sharon Mayell
Keyword(s):  
Older Adults ◽  
Cognitive Aging ◽  
Attention And Memory ◽  
Younger Adults ◽  
Media Messages ◽  
Two Factors ◽  
The Difference

The study reported here compared how younger and older adults processed the same set of media messages which were selected to vary on two factors, arousing content and valence. Results showed that older and younger adults had similar arousal responses but different patterns of attention and memory. Older adults paid more attention to all messages than did younger adults. However, this attention did not translate into greater memory. Older and younger adults had similar levels of memory for slow-paced messages, but younger adults outperformed older adults significantly as pacing increased, and the difference was larger for arousing compared with calm messages. The differences found are in line with predictions made based on the cognitive-aging literature.

Gene expression patterns in blood predict future severe endpoints in community acquired pneumonia

Pneumologie ◽  
2018 ◽  
Vol 72 (S 01) ◽  
pp. S8-S9
Author(s):  
M Bauer ◽  
H Kirsten ◽  
E Grunow ◽  
P Ahnert ◽  
M Kiehntopf ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Community Acquired Pneumonia ◽  
Gene Expression Patterns

Penerapan Rinfo Sebagai Media Pendukung Untuk Proses Pembelajaran Pada Perguruan Tinggi Raharja

CCIT Journal ◽  
2014 ◽  
Vol 8 (1) ◽  
pp. 101-115
Author(s):  
Untung Rahardja ◽  
Khanna Tiara ◽  
Ray Indra Taufik Wijaya
Keyword(s):  
Learning Process ◽  
Human Life ◽  
Learning Tools ◽  
Integrated Learning ◽  
Civilizing Process ◽  
The World ◽  
The Future ◽  
Two Factors ◽  
Life Education ◽  
New Generation

Education is an important factor in human life. According to Ki Hajar Dewantara, education is a civilizing process that a business gives high values ??to the new generation in a society that is not only maintenance but also with a view to promote and develop the culture of the nobility toward human life. Education is a human investment that can be used now and in the future. One other important factor in supporting human life in addition to education, which is technology. In this globalization era, technology has touched every joint of human life. The combination of these two factors will be a new innovation in the world of education. The innovation has been implemented by Raharja College, namely the use of the method iLearning (Integrated Learning) in the learning process. Where such learning has been online based. ILearning method consists of TPI (Ten Pillars of IT iLearning). Rinfo is one of the ten pillars, where it became an official email used by the whole community’s in Raharja College to communicate with each other. Rinfo is Gmail, which is adapted from the Google platform with typical raharja.info as its domain. This Rinfo is a medium of communication, as well as a tool to support the learning process in Raharja College. Because in addition to integrated with TPi, this Rinfo was connected also support with other learning tools, such as Docs, Drive, Sites, and other supporting tools.

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