scholarly journals Abitudini ed ereditarietà: la rivincita di Lamarck?

2021 ◽  
Vol 33 ◽  
pp. 88-90
Author(s):  
Alessandro Capitanini ◽  
Francesca Capitanini
Keyword(s):  
Gene Expression ◽  
Significant Influence ◽  
Genetic Information ◽  
Living Organism ◽  
Human Behaviour ◽  
Human Phenotype ◽  
Phenotypic Response ◽  
New Concepts ◽  
Genetic Modifications

Human phenotype, the set of characteristics manifested by a living organism, is determined by genetic information expression dependent on genome, epigenome and microbiome. There is a kind of bidirectionality between humans and their genome with significant influence by environment and human behaviour. In the timeline of evolution we see that genetic modifications take millions of years to take place and consolidate, as per Darwinian principles, but environment and our habits are able much more rapidly to influence our phenotypic response, through epigenetic and microbiotic pathways, as per Lamarckian hypothesis (Fig. 1). Our habits (physical, psychological, environment) are able to determine changes in gene expression and potentially influence our children’s one. The evidence of these new concepts should be a further stimulus to a more conscious lifestyle.

scholarly journals Cell-free genetic devices confer autonomic and adaptive properties to hydrogels

2019 ◽  
Author(s):  
Colette J. Whitfield ◽  
Alice M. Banks ◽  
Gema Dura ◽  
John Love ◽  
Jonathan E. Fieldsend ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Information Processing ◽  
Synthetic Biology ◽  
Smart Materials ◽  
Living Organism ◽  
Chemical Diversity ◽  
Biological Information ◽  
Self Healing ◽  
Wide Range

AbstractSmart materials are able to alter one or more of their properties in response to defined stimuli. Our ability to design and create such materials, however, does not match the diversity and specificity of responses seen within the biological domain. We propose that relocation of molecular phenomena from living cells into hydrogels can be used to confer smart functionality to materials. We establish that cell-free protein synthesis can be conducted in agarose hydrogels, that gene expression occurs throughout the material and that co-expression of genes is possible. We demonstrate that gene expression can be controlled transcriptionally (using in gel gene interactions) and translationally in response to small molecule and nucleic acid triggers. We use this system to design and build a genetic device that can alter the structural property of its chassis material in response to exogenous stimuli. Importantly, we establish that a wide range of hydrogels are appropriate chassis for cell-free synthetic biology, meaning a designer may alter both the genetic and hydrogel components according to the requirements of a given application. We probe the relationship between the physical structure of the gel and in gel protein synthesis and reveal that the material itself may act as a macromolecular crowder enhancing protein synthesis. Given the extensive range of genetically encoded information processing networks in the living kingdom and the structural and chemical diversity of hydrogels, this work establishes a model by which cell-free synthetic biology can be used to create autonomic and adaptive materials.Significance statementSmart materials have the ability to change one or more of their properties (e.g. structure, shape or function) in response to specific triggers. They have applications ranging from light-sensitive sunglasses and drug delivery systems to shape-memory alloys and self-healing coatings. The ability to programme such materials, however, is basic compared to the ability of a living organism to observe, understand and respond to its environment. Here we demonstrate the relocation of biological information processing systems from cells to materials. We achieved this by operating small, programmable genetic devices outside the confines of a living cell and inside hydrogel matrices. These results establish a method for developing materials functionally enhanced with molecular machinery from biological systems.

scholarly journals PredicTF: a tool to predict bacterial transcription factors in complex microbial communities

2021 ◽  
Author(s):  
Lummy Maria Oliveira Monteiro ◽  
Joao Saraiva ◽  
Rodolfo Brizola Toscan ◽  
Peter F Stadler ◽  
Rafael Silva-Rocha ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Microbial Communities ◽  
Open Source ◽  
Genetic Information ◽  
Environmental Isolate ◽  
Ammonium Oxidation ◽  
Cellular Gene ◽  
Bacterial Transcription

AbstractTranscription Factors (TFs) are proteins that control the flow of genetic information by regulating cellular gene expression. Here we describe PredicTF, a first platform supporting the prediction and classification of novel bacterial TF in complex microbial communities. We evaluated PredicTF using a two-step approach. First, we tested PredictTF’s ability to predict TFs for the genome of an environmental isolate. In the second evaluation step, PredicTF was used to predict TFs in a metagenome and 11 metatranscriptomes recovered from a community performing anaerobic ammonium oxidation (anammox) in a bioreactor. PredicTF is open source pipeline available at https://github.com/mdsufz/PredicTF.

scholarly journals John Arthur Joseph Pateman. 18 May 1926—18 May 2011

2018 ◽  
Vol 65 ◽  
pp. 299-315
Author(s):  
Claudio Scazzocchio
Keyword(s):  
Gene Expression ◽  
Protein Structure ◽  
Genetic Information ◽  
Positive Control ◽  
Control Of Gene Expression ◽  
Academic Background ◽  
Eukaryotic Microorganisms ◽  
The Subject ◽  
Relationship Of ◽  
The Relationship

John Pateman was a distinguished British microbial geneticist. He came from a working-class area of London and a non-academic background. His earliest contribution to genetics was the discovery (together with John Fincham) of intracistronic complementation, an important phenomenon to understand the relationship of genetic information and protein structure; this at a time when the actual coding relationships of DNA and proteins were not yet worked out. Later on, he and his students made a fundamental contribution to the understanding of control of gene expression in eukaryotic microorganisms, providing some of the earliest examples of positive control. This work also led to the discovery of a new enzyme cofactor, the only one discovered through purely genetic evidence. He worked at various universities in Britain and Australia and trained a number of students who further developed the subject.

scholarly journals Fidelity in Archaeal Information Processing

Archaea ◽  
2010 ◽  
Vol 2010 ◽  
pp. 1-15 ◽  
Author(s):  
Bart de Koning ◽  
Fabian Blombach ◽  
Stan J. J. Brouns ◽  
John van der Oost
Keyword(s):  
Gene Expression ◽  
Quality Control ◽  
Information Processing ◽  
Genome Size ◽  
Genetic Information ◽  
Important Determinant ◽  
Current Knowledge ◽  
The Other ◽  
Living Systems ◽  
Evolution Of Life

A key element during the flow of genetic information in living systems is fidelity. The accuracy of DNA replication influences the genome size as well as the rate of genome evolution. The large amount of energy invested in gene expression implies that fidelity plays a major role in fitness. On the other hand, an increase in fidelity generally coincides with a decrease in velocity. Hence, an important determinant of the evolution of life has been the establishment of a delicate balance between fidelity and variability. This paper reviews the current knowledge on quality control in archaeal information processing. While the majority of these processes are homologous in Archaea, Bacteria, and Eukaryotes, examples are provided of nonorthologous factors and processes operating in the archaeal domain. In some instances, evidence for the existence of certain fidelity mechanisms has been provided, but the factors involved still remain to be identified.

scholarly journals Overexpression of Acyl-ACP Thioesterases, CpFatB4 and CpFatB5, Induce Distinct Gene Expression Reprogramming in Developing Seeds of Brassica napus

2019 ◽  
Vol 20 (13) ◽  
pp. 3334 ◽  
Author(s):  
Jeong-Won Nam ◽  
Jinouk Yeon ◽  
Jiseong Jeong ◽  
Eunyoung Cho ◽  
Ho Bang Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Transgenic Plants ◽  
Palmitic Acid ◽  
Acyl Carrier Protein ◽  
Carrier Protein ◽  
Rna Seq ◽  
Oleate Desaturase ◽  
Fa Composition ◽  
Genetic Modifications

We examined the substrate preference of Cuphea paucipetala acyl-ACP thioesterases, CpFatB4 and CpFatB5, and gene expression changes associated with the modification of lipid composition in the seed, using Brassica napus transgenic plants overexpressing CpFatB4 or CpFatB5 under the control of a seed-specific promoter. CpFatB4 seeds contained a higher level of total saturated fatty acid (FA) content, with 4.3 times increase in 16:0 palmitic acid, whereas CpFatB5 seeds showed approximately 3% accumulation of 10:0 and 12:0 medium-chain FAs, and a small increase in other saturated FAs, resulting in higher levels of total saturated FAs. RNA-Seq analysis using entire developing pods at 8, 25, and 45 days after flowering (DAF) showed up-regulation of genes for β-ketoacyl-acyl carrier protein synthase I/II, stearoyl-ACP desaturase, oleate desaturase, and linoleate desaturase, which could increase unsaturated FAs and possibly compensate for the increase in 16:0 palmitic acid at 45 DAF in CpFatB4 transgenic plants. In CpFatB5 transgenic plants, many putative chloroplast- or mitochondria-encoded genes were identified as differentially expressed. Our results report comprehensive gene expression changes induced by alterations of seed FA composition and reveal potential targets for further genetic modifications.

scholarly journals Comprehensive Multiple eQTL Detection and Its Application to GWAS Interpretation

Genetics ◽  
2019 ◽  
Vol 212 (3) ◽  
pp. 905-918 ◽  
Author(s):  
Biao Zeng ◽  
Luke R. Lloyd-Jones ◽  
Grant W. Montgomery ◽  
Andres Metspalu ◽  
Tonu Esko ◽  
...  
Keyword(s):  
Gene Expression ◽  
Peripheral Blood ◽  
Complex Traits ◽  
Regulation Of Gene Expression ◽  
Credible Interval ◽  
Causal Variant ◽  
Human Phenotype ◽  
Disease States ◽  
Heart Study ◽  
Microarray Studies

Expression QTL (eQTL) detection has emerged as an important tool for unraveling the relationship between genetic risk factors and disease or clinical phenotypes. Most studies are predicated on the assumption that only a single causal variant explains the association signal in each interval. This greatly simplifies the statistical modeling, but is liable to biases in scenarios where multiple local causal-variants are responsible. Here, our primary goal was to address the prevalence of secondary cis-eQTL signals regulating peripheral blood gene expression locally, utilizing two large human cohort studies, each >2500 samples with accompanying whole genome genotypes. The CAGE (Consortium for the Architecture of Gene Expression) dataset is a compendium of Illumina microarray studies, and the Framingham Heart Study is a two-generation Affymetrix dataset. We also describe Bayesian colocalization analysis of the extent of sharing of cis-eQTL detected in both studies as well as with the BIOS RNAseq dataset. Stepwise conditional modeling demonstrates that multiple eQTL signals are present for ∼40% of over 3500 eGenes in both microarray datasets, and that the number of loci with additional signals reduces by approximately two-thirds with each conditioning step. Although <20% of the peak signals across platforms fine map to the same credible interval, the colocalization analysis finds that as many as 50–60% of the primary eQTL are actually shared. Subsequently, colocalization of eQTL signals with GWAS hits detected 1349 genes whose expression in peripheral blood is associated with 591 human phenotype traits or diseases, including enrichment for genes with regulatory functions. At least 10%, and possibly as many as 40%, of eQTL-trait colocalized signals are due to nonprimary cis-eQTL peaks, but just one-quarter of these colocalization signals replicated across the gene expression datasets. Our results are provided as a web-based resource for visualization of multi-site regulation of gene expression and its association with human complex traits and disease states.

Transmembrane Signaling in the Brain by Serotonin, A Key Regulator of Physiology and Emotion

2005 ◽  
Vol 25 (5-6) ◽  
pp. 363-385 ◽  
Author(s):  
Tatyana Adayev ◽  
Buddima Ranasinghe ◽  
Probal Banerjee
Keyword(s):  
Gene Expression ◽  
Immune Cells ◽  
Functional Role ◽  
Living Organism ◽  
Covalent Modification ◽  
G Protein Coupled Receptors ◽  
And Behavior ◽  
G Protein Coupled ◽  
Compare And Contrast ◽  
The Brain

Serotonin (5-HT) is an ancient chemical that plays a crucial functional role in almost every living organism. It regulates platelet aggregation, activation of immune cells, and contraction of stomach and intestinal muscles. In addition, serotonin acts as a neurotransmitter in the brain and the peripheral nervous system. These activities are initiated by the binding of serotonin to 15 or more receptors that are pharmacologically classified into seven groups, 5-HT1 through 5-HT7. Each group is further divided into subgroups of receptors that are homologous but are encoded by discrete genes. With the exception of the 5-HT3 receptor-a cation channel—all of the others are G protein-coupled receptors that potentially activate or inhibit a large number of biochemical cascades. This review will endeavor to compare and contrast such signaling pathways with special attention to their tissue-specific occurrence, their possible role in immediate effects on covalent modification of other proteins, and relatively slower effects on gene expression, physiology and behavior.

scholarly journals Genomic signatures of diet-related shifts during human origins

2010 ◽  
Vol 278 (1708) ◽  
pp. 961-969 ◽  
Author(s):  
Courtney C. Babbitt ◽  
Lisa R. Warner ◽  
Olivier Fedrigo ◽  
Christine E. Wall ◽  
Gregory A. Wray
Keyword(s):  
Gene Expression ◽  
New Technologies ◽  
Morphological Changes ◽  
Current Evidence ◽  
Human Origins ◽  
Human Phenotype ◽  
Genomic Signatures ◽  
Profound Influence ◽  
Genomic Studies ◽  
Morphological Differences

There are numerous anthropological analyses concerning the importance of diet during human evolution. Diet is thought to have had a profound influence on the human phenotype, and dietary differences have been hypothesized to contribute to the dramatic morphological changes seen in modern humans as compared with non-human primates. Here, we attempt to integrate the results of new genomic studies within this well-developed anthropological context. We then review the current evidence for adaptation related to diet, both at the level of sequence changes and gene expression. Finally, we propose some ways in which new technologies can help identify specific genomic adaptations that have resulted in metabolic and morphological differences between humans and non-human primates.

scholarly journals Phase Transitions in Virology

2020 ◽  
Author(s):  
Ricard Sole ◽  
Josep Sardanyes ◽  
Santiago F. Elena
Keyword(s):  
Phase Transitions ◽  
Genetic Information ◽  
Molecular Mechanisms ◽  
Evolutionary Dynamics ◽  
Living Organism ◽  
Genome Replication ◽  
Minimal Models ◽  
Biological Organization ◽  
Symbiotic Relationships ◽  
Replication Gene

Viruses have established symbiotic relationships with almost every other living organism on Earth and at all levels of biological organization, from other viruses up to entire ecosystems. In most cases, peacefully coexisting with their hosts, but in most relevant cases, parasitizing them and inducing diseases. Viruses are playing an essential role in shaping the eco-evolutionary dynamics of their hosts, and also have been involved in some of the major evolutionary innovations either by working as vectors of genetic information or by being themselves coopted by the host into their genomes. Viruses can be studied at different levels of biological organization, from the molecular mechanisms of genome replication, gene expression and encapsidation to global pandemics. All these levels are different and yet connected through the presence of threshold conditions allowing for the formation of a capsid, the loss of genetic information or epidemic spreading. These thresholds, as it occurs with temperatures separating phases in a liquid, define sharp qualitative types of behaviour. These {\em phase transitions} are very well known in physics. They have been studied by means of simple, but powerful models able to capture their essential properties, allowing to understand them. Can the physics of phase transitions be an inspiration for our understanding of viral dynamics at different scales? Here we review the best-known examples of transition phenomena in virology and their simplest mathematical modelling approaches. We suggest that the advantages of abstract, simplified pictures used in physics are also the key to properly understand the origins and evolution of complexity in viruses. By means of several examples, we explore this multilevel landscape and how minimal models provide deep insights into a diverse array of problems. The relevance of these transitions in connecting dynamical patterns across levels and their evolutionary and clinical implications are outlined.

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