Hydrothermal Chemistry and the Origin of Cellular Life

Astrobiology ◽  
2019 ◽  
Vol 19 (12) ◽  
pp. 1523-1537 ◽  
Author(s):  
David Deamer ◽  
Bruce Damer ◽  
Vladimir Kompanichenko
Keyword(s):  
Cellular Life ◽  
Hydrothermal Chemistry

A Survey on Computational Methods for Essential Proteins and Genes Prediction

2019 ◽  
Vol 14 (3) ◽  
pp. 211-225 ◽  
Author(s):  
Ming Fang ◽  
Xiujuan Lei ◽  
Ling Guo
Keyword(s):  
Computational Methods ◽  
Drug Targets ◽  
Disease Genes ◽  
Essential Proteins ◽  
Experimental Identification ◽  
Cellular Life ◽  
Different Types ◽  
The Stability ◽  
Human Disease Genes ◽  
Biology Research

Background: Essential proteins play important roles in the survival or reproduction of an organism and support the stability of the system. Essential proteins are the minimum set of proteins absolutely required to maintain a living cell. The identification of essential proteins is a very important topic not only for a better comprehension of the minimal requirements for cellular life, but also for a more efficient discovery of the human disease genes and drug targets. Traditionally, as the experimental identification of essential proteins is complex, it usually requires great time and expense. With the cumulation of high-throughput experimental data, many computational methods that make useful complements to experimental methods have been proposed to identify essential proteins. In addition, the ability to rapidly and precisely identify essential proteins is of great significance for discovering disease genes and drug design, and has great potential for applications in basic and synthetic biology research. Objective: The aim of this paper is to provide a review on the identification of essential proteins and genes focusing on the current developments of different types of computational methods, point out some progress and limitations of existing methods, and the challenges and directions for further research are discussed.

scholarly journals An Imbalanced Image Classification Method for the Cell Cycle Phase

Information ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 249
Author(s):  
Xin Jin ◽  
Yuanwen Zou ◽  
Zhongbing Huang
Keyword(s):  
Cell Cycle ◽  
Deep Learning ◽  
Image Classification ◽  
Classification Accuracy ◽  
Data Augmentation ◽  
Cycle Phase ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Cellular Life

The cell cycle is an important process in cellular life. In recent years, some image processing methods have been developed to determine the cell cycle stages of individual cells. However, in most of these methods, cells have to be segmented, and their features need to be extracted. During feature extraction, some important information may be lost, resulting in lower classification accuracy. Thus, we used a deep learning method to retain all cell features. In order to solve the problems surrounding insufficient numbers of original images and the imbalanced distribution of original images, we used the Wasserstein generative adversarial network-gradient penalty (WGAN-GP) for data augmentation. At the same time, a residual network (ResNet) was used for image classification. ResNet is one of the most used deep learning classification networks. The classification accuracy of cell cycle images was achieved more effectively with our method, reaching 83.88%. Compared with an accuracy of 79.40% in previous experiments, our accuracy increased by 4.48%. Another dataset was used to verify the effect of our model and, compared with the accuracy from previous results, our accuracy increased by 12.52%. The results showed that our new cell cycle image classification system based on WGAN-GP and ResNet is useful for the classification of imbalanced images. Moreover, our method could potentially solve the low classification accuracy in biomedical images caused by insufficient numbers of original images and the imbalanced distribution of original images.

scholarly journals Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 63
Author(s):  
Lakshminarayan M. Iyer ◽  
Vivek Anantharaman ◽  
Arunkumar Krishnan ◽  
A. Maxwell Burroughs ◽  
L. Aravind
Keyword(s):  
Genome Size ◽  
Principal Component ◽  
Comparative Genomic ◽  
Rna Repair ◽  
Cellular Life ◽  
Rna Targeting ◽  
Conserved Genes ◽  
Comparative Genomics Analysis ◽  
Phage Proteins ◽  
Novel Protein

Jumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects of biology. By performing a comparative genomics analysis of 224 jumbo phages, we suggest an objective inclusion criterion based on genome size distributions and present a synthetic overview of their manifold adaptations across major biological systems. By means of clustering and principal component analysis of the phyletic patterns of conserved genes, all known jumbo phages can be classified into three higher-order groups, which include both myoviral and siphoviral morphologies indicating multiple independent origins from smaller predecessors. Our study uncovers several under-appreciated or unreported aspects of the DNA replication, recombination, transcription and virion maturation systems. Leveraging sensitive sequence analysis methods, we identify novel protein-modifying enzymes that might help hijack the host-machinery. Focusing on host–virus conflicts, we detect strategies used to counter different wings of the bacterial immune system, such as cyclic nucleotide- and NAD+-dependent effector-activation, and prevention of superinfection during pseudolysogeny. We reconstruct the RNA-repair systems of jumbo phages that counter the consequences of RNA-targeting host effectors. These findings also suggest that several jumbo phage proteins provide a snapshot of the systems found in ancient replicons preceding the last universal ancestor of cellular life.

scholarly journals Role for Human SIRT2 NAD-Dependent Deacetylase Activity in Control of Mitotic Exit in the Cell Cycle

2003 ◽  
Vol 23 (9) ◽  
pp. 3173-3185 ◽  
Author(s):  
Sylvia C. Dryden ◽  
Fatimah A. Nahhas ◽  
James E. Nowak ◽  
Anton-Scott Goustin ◽  
Michael A. Tainsky
Keyword(s):  
Cell Cycle ◽  
Protein A ◽  
Proteasome Inhibitors ◽  
26S Proteasome ◽  
Functional Studies ◽  
Cellular Life ◽  
Subsequent Decrease ◽  
Subsequent Degradation ◽  
Phosphorylation Cascade ◽  
And Control

ABSTRACT Studies of yeast have shown that the SIR2 gene family is involved in chromatin structure, transcriptional silencing, DNA repair, and control of cellular life span. Our functional studies of human SIRT2, a homolog of the product of the yeast SIR2 gene, indicate that it plays a role in mitosis. The SIRT2 protein is a NAD-dependent deacetylase (NDAC), the abundance of which increases dramatically during mitosis and is multiply phosphorylated at the G2/M transition of the cell cycle. Cells stably overexpressing the wild-type SIRT2 but not missense mutants lacking NDAC activity show a marked prolongation of the mitotic phase of the cell cycle. Overexpression of the protein phosphatase CDC14B, but not its close homolog CDC14A, results in dephosphorylation of SIRT2 with a subsequent decrease in the abundance of SIRT2 protein. A CDC14B mutant defective in catalyzing dephosphorylation fails to change the phosphorylation status or abundance of SIRT2 protein. Addition of 26S proteasome inhibitors to human cells increases the abundance of SIRT2 protein, indicating that SIRT2 is targeted for degradation by the 26S proteasome. Our data suggest that human SIRT2 is part of a phosphorylation cascade in which SIRT2 is phosphorylated late in G2, during M, and into the period of cytokinesis. CDC14B may provoke exit from mitosis coincident with the loss of SIRT2 via ubiquitination and subsequent degradation by the 26S proteasome.

scholarly journals Hydrothermal Conditions and the Origin of Cellular Life

Astrobiology ◽  
2015 ◽  
Vol 15 (12) ◽  
pp. 1091-1095 ◽  
Author(s):  
David W. Deamer ◽  
Christos D. Georgiou
Keyword(s):  
Hydrothermal Conditions ◽  
Cellular Life

scholarly journals CopR, a global regulator of transcription to maintain copper homeostasis in Pyrococcus furiosus

2020 ◽  
Author(s):  
Felix Grünberger ◽  
Robert Reichelt ◽  
Ingrid Waege ◽  
Verena Ned ◽  
Korbinian Bronner ◽  
...  
Keyword(s):  
Essential Role ◽  
Pyrococcus Furiosus ◽  
Copper Homeostasis ◽  
Negative Stain ◽  
Cellular Life ◽  
Transmission Electron ◽  
Genome Wide ◽  
Binding Data ◽  
Differential Gene

AbstractAlthough copper is in many cases an essential micronutrient for cellular life, higher concentrations are toxic. Therefore, all living cells have developed strategies to maintain copper homeostasis. In this manuscript, we have analysed the transcriptome-wide response of Pyrococcus furiosus to increased copper concentrations and described the essential role of the putative copper-sensing metalloregulator CopR in the detoxification process.To this end, we employed biochemical and biophysical methods to characterise the role of CopR. Additionally, a copR knockout strain revealed an amplified sensitivity in comparison to the parental strain towards increased copper levels, which designates an essential role of CopR for copper homeostasis. To learn more about the CopR-regulated gene network, we performed differential gene expression and ChIP-seq analysis under normal and 20 μM copper-shock conditions. By integrating the transcriptome and genome-wide binding data, we found that CopR binds to the upstream regions of many copper-induced genes. Negative-stain transmission electron microscopy and 2D class averaging revealed an octameric assembly formed from a tetramer of dimers for CopR, similar to published crystal structures from the Lrp family. In conclusion, we propose a model for CopR-regulated transcription and highlight the complex regulatory network that enables Pyrococcus to respond to increased copper concentrations.

scholarly journals Chaos, Order and Systematics in Evolution of the Genetic Code

2020 ◽  
Author(s):  
Lei Lei ◽  
Zachary F. Burton
Keyword(s):  
Genetic Code ◽  
Life Transition ◽  
Life World ◽  
Phase Separations ◽  
Fiber Production ◽  
Trna Synthetases ◽  
Cellular Life ◽  
Aminoacyl Trna Synthetases ◽  
Translation Systems ◽  
Liquid Liquid Phase Separation

The genetic code evolved by parallel tracks of chaotic and ordered processes. Liquid-liquid phase separation (hydrogels), a chaotic process, constructs diverse membraneless compartments within cells, resulting in regulated hydration and sequestration and concentration of reaction components. Hydrogels relate to chaotic amyloid fiber production. We propose that polyglycine and related hydrogels (i.e. GADV; G is glycine), phase separations, membraneless droplets and amyloid accretions organized protocell domains to drive the earliest evolution of the genetic code and the pre-life to cellular life transition. By contrast, evolution of tRNA, tRNAomes, aminoacyl-tRNA synthetases and translation systems followed highly ordered and systematic pathways, described by well-defined mechanisms and rules. The pathway of evolution of aminoacyl-tRNA synthetases, which tracked evolution of the genetic code, is clarified. Hydrogels and amyloids form a chaotic component, therefore, that complemented otherwise systematic processes. We describe with detail a pre-life world in which hydrogels and amyloids provided the selections of the first life.

Ecology Emergent

2017 ◽  
Author(s):  
John L. Culliney ◽  
David Jones
Keyword(s):  
Big Bang ◽  
Competition And Cooperation ◽  
Evolving Systems ◽  
Chemical Structures ◽  
Edge Of Chaos ◽  
Cellular Life ◽  
The World ◽  
Complex Carbon ◽  
Living Organisms ◽  
Self Replication

Ever since life’s debut on the earth, biotic evolution has been a near-balancing act. On virtually every level, competition and cooperation, shifting endlessly between foreground and background, have tugged and teased evolving systems as they have wobbled through time along the edge of chaos. The emergence of cellular life from the world of complex carbon-based chemistry appears to have happened only once in the primordial dreamtime of planet Earth. Scientists base this conjecture on a number of virtually universal distributions of chemical structures and processes across the spectrum of living organisms. Despite their perhaps tenuous hold on life, the earliest cells, primitive bacteria and archea, possessed the keys to the opening of new potential for matter and energy—the capabilities of self-replication, controlled energy transduction, directed locomotion, and the regulation of an internal environment. Out of this cellular Big Bang there arose a totally new force field on planet Earth superimposed over the physical, chemical, and geological, but with tendrils pervading all of those realms. It was the beginning of the biosphere. Life pervaded and began to transform the lithosphere, hydrosphere, and atmosphere. The chapter highlights transitions of prokaryote to eukaryote via endosymbiosis. Also featured are: biofilms, bioluminescence, coral reefs, and ecological succession.

Three Lives and Astrobiology

2020 ◽  
pp. 57-78 ◽  
Author(s):  
Lucas Mix
Keyword(s):  
Anthropic Principle ◽  
Biological Organization ◽  
Cellular Life ◽  
Hard Problems ◽  
Life On Earth ◽  
Different Origins ◽  
Three Lives

This chapter explores the concept of life across traditions, from science to philosophy to theology. The term “life” covers at least three constellations of meaning or life-concepts: biological life, internal life, and rational life. Biological life shares traits with all cellular life on Earth (archaea, eubacteria, and eukarya). Internal or conscious life shares subjective interiority with humans. Rational life shares intellect with all minds that can distinguish truth from non-truth. These three lives possess different origins, extents, and futures. The chapter then identifies three distinct “hard problems of life” relating to the origin and extent of biological organization, consciousness, and reason: moving from non-life to life, from life to sentience, and from sentience to rationality. The Drake equation, the Fermi paradox, and the anthropic principle provide concrete examples in astrobiology.

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