Evolution and Development of the Information Concept in Biological Systems: From Empirical Description to Informational Modeling of the Living Structures

With the purpose to smooth the way of a correct understanding of information concepts and their evolution,in this paper,is discussed the evolution and development of the concept of information in biological systems,showing that this concept was intuitively perceived even since ancient times by our predecessors,and described according to their language level of that times,but the crystallization of the real meaning of information is an achievement of our nowadays,by successive contribution of various scientific branches and personalities of the scientific community of the world,leading to a modern description/modeling of reality,in which information plays a fundamental role.It is shown that our reality can be understood as a contribution of matter/energy/information and represented/discussed as the model of the Universal Triangle of Reality(UTR),where various previous models can be suggestively inserted,as a function of their basic concern.The modern concepts on information starting from a theoretic experiment which would infringe the thermodynamics laws and reaching the theory of information and modern philosophic concepts on the world structuration allow us to show that information is a fundamental component of the material world and of the biological structures,in correlation with the structuration/destructuration processes of matter,involving absorption/release of information.Based on these concepts,is discussed the functionality of the biologic structures and is presented the informational model of the human body and living structures,as a general model of info-organization on the entire biological scale,showing that a rudimentary proto-consciousness should be operative even at the low-scale biological systems,because they work on the same principles,like the most developed bio-systems.The operability of biologic structures as informational devices is also pointed out.

Optimal Size for Maximal Energy Efficiency in Information Processing of Biological Systems Due to Bistability

Energy efficiency is closely related to the evolution of biological systems and is important to their information processing. In this work, we calculate the excitation probability of a simple model of a bistable biological unit in response to pulsatile inputs, and its spontaneous excitation rate due to noise perturbation. Then we analytically calculate the mutual information, energy cost, and energy efficiency of an array of these bistable units. We find that the optimal number of units could maximize this array＇s energy efficiency in encoding pulse inputs, which depends on the fixed energy cost. We conclude that demand for energy efficiency in biological systems may strongly influence the size of these systems under the pressure of natural selection.

Information-Body Relation and Information as a Solution of the Consciousness Problem in the Biological Structures

This paper approaches two main philosophical questions concerning the biological structures,from unicellular to multicellular organisms:one of them(i),referred to the information-body relation,as an extension of the mind-body relation at human,and another one(ii),to the consciousness problem,concerning the existence and nature of consciousness(if any),at the inferior organisms on the complexity scale,as this concept is known at humans.As philosophy benefits of the privilege to use data/concepts from other sciences to obtain philosophical conclusions,there were included detailed descriptions of some key biologic mechanisms,analyzed from informational perspective,necessary just to support/demonstrate/reinforce the informational nature/substrate of the mentioned relations.The analysis of the close relation between information and body,related to the structuration and functional properties of the biological organisms,from cells to multicellular structures,shows that all of them are able to“embody/disembody”information during/by structuration/destructuration processes of matter,in particular that of DNA/RNA/proteins,their functions appearing as a result of their informational capabilities to internally manage the inter-connection with environment,primarily due to their permanent dependence on the food resources and adaptation/survival needs.The experimental and theoretical studies,revealing/documenting on one hand the automatic management of maintenance metabolic processes,the reproduction,and growth/development,and on the other hand the adaptive decision-making/sentient processes as a responsive reaction to the environmental cues,show/support the consistency of the informational model of the human body and living structures on the entire biological scale,providing support to the informational solution of the stated problems(i)and(ii).A distinct attention is paid to plants,which are organisms without nervous system,but which show/manifest also informational capabilities to detect/react to information and to modulate their behavior accordingly.The question if the living organisms possess a pseudo/proto-consciousness level as a consequence of the informational activity of their body,distinct from human,but active in any biological structure under certain conditions is furthermore discussed,and a reliable definition of rudimentary pseudo/proto-consciousness level is given/described and compared with other empirical/theoretical concepts.

Information standardization for typical toxic and harmful algae in China's coastal waters——a case study of Karenia mikimotoi

To assist the researches of toxic and harmful algae and provide government workers with judgment basis for decision-making related events,we established a biological information management system for toxic and harmful algae in China’s of fshore to assist relevant research.In this study,Karenia mikimotoi was studied as a typical toxic and harmful algae species,and the basic biological information and biogeographic distribution information of K.mikimotoi were systematically studied and collected.In the part of basic biological information,the name,toxin,and molecular characteristic sequence of K.mikimotoi were sorted out by literature searching and website browsing.Through experimental means,the relevant information of morphological identifi cation,pigment composition,and lipid composition were obtained.In the part of biogeographic distribution information,this study sorted out the information of K.mikimotoi,analyzed the characteristics of its occurrence,and completed the standardized construction of biogeographic distribution information.Through the collation of basic biological information and biogeographic distribution information of K.mikimotoi,the standardization of related information was completed,which provided template and method reference for information collection of other toxic and harmful algae species,which was benefi cial to the database analysis and design.

Investigation of GhFAT Genes Related to Seed Oil Content and Fatty Acid Composition in Gossypium hirsutum L.

Fatty Acyl-ACP thioesterase(FAT)is a key enzyme controlling oil biosynthesis in plant seeds.FATs can be divided into two subfamilies,FATA and FATB according to their amino acid sequences and substrate specificity.The Upland cotton genome contains 20 GhFAT genes,amongst which 6 genes were of the GhFATA subfamily and 14 of the GhFATB subfamily.The 20 GhFAT genes are unevenly distributed on 14 chromosomes.The GhFATA genes have 5 or 7 exons and the GhFATB genes have 6 or 7 exons.All GhFAT proteins have the conserved Acyl-ACP_TE domain and PLN02370 super family,the typical characteristics of plant thioesterases.Analyses of the expression level of GhFATs and the compositions of fatty acid in 5-60 days-post-anthesis seeds showed that the ratio of saturated fatty acids to unsaturated fatty acids was consistent with the expression profile of GhFATB12,GhFATB3,and GhFATB10;the ratio of monounsaturated fatty acid to polyunsaturated fatty acids was consistent with the expression profile of GhFATA3.The oil contents of mature cottonseeds were positively correlated with the contents of palmitic acid and linolenic acid as well as seed vigor.These results provide essential information for further exploring the role(s)of the specific GhFATs in determining oil biosynthesis and cottonseed compositions.

Bioinformatics screening of breast cancer-related genes and potential drug research

Objective:To search the the differentially expressed genes between breast cell carcinoma tissues and normal tissues by using bioinformatics technology,and the potential therapeutic drugs for breast cancer were identified,which can provide reference for clinical immune targeted therapy and drug therapy of breast cancer in the future.Methods:"Breast cancer"was searched by using Gene Expression Omnibus(GEO),and GSE79586 chip data was downloaded.The differentially expressed genes in the control group and the breast cancer model group were screened by using bio-communication technology and subjected to GO function analysis,KEGG pathway analysis,differential gene characteristic expression analysis and protein-protein interaction network(PPI)analysis,and the analysis results were further visualized.Prognosis analysis,related function prediction and immune infiltration analysis were performed using the GEPIA,GeneMANIA,and Timer2.0 databases,respectively.Finally,the compounds with potential therapeutic effects on breast cancer are identified through Connectivity Map(CMap).Western blotting and real-time PCR(RT-PCR)were used to verify the core genes and potential therapeutic agents with the highest correlation in vitro.Results:A total of 3916 differentially expressed genes including 1786 up-regulated genes and 2130 down-regulated genes were screened.GO analysis showed that the differential genes were mainly involved in the positive regulation of phosphorylation,secretory vesicles,racemase and epimerase activities.KEGG analysis showed that differential genes were involved in systemic lupus erythematosus,alcoholism,sticky spots,amoebic dysentery Ras signal pathways and other disease pathways.The characteristic expression analysis of differential genes showed that MEK inhibitors,HSP90 inhibitors and signal transduction pathway kinase inhibitors were drugs similar to the differential genes.PPI results showed that H2AFJ,TFF1,GATA3,FOXA1,and CDH1 were core genes related to breast cancer.Two core genes of H2AFJ and TFF1 with the highest correlation were further selected for GEPIA analysis.The results of the analysis showed that the mRNA expression levels of H2AFJ and TFF1 in breast cancer cells were significantly higher than those in normal tissues,and there was a significant correlation with the pathological staging,overall survival rate and disease-free survival rate of breast cancer patients.H2AFJ and TFF1 may be potential prognostic biomarkers for survival of breast cancer patients.The functions of differentially expressed H2AFJ and TFF1 are mainly related to hormone receptor binding,epithelial structure maintenance and epigenetic negative regulation of genes,chromatin tissue involved in negative regulation of transcription,etc.The results of immune infiltration showed that the expressions of H2AFJ and TFF1 had a significant correlation with the infiltration of macrophages,neutrophils,monocytes,CD4+T,CD8+T,B lymphocytes and other immune cells.CMap results showed that compounds such as Gefitinib,Alpelisib,Sorafenib,and Sunitinib had potential therapeutic effects on breast cancer.Western blot and RT-PCR results showed that H2AFJ and TFF1 were significantly overexpressed in breast cancer cells.Gefitinib significantly inhibited the expression of H2AFJ and TFF1 in breast cancer cells(P<0.05,P<0.01).Conclusion:In this study,differentially expressed genes between breast cell carcinoma tissues and normal tissues were screened out by bioinformatics means to further identify key genes and compounds with potential therapeutic effects in the onset process of breast cancer and to further verify the effectiveness of the screened drugs on breast cancer through experiments.It will provide reference for clinical research and development of new drugs against breast cancer in the future in order to develop more effective treatment options.

Sequence-Based Predicting Bacterial Essential ncRNAs Algorithm by Machine Learning

Essential ncRNA is a type of ncRNAwhich is indispensable for the sur-vival of organisms.Although essential ncRNAs cannot encode proteins,they are as important as essential coding genes in biology.They have got wide variety of applications such as antimicrobial target discovery,minimal genome construction and evolution analysis.At present,the number of species required for the deter-mination of essential ncRNAs in the whole genome scale is still very few due to the traditional methods are time-consuming,laborious and costly.In addition,tra-ditional experimental methods are limited by the organisms as less than 1%of bacteria can be cultured in the laboratory.Therefore,it is important and necessary to develop theories and methods for the recognition of essential non-coding RNA.In this paper,we present a novel method for predicting essential ncRNA by using both compositional and derivative features calculated by information theory of ncRNA sequences.The method was developed with Support Vector Machine(SVM).The accuracy of the method was evaluated through cross-species cross-vali-dation and found to be between 0.69 and 0.81.It shows that the features we selected have good performance for the prediction of essential ncRNA using SVM.Thus,the method can be applied for discovering essential ncRNAs in bacteria.

A Study on the Utility of an Electroencephalogram-Based Stress Analysis Method for Seaside and Road Space

Modern society is called the stress society, there has been a growing interest in comfortable living space. Therefore, a lot of studies using biological information have been done to quantitatively assess the effects on the human body in recent years. This study verified quantitatively difference between healing effect and stress reduction effect of sea space and general street space using an inexpensive EEG (Electroencephalogram) machine. The purpose of this study is to verify quantitatively healing effect and stress reduction effect of sea space using the EEG measurement from the psychological analysis by questionnaire survey and the SD (Semantic Differential) method. As a result, EEG and questionnaire results, psychological analysis results can be seen to match, and the effectiveness of the EEG measurement was confirmed.

Novel Scheme for Essential Proteins Identification Based on Improved Multicriteria Decision Making

Identifying essential proteins from protein-protein interaction networks is important for studies onbiological evolution and new drug’s development.Most of the presented criteria for prioritizing essential proteinsonly focus on a certain attribute of the proteins in the network,which suffer from information loss.In order toovercome this problem,a relatively comprehensive and effective novel method for essential proteins identificationbased on improved multicriteria decision making(MCDM),called essential proteins identification-technique fororder preference by similarity to ideal solution(EPI-TOPSIS),is proposed.First,considering different attributes ofproteins,we propose three methods from different aspects to evaluate the significance of the proteins:gene-degreecentrality(GDC)for gene expression sequence;subcellular-neighbor-degree centrality(SNDC)and subcellular-indegree centrality(SIDC)for subcellular location information and protein complexes.Then,betweenness centrality(BC)and these three methods are considered together as the multiple criteria of the decision-making model.Analytic hierarchy process is used to evaluate the weights of each criterion,and the essential proteins are prioritizedby an ideal solution of MCDM,i.e.,TOPSIS.Experiments are conducted on YDIP,YMIPS,Krogan and BioGRIDnetworks.The results indicate that EPI-TOPSIS outperforms several state-of-the-art approaches for identifyingthe essential proteins through the performance measures.