Information In Biological Systems Research Articles

Information support for the bioresource collection: a biological information system «NeuroOnc»

The manuscript is devoted to development of information support system for a bioresource collection - biological information system «NeuroOnc». Architecture and main functions of system are presented. This system was formed in the project «Development of bioresource collection of tumors of the human nervous system with molecular genetic certification for personalized treatment of patients with neuro-oncological diseases». The purpose of this project was not only formation of bioresource collection, but also development of various molecular genetic methods for analysis of biospecimens in context of clinical researches. Biological information systems created to support the work of bioresource collections in hospitals should become a natural part of information infrastructure. Information support of bioresource collections cannot imply only «warehouse» functions. This system should have tools to support various scientific and clinical researches. Biological information systems can sometimes expand medical information systems but remain sufficiently autonomous. It is advisable to develop biological information systems in large specialized companies that can support their products for many years.

Uncovering Patterns Beneath the Surface: A Glimpse into the Applications of Algebraic Topology

This paper explores the significant impact of algebraic topology on diverse real-world applications. Starting with an introduction to the historical development and essence of algebraic topology, it delves into its applications in neuroscience, physics, biology, engineering, data analysis, and Geographic Information Systems (GIS). Remarkable applications incorporate the analysis of neural networks, quantum mechanics, materials science, and disaster management, showcasing its boundless significance. Despite computational challenges, this study outlines prospects, emphasizing the requirement for proficient algorithms, noise robustness, multi-scale analysis, machine learning integration, user-friendly tools, and interdisciplinary collaborations. In essence, algebraic topology provides a transformative lens for uncovering stowed-away topological structures in complex data, offering solutions to perplexing problems in science, engineering, and society, with vast potential for future exploration and innovation.

Development ofmarine biodiversity database (BISMaL) to enable estimations past habitat conditions formarine life inthe northwestern Pacific.

Global activities involving the collection of marine biodiversity information have provided a large amount of biological observation records that cover various spatiotemporal areas. To predict biological responses or distribution changes in response to environmental changes by using these observation records, it is essential to analyze not only the current marine physicochemical environmental conditions but also the past conditions when the organisms were observed. We developed a new function to estimate the past marine environmental conditions for the observation records in our marine biodiversity database (Biological Information System for Marine Life: BISMaL) and examine whether the database can reliably estimate thermal habitats for both benthic and planktonic marine organisms. For the benthic squat lobster Shinkaia crosnieri, the estimated and observed in situ temperatures were similar to each other. For the planktonic chaetognaths Krohnitta pacifica and K. subtilis, the estimated temperatures showed clear seasonal changes specific to their distribution areas. These results indicated that BISMaL can reliably provide past habitat conditions regardless of planktonic or benthic lifestyles. BISMaL, which provides both biological observations and estimated past environmental conditions through web services, could lower the barrier to data access and use and make data-driven science available not only for data scientists but also for various marine scientists, such as taxonomists, ecologists and field scientists. Database URL: https://www.godac.jamstec.go.jp/bismal/e/.

NGS and Mutational Profile Analysis of Non-Small-Cell Lung Carcinoma (NSCLC)

Abstract: Computational analysis imitates the functioning of biological information systems to anticipate and offer novel perspectives on the biological realm. Genome sequencing analysis interactive techniques with the aim of improving the standards of cancer patient, has progressed greatly over the last decades, and is now considered to be one of the major scientific fields that promote innovation in the technology and healthcare sectors. In the field of bioinformatics, the first widespread application of data analysis was the creation of the first collection of systematic data representing the genome sequences of the eukaryotic organisms, termed as the eukaryotic genome, or the "de novo" genome. Tumor suppressor proteins are a class of proteins that are involved in preventing cancer from occurring. Several tumor suppressor proteins have been found to be mutated in certain forms of cancer, resulting in the loss of their tumor suppressing properties. Lung cancer develops when normal lung cells change, or mutate, in a way that alters their natural growth and death cycle, resulting in unregulated cell division that produces too many cells.Deep sequence analysis of non-small cell lung cancer and integrated analysis of gene expression. Understanding the biology of cancer is required to improve patient outcomes. Next-generation sequencing (NGS) is a powerful tool for whole genome characterization, enabling comprehensive exploration and understanding of the complex interactions between genes, proteins and their environment. NGS in the field of oncology is still in its infancy and the wealth of data that it is capable of generating is revolutionizing our understanding of cancer. ORFs have led to many exciting discoveries in the field of oncology, including the identification of tumor suppressor proteins. One of the most exciting recent discoveries is in the field of tumor suppressor proteins. Tumor suppressor proteins are proteins that play a role in the regulation of cell proliferation and division. Mutations in certain tumor suppressor genes cause cancer, and as a result, a great deal of research has gone into the identification of new tumor suppressor genes

Major Transitions as Groupoid Symmetry-Breaking in Nonergodic Prebiotic, Biological and Social Information Systems.

We extend the comparatively simple processes of group symmetry-breaking in physical systems to groupoid/equivalence class phase transitions characterizing adiabatically, piecewise stationary, information transmission in prebiotic, biological, and social phenomena: High vs. Low probability paths [Formula: see text] Interior and Exterior Interact [Formula: see text] Multiple Interacting Tunable Workspaces Application to nonstationary processes seems possible via generalizations of the symmetry algebra, for example, to semigroupoids. The dynamic probability models explored here can be transformed into statistical tools for the analysis of real-time and other data across a spectrum of important disciplines confronted by biological and other forms of cognition and their dysfunctions.

A resource scheduling method for reliable and trusted distributed composite services in cloud environment based on deep reinforcement learning.

With the vigorous development of Internet technology, applications are increasingly migrating to the cloud. Cloud, a distributed network environment, has been widely extended to many fields such as digital finance, supply chain management, and biomedicine. In order to meet the needs of the rapid development of the modern biomedical industry, the biological cloud platform is an inevitable choice for the integration and analysis of medical information. It improves the work efficiency of the biological information system and also realizes reliable and credible intelligent processing of biological resources. Cloud services in bioinformatics are mainly for the processing of biological data, such as the analysis and processing of genes, the testing and detection of human tissues and organs, and the storage and transportation of vaccines. Biomedical companies form a data chain on the cloud, and they provide services and transfer data to each other to create composite services. Therefore, our motivation is to improve process efficiency of biological cloud services. Users’ business requirements have become complicated and diversified, which puts forward higher requirements for service scheduling strategies in cloud computing platforms. In addition, deep reinforcement learning shows strong perception and continuous decision-making capabilities in automatic control problems, which provides a new idea and method for solving the service scheduling and resource allocation problems in the cloud computing field. Therefore, this paper designs a composite service scheduling model under the containers instance mode which hybrids reservation and on-demand. The containers in the cluster are divided into two instance modes: reservation and on-demand. A composite service is described as a three-level structure: a composite service consists of multiple services, and a service consists of multiple service instances, where the service instance is the minimum scheduling unit. In addition, an improved Deep Q-Network (DQN) algorithm is proposed and applied to the scheduling algorithm of composite services. The experimental results show that applying our improved DQN algorithm to the composite services scheduling problem in the container cloud environment can effectively reduce the completion time of the composite services. Meanwhile, the method improves Quality of Service (QoS) and resource utilization in the container cloud environment.

The Coevolution of Biomolecules and Prebiotic Information Systems in the Origin of Life: A Visualization Model for Assembling the First Gene.

Prebiotic information systems exist in three forms: analog, hybrid, and digital. The Analog Information System (AIS), manifested early in abiogenesis, was expressed in the chiral selection, nucleotide formation, self-assembly, polymerization, encapsulation of polymers, and division of protocells. It created noncoding RNAs by polymerizing nucleotides that gave rise to the Hybrid Information System (HIS). The HIS employed different species of noncoding RNAs, such as ribozymes, pre-tRNA and tRNA, ribosomes, and functional enzymes, including bridge peptides, pre-aaRS, and aaRS (aminoacyl-tRNA synthetase). Some of these hybrid components build the translation machinery step-by-step. The HIS ushered in the Digital Information System (DIS), where tRNA molecules become molecular architects for designing mRNAs step-by-step, employing their two distinct genetic codes. First, they created codons of mRNA by the base pair interaction (anticodon–codon mapping). Secondly, each charged tRNA transferred its amino acid information to the corresponding codon (codon–amino acid mapping), facilitated by an aaRS enzyme. With the advent of encoded mRNA molecules, the first genes emerged before DNA. With the genetic memory residing in the digital sequences of mRNA, a mapping mechanism was developed between each codon and its cognate amino acid. As more and more codons ‘remembered’ their respective amino acids, this mapping system developed the genetic code in their memory bank. We compared three kinds of biological information systems with similar types of human-made computer systems.

A flexible selection tool for the inclusion of soil biology methods in the assessment of soil multifunctionality

Soil biota contribute to the delivery of multiple soil functions. However, soil biological methods are highly underrepresented in the assessment of soil functionality in agricultural production systems. Here we present a flexible tool to support decision-making during the selection process of soil biological methods for monitoring soil functions. This tool is based on a structured and conceptual framework that connects soil biota to soil functions through their contribution to different soil processes. The methods assessed by the tool were selected as a result of a thorough literature review. Soil biology experts supported the development of the tool (i) by providing feedback on the reviewed methods through a survey and (ii) by determining the relevance of different soil biota to the soil processes related to soil multifunctionality during a workshop. The tool is freely accessible online at the Biological Soil Information System (BIOSIS) platform, where researchers or users with an understanding of research practices can interact with the tool to define the context of their assessment and preferences for technical criteria of the methods. By incorporating user input, this flexible tool can help inform a wide variety of research and assessment programs interested in applying soil biological methods to monitor soil multifunctionality at different scales.

Differential Gene Expression Responding to Low Phosphate Stress in Leaves and Roots of Maize by cDNA-SRAP.

Phosphate (Pi) deficiency in soil can have severe impacts on the growth, development, and production of maize worldwide. In this study, a cDNA-sequence-related amplified polymorphism (cDNA-SRAP) transcript profiling technique was used to evaluate the gene expression in leaves and roots of maize under Pi stress for seven days. A total of 2494 differentially expressed fragments (DEFs) were identified in response to Pi starvation with 1202 and 1292 DEFs in leaves and roots, respectively, using a total of 60 primer pairs in the cDNA-SRAP analysis. These DEFs were categorized into 13 differential gene expression patterns. Results of sequencing and functional analysis showed that 63 DEFs (33 in leaves and 30 in roots) were annotated to a total of 54 genes involved in diverse groups of biological pathways, including metabolism, photosynthesis, signal transduction, transcription, transport, cellular processes, genetic information, and organismal system. This study demonstrated that (1) the cDNA-SRAP transcriptomic profiling technique is a powerful method to analyze differential gene expression in maize showing advantageous features among several transcriptomic methods; (2) maize undergoes a complex adaptive process in response to low Pi stress; and (3) a total of seven differentially expressed genes were identified in response to low Pi stress in leaves or roots of maize and could be used in the genetic modification of maize.

What is Genetic Entropy. An Equilibrium or a Non Equilibrium Entropy

It is the genetic degeneration of living things. Genetic entropy is the systematic breakdown of the internal biological information systems that make life alive. Genetic entropy results from genetic mutations. The important aspect to understand here is if each of these mutations follow a pattern or proportionality to any physical quantity. Do these mutations behave in a way which is already known to us or does it require a deeper understanding. We have tried to understand the behavior of mutations based on non-equilibrium entropy arising from the Fokker-Planck equations. This study shows the calculation of entropy production of mutations in general and if they follow a specific behavior or if they follow an underlying principle or not.

Design and self-assembly of information systems

ABSTRACTThe existence of biological information systems is generally taken as given in discussions of their function. However, any theory of such systems must be considered incomplete unless it can also explain how the system comes to exist. This article describes the ways in which complex functional systems in general can be created through design, self-assembly and evolution. The differences and relationship between physical and informational entities, organization, processes and dimensionality are also discussed. Through comparison with information technologies, whose origins we understand, conclusions are drawn concerning the creation of functional biological neural networks: specifically, that this involves the self-assembly of information entities into a number of strongly emergent levels of organization. Finally, potential approaches are considered to overcome the hurdles to scientific investigation of emergent information-based systems and the processes by which they are created.

Effect of ketamine anesthesia on proteome in hippocampus of aged rats

Objective To evaluate the effects of ketamine anesthesia on proteome in hippocampus in aged rats. Methods Thirty healthy male Wistar rats, aged 20 months, weighing 560-610 g, were divided into 2 groups (n=15 each) using a random number table method: control group (group C) and ketamine group (group K). In group K, ketamine 80 mg/kg was intraperitoneally injected, additional 1/2 initial dose was given when the righting reflex was recovered, and anesthesia was maintained for 3 h. Morris water maze test was performed starting from 1st day after the end of anesthesia.Five rats were selected at days 1 and 7 after the end of anesthesia and sacrificed, and hippocampal tissues were obtained to extract proteins.Proteins extracted from rat hippocampi were identified by 2-dimensional electrophoresis (2-DE). The differentially expressed proteins were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and biological information system. Results Compared with group C, the escape latency and total swimming distance to find the submerged platform in Morris water maze at the 1st day after anesthesia were significantly prolonged in group K (P<0.05 or 0.01). The MALDI-TOF-MS analysis showed that there were 21 differentially expressed proteins at 1st day after ketamine anesthesia, of which 6 proteins (involving maintenance of intracellular protein homeostasis, energy metabolism, etc.) presented with up-regulated expression and 15 proteins (involving synaptic vesicle transport efficiency, synaptic structural and functional plasticity, maintenance of intracellular protein homeostasis, NMDA-mediated Ca2+ signal transport, energy metabolism, etc.) presented with down-regulated expression.There were 8 differentially expressed proteins at 7th day, including 3 proteins with up-regulated expression and 5 proteins with down-regulated expression (P<0.05). Conclusion Ketamine anesthesia can induce 21 differentially expressed proteins in hippocampi of aged rats, involving synaptic vesicle transport efficiency, synaptic structural and functional plasticity, intracellular protein homeostasis, NMDA-mediated Ca2+ signal transport, energy metabolism, and etc.which may be involved in the mechanism of ketamine-induced temporary cognitive dysfunction. Key words: Ketamine; Cognitive function; Hippocampus; Proteome; Aged

Development of the Biological Information Measurement System for STEM Education and High School/University Articulation

Development of human resources in the field of science and technology is a necessity in the modern world. To encourage the development of the nation, it is important to educate forward-thinking engineers in cooperation with the education system, with the requirements of modern society as the background of their efforts. In Western countries, STEM (Science, Technology, Engineering, and Mathematics) education is provided as a national strategy for development, and this type of education is also spreading to Japan. On the other hand, in the context of high school/university articulation, it is argued that the abilities required by high schools, universities, and society are different from one another, and that it is necessary to inter-link them. Accordingly, comprehensive content that includes all levels, from primary to higher education, is required. On the basis of this background and the current problem of STEM education and high school/university articulation, this research aims to aid in the development of a curriculum and educational study materials through which the technology of universities could be integrated into high school classes. This report includes the development of educational study material on biological information systems because it reflects the features of the department to which the authors belong and there is already a lot of research on, and technology related to, biological information. Using the educational study material, we carry out an in-class practice session including task-oriented research at a high school with cooperation from a university and discuss the educational effect that results from it.

Applications of Biological Diversity Information Systems towards Conservation at Lawachara National Park in Bangladesh

The study investigates a framework for Integrated Biological Diversity Information Systems (BDIS) with relevant rules and regulations that emphasize the need for interdisciplinary research collaborations at national, regional and global scales on nature conservation mechanisms at Lawachara National Park (LNP) in Bangladesh. To date, Bangladesh has no Integrated National Biodiversity Database with Clearing House Mechanisms. So, there is a lot of nature conserving problems faced on biodiversity management systems. The study integrates technological information from stakeholders like park manager, biological diversity specialists, network officers, ecological specialists, policy-makers, wildlife managers, academicians and relevant bodies. The study represents the uniqueness of the tools used to enhance conservation professionals on the national biodiversity strategic action plan through existing policies and technology, literature reviews, observations, interviews and reconnaissance findings. Approximately 64% of the respondents agreed for the development of Biological Diversity Information Systems (BDIS) for conserving nature at LNP. The study describes the essential information needed for comprehensive data exchange, data indexing, web-publication and reports on Convention on Biological Diversity with the help of Resources Information Management System. Finally, the study suggests future research trajectories using a new collaborative approach to drive the methodological agenda and recommends ways to further incorporate the information systems integrating next generations’ biodiversity conservation perspectives.&#x0D;

Физические основы функционированияи эволюционные истоки биологических информационных систем

Физические основы функционированияи эволюционные истоки биологических информационных систем

Analysis of population genetic diversity of mosquitoes from Shandong Province based on mitochondrial DNA cytochrome oxidase subunit I gene fragment

To explore the characteristics of gene sequence of mtDNA-COⅠ of Culex pipiens pallens from different geographical regions in Shandong Province and different resistant strains from the lab and five common mosquito species, and analyze the genetic diversity of these mosquitoes. Adult mosquitoes were collected from Jinan, Jining, Qingdao cities and other places in Shandong Province. The sensitive, dichlorvos-resistant, pyrethroid-resistant and propoxur-resistant strains were reared in the lab. Five species of mosquito (Cx. pipiens pallens, Cx. tritaeniorhynchus, Anopheles sinensis, Aedes albopictus, and Armigeres subalbatus) were collected from Jining City and identified in the lab. mtDNA-COⅠwas specifically amplified by PCR and sequenced. The gene sequences were compared and analyzed by the biological information systems, and the phylogenetic tree was constructed. The amplified mtDNA-COⅠfragments of Cx. pipiens pallens from eight different cities and four different resistant strains were 528 bp in length, with 67.4% A+T contents and two mutation sites. The nucleotide sequence homology among the different geographic strains was 99.95% and the gene sequences of the four resistant strains were the same, showing a high homogeny. The amplified mtDNA-COⅠfragments of the five species of mosquitoes were 528 bp with 408 conserved sites, 120 variable sites, 42 parsimony informative sites and 78 singleton sites. The A+T contents were between 65.7% and 68.0%. The nucleotide sequence homology among the different mosquito species was between 86.17% and 92.05%, and the molecular identification was consistent with the traditional morphological identification. The molecular phylogenetic study showed that the different species were clustered at their own branch at the species and genus levels, while genera Armigeres was distantly related to the others. mtDNA-COⅠcould not serve as the molecular marker to analyze the population genetic variation and phylogenesis of Cx. pipiens pallens from different geographical regions and different resistant strains, but it has species and genus specificities, which could be used for the identification of the mosquito species and genus.

Методи оцінювання антропогенних загроз біорізноманіттю прісноводних екосистем

The industrial and agricultural activities of mankind, which includes chemical pollution, building of dams and hydroelectric power stations and their use of the biomass of freshwater ecosystems, have had considerable impacts on freshwater ecosystems, the abundance of aquatic species, and the vital capacity of those species’ populations. A variety of aquatic organisms are feasible indicators and they can be used for evaluation water quality through analysis of their population diversity, composition and abundance. The most significant threats for freshwater biodiversity and the integrity of aquatic ecosystems are activities in the watershed’s terrestrial realm, disturbances occurring in aquatic and riparian environments and threats that affect freshwater organisms. There are changes of functional structure of biological community due to reducing biodiversity and the dominance of opportunistic species. A lot of changes in characteristics of biological communities can be assessed by using different kinds of evaluations, including the index of biological integrity, saprobity system and geographic information system technology. An effective predictor of great number of disturbances to freshwater ecosystems is the density of human population. Approaches that directly evaluate the level of threat to freshwater biodiversity typically use species composition and abundance data. Methods that indirectly assess the biotic community evaluate the ecological integrity of aquatic ecosystems. For large-scale, resource-limited, time-constrained biodiversity conservation planning, the most appropriate method for assessing the impairment of freshwater systems is relativistic evaluation of biological integrity using geospatial data. For aquatic threat assessments, the most meaningful level of analysis is the drainage basin and its subbasins. The concept of ecoregions covers all freshwater ecosystems. This approach provides biologically meaningful units for further large-scale studies of existing and potential threats to biodiversity. The size of drainage basins can be defined from digital elevation models, which exist as global network in high quality resolution. At the level of drainage basin, using high-resolution remote sensing imagery is often feasible from a financial and workload perspective.

Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing.

Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche.

Best-in-class and strategic benchmarking of scientific subject categories of Web of Science in 2010

Here we show a novel technique for comparing subject categories, where the prestige of academic journals in each category is represented statistically by an impact-factor histogram. For each subject category we compute the probability of occurrence of scholarly journals with impact factor in different intervals. Here impact factor is measured with Thomson Reuters Impact Factor, Eigenfactor Score, and Immediacy Index. Assuming the probabilities associated with a pair of subject categories our objective is to measure the degree of dissimilarity between them. To do so, we use an axiomatic characterization for predicting dissimilarity between subject categories. The scientific subject categories of Web of Science in 2010 were used to test the proposed approach for benchmarking Cell Biology and Computer Science Information Systems with the rest as two case studies. The former is best-in-class benchmarking that involves studying the leading competitor category; the latter is strategic benchmarking that involves observing how other scientific subject categories compete.

Cloud computing: increasing the 'T' pipeline in STEM majors

Science, technology, engineering and mathematics (STEM) are driving forces in the world’s economy. Unfortunately, it is estimated that the USA may have a shortage of as many as three million STEM workers by 2018. One way to mitigate this potential shortage is to introduce STEM programmes in K-12 using cloud computing. Cloud computing, specifically the Virtual Computing Lab (VCL), allows users to have remote access to a wide range of computing environments and applications. This article discusses VCL as it was introduced to high school students during a summer programme. The FUTURES/T.A.G.S. programme was a collaborative effort between faculty members in the Biology and Computer Information Systems programmes. The theme for the FUTURES/T.A.G.S. summer programme was ‘Addressing global obesity’. The results of the programme show that through the use of innovative and collaborative STEM programmes strides can be made with students’ perceptions of STEM careers while increasing their aptitude.