scholarly journals Honey bee as an alternative model invertebrate organism

2025 ◽  
Vol 74 (10) ◽  
pp. 6140-2025
Author(s):  
ALEKSANDRA ŁOŚ ◽  
MAŁGORZATA BIEŃKOWSKA ◽  
ANETA STRACHECKA
Keyword(s):  
Collective Intelligence ◽  
Lethal Dose ◽  
Genetic Research ◽  
Model Organism ◽  
Model Organisms ◽  
Cellular Mechanisms ◽  
Bee Colony ◽  
Proboscis Extension ◽  
The Individual ◽  
Explosive Devices

Insects perfectly fit the flagship principle of animal research – 3R: to reduce (the number of animals), to replace (animals with alternative models) and to refine (methods). Bees have the most important advantages of a model organism: they cause minimal ethical controversy, they have a small and fully known genome, and they permit the use of many experimental techniques. Bees have a fully functional DNMT toolkit. Therefore, they are used as models in biomedical/genetic research, e.g. in research on the development of cancer or in the diagnostics of mental and neuroleptic diseases in humans. The reversion of aging processes in bees offers hope for progress in gerontology research. The cellular mechanisms of learning and memory coding, as well as the indicators of biochemical immunity parameters, are similar or analogous to those in humans, so bees may become useful in monitoring changes in behavior and metabolism. Bees are very well suited for studies on the dose of the substance applied to determine the lethal dose or the effect of a formula on life expectancy. Honeybees have proven to be an effective tool for studying the effects of a long-term consumption of stimulants, as well as for observing behavioral changes and developing addictions at the individual and social levels, as well as for investigating the effects of continuously delivering the same dose of a substance. The genomic and physiological flexibility of bees in dividing tasks among workers in a colony makes it possible to create a Single- Cohort Colony (SCC) in which peers compared perform different tasks. Moreover behavioral methods (e.g. Proboscis Extension Reflex – PER, Sting Extension Reflex – SER, free flying target discrimination tasks or the cap pushing response) make it possible to analyse changes occurring in honeybee brains during learning and remembering. Algorithms of actions are created based on the behavior of a colony or individual, e.g. Artificial Bee Colony Algorithm (ABCA). Honeybees are also model organisms for profiling the so-called intelligence of a swarm or collective intelligence. Additionally, they serve as models for guidance systems and aviation technologies. Bees have inspired important projects in robotics, such as B-droid, Robobee and The Green Brain Project. It has also been confirmed that the apian sense of smell can be used to detect explosive devices, such as TNT, or drugs (including heroin, cocaine, amphetamines and cannabis). This inconspicuous little insect can revolutionize the world of science and contribute to the solution of many scientific problems as a versatile model.

scholarly journals In silicoidentification of non-coding RNAs inHalobacterium salinarum NRC-1, a model archeon organism

2017 ◽  
Author(s):  
M. A. S. Fonseca ◽  
R. Z. N. Vêncio
Keyword(s):  
Model Organism ◽  
Regulatory Elements ◽  
Halobacterium Salinarum ◽  
Biological Information ◽  
Model Organisms ◽  
Cellular Mechanisms ◽  
Information Processing Model ◽  
Rna Molecules ◽  
Candidate Ncrnas ◽  
Genomic Regions

AbstractBackgroundIn addition to the regulatory elements already known, for instance, transcription factors or post-translation modifications, there is growing interest in the regulatory role played by non-coding RNA molecules (ncRNA), whose functions are performed at a different level of biological information processing. Model organisms provide a convenient way of working in the laboratory, and different research groups use these models to conduct studies on the cellular mechanisms present in these organisms. Although some ncRNAs elements have been found in theHalobacterium salinarummodel organism, we believe that not enough is known about these genomic regions.MethodsTherefore, anin silicoanalysis for ncRNA identification was conducted onH. salinarumNRC-1. Considering a data integration perspective and some available methodologies, several machine learning models were built and used to designate candidate ncRNAs genome regions.ResultsA total of 42 new ncRNAs were identified. Combing analysis with other available tools, it had been observed that some suggested candidates also was found with different methodologies and thus, it highlights the proposed results.

scholarly journals New Roles for Model Genetic Organisms in Understanding and Treating Human Disease: Report From The 2006 Genetics Society of America Meeting

Genetics ◽  
2006 ◽  
Vol 172 (4) ◽  
pp. 2025-2032
Author(s):  
Allan Spradling ◽  
Barry Ganetsky ◽  
Phil Hieter ◽  
Mark Johnston ◽  
Maynard Olson ◽  
...  
Keyword(s):  
Human Disease ◽  
Medical Science ◽  
Genetic Research ◽  
Model Organism ◽  
Model Systems ◽  
Neurological Dysfunction ◽  
Model Organisms ◽  
Biological Knowledge ◽  
Medical Disorders ◽  
The Future

Abstract Fundamental biological knowledge and the technology to acquire it have been immeasurably advanced by past efforts to understand and manipulate the genomes of model organisms. Has the utility of bacteria, yeast, worms, flies, mice, plants, and other models now peaked and are humans poised to become the model organism of the future? The Genetics Society of America recently convened its 2006 meeting entitled “Genetic Analysis: Model Organisms to Human Biology” to examine the future role of genetic research. (Because of time limitations, the meeting was unable to cover the substantial contributions and future potential of research on model prokaryotic organisms.) In fact, the potential of model-organism-based studies has grown substantially in recent years. The genomics revolution has revealed an underlying unity between the cells and tissues of eukaryotic organisms from yeast to humans. No uniquely human biological mechanisms have yet come to light. This common evolutionary heritage makes it possible to use genetically tractable organisms to model important aspects of human medical disorders such as cancer, birth defects, neurological dysfunction, reproductive failure, malnutrition, and aging in systems amenable to rapid and powerful experimentation. Applying model systems in this way will allow us to identify common genes, proteins, and processes that underlie human medical conditions. It will allow us to systematically decipher the gene–gene and gene–environment interactions that influence complex multigenic disorders. Above all, disease models have the potential to address a growing gap between our ability to collect human genetic data and to productively interpret and apply it. If model organism research is supported with these goals in mind, we can look forward to diagnosing and treating human disease using information from multiple systems and to a medical science built on the unified history of life on earth.

scholarly journals In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2226
Author(s):  
Sazia Kunvar ◽  
Sylwia Czarnomska ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Model Organism ◽  
Genotyping By Sequencing ◽  
Model Organisms ◽  
European Bison ◽  
Model Animal ◽  
Pcr Duplicates ◽  
Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

scholarly journals Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Bing He ◽  
Ping Chen ◽  
Sonia Zambrano ◽  
Dina Dabaghie ◽  
Yizhou Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Human Kidney ◽  
Cell Types ◽  
Model Organisms ◽  
Mural Cell ◽  
Glomerular Cell ◽  
Individual Gene ◽  
The Individual

AbstractMolecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research. Previous studies have uncovered gene expression profiles of several kidney glomerular cell types, however, important cells, including mesangial (MCs) and glomerular parietal epithelial cells (PECs), are missing or incompletely described, and a systematic comparison between mouse and human kidney is lacking. To this end, we use Smart-seq2 to profile 4332 individual glomerulus-associated cells isolated from human living donor renal biopsies and mouse kidney. The analysis reveals genetic programs for all four glomerular cell types (podocytes, glomerular endothelial cells, MCs and PECs) as well as rare glomerulus-associated macula densa cells. Importantly, we detect heterogeneity in glomerulus-associated Pdgfrb-expressing cells, including bona fide intraglomerular MCs with the functionally active phagocytic molecular machinery, as well as a unique mural cell type located in the central stalk region of the glomerulus tuft. Furthermore, we observe remarkable species differences in the individual gene expression profiles of defined glomerular cell types that highlight translational challenges in the field and provide a guide to design translational studies.

scholarly journals Alliance of Genome Resources Portal: unified model organism research platform

2019 ◽  
Vol 48 (D1) ◽  
pp. D650-D658 ◽  
Author(s):  
◽  
Julie Agapite ◽  
Laurent-Philippe Albou ◽  
Suzi Aleksander ◽  
Joanna Argasinska ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Model Organism ◽  
Model Organisms ◽  
Data Types ◽  
Primary Model ◽  
Genomic Studies ◽  
Health And Disease ◽  
Extensive Body ◽  
Access To Data ◽  
Model Organism Databases

Abstract The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource.

scholarly journals How Can Satellite DNA Divergence Cause Reproductive Isolation? Let Us Count the Chromosomal Ways

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Patrick M. Ferree ◽  
Satyaki Prasad
Keyword(s):  
Reproductive Isolation ◽  
Developmental Stages ◽  
Rapid Evolution ◽  
Model Organisms ◽  
Cellular Mechanisms ◽  
Closely Related Species ◽  
Heterochromatin Formation ◽  
Interspecies Hybrids ◽  
Postzygotic Reproductive Isolation ◽  
And Function

Satellites are one of the most enigmatic parts of the eukaryotic genome. These highly repetitive, noncoding sequences make up as much as half or more of the genomic content and are known to play essential roles in chromosome segregation during meiosis and mitosis, yet they evolve rapidly between closely related species. Research over the last several decades has revealed that satellite divergence can serve as a formidable reproductive barrier between sibling species. Here we highlight several key studies on Drosophila and other model organisms demonstrating deleterious effects of satellites and their rapid evolution on the structure and function of chromosomes in interspecies hybrids. These studies demonstrate that satellites can impact chromosomes at a number of different developmental stages and through distinct cellular mechanisms, including heterochromatin formation. These findings have important implications for how loci that cause postzygotic reproductive isolation are viewed.

scholarly journals Transgenic Epigenetics: Using Transgenic Organisms to Examine Epigenetic Phenomena

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Lori A. McEachern
Keyword(s):  
Molecular Mechanisms ◽  
Model Organism ◽  
Evolutionary Conservation ◽  
Model Organisms ◽  
Valuable Insight ◽  
Epigenetic Control ◽  
Transgenic Organisms ◽  
Epigenetic Analysis ◽  
Insight Into ◽  
Epigenetic Processes

Non-model organisms are generally more difficult and/or time consuming to work with than model organisms. In addition, epigenetic analysis of model organisms is facilitated by well-established protocols, and commercially-available reagents and kits that may not be available for, or previously tested on, non-model organisms. Given the evolutionary conservation and widespread nature of many epigenetic mechanisms, a powerful method to analyze epigenetic phenomena from non-model organisms would be to use transgenic model organisms containing an epigenetic region of interest from the non-model. Interestingly, while transgenic Drosophila and mice have provided significant insight into the molecular mechanisms and evolutionary conservation of the epigenetic processes that target epigenetic control regions in other model organisms, this method has so far been under-exploited for non-model organism epigenetic analysis. This paper details several experiments that have examined the epigenetic processes of genomic imprinting and paramutation, by transferring an epigenetic control region from one model organism to another. These cross-species experiments demonstrate that valuable insight into both the molecular mechanisms and evolutionary conservation of epigenetic processes may be obtained via transgenic experiments, which can then be used to guide further investigations and experiments in the species of interest.

1,2-dichloroethane removal by Bruguiera gymnorrhiza (L.) Lamk and Pseudomonas putida BCC 23535

2016 ◽  
Vol 16 (5) ◽  
pp. 1313-1319 ◽  
Author(s):  
Sawitree Saiyood ◽  
Duangrat Inthorn ◽  
Alisa Vangnai ◽  
Paitip Thiravetyan
Keyword(s):  
Adverse Effect ◽  
Pseudomonas Putida ◽  
Lethal Dose ◽  
Contaminated Water ◽  
Bruguiera Gymnorrhiza ◽  
Mangrove Plant ◽  
The Individual ◽  
Hydroponic Conditions

The purpose of this work was to investigate the ability of Bruguiera gymnorrhiza (L.) Lamk and Pseudomonas putida BCC 23535 to remove 1,2-dichloroethane (1,2-DCA) in contaminated water under hydroponic conditions. B. gymnorrhiza (L.) Lamk is a representative mangrove plant that can tolerate high levels of 1,2-DCA with a lethal dose 50 (LD50) of 34.67 mM. A concentration of 10 mM 1,2-DCA was chosen in the present study because it had no adverse effect on the plant. Using B. gymnorrhiza (L.) Lamk alone could completely remove 1,2-DCA over four cycles of 1,2-DCA exposure. P. putida BCC 23535 alone could also remove 1,2-DCA but the efficiency was lower than B. gymnorrhiza (L.) Lamk. The combination of B. gymnorrhiza (L.) Lamk and P. putida BCC 23535 could completely remove 1,2-DCA within 6 days, which was more effective than the individual plants alone. P. putida BCC 23535 can be applied in 1,2-DCA contaminated water in groundwater which B. gymnorrhiza (L.) Lamk can be used in above ground contaminated environments. Therefore, this study suggests that both B. gymnorrhiza (L.) Lamk and P. putida BCC 23535 are alternative ways to treat 1,2-DCA in contaminated environments.

scholarly journals Individualization of Products and Services with Artificial General Intelligence and General Collective Intelligence

2020 ◽  
Author(s):  
Andy E Williams
Keyword(s):  
Online Education ◽  
News Media ◽  
Intelligent Agents ◽  
Collective Intelligence ◽  
Online News ◽  
General Intelligence ◽  
Entertainment Media ◽  
Individual User ◽  
Artificial General Intelligence ◽  
The Individual

INTRODUCTION: With advances in big data techniques having already led to search results and advertising being customized to the individual user, the concept of an online education designed solely for an individual, or the concept of online news or entertainment media, or any other virtual service being designed uniquely for each individual, no longer seems as far fetched. However, designing services that maximize user outcomes as opposed to services that maximize outcomes for the corporation owning them, requires modeling user processes and the outcomes they target.OBJECTIVES: To explore the use of Human-Centric Functional Modeling (HCFM) to define functional state spaces within which human processes are well-defined paths, and within which products and services solve specific navigation problems, so that by considering all of any given individual’s desired paths through a given state space, it is possible to automate the customization of those products and services for that individual or to groups of individuals.METHODS: An analysis is performed to assess how and whether intelligent agents based on some subset of functionality required for Artificial General Intelligence (AGI) might be used to optimize for the individual user. And an analysis is performed to determine whether and if so how General Collective Intelligence (GCI) might be used to optimize across all users.RESULTS: AGI and GCI create the possibility to individualize products and services, even shared services such as the Internet, or news services so that every individual sees a different version.CONCLUSION: The conceptual example of customizing a news media website for two individual users of opposite political persuasions suggests that while the overhead of customizing such services might potentially result in massively increased storage and processing overhead, within a network of cooperating services in which this customization reliably creates value, this is potentially a significant opportunity.

scholarly journals Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

FACETS ◽  
2017 ◽  
Vol 2 (2) ◽  
pp. 610-641 ◽  
Author(s):  
Rebekah A. Oomen ◽  
Jeffrey A. Hutchings
Keyword(s):  
Climate Change ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Environmental Variability ◽  
Global Climate ◽  
Genetic Research ◽  
Model Organisms ◽  
Rna Seq ◽  
Transcriptomic Responses ◽  
Ecological Importance

The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short- and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.

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