Metagrowth: a new resource for the building of metabolic hypotheses in microbiology.
Ontology highlight
ABSTRACT:
SUBMITTER: Ogata H
PROVIDER: S-EPMC539996 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:New educational resources are being implemented as an initiative to foster learning. In order to contribute to the toolkit of innovative educational resources, we developed a microbiology comic book. The aim of this comic is to provide educators with a fun, accessible, and rigorous way to generate awareness of the invisible world that surrounds us and that inhabits us. Bacteria have a reputation as harmful and disgusting entities. Mass media, with advertisements of disinfectants, soaps, and house cleaning products, are sending a distorted message about microbes. We must debunk these misconceptions and emphasize the importance of microorganisms, and particularly bacteria, in the environment and our lives. Education is the means to this end, and therefore this comic is intended to help educators teach microbiology in an attractive, accurate, and straightforward way. Here, we present this educational tool and give some tips on the different themes that can be addressed in the classroom using this resource.
| S-EPMC6508913 | biostudies-literature
Project description:Introduction:The National Academy of Medicine recently published "A Multifaceted Systems Approach to Addressing Stress Within Health Professions Education and Beyond," which calls for greater attention to the wellness of health care providers, students, and educators. Suggested actions include "creating and training positive role models." In order for faculty to role-model behaviors of wellness, they need to understand what this means and how to incorporate it into their lives. At present, there is only one other MedEdPORTAL resource on wellness and resilience that includes faculty as audience members. Methods:This 60-minute workshop is designed to provide faculty with a basic framework for wellness, with an emphasis on the emotional process aspect of resilience. Strategies for stress and anxiety management are reviewed. The workshop is interactive, with large- and small-group discussions, as well as a guided meditation. Results:This workshop was given at the 2017 Council of Faculties Business Meeting at the American Dental Education Association Annual Session, with 40 participants. Workshop evaluations, completed by 34 (85%) attendees, showed an overall rating of 4.0 on a 5-point Likert scale, with 5 = excellent. The workshop was repeated at the School of Dentistry at the University of California, San Francisco, with 11 attendees; there, the overall rating was 4.7. Discussion:In order to contribute to a culture of wellness and resilience in their organization, faculty need training on the concepts, as well as practical skills for implementation. This workshop provides introductory-level knowledge and skills.
| S-EPMC6338201 | biostudies-other
Project description:Systems biology and functional genomics require genome-wide datasets and resources. Complete sets of cloned open reading frames (ORFs) have been made for about a dozen bacterial species and allow researchers to express and study complete proteomes in a high-throughput fashion.We have constructed an open reading frame (ORFeome) collection of 3974 or 94% of the known Escherichia coli K-12 ORFs in Gateway entry vector pENTR/Zeo. The collection has been used for protein expression and protein interaction studies. For example, we have compared interactions among YgjD, YjeE and YeaZ proteins in E. coli, Streptococcus pneumoniae, and Staphylococcus aureus. We also compare this ORFeome with other Gateway-compatible bacterial ORFeomes and show its utility for comparative functional genomics.The E. coli ORFeome provides a useful resource for functional genomics and other areas of protein research in a highly flexible format. Our comparison with other ORFeomes makes comparative analyses straighforward and facilitates direct comparisons of many proteins across many genomes.
| S-EPMC3091666 | biostudies-literature
Project description:Undergraduate microbiology curriculum should be amenable to periodic changes to incorporate new developments and ideas. The curriculum should be used not merely as a way to disseminate facts but also as a way to allow students to experience the process of science. In the context of undergraduate microbiology education in Osmania University (Hyderabad, India), existing curriculum does not explicitly allow students to engage in deeper understanding of concepts and understanding of the process of science, both in lecture and laboratory courses. The assessment methods that are currently used are limited in scope as they only test factual recall and superficial understanding of the subject and very minimally assess critical thinking skills. Another factor hampering innovation in the broader context of undergraduate education is the unavailability and inaccessibility to adequate resources. To address the issue of resource-limitations in implementing activities that expose undergraduate students to real-world microbiology experiences, a collaboration between a research institute and two teaching colleges was formed. This collaboration involved teacher and student workshops on exploring microbial diversity using 16S rRNA analysis with a view of blending novel research questions with technical skills in the undergraduate microbiology lab. This effort is an example of educators providing students with authentic experiences and, helping them gain critical knowledge and research skills in microbiology even under resource constraints, and students demonstrating motivation to participate in similar activities in the future. The collaborative effort described here can be a broadly sustainable model to improve overall undergraduate education in relatively resource-limited environments.
| S-EPMC7752863 | biostudies-literature
Project description:BackgroundMetabolic network reconstructions formalize our knowledge of metabolism. Gaps in these networks pinpoint regions of metabolism where biological components and functions are "missing." At the same time, a major challenge in the post genomic era involves characterisation of missing biological components to complete genome annotation.ResultsWe used the human metabolic network reconstruction RECON 1 and established constraint-based modelling tools to uncover novel functions associated with human metabolism. Flux variability analysis identified 175 gaps in RECON 1 in the form of blocked reactions. These gaps were unevenly distributed within metabolic pathways but primarily found in the cytosol and often caused by compounds whose metabolic fate, rather than production, is unknown. Using a published algorithm, we computed gap-filling solutions comprised of non-organism specific metabolic reactions capable of bridging the identified gaps. These candidate solutions were found to be dependent upon the reaction environment of the blocked reaction. Importantly, we showed that automatically generated solutions could produce biologically realistic hypotheses of novel human metabolic reactions such as of the fate of iduronic acid following glycan degradation and of N-acetylglutamate in amino acid metabolism.ConclusionsThe results demonstrate how metabolic models can be utilised to direct hypotheses of novel metabolic functions in human metabolism; a process that we find is heavily reliant upon manual curation and biochemical insight. The effectiveness of a systems approach for novel biochemical pathway discovery in mammals is demonstrated and steps required to tailor future gap filling algorithms to mammalian metabolic networks are proposed.
| S-EPMC3224382 | biostudies-literature
Project description:The Tara Oceans Expedition has provided large, publicly-accessible microbial metagenomic datasets from a circumnavigation of the globe. Utilizing several size fractions from the samples originating in the Mediterranean Sea, we have used current assembly and binning techniques to reconstruct 290 putative draft metagenome-assembled bacterial and archaeal genomes, with an estimated completion of ?50%, and an additional 2,786 bins, with estimated completion of 0-50%. We have submitted our results, including initial taxonomic and phylogenetic assignments, for the putative draft genomes to open-access repositories for the scientific community to use in ongoing research.
| S-EPMC5507172 | biostudies-literature
Project description:Biologists are required to integrate large amounts of data to construct a working model of the system under investigation. This model is often informal and stored mentally or textually, making it prone to contain undetected inconsistencies, inaccuracies, or even contradictions, not much less than a representation in free natural language. Using Object-Process Methodology (OPM), a formal yet visual and humanly accessible conceptual modeling language, we have created an executable working model of the mRNA decay process in Saccharomyces cerevisiae, as well as the import of its components to the nucleus following mRNA decay. We show how our model, which incorporates knowledge from 43 articles, can reproduce outcomes that match the experimental findings, evaluate hypotheses, and predict new possible outcomes. Moreover, we were able to analyze the effects of the mRNA decay model perturbations related to gene and interaction deletions, and predict the nuclear import of certain decay factors, which we then verified experimentally. In particular, we verified experimentally the hypothesis that Rpb4p, Lsm1p, and Pan2p remain bound to the RNA 3'-untranslated region during the entire process of the 5' to 3' degradation of the RNA open reading frame. The model has also highlighted erroneous hypotheses that indeed were not in line with the experimental outcomes. Beyond the scientific value of these specific findings, this work demonstrates the value of the conceptual model as an in silico vehicle for hypotheses generation and testing, which can reinforce, and often even replace, risky, costlier wet lab experiments.
| S-EPMC4177816 | biostudies-literature
Project description: Not available
| S-EPMC5577975 | biostudies-literature
Project description:There is increasing appreciation that the immune system plays critical roles not only in the traditional domains of infection and inflammation but also in many areas of biology, including tumorigenesis, metabolism, and even neurobiology. However, one of the major barriers for understanding human immunological mechanisms is that immune assays have not been reproducibly characterized for a sufficiently large and diverse healthy human cohort. Here, we present the 10,000 Immunomes Project (10KIP), a framework for growing a diverse human immunology reference, from ImmPort, a publicly available resource of subject-level immunology data. Although some measurement types are sparse in the presently deposited ImmPort database, the extant data allow for a diversity of robust comparisons. Using 10KIP, we describe variations in serum cytokines and leukocytes by age, race, and sex; define a baseline cell-cytokine network; and describe immunologic changes in pregnancy. All data in the resource are available for visualization and download at http://10kimmunomes.org/.
| S-EPMC6263160 | biostudies-literature
Project description:Bioinformatics looks to many microbiologists like a service industry. In this view, annotation starts with what is known from experiments in the lab, makes reasonable inferences of which genes match other genes in function, builds databases to make all that we know accessible, but creates nothing truly new. Experiments lead, then biocuration and computational biology follow. But the astounding success of genome sequencing is changing the annotation paradigm. Every genome sequenced is an intercepted coded message from the microbial world, and as all cryptographers know, it is easier to decode a thousand messages than a single message. Some biology is best discovered not by phenomenology, but by decoding genome content, forming hypotheses, and doing the first few rounds of validation computationally. Through such reasoning, a role and function may be assigned to a protein with no sequence similarity to any protein yet studied. Experimentation can follow after the discovery to cement and to extend the findings. Unfortunately, this approach remains so unfamiliar to most bench scientists that lab work and comparative genomics typically segregate to different teams working on unconnected projects. This review will discuss several themes in comparative genomics as a discovery method, including highly derived data, use of patterns of design to reason by analogy, and in silico testing of computationally generated hypotheses.
| S-EPMC4325363 | biostudies-literature