Assessing Students' Ability to Trace Matter in Dynamic Systems in Cell Biology

College-level biology courses contain many complex processes that are often taught and learned as detailed narratives. These processes can be better understood by perceiving them as dynamic systems that are governed by common fundamental principles. Conservation of matter is such a principle, and thus tracing matter is an essential step in learning to reason about biological processes. We present here multiple-choice questions that measure students' ability and inclination to trace matter through photosynthesis and cellular respiration. Data associated with each question come from students in a large undergraduate biology course that was undergoing a shift in instructional strategy toward making fundamental principles (such as tracing matter) a central theme. We also present findings from interviews with students in the course. Our data indicate that 1) many students are not using tracing matter as a tool to reason about biological processes, 2) students have particular difficulties tracing matter between systems and have a persistent tendency to interconvert matter and energy, and 3) instructional changes seem to be effective in promoting application of the tracing matter principle. Using these items as diagnostic tools allows instructors to be proactive in addressing students' misconceptions and ineffective reasoning.

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Using "Orals" as a Peer-Led Instructional Strategy to Improve Undergraduate Performance

Innovations in Teaching & Learning Conference Proceedings ◽

10.13021/g84c79 ◽

2015 ◽

Vol 7 (1) ◽

Author(s):

Reid Schwebach ◽

Caroline Thomas ◽

Claudette Davis

Keyword(s):

Small Group ◽

Cell Biology ◽

Instructional Strategy ◽

Group Discussion ◽

Visual Learning ◽

Calvin Cycle ◽

Time Frame ◽

Biological Processes ◽

Student Interactions ◽

Biology Courses

Learning Assistants (LAs), Faculty, and GTAs will learn how to hold small group oral review sessions in undergraduate Biology courses using five small group strategies. These sessions were designed to help undergraduates prepare for semester examinations. Within a two-hour time frame, orals blend kinesthetic, audial, and visual learning prompts to help students understand biological topics. These strategies are highly adoptable for other STEM courses. The five techniques that will be explored include: (1) student utilization of the whiteboard, (2) LA utilization of the whiteboard, (3) student-to-LA interactions, (4) small group discussion, and (5) student-to-student interactions. (1) Students will use the whiteboard to draw pictorial representations of biological processes while other students provide feedback. (2) LAs will draw out cellular processes (for example, glycolysis and the Calvin cycle) on the whiteboard while students instruct the LA on what to draw. (3) LAs provide a list of guiding questions to students that act as a basis for student and LA discussion. (4) LAs also provide a packet containing key lecture PowerPoint slides—the figures contained in these slides force students to provide the context to slides. (5) Student-to-student pair interactions force students to discuss, draw, or act out biological processes. Importantly, in a cell biology courses, these strategies are associated with underperforming students improving their grades by a full letter grade (D students make C grades), and higher-performing students report the strategies to be highly beneficial.

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Simulation of Indicators of the Functional Systems of Human Body on the Basis of Three Compartmental Two-Cluster Control System

Journal of New Medical Technologies ◽

10.12737/7259 ◽

2014 ◽

Vol 21 (4) ◽

pp. 7-11 ◽

Cited By ~ 1

Author(s):

Берестин ◽

D. Berestin ◽

Даянова ◽

D. Dayanova ◽

Вохмина ◽

...

Keyword(s):

Dynamic Systems ◽

Chaotic Dynamics ◽

Simulation Software ◽

External Control ◽

Biological Processes ◽

Systems Management ◽

Cluster Systems ◽

Complex Processes ◽

Control Actions ◽

Main Components

Processes simulation is one of the main directions in science and technology. In the presence of a simple model of the process, the results of the process before it starts can be obtained. The simulation of complex processes (systems) within the standard methods of computing and simulation software runs into difficulties because of the chaotic dynamics of such systems. The number of models that allow to describe the complex biological processes of dynamic systems is extremely small, because it is impossible to repeat the same results of experiments based on deterministic or stochastic models. The authors propose a model that allows the description of the state vector of a person within tree compartmental two-cluster systems management. The model is implemented using the package of applied programs that demonstrate the performance of each cluster separately. On the model output signals are obtained, they are compared with real experiments and the resulting signals. Signals obtained at the output of the simulation model signals show different values of external control actions in which the change in the properties of the output signal. Control signal and the output signals respectively were divided into four main components that have the same name counterparts with complex biological dynamical systems.

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A Classroom Simulation Activity to Visualize Energy and Matter Transformation in Cellular Respiration and Photosynthesis

The American Biology Teacher ◽

10.1525/abt.2017.79.7.552 ◽

2017 ◽

Vol 79 (7) ◽

pp. 552-561

Author(s):

Lace A. Svec

Keyword(s):

High School Students ◽

Cell Biology ◽

Cellular Respiration ◽

Introductory Biology ◽

School Students ◽

Biology Students ◽

Complex Processes ◽

University Level ◽

The University ◽

Classroom Simulation

Undergraduate introductory biology students at the university level often struggle to trace movement of matter and energy through catabolic and anabolic processes in biological systems. A sequential guided simulation of cellular respiration and photosynthesis provides students an opportunity to actively model and visualize matter transformation and energy accumulation and degradation through the movement of molecular and energy “game pieces.” The activity was designed to help students generate a simplified outline of these two highly complex processes, while reinforcing the principles of conservation of matter and energy. My students participated in this activity during peer-led review sessions in an undergraduate, introductory, majors biology course (ca.150 students in 18 SI sessions over two semesters), but instructors could also easily adapt it for use in small lecture or laboratory classrooms, introductory cell biology, physiology, and ecology courses, or with high school students.

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A Dynamic Systems Approach to Personality

European Psychologist ◽

10.1027//1016-9040.6.3.172 ◽

2001 ◽

Vol 6 (3) ◽

pp. 172-176 ◽

Cited By ~ 14

Author(s):

Lawrence A. Pervin

Keyword(s):

Dynamic Systems ◽

Systems Approach ◽

Biological Processes ◽

Recent Advances ◽

Dynamic View ◽

The Future ◽

History Of

David Magnusson has been the most articulate spokesperson for a holistic, systems approach to personality. This paper considers three concepts relevant to a dynamic systems approach to personality: dynamics, systems, and levels. Some of the history of a dynamic view is traced, leading to an emphasis on the need for stressing the interplay among goals. Concepts such as multidetermination, equipotentiality, and equifinality are shown to be important aspects of a systems approach. Finally, attention is drawn to the question of levels of description, analysis, and explanation in a theory of personality. The importance of the issue is emphasized in relation to recent advances in our understanding of biological processes. Integrating such advances into a theory of personality while avoiding the danger of reductionism is a challenge for the future.

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Molecular regulation of Snai2 in development and disease

Journal of Cell Science ◽

10.1242/jcs.235127 ◽

2019 ◽

Vol 132 (23) ◽

Author(s):

Wenhui Zhou ◽

Kayla M. Gross ◽

Charlotte Kuperwasser

Keyword(s):

Transcription Factor ◽

Cell Biology ◽

Molecular Mechanisms ◽

Epithelial To Mesenchymal Transition ◽

Zinc Finger Protein ◽

Main Role ◽

Biological Processes ◽

Developmental Defects ◽

Mesenchymal Transition ◽

Damage Repair

ABSTRACT The transcription factor Snai2, encoded by the SNAI2 gene, is an evolutionarily conserved C2H2 zinc finger protein that orchestrates biological processes critical to tissue development and tumorigenesis. Initially characterized as a prototypical epithelial-to-mesenchymal transition (EMT) transcription factor, Snai2 has been shown more recently to participate in a wider variety of biological processes, including tumor metastasis, stem and/or progenitor cell biology, cellular differentiation, vascular remodeling and DNA damage repair. The main role of Snai2 in controlling such processes involves facilitating the epigenetic regulation of transcriptional programs, and, as such, its dysregulation manifests in developmental defects, disruption of tissue homeostasis, and other disease conditions. Here, we discuss our current understanding of the molecular mechanisms regulating Snai2 expression, abundance and activity. In addition, we outline how these mechanisms contribute to disease phenotypes or how they may impact rational therapeutic targeting of Snai2 dysregulation in human disease.

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Microfluidic Based Physical Approaches towards Single-Cell Intracellular Delivery and Analysis

Micromachines ◽

10.3390/mi12060631 ◽

2021 ◽

Vol 12 (6) ◽

pp. 631

Author(s):

Kiran Kaladharan ◽

Ashish Kumar ◽

Pallavi Gupta ◽

Kavitha Illath ◽

Tuhin Subhra Santra ◽

...

Keyword(s):

Single Cell ◽

Cell Biology ◽

Transfection Efficiency ◽

Intracellular Delivery ◽

Diagnostic Tools ◽

Delivery Methods ◽

Physical Methods ◽

Cell Measurement ◽

Therapeutic Development ◽

Single Living

The ability to deliver foreign molecules into a single living cell with high transfection efficiency and high cell viability is of great interest in cell biology for applications in therapeutic development, diagnostics, and drug delivery towards personalized medicine. Various physical delivery methods have long demonstrated the ability to deliver cargo molecules directly to the cytoplasm or nucleus and the mechanisms underlying most of the approaches have been extensively investigated. However, most of these techniques are bulk approaches that are cell-specific and have low throughput delivery. In comparison to bulk measurements, single-cell measurement technologies can provide a better understanding of the interactions among molecules, organelles, cells, and the microenvironment, which can aid in the development of therapeutics and diagnostic tools. To elucidate distinct responses during cell genetic modification, methods to achieve transfection at the single-cell level are of great interest. In recent years, single-cell technologies have become increasingly robust and accessible, although limitations exist. This review article aims to cover various microfluidic-based physical methods for single-cell intracellular delivery such as electroporation, mechanoporation, microinjection, sonoporation, optoporation, magnetoporation, and thermoporation and their analysis. The mechanisms of various physical methods, their applications, limitations, and prospects are also elaborated.

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The Etiology and Pathophysiology Genesis of Benign Prostatic Hyperplasia and Prostate Cancer: A New Perspective

Medicines ◽

10.3390/medicines8060030 ◽

2021 ◽

Vol 8 (6) ◽

pp. 30

Author(s):

Teow J. Phua

Keyword(s):

Prostate Cancer ◽

Benign Prostatic Hyperplasia ◽

Cell Biology ◽

Cancer Biology ◽

Cost Savings ◽

Prostatic Hyperplasia ◽

Biological Processes ◽

New Perspective ◽

Prostatic Diseases

Background: The etiology of benign prostatic hyperplasia and prostate cancer are unknown, with ageing being the greatness risk factor. Methods: This new perspective evaluates the available interdisciplinary evidence regarding prostate ageing in terms of the cell biology of regulation and homeostasis, which could explain the timeline of evolutionary cancer biology as degenerative, inflammatory and neoplasm progressions in these multifactorial and heterogeneous prostatic diseases. Results: This prostate ageing degeneration hypothesis encompasses the testosterone-vascular-inflamm-ageing triad, along with the cell biology regulation of amyloidosis and autophagy within an evolutionary tumorigenesis microenvironment. Conclusions: An understanding of these biological processes of prostate ageing can provide potential strategies for early prevention and could contribute to maintaining quality of life for the ageing individual along with substantial medical cost savings.

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Rescaling Biology: Increasing Integration Across Biological Scales and Subdisciplines to Enhance Understanding and Prediction

Integrative and Comparative Biology ◽

10.1093/icb/icab191 ◽

2021 ◽

Author(s):

Colette St. Mary ◽

Thomas H Q Powell ◽

John S Kominoski ◽

Emily Weinert

Keyword(s):

Multiple Scales ◽

Genomic Variation ◽

Biological Processes ◽

Explicit Integration ◽

Fully Integrated ◽

Community Or ◽

Complex Processes ◽

Spatiotemporal Scales ◽

Patterns And Processes ◽

Vast Range

Synopsis The organization of the living world covers a vast range of spatiotemporal scales, from molecules to the biosphere, seconds to centuries. Biologists working within specialized subdisciplines tend to focus on different ranges of scales. Therefore, developing frameworks that enable testing questions and predictions of scaling requires sufficient understanding of complex processes across biological subdisciplines and spatiotemporal scales. Frameworks that enable scaling across subdisciplines would ideally allow us to test hypotheses about the degree to which explicit integration across spatiotemporal scales is needed for predicting the outcome of biological processes. For instance, how does genomic variation within populations allow us to explain community structure? How do the dynamics of cellular metabolism translate to our understanding of whole-ecosystem metabolism? Do patterns and processes operate seamlessly across biological scales, or are there fundamental laws of biological scaling that limit our ability to make predictions from one scale to another? Similarly, can sub-organismal structures and processes be sufficiently understood in isolation of potential feedbacks from the population, community, or ecosystem levels? And can we infer the sub-organismal processes from data on the population, community, or ecosystem scale? Concerted efforts to develop more cross-disciplinary frameworks will open doors to a more fully integrated field of biology. In this paper, we discuss how we might integrate across scales, specifically by (1) identifying scales and boundaries, (2) determining analogous units and processes across scales, (3) developing frameworks to unite multiple scales, and (4) extending frameworks to new empirical systems.

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An Algorithm for Cellular Reprogramming

10.1101/162974 ◽

2017 ◽

Cited By ~ 1

Author(s):

Scott Ronquist ◽

Geoff Patterson ◽

Markus Brown ◽

Stephen Lindsly ◽

Haiming Chen ◽

...

Keyword(s):

Cell Cycle ◽

Transcription Factor ◽

Transcription Factors ◽

Cell Biology ◽

Human Fibroblasts ◽

Cell Types ◽

Approximate Model ◽

Cellular Reprogramming ◽

Biological Processes ◽

Moderate Complexity

AbstractThe day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton’s laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology, providing data-guided frameworks that allow us to develop better predictions about, and methods for, control over specific biological processes and system-wide cell behavior. In this paper, we describe an approach to optimizing the use of transcription factors (TFs) in the context of cellular reprogramming. We construct an approximate model for the natural evolution of a cell cycle synchronized population of human fibroblasts, based on data obtained by sampling the expression of 22,083 genes at several time points along the cell cycle. In order to arrive at a model of moderate complexity, we cluster gene expression based on the division of the genome into topologically associating domains (TADs) and then model the dynamics of the TAD expression levels. Based on this dynamical model and known bioinformatics, such as transcription factor binding sites (TFBS) and functions, we develop a methodology for identifying the top transcription factor candidates for a specific cellular reprogramming task. The approach used is based on a device commonly used in optimal control. Our data-guided methodology identifies a number of transcription factors previously validated for reprogramming and/or natural differentiation. Our findings highlight the immense potential of dynamical models, mathematics, and data-guided methodologies for improving strategies for control over biological processes.Significance StatementReprogramming the human genome toward any desirable state is within reach; application of select transcription factors drives cell types toward different lineages in many settings. We introduce the concept of data-guided control in building a universal algorithm for directly reprogramming any human cell type into any other type. Our algorithm is based on time series genome transcription and architecture data and known regulatory activities of transcription factors, with natural dimension reduction using genome architectural features. Our algorithm predicts known reprogramming factors, top candidates for new settings, and ideal timing for application of transcription factors. This framework can be used to develop strategies for tissue regeneration, cancer cell reprogramming, and control of dynamical systems beyond cell biology.

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Trace elements during primordial plexiform network formation in human cerebral organoids

10.7287/peerj.preprints.2126 ◽

2016 ◽

Author(s):

Rafaela C Sartore ◽

Simone C Cardoso ◽

Yuri V Lages ◽

Julia M Paraguassu ◽

Rodrigo F Madeiro da Costa ◽

...

Keyword(s):

Trace Elements ◽

Human Brain ◽

Pluripotent Stem Cells ◽

Cell Biology ◽

Network Formation ◽

Biological Processes ◽

Human Brain Tissue ◽

Human Brain Development ◽

Calcium Iron ◽

Human Telencephalon

Systematic studies of micronutrients during brain formation are hindered by restrictions to animal models and adult post-mortem tissues. Recently, advances in stem cell biology have enabled recapitulation of the early stages of human telencephalon development. In the present work, we exposed cerebral organoids derived from human pluripotent stem cells to synchrotron radiation in order to measure how biologically valuable micronutrients are incorporated and distributed in the exogenously developing brain. Our findings indicate that elemental inclusion in organoids is consistent with human brain tissue and involves calcium, iron, phosphorus, potassium, sulfur, and zinc. Local trends in concentrations suggest a switch from passive to actively mediated transport across cell membranes. Finally, correlational analysis for pairs of elements shows spatially conserved patterns, suggesting they may physically associate, be stored in similar compartments or used in related biological processes. These findings might reflect which trace elements are important during human brain development and will support studies aimed to unravel the consequences of disrupted metal homeostasis for neurodevelopmental diseases, including those manifested in adulthood.

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