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1.
Integr Comp Biol ; 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38982316

ABSTRACT

The striking appearance of wax 'tails' - posterior wax projections on planthopper nymphs - has captivated entomologists and naturalists alike. Despite their intriguing presence, the functional roles of these formations remain largely unexplored. This study leverages high-speed imaging to uncover the biomechanical implications of wax structures in the aerial dynamics of planthopper nymphs (Ricania sp.). We quantitatively demonstrate that removing wax tails significantly increases body rotations during jumps. Specifically, nymphs without wax undergo continuous rotations, averaging 4.2 ± 1.8 per jump, in contrast to wax-intact nymphs, who do not complete a full rotation, averaging only 0.7 ± 0.2 per jump. This along with significant reductions in angular and translational velocity from takeoff to landing suggest that aerodynamic drag forces on wax structures effectively counteract rotation. These stark differences in body rotation correlate with landing success: nymphs with wax intact achieve a near perfect landing rate of 98.5%, while those without wax manage only a 35.5% success rate. Jump trajectory analysis reveals that wax-intact jumps transition from parabolic to asymmetric shapes at higher take-off velocities and show a significantly greater reduction in velocity from takeoff to landing compared to wax-removed jumps, demonstrating how wax structures help nymphs achieve more stable, controlled descents. Our findings confirm the aerodynamic self-righting functionality of wax tails in stabilizing planthopper nymph landings, advancing our understanding of the complex relationship between wax morphology and aerial maneuverability, with broader implications for wingless insect aerial adaptations and bioinspired robotics.

2.
bioRxiv ; 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38659822

ABSTRACT

The striking appearance of wax 'tails' - posterior wax projections on planthopper nymphs - has captivated entomologists and naturalists alike. Despite their intriguing presence, the functional roles of these structures remain largely unexplored. This study leverages high-speed imaging to uncover the biomechanical implications of these wax formations in the aerial dynamics of planthopper nymphs (Ricania sp.). We quantitatively demonstrate that removing wax tails significantly increases body rotations during jumps. Specifically, nymphs without wax projections undergo continuous rotations, averaging 4.3 ± 1.9 per jump, in contrast to wax-intact nymphs, who narrowly complete a full rotation, averaging only 0.7 ± 0.2 per jump. This suggests that wax structures effectively counteract rotation through aerodynamic drag forces. These stark differences in body rotation correlate with landing success: nymphs with wax intact achieve a near perfect landing rate of 98.5%, while those without wax manage only a 35.5% success rate. Jump trajectory analysis reveals transitions from parabolic to Tartaglia shapes at higher take-off velocities for wax-intact nymphs, illustrating how wax structures assist nymphs in achieving stable, controlled descents. Our findings confirm the aerodynamic self-righting functionality of wax tails in stabilizing planthopper landings, advancing our understanding of the complex interplay between wax morphology and aerial maneuverability, with broader implications for the evolution of flight in wingless insects and bioinspired robotics.

3.
Diabetes Technol Ther ; 26(1): 11-23, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37850941

ABSTRACT

Background: The Omnipod® 5 Automated Insulin Delivery (AID) System was shown to be safe and effective following 3 months of use in people with type 1 diabetes (T1D); however, data on the durability of these results are limited. This study evaluated the long-term safety and effectiveness of Omnipod 5 use in people with T1D during up to 2 years of use. Materials and Methods: After a 3-month single-arm, multicenter, pivotal trial in children (6-13.9 years) and adolescents/adults (14-70 years), participants could continue system use in an extension phase. HbA1c was measured every 3 months for up to 15 months; continuous glucose monitor metrics were collected for up to 2 years. Results: Participants (N = 224) completed median (interquartile range) 22.3 (21.7, 22.7) months of AID. HbA1c was reduced in the pivotal trial from 7.7% ± 0.9% in children and 7.2% ± 0.9% in adolescents/adults to 7.0% ± 0.6% and 6.8% ± 0.7%, respectively, (P < 0.0001), and was maintained at 7.2% ± 0.7% and 6.9% ± 0.6% after 15 months (P < 0.0001 from baseline). Time in target range (70-180 mg/dL) increased from 52.4% ± 15.6% in children and 63.6% ± 16.5% in adolescents/adults at baseline to 67.9% ± 8.0% and 73.8% ± 10.8%, respectively, during the pivotal trial (P < 0.0001) and was maintained at 65.9% ± 8.9% and 72.9% ± 11.3% during the extension (P < 0.0001 from baseline). One episode of diabetic ketoacidosis and seven episodes of severe hypoglycemia occurred during the extension. Children and adolescents/adults spent median 96.1% and 96.3% of time in Automated Mode, respectively. Conclusion: Our study supports that long-term use of the Omnipod 5 AID System can safely maintain improvements in glycemic outcomes for up to 2 years of use in people with T1D. Clinical Trials Registration Number: NCT04196140.


Subject(s)
Diabetes Mellitus, Type 1 , Adult , Child , Humans , Adolescent , Diabetes Mellitus, Type 1/drug therapy , Hypoglycemic Agents/therapeutic use , Insulin/therapeutic use , Glycated Hemoglobin , Insulin Infusion Systems , Blood Glucose , Blood Glucose Self-Monitoring
4.
Diabetes Res Clin Pract ; 190: 109998, 2022 Aug.
Article in English | MEDLINE | ID: mdl-35853530

ABSTRACT

AIMS: To evaluate psychosocial outcomes for adults with type 1 diabetes (T1D) using the tubeless Omnipod® 5 Automated Insulin Delivery (AID) System. METHODS: A single-arm, multicenter (across the United States), prospective safety and efficacy study of the tubeless AID system included 115 adults with T1D. Participants aged 18-70 years completed questionnaires assessing psychosocial outcomes - diabetes distress (T1-DDS), hypoglycemic confidence (HCS), well-being (WHO-5), sleep quality (PSQI), insulin delivery satisfaction (IDSS), diabetes treatment satisfaction (DTSQ), and system usability (SUS) - before and after 3 months of AID use. Associations among participant characteristics, psychosocial measures and glycemic outcomes were evaluated using linear regression analyses. RESULTS: Adults using the tubeless AID system demonstrated improvements in diabetes-specific psychosocial measures, including diabetes distress, hypoglycemic confidence, insulin delivery satisfaction, diabetes treatment satisfaction, and system usability after 3 months (all P < 0.001). No changes in general well-being or sleep quality were observed. The psychosocial outcomes assessed were not consistently associated with baseline participant characteristics (i.e., age, sex, diabetes duration, glycemic outcomes including percent time in range 70-180 mg/dL, percent time below range < 70 mg/dL, hemoglobin A1c, or insulin regimen). CONCLUSIONS: Use of the Omnipod 5 AID system was associated with significant improvements in diabetes-related psychosocial outcomes for adults with T1D. CLINICAL TRIALS REGISTRATION NUMBER: NCT04196140.


Subject(s)
Diabetes Mellitus, Type 1 , Adult , Blood Glucose , Blood Glucose Self-Monitoring , Diabetes Mellitus, Type 1/drug therapy , Diabetes Mellitus, Type 1/psychology , Humans , Hypoglycemic Agents/therapeutic use , Insulin/therapeutic use , Insulin Infusion Systems , Insulin, Regular, Human/therapeutic use , Prospective Studies
5.
ASN Neuro ; 13: 17590914211055064, 2021.
Article in English | MEDLINE | ID: mdl-34812056

ABSTRACT

This study investigated the effects of the pharmacological manipulation of noradrenergic activities on dopaminergic phenotypes in aged rats. Results showed that the administration of L-threo-3,4-dihydroxyphenylserine (L-DOPS) for 21 days significantly increased the expression of tyrosine hydroxylase (TH) and dopamine transporter (DAT) in the striatum and substantia nigra (SN) of 23-month-old rats. Furthermore, this treatment significantly increased norepinephrine/DA concentrations in the striatum and caused a deficit of sensorimotor gating as measured by prepulse inhibition (PPI). Next, old rats were injected with the α2-adrenoceptor antagonist 2-methoxy idazoxan or ß2-adrenoceptor agonist salmeterol for 21 days. Both drugs produced similar changes of TH and DAT in the striatum and SN. Moreover, treatments with L-DOPS, 2-methoxy idazoxan, or salmeterol significantly increased the protein levels of phosphorylated Akt in rat striatum and SN. However, although a combination of 2-methoxy idazoxan and salmeterol resulted in a deficit of PPI in these rats, the administration of 2-methoxy idazoxan alone showed an opposite behavioral change. The in vitro experiments revealed that treatments with norepinephrine markedly increased mRNAs and proteins of ATF2 and CBP/p300 and reduced mRNA and proteins of HDAC2 and HDAC5 in MN9D cells. A ChIP assay showed that norepinephrine significantly increased CBP/p300 binding or reduced HDAC2 and HDAC5 binding on the TH promoter. The present results indicate that facilitating noradrenergic activity in the brain can improve the functions of dopaminergic neurons in aged animals. While this improvement may have biochemically therapeutic indication for the status involving the degeneration of dopaminergic neurons, it may not definitely include behavioral improvements, as indicated by using 2-methoxy idazoxan only.


Subject(s)
Dopamine , Norepinephrine , Animals , Histone Deacetylases , Phenotype , Rats , Substantia Nigra/metabolism , Tyrosine 3-Monooxygenase/metabolism
6.
Diabetes Care ; 44(7): 1630-1640, 2021 07.
Article in English | MEDLINE | ID: mdl-34099518

ABSTRACT

OBJECTIVE: Advances in diabetes technology have transformed the treatment paradigm for type 1 diabetes, yet the burden of disease is significant. We report on a pivotal safety study of the first tubeless, on-body automated insulin delivery system with customizable glycemic targets. RESEARCH DESIGN AND METHODS: This single-arm, multicenter, prospective study enrolled 112 children (age 6-13.9 years) and 129 adults (age 14-70 years). A 2-week standard therapy phase (usual insulin regimen) was followed by 3 months of automated insulin delivery. Primary safety outcomes were incidence of severe hypoglycemia and diabetic ketoacidosis. Primary effectiveness outcomes were change in HbA1c and percent time in sensor glucose range 70-180 mg/dL ("time in range"). RESULTS: A total of 235 participants (98% of enrolled, including 111 children and 124 adults) completed the study. HbA1c was significantly reduced in children by 0.71% (7.8 mmol/mol) (mean ± SD: 7.67 ± 0.95% to 6.99 ± 0.63% [60 ± 10.4 mmol/mol to 53 ± 6.9 mmol/mol], P < 0.0001) and in adults by 0.38% (4.2 mmol/mol) (7.16 ± 0.86% to 6.78 ± 0.68% [55 ± 9.4 mmol/mol to 51 ± 7.4 mmol/mol], P < 0.0001). Time in range was improved from standard therapy by 15.6 ± 11.5% or 3.7 h/day in children and 9.3 ± 11.8% or 2.2 h/day in adults (both P < 0.0001). This was accomplished with a reduction in time in hypoglycemia <70 mg/dL among adults (median [interquartile range]: 2.00% [0.63, 4.06] to 1.09% [0.46, 1.75], P < 0.0001), while this parameter remained the same in children. There were three severe hypoglycemia events not attributable to automated insulin delivery malfunction and one diabetic ketoacidosis event from an infusion site failure. CONCLUSIONS: This tubeless automated insulin delivery system was safe and allowed participants to significantly improve HbA1c levels and time in target glucose range with a very low occurrence of hypoglycemia.


Subject(s)
Diabetes Mellitus, Type 1 , Insulin , Adolescent , Adult , Aged , Blood Glucose , Child , Diabetes Mellitus, Type 1/drug therapy , Glycated Hemoglobin/analysis , Humans , Hypoglycemic Agents , Insulin Infusion Systems , Middle Aged , Prospective Studies , Young Adult
7.
ASN Neuro ; 13: 17590914211009730, 2021.
Article in English | MEDLINE | ID: mdl-33940943

ABSTRACT

Dysfunction of the central noradrenergic and dopaminergic systems is the primary neurobiological characteristic of Parkinson's disease (PD). Importantly, neuronal loss in the locus coeruleus (LC) that occurs in early stages of PD may accelerate progressive loss of dopaminergic neurons. Therefore, restoring the activity and function of the deficient noradrenergic system may be an important therapeutic strategy for early PD. In the present study, the lentiviral constructions of transcription factors Phox2a/2b, Hand2 and Gata3, either alone or in combination, were microinjected into the LC region of the PD model VMAT2 Lo mice at 12 and 18 month age. Biochemical analysis showed that microinjection of lentiviral expression cassettes into the LC significantly increased mRNA levels of Phox2a, and Phox2b, which were accompanied by parallel increases of mRNA and proteins of dopamine ß-hydroxylase (DBH) and tyrosine hydroxylase (TH) in the LC. Furthermore, there was considerable enhancement of DBH protein levels in the frontal cortex and hippocampus, as well as enhanced TH protein levels in the striatum and substantia nigra. Moreover, these manipulations profoundly increased norepinephrine and dopamine concentrations in the striatum, which was followed by a remarkable improvement of the spatial memory and locomotor behavior. These results reveal that over-expression of these transcription factors in the LC improves noradrenergic and dopaminergic activities and functions in this rodent model of PD. It provides the necessary groundwork for the development of gene therapies of PD, and expands our understanding of the link between the LC-norepinephrine and dopamine systems during the progression of PD.


Subject(s)
Adrenergic Neurons/metabolism , Locus Coeruleus/metabolism , Norepinephrine/biosynthesis , Parkinsonian Disorders/metabolism , Vesicular Monoamine Transport Proteins/biosynthesis , Animals , Dopamine beta-Hydroxylase/biosynthesis , Dopamine beta-Hydroxylase/genetics , Female , Male , Mice , Mice, Transgenic , Microinjections/methods , Norepinephrine/genetics , Parkinsonian Disorders/genetics , Tyrosine 3-Monooxygenase/biosynthesis , Tyrosine 3-Monooxygenase/genetics , Vesicular Monoamine Transport Proteins/genetics
8.
Gen Comp Endocrinol ; 299: 113580, 2020 12 01.
Article in English | MEDLINE | ID: mdl-32827514

ABSTRACT

Monoamine oxidase (MAO) is a mitochondrial membrane-bound enzyme that catalyzes the oxidative deamination of monoamines in a wide array of organisms. While the enzyme monoamine oxidase has been studied extensively in its role in moderating behavior in mammals, there is a paucity of research investigating this role in invertebrates, where the latter utilizes this enzyme in a major pathway to degrade monoamines. There is especially a dismal lack of information on how MAO influences activity in invertebrates, particularly in account of the circadian cycle. Previous studies revealed MAO degrades serotonin and norepinephrine in arachnids, but did not investigate other critically important compounds like octopamine. Larinioides cornutus is a species of orb-weaving spider that exhibits diel fluctuations in behavior, specifically levels of aggression. The monoamines octopamine and serotonin have been shown to influence aggressive behaviors in L. cornutus, thus this species was used to investigate if MAO is a potential site of regulation throughout the day. Not only did gene expression of MAO orthologs and MAO activity fluctuate at different times of day, but the enzymatic activity was substrate-specific producing a higher level of degradation of octopamine as compared to serotonin in vitro. This study further supports evidence that MAO has an active role in monoamine inactivation in invertebrates and provides a first look at how MAO ultimately may be regulating behavior in an invertebrate.


Subject(s)
Monoamine Oxidase/metabolism , Serotonin/metabolism , Animals , Spiders
9.
Neurotox Res ; 38(3): 793-807, 2020 Oct.
Article in English | MEDLINE | ID: mdl-32617854

ABSTRACT

The present study investigated the effects of forced overexpression of Phox2a/2b, two transcription factors, in the locus coeruleus (LC) of aged rats on noradrenergic and dopaminergic phenotypes in brains. Results showed that a significant increase in Phox2a/2b mRNA levels in the LC region was paralleled by marked enhancement in expression of DBH and TH per se. Furthermore, similar increases in TH protein levels were observed in the substantial nigra and striatum, as well as in the hippocampus and frontal cortex. Overexpression of Phox2 genes also significantly increased BrdU-positive cells in the hippocampal dentate gyrus and NE levels in the striatum. Moreover, this manipulation significantly improved the cognition behavior. The in vitro experiments revealed that norepinephrine treatments may increase the transcription of TH gene through the epigenetic action on the TH promoter. The results indicate that Phox2 genes may play an important role in improving the function of the noradrenergic and dopaminergic neurons in aged animals, and regulation of Phox2 gene expression may have therapeutic utility in aging or disorders involving degeneration of noradrenergic neurons.


Subject(s)
Aging , Dopamine/metabolism , Norepinephrine/metabolism , Transcription Factors/metabolism , Animals , Female , Male , Nerve Tissue Proteins/metabolism , Neurons/metabolism , Promoter Regions, Genetic , Rats, Inbred F344 , Substantia Nigra/metabolism , Transcriptional Activation/physiology , Tyrosine 3-Monooxygenase/metabolism
10.
Article in English | MEDLINE | ID: mdl-32219511

ABSTRACT

We examined the circadian rhythms of locomotor activity in three spider species in the Family Theridiidae under light-dark cycles and constant darkness. Contrary to previous findings in other organisms, we found exceptionally high variability in endogenous circadian period both within and among species. Many individuals exhibited circadian periods much lower (19-22 h) or much higher (26-30 h) than the archetypal circadian period. These results suggest relaxed selection on circadian period as well as an ability to succeed in nature despite a lack of circadian resonance with the 24-h daily cycle. Although displaying similar entrainment waveforms under light-dark cycles, there were remarkable differences among the three species with respect to levels of apparent masking and dispersion of activity under constant dark conditions. These behavioral differences suggest an aspect of chronotype adapted to the particular ecologies of the different species.


Subject(s)
Spiders/classification , Spiders/physiology , Animals , Circadian Rhythm , Locomotion , Photoperiod
11.
Methods Mol Biol ; 1945: 119-139, 2019.
Article in English | MEDLINE | ID: mdl-30945244

ABSTRACT

Biologists seek to create increasingly complex molecular regulatory network models. Writing such a model is a creative effort that requires flexible analysis tools and better modeling languages than offered by many of today's biochemical model editors. Our Multistate Model Builder (MSMB) supports multistate models created using different modeling styles that suit the modeler rather than the software. MSMB defines a simple but powerful syntax to describe multistate species. Our syntax reduces the number of reactions needed to encode the model, thereby reducing the cognitive load involved with model creation. MSMB gives extensive feedback during all stages of model creation. Users can activate error notifications, and use these notifications as a guide toward a consistent, syntactically correct model. Any consistent model can be exported to SBML or COPASI formats. We show the effectiveness of MSMB's multistate syntax through realistic models of cell cycle regulation and mRNA transcription. MSMB is an open-source project implemented in Java and it uses the COPASI API. Complete information and the installation package can be found at http://copasi.org/Projects/ .


Subject(s)
Computational Biology/methods , Models, Biological , Software , Systems Biology/methods , Algorithms , Computer Graphics , Computer Simulation , Programming Languages
12.
Am Nat ; 191(1): 74-87, 2018 Jan.
Article in English | MEDLINE | ID: mdl-29244567

ABSTRACT

Daily rhythms occur in numerous physiological and behavioral processes across an immense diversity of taxa, but there remain few cases in which mechanistic links between rhythms of trait expression and organismal fitness have been established. We construct a dynamic optimization model to determine whether risk allocation provides an adaptive explanation for the daily foraging rhythm observed in many species using the orb-weaving spider Cyclosa turbinata as a case study. Our model predicts that female C. turbinata should generally start foraging at lower levels of energy reserves (i.e., should be less bold) during midday when predators are most abundant. We also find that individuals' foraging efficacy determines whether daily rates of encounters with predators or prey more strongly influences boldness under high risk. The qualitative model predictions are robust to variation in our parameter estimates and likely apply to a wide range of taxa. The predictions are also consistent with observed patterns of foraging behavior under both laboratory and field conditions. We discuss the implications of our study for understanding the evolution of daily rhythms and the importance of model predictions for interpreting empirical studies and generating additional hypotheses regarding behavioral evolution.


Subject(s)
Food Chain , Predatory Behavior , Spiders/physiology , Animals , Circadian Rhythm , Female , Models, Biological , Risk , Time Factors
13.
Simulation ; 94(11): 993-1008, 2018 Nov.
Article in English | MEDLINE | ID: mdl-31303682

ABSTRACT

The growing size and complexity of molecular network models makes them increasingly difficult to construct and understand. Modifying a model that consists of tens of reactions is no easy task. Attempting the same on a model containing hundreds of reactions can seem nearly impossible. We present the JigCell Model Connector, a software tool that supports large-scale molecular network modeling. Our approach to developing large models is to combine smaller models, making the result easier to comprehend. At the base, the smaller models (called modules) are defined by small collections of reactions. Modules connect together to form larger modules through clearly defined interfaces, called ports. In this work, we enhance the port concept by defining three types of ports. An output port is linked to an internal component that will send a value. An input port is linked to an internal component that will receive a value. An equivalence port is linked to an internal component that will both receive and send values. Not all modules connect together in the same way; therefore, multiple connection options need to exist.

14.
J Neurochem ; 139(2): 197-207, 2016 10.
Article in English | MEDLINE | ID: mdl-27501468

ABSTRACT

MicroRNAs are short non-coding RNAs that provide global regulation of gene expression at the post-transcriptional level. Such regulation has been found to play a role in stress-induced epigenetic responses in the brain. The norepinephrine transporter (NET) and glucocorticoid receptors are closely related to the homeostatic integration and regulation after stress. Our previous studies demonstrated that NET mRNA and protein levels in rats are regulated by chronic stress and by administration of corticosterone, which is mediated through glucocorticoid receptors. Whether miRNAs are intermediaries in the regulation of these proteins remains to be elucidated. This study was undertaken to determine possible regulatory effects of miRNAs on the expression of NET and glucocorticoid receptors in the noradrenergic neuronal cell line. Using computational target prediction, we identified several candidate miRNAs potentially targeting NET and glucocorticoid receptors. Western blot results showed that over-expression of miR-181a and miR-29b significantly repressed protein levels of NET, which is accompanied by a reduced [3 H] norepinephrine uptake, and glucocorticoid receptors in PC12 cells. Luciferase reporter assays verified that both miR-181a and miR-29b bind the 3'UTR of mRNA of NET and glucocorticoid receptors. Furthermore, exposure of PC12 cells to corticosterone markedly reduced the endogenous levels of miR-29b, which was not reversed by the application of glucocorticoid receptor antagonist mifepristone. These observations indicate that miR-181a and miR-29b can function as the negative regulators of NET and glucocorticoid receptor translation in vitro. This regulatory effect may be related to stress-induced up-regulation of the noradrenergic phenotype, a phenomenon observed in stress models and depressive patients. This study demonstrated that miR-29b and miR-181a, two short non-coding RNAs that provide global regulation of gene expression, markedly repressed protein levels of norepinephrine (NE) transporter and glucocorticoid receptor (GR), as well as NE uptake by binding the 3'UTR of their mRNAs in PC12 cells. Also, exposure of cells to corticosterone significantly reduced miR-29b levels through a GR-independent way.


Subject(s)
MicroRNAs/genetics , Norepinephrine Plasma Membrane Transport Proteins/biosynthesis , Receptors, Glucocorticoid/biosynthesis , 3' Untranslated Regions , Animals , Computer Simulation , Corticosterone/pharmacology , Down-Regulation/drug effects , Gene Expression Regulation/drug effects , Gene Expression Regulation/genetics , MicroRNAs/biosynthesis , Mifepristone/pharmacology , Norepinephrine/metabolism , Norepinephrine Plasma Membrane Transport Proteins/drug effects , Norepinephrine Plasma Membrane Transport Proteins/genetics , PC12 Cells , Rats , Receptors, Glucocorticoid/drug effects , Receptors, Glucocorticoid/genetics
15.
J Theor Biol ; 408: 243-259, 2016 11 07.
Article in English | MEDLINE | ID: mdl-27544421

ABSTRACT

In this paper, we develop a model for predation movements of a subsocial spider species, Anelosimus studiosus. We expand on a previous model to include multiple spider interaction on the web as well as a latency period during predation. We then use the model to test different spatial configurations to determine the optimal spacing of spiders within a colony for successful capture during predation. The model simulations indicate that spiders uniformly spacing out along the edge of the web results in the most successful predation strategy. This is similar to the behavior observed by Ross (2013) in which it was determined to be statistically significant that during certain times of the day, spiders were positioned along the edge more than expected under complete spatial randomness.


Subject(s)
Predatory Behavior , Spatio-Temporal Analysis , Spiders/physiology , Animals , Models, Theoretical , Social Behavior
16.
BMC Syst Biol ; 9: 95, 2015 Dec 24.
Article in English | MEDLINE | ID: mdl-26704692

ABSTRACT

BACKGROUND: Most biomolecular reaction modeling tools allow users to build models with a single list of parameter values. However, a common scenario involves different parameterizations of the model to account for the results of related experiments, for example, to define the phenotypes for a variety of mutations (gene knockout, over expression, etc.) of a specific biochemical network. This scenario is not well supported by existing model editors, forcing the user to manually generate, store, and maintain many variations of the same model. RESULTS: We developed an extension to our modeling editor called the JigCell Run Manager (JC-RM). JC-RM allows the modeler to define a hierarchy of parameter values, simulations, and plot settings, and to save them together with the initial model. JC-RM supports generation of simulation plots, as well as export to COPASI and SBML (L3V1) for further analysis. CONCLUSIONS: Developing a model with its initial list of parameter values is just the first step in modeling a biological system. Models are often parameterized in many different ways to account for mutations of the organism and/or for sets of related experiments performed on the organism. JC-RM offers two critical features: it supports the everyday management of a large model, complete with its parameterizations, and it facilitates sharing this information before and after publication. JC-RM allows the modeler to define a hierarchy of parameter values, simulation, and plot settings, and to maintain a relationship between this hierarchy and the initial model. JC-RM is implemented in Java and uses the COPASI API. JC-RM runs on all major operating systems, with minimal system requirements. Installers, source code, user manual, and examples can be found at the COPASI website ( http://www.copasi.org/Projects ).


Subject(s)
Models, Biological , Software , Systems Biology/methods , Computer Graphics , Time Factors
18.
Math Biosci Eng ; 11(6): 1411-29, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25365607

ABSTRACT

In this paper, we develop a stochastic differential equation model to simulate the movement of a social/subsocial spider species, Anelosimus studiosus, during prey capture using experimental data collected in a structured environment. In a subsocial species, females and their maturing offspring share a web and cooperate in web maintenance and prey capture. Furthermore, observations indicate these colonies change their positioning throughout the day, clustered during certain times of the day while spaced out at other times. One key question was whether or not the spiders spaced out ``optimally'' to cooperate in prey capture. In this paper, we first show the derivation of the model where experimental data is used to determine key parameters within the model. We then use this model to test the success of prey capture under a variety of different spatial configurations for varying colony sizes to determine the best spatial configuration for prey capture.


Subject(s)
Models, Theoretical , Predatory Behavior , Social Behavior , Spiders , Animals , Computer Simulation , Female , Stochastic Processes
20.
BMC Syst Biol ; 8: 42, 2014 Apr 04.
Article in English | MEDLINE | ID: mdl-24708852

ABSTRACT

BACKGROUND: Building models of molecular regulatory networks is challenging not just because of the intrinsic difficulty of describing complex biological processes. Writing a model is a creative effort that calls for more flexibility and interactive support than offered by many of today's biochemical model editors. Our model editor MSMB - Multistate Model Builder - supports multistate models created using different modeling styles. RESULTS: MSMB provides two separate advances on existing network model editors. (1) A simple but powerful syntax is used to describe multistate species. This reduces the number of reactions needed to represent certain molecular systems, thereby reducing the complexity of model creation. (2) Extensive feedback is given during all stages of the model creation process on the existing state of the model. Users may activate error notifications of varying stringency on the fly, and use these messages as a guide toward a consistent, syntactically correct model. MSMB default values and behavior during model manipulation (e.g., when renaming or deleting an element) can be adapted to suit the modeler, thus supporting creativity rather than interfering with it. MSMB's internal model representation allows saving a model with errors and inconsistencies (e.g., an undefined function argument; a syntactically malformed reaction). A consistent model can be exported to SBML or COPASI formats. We show the effectiveness of MSMB's multistate syntax through models of the cell cycle and mRNA transcription. CONCLUSIONS: Using multistate reactions reduces the number of reactions need to encode many biochemical network models. This reduces the cognitive load for a given model, thereby making it easier for modelers to build more complex models. The many interactive editing support features provided by MSMB make it easier for modelers to create syntactically valid models, thus speeding model creation. Complete information and the installation package can be found at http://www.copasi.org/SoftwareProjects. MSMB is based on Java and the COPASI API.


Subject(s)
Models, Biological , Software , Algorithms , Binding Sites , Phosphorylation , Protein Biosynthesis , RNA, Messenger/genetics , Systems Biology , User-Computer Interface
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