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Full-Text Articles in Life Sciences
An Approach For Determining And Measuring Network Hierarchy Applied To Comparing The Phosphorylome And The Regulome, Chao Cheng, Erik Andrews, Koon-Kiu Yan, Matthew Ung, Daifeng Wang, Mark Gerstein
An Approach For Determining And Measuring Network Hierarchy Applied To Comparing The Phosphorylome And The Regulome, Chao Cheng, Erik Andrews, Koon-Kiu Yan, Matthew Ung, Daifeng Wang, Mark Gerstein
Dartmouth Scholarship
Many biological networks naturally form a hierarchy with a preponderance of downward information flow. In this study, we define a score to quantify the degree of hierarchy in a network and develop a simulated-annealing algorithm to maximize the hierarchical score globally over a network. We apply our algorithm to determine the hierarchical structure of the phosphorylome in detail and investigate the correlation between its hierarchy and kinase properties. We also compare it to the regulatory network, finding that the phosphorylome is more hierarchical than the regulome.
Collapse Of An Ecological Network In Ancient Egypt, Justin Yeakel, Mathias Pires, Lars Rudolf, Nathaniel Dominy
Collapse Of An Ecological Network In Ancient Egypt, Justin Yeakel, Mathias Pires, Lars Rudolf, Nathaniel Dominy
Dartmouth Scholarship
The dynamics of ecosystem collapse are fundamental to determining how and why biological communities change through time, as well as the potential effects of extinctions on ecosystems. Here, we integrate depictions of mammals from Egyptian antiquity with direct lines of paleontological and archeological evidence to infer local extinctions and community dynamics over a 6,000-y span. The unprecedented temporal resolution of this dataset enables examination of how the tandem effects of human population growth and climate change can disrupt mammalian communities. We show that the extinctions of mammals in Egypt were nonrandom and that destabilizing changes in community composition coincided with …
Natural Selection On Thermal Performance In A Novel Thermal Environment, Michael L. Logan, Robert M. Cox, Ryan Calsbeek
Natural Selection On Thermal Performance In A Novel Thermal Environment, Michael L. Logan, Robert M. Cox, Ryan Calsbeek
Dartmouth Scholarship
Tropical ectotherms are thought to be especially vulnerable to climate change because they are adapted to relatively stable temperature regimes, such that even small increases in environmental temperature may lead to large decreases in physiological performance. One way in which tropical organisms may mitigate the detrimental effects of warming is through evolutionary change in thermal physiology. The speed and magnitude of this response depend, in part, on the strength of climate-driven selection. However, many ectotherms use behavioral adjustments to maintain preferred body temperatures in the face of environmental variation. These behaviors may shelter individuals from natural selection, preventing evolutionary adaptation …
Recent Shifts In The Occurrence, Cause, And Magnitude Of Animal Mass Mortality Events, Samuel B. Fey, Adam M. Siepielski, Sébastien Nusslé, Kristina Cervantes-Yoshida, Jason L. Hwan, Eric R. Huber, Maxfield J. Fey, Alessandro Catenazzi, Stephanie M. Carlson
Recent Shifts In The Occurrence, Cause, And Magnitude Of Animal Mass Mortality Events, Samuel B. Fey, Adam M. Siepielski, Sébastien Nusslé, Kristina Cervantes-Yoshida, Jason L. Hwan, Eric R. Huber, Maxfield J. Fey, Alessandro Catenazzi, Stephanie M. Carlson
Dartmouth Scholarship
Mass mortality events (MMEs) are rapidly occurring catastrophic demographic events that punctuate background mortality levels. Individual MMEs are staggering in their observed magnitude: re- moving more than 90% of a population, resulting in the death of more than a billion individuals, or producing 700 million tons of dead biomass in a single event. Despite extensive documentation of individual MMEs, we have no understanding of the major features characterizing the occurrence and magnitude of MMEs, their causes, or trends through time. Thus, no framework exists for contextualizing MMEs in the wake of ongoing global and regional perturbations to natural systems. Here …
Arabidopsis Bhlh100 And Bhlh101 Control Iron Homeostasis Via A Fit-Independent Pathway, Alicia B. Sivitz, Victor Hermand, Catherine Curie, Grégory Vert
Arabidopsis Bhlh100 And Bhlh101 Control Iron Homeostasis Via A Fit-Independent Pathway, Alicia B. Sivitz, Victor Hermand, Catherine Curie, Grégory Vert
Dartmouth Scholarship
Iron deficiency induces a complex set of responses in plants, including developmental and physiological changes, to increase iron uptake from soil. In Arabidopsis, many transporters involved in the absorption and distribution of iron have been identified over the past decade. However, little is known about the signaling pathways and networks driving the various responses to low iron. Only the basic helix–loop–helix (bHLH) transcription factor FIT has been shown to control the expression of the root iron uptake machinery genes FRO2 and IRT1. Here, we characterize the biological role of two other iron-regulated transcription factors, bHLH100 and bHLH101, in iron homeostasis. …
Integration Without Unification: An Argument For Pluralism In The Biological Sciences, Sandra D. Mitchell, Michael R. Dietrich
Integration Without Unification: An Argument For Pluralism In The Biological Sciences, Sandra D. Mitchell, Michael R. Dietrich
Dartmouth Scholarship
In this article, we consider the tension between unification and pluralism in biological theory. We begin with a consideration of historical efforts to establish a unified understanding of evolution in the neo‐Darwinian synthesis. The fragmentation of the evolutionary synthesis by molecular evolution suggests the limitations of the general unificationist ideal for biology but not necessarily for integrating explanations. In the second half of this article, we defend a specific variety of pluralism that allows for the integration required for explanations of complex phenomena without unification on a large scale.
The Relationship Between Frq-Protein Stability And Temperature Compensation In The Neurospora Circadian Clock, Peter Ruoff, Jennifer J. Loros, Jay C. Dunlap
The Relationship Between Frq-Protein Stability And Temperature Compensation In The Neurospora Circadian Clock, Peter Ruoff, Jennifer J. Loros, Jay C. Dunlap
Dartmouth Scholarship
Temperature compensation is an important property of all biological clocks. In Neurospora crassa, negative-feedback regulation on the frequency (frq) gene's transcription by the FRQ protein plays a central role in the organism's circadian pacemaker. Earlier model calculations predicted that the stability of FRQ should determine the period length of Neurospora's circadian rhythm as well as the rhythm's temperature compensation. Here, we report experimental FRQ protein stabilities in frq mutants at 20 degrees C and 25 degrees C, and estimates of overall activation energies for mutant FRQ protein degradation. The results are consistent with earlier model predictions, i.e., temperature compensation of …