Journal Club: PNAS, Science, PLoS papers to read


DNAHere are some papers with interesting titles and abstracts:

  • Tracing the protectors path from the germ line to the genome One of the basic principles that nature uses in evolution is to recycle successful concepts and create new functions by… (PNAS)
  • RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription A structurally conserved element, the trigger loop, has been suggested to play a key role in substrate selection and catalysis… (PNAS)
  • Limited taste discrimination in Drosophila In the gustatory systems of mammals and flies, different populations of sensory cells recognize different taste modalities, such that there… (PNAS)
  • Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict Genetic conflicts between sexes and generations provide a foundation for understanding the functional evolution of sex chromosomes and sexually dimorphic… (PNAS)
  • One Rule to Grow Them All: A General Theory of Neuronal Branching and Its Practical Application More than a century has passed since Ramón y Cajal presented a set of fundamental biological laws of neuronal branching. He described how the shape of the core elements of the neural circuitry – axons and dendrites – are constrained by physical parameters such as space, cytoplasmic volume, and conduction time. The existence of these laws enabled him to organize his histological observations, to formulate the neuron doctrine, and to infer directionality in signal flow in the nervous system. We show that Cajal’s principles can be used computationally to generate synthetic neural circuits. These principles rigorously constrain the shape of real neuronal structures, providing direct validation of his theories. At the same time, this strategy provides us with a powerful set of tools for generating synthetic neurons, as well as a model-based approach for automated reconstructions of neuronal trees from confocal image stacks. (PLoS Comp Biol)
  • A Simple Self-Maintaining Metabolic System: Robustness, Autocatalysis, Bistability The question of whether a whole organism (as opposed to particular properties of an organism) can be modeled in the computer has been controversial. As a step towards resolving it, we have studied the feasibility of simulating the behavior of a simple theoretical model in which all the catalysts needed for the metabolism of a system are themselves products of the metabolism itself, and in which there is a continuous loss of catalysts in unavoidable degradation reactions. In addition to a trivial (“dead”) steady state in which all rates are zero, the model is capable of establishing a stable non-trivial steady state with finite and reproducible fluxes. This can be achieved by “seeding” it with a sufficient quantity of at least one of the catalysts needed for functioning. It is also robust, because it can recover from a catastrophic disappearance of a catalyst. (PLoS Comp Biol)
  • Females Use Multiple Mating and Genetically Loaded Sperm Competition to Target Compatible Genes Female birds that have multiple mates favor fertilization by the most genetically compatible father. (Science)

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