Biology subjects

Fox, G. E.

Publications and source records attributed to Fox, G. E..

3 recordsLinked to original sources

bioRxiv2018

Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: A Whole Genome Comparison of Two Spacecraft Assembly Facility Isolates

BackgroundBacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spore resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, as well as draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. In addition, comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis.\n\nResultsThe FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains [1]. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by either MERTA or ATCC7061T. The FO-36b genome was found to have ten unique reading frames and two phage-like regions, which have homology with the Bacillus bacteriophage SPP1 (NC_004166) and Brevibacillus phage Jimmer1 (NC_029104). Differing remnants of the Jimmer1 phage are found in essentially all safensis/pumilus strains. Seven unique genes are part of these phage elements. Comparison of gyrA sequences from FO-36b, SAFR-032, ATCC7061T, and 61 other draft genomes separate the various strains into three distinct clusters. Two of these are subgroups of B. pumilus while the other houses all the B. safensis strains.\n\nConclusionsIt is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can change the level of expression of key proteins thereby changing the organisms resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. The larger comparison of multiple strains indicates that many strains named as B. pumilus actually belong to the B. safensis group.

genomics↗

bioRxiv2017

Neural code uses self-information principle to organize the brain’s universal cell-assembly coding

The brain generates cognition and behavior through firing changes of its neurons, yet, with enormous firing variability, the organizing principle underlying real-time neural code remains unclear. Here, we test the Neural Self-Information Theory that neural code is constructed via the self-information principle under which each inter-spike-interval (ISI) is inherently self-tagged with discrete information based on its relation to ISI variability-probability distribution - higher-probability ISIs, which reflect the balanced excitation-inhibition ground state, convey minimal information, whereas lower-probability ISIs, which signify statistical surprisals, carry more information. Moreover, temporally coordinated ISI surprisals across neural cliques intrinsically give rise to real-time cell-assembly neural code. As a result, this self-information-based neural coding is uniquely intrinsic to the neurons themselves, with no need for outside observers to set any reference point to manually mark external or internal inputs. Applying this neural self-information concept, we devised an unbiased general decoding strategy and successfully uncovered 15 distinct cell-assembly patterns from multiple cortical and hippocampal circuits associated with different sleep cycles, earthquake, elevator-drop, foot-shock experiences, navigation or various actions in five-choice visual-discrimination operant-conditioning tasks. Detailed analyses of all 15 cell assemblies revealed that ~20% of the skewed ISI distribution tails were responsible for the emergence of robust cell-assembly codes, conforming to the Pareto Principle. These findings support the notion that neural coding is organized via the self-information principle to generate real-time information across brain regions, cognitive modalities, and behaviors.

neuroscience↗

bioRxiv2017

Spike-Timing Patterns Conform to Gamma Distribution with Regional and Cell Type-Specific Characteristics

Spike-timing patterns - crucial for synaptic plasticity and neural computation - are often modeled as Poisson-like random processes, log-normal distribution or gamma-distribution patterns, each with different underlying assumptions that may or may not be biologically true. However, it is not entirely clear whether (and how well) these different models would or would not capture spike-timing statistical patterns across different neurons, regions, animal species and cognitive states. Here, we examine statistical patterns of spike-timing irregularity in 13 different cortical and subcortical regions from mouse, hamster, cat and monkey brains. In contrast to the widely-assumed Poisson or log-normal distribution patterns, we show that spike-timing patterns of various projection neurons-including cortical excitatory principal cells, hippocampal pyramidal cells, inhibitory striatal medium spiny neurons and dopaminergic neurons, as well as fast-spiking interneurons - all invariantly conform to the gamma-distribution model. While higher regularity in spike-timing patterns are observed in a few cases, such as mouse DA neurons and monkey motor cortical neurons, there is no clear tendency in increased firing regularity from the sensory and subcortical neurons to prefrontal or motor cortices, as previously entertained. Moreover, gamma shapes of spike-timing patterns remain robust over various natural cognitive states, such as sleep, awake periods, or during fearful episodic experiences. Interestingly, ketamine-induced general anesthesia or unconsciousness is associated with the breakdown of forebrain spike patterns from a singular gamma distribution into two distinct subtypes of gamma distributions, suggesting the importance of this spike-timing pattern in supporting natural cognitive states. These results suggest that gamma-distribution patterns of spike timing reflect not only a fundamental property conserved across different neurons, regions and animal species, but also an operation crucial for supporting natural cognitive states. Such gamma-distribution-based spike-timing patterns can also have important implications for real-time neural coding and realistic neuromorphic computing.

neuroscience↗