Perspectives on the use of transcriptomics to advance biofuels

As a field within the energy research sector, bioenergy is continuously expanding. Although much has been achieved and the yields of both ethanol and butanol have been improved, many avenues of research to further increase these yields still remain. This review covers current research related with transcriptomics and the application of this high-throughput analytical tool to engineer both microbes and plants with the penultimate goal being better biofuel production and yields. The initial focus is given to the responses of fermentative microbes during the fermentative production of acids, such as butyric acid, and solvents, including ethanol and butanol. As plants offer the greatest natural renewable source of fermentable sugars within the form of lignocellulose, the second focus area is the transcriptional responses of microbes when exposed to plant hydrolysates and lignin-related compounds. This is of particular importance as the acid/base hydrolysis methods commonly employed to make the plant-based cellulose available for enzymatic hydrolysis to sugars also generates significant amounts of lignin-derivatives that are inhibitory to fermentative bacteria and microbes. The article then transitions to transcriptional analyses of lignin-degrading organisms, such as Phanerochaete chrysosporium, as an alternative to acid/base hydrolysis. The final portion of this article will discuss recent transcriptome analyses of plants and, in particular, the genes involved in lignin production. The rationale behind these studies is to eventually reduce the lignin content present within these plants and, consequently, the amount of inhibitors generated during the acid/base hydrolysis of the lignocelluloses. All four of these topics represent key areas where transcriptomic research is currently being conducted to identify microbial genes and their responses to products and inhibitors as well as those related with lignin degradation/formation.clos

Caught in the rhythm: how satellites settle into a plane around their central galaxy

Using the cosmological hydrodynamics simulation Horizon-AGN, we investigate the spatial distribution of satellite galaxies relative to their central counterpart in the redshift range between 0.3 and 0.8. We find that, on average, these satellites tend to be located on the galactic plane of the central object. This effect is detected for central galaxies with a stellar mass larger than 10^10 solar masses and found to be strongest for red passive galaxies, while blue galaxies exhibit a weaker trend. For galaxies with a minor axis parallel to the direction of the nearest filament, we find that the coplanarity is stronger in the vicinity of the central galaxy, and decreases when moving towards the outskirts of the host halo. By contrast, the spatial distribution of satellite galaxies relative to their closest filament follows the opposite trend: their tendency to align with them dominates at large distances from the central galaxy, and fades away in its vicinity. Relying on mock catalogs of galaxies in that redshift range, we show that massive red centrals with a spin perpendicular to their filament also have corotating satellites well aligned with both the galactic plane and the filament. On the other hand, lower-mass blue centrals with a spin parallel to their filament have satellites flowing straight along this filament, and hence orthogonally to their galactic plane. The orbit of these satellites is then progressively bent towards a better alignment with the galactic plane as they penetrate the central region of their host halo. The kinematics previously described are consistent with satellite infall and spin build-up via quasi-polar flows, followed by a re-orientation of the spin of massive red galaxies through mergers

Caught in the rhythm: how satellites settle into a plane around their central galaxy

Using the cosmological hydrodynamics simulation Horizon-AGN, we investigate the spatial distribution of satellite galaxies relative to their central counterpart in the redshift range between 0.3 and 0.8. We find that, on average, these satellites tend to be located on the galactic plane of the central object. This effect is detected for central galaxies with a stellar mass larger than 10^10 solar masses and found to be strongest for red passive galaxies, while blue galaxies exhibit a weaker trend. For galaxies with a minor axis parallel to the direction of the nearest filament, we find that the coplanarity is stronger in the vicinity of the central galaxy, and decreases when moving towards the outskirts of the host halo. By contrast, the spatial distribution of satellite galaxies relative to their closest filament follows the opposite trend: their tendency to align with them dominates at large distances from the central galaxy, and fades away in its vicinity. Relying on mock catalogs of galaxies in that redshift range, we show that massive red centrals with a spin perpendicular to their filament also have corotating satellites well aligned with both the galactic plane and the filament. On the other hand, lower-mass blue centrals with a spin parallel to their filament have satellites flowing straight along this filament, and hence orthogonally to their galactic plane. The orbit of these satellites is then progressively bent towards a better alignment with the galactic plane as they penetrate the central region of their host halo. The kinematics previously described are consistent with satellite infall and spin build-up via quasi-polar flows, followed by a re-orientation of the spin of massive red galaxies through mergers

Experience-dependent plasticity of dendritic spines in the developing rat barrel cortex in vivo

Do changes in neuronal structure underlie cortical plasticity(1,2)? Here we used time-lapse two-photon microscopy(3,4) of pyramidal neurons in layer 2/3 of developing rat barrel cortex(5) to image the structural dynamics of dendritic spines and filopodia. We found that these protrusions were highly motile: spines and filopodia appeared, disappeared or changed shape over tens of minutes. To test whether sensory experience drives this motility we trimmed whiskers one to three days before imaging. Sensory deprivation markedly (similar to 40%) reduced protrusive motility in deprived regions of the barrel cortex during a critical period around postnatal days (P)11-13, but had no effect in younger (P8-10) or older (P14-16) animals. Unexpectedly, whisker trimming did not change the density, length or shape of spines and filopodia. However, sensory deprivation during the critical period degraded the tuning of layer 2/3 receptive fields. Thus sensory experience drives structural plasticity in dendrites, which may underlie the reorganization of neural circuits

Spine growth precedes synapse formation in the adult neocortex in vivo

Dendritic spines appear and disappear in an experience-dependent manner. Although some new spines have been shown to contain synapses, little is known about the relationship between spine addition and synapse formation, the relative time course of these events, or whether they are coupled to de novo growth of axonal boutons. We imaged dendrites in barrel cortex of adult mice over 1 month, tracking gains and losses of spines. Using serial section electron microscopy, we analyzed the ultrastructure of spines and associated boutons. Spines reconstructed shortly after they appeared often lacked synapses, whereas spines that persisted for 4 d or more always had synapses. New spines had a large surface-to-volume ratio and preferentially contacted boutons with other synapses. In some instances, two new spines contacted the same axon. Our data show that spine growth precedes synapse formation and that new synapses form preferentially onto existing boutons