Molecular and Cellular Approaches for Diversifying and Extending Optogenetics

Optogenetic technologies employ light to control biological processes within targeted cells in vivo with high temporal precision. Here, we show that application of molecular trafficking principles can expand the optogenetic repertoire along several long-sought dimensions. Subcellular and transcellular trafficking strategies now permit (1) optical regulation at the far-red/infrared border and extension of optogenetic control across the entire visible spectrum, (2) increased potency of optical inhibition without increased light power requirement (nanoampere-scale chloride-mediated photocurrents that maintain the light sensitivity and reversible, step-like kinetic stability of earlier tools), and (3) generalizable strategies for targeting cells based not only on genetic identity, but also on morphology and tissue topology, to allow versatile targeting when promoters are not known or in genetically intractable organisms. Together, these results illustrate use of cell-biological principles to enable expansion of the versatile fast optogenetic technologies suitable for intact-systems biology and behavior

On RAF Sets and Autocatalytic Cycles in Random Reaction Networks

The emergence of autocatalytic sets of molecules seems to have played an important role in the origin of life context. Although the possibility to reproduce this emergence in laboratory has received considerable attention, this is still far from being achieved. In order to unravel some key properties enabling the emergence of structures potentially able to sustain their own existence and growth, in this work we investigate the probability to observe them in ensembles of random catalytic reaction networks characterized by different structural properties. From the point of view of network topology, an autocatalytic set have been defined either in term of strongly connected components (SCCs) or as reflexively autocatalytic and food-generated sets (RAFs). We observe that the average level of catalysis differently affects the probability to observe a SCC or a RAF, highlighting the existence of a region where the former can be observed, whereas the latter cannot. This parameter also affects the composition of the RAF, which can be further characterized into linear structures, autocatalysis or SCCs. Interestingly, we show that the different network topology (uniform as opposed to power-law catalysis systems) does not have a significantly divergent impact on SCCs and RAFs appearance, whereas the proportion between cleavages and condensations seems instead to play a role. A major factor that limits the probability of RAF appearance and that may explain some of the difficulties encountered in laboratory seems to be the presence of molecules which can accumulate without being substrate or catalyst of any reaction.Comment: pp 113-12

Double Dissociation of Format-Dependent and Number-Specific Neurons in Human Parietal Cortex

Based on neuroimaging methods, it is a commonly held view that numerical representation in the human parietal lobes is format independent. We used a transcranial magnetic stimulation adaptation paradigm to examine the existence of functionally segregated overlapping populations of neurons for different numerical formats and to reveal how numerical information is encoded and represented. Based on 2 experiments, we found that right parietal lobe stimulation showed a dissociation between digits and verbal numbers, whereas the left parietal lobe showed a double dissociation between the different numerical formats. Further analysis and modeling also excluded pre- or postrepresentational components as the source of the current effects. These results demonstrate that both parietal lobes are equipped with format-dependent neurons that encode quantity

Radiation of Extant Cetaceans Driven by Restructuring of the Oceans

The remarkable fossil record of whales and dolphins (Cetacea) has made them an exemplar of macroevolution. Although their overall adaptive transition from terrestrial to fully aquatic organisms is well known, this is not true for the radiation of modern whales. Here, we explore the diversification of extant cetaceans by constructing a robust molecular phylogeny that includes 87 of 89 extant species. The phylogeny and divergence times are derived from nuclear and mitochondrial markers, calibrated with fossils. We find that the toothed whales are monophyletic, suggesting that echolocation evolved only once early in that lineage some 36–34 Ma. The rorqual family (Balaenopteridae) is restored with the exclusion of the gray whale, suggesting that gulp feeding evolved 18–16 Ma. Delphinida, comprising all living dolphins and porpoises other than the Ganges/Indus dolphins, originated about 26 Ma; it contains the taxonomically rich delphinids, which began diversifying less than 11 Ma. We tested 2 hypothesized drivers of the extant cetacean radiation by assessing the tempo of lineage accumulation through time. We find no support for a rapid burst of speciation early in the history of extant whales, contrasting with expectations of an adaptive radiation model. However, we do find support for increased diversification rates during periods of pronounced physical restructuring of the oceans. The results imply that paleogeographic and paleoceanographic changes, such as closure of major seaways, have influenced the dynamics of radiation in extant cetaceans

Decrease in coccolithophore calcification and CO2 since the middle Miocene

International audienceMarine algae are instrumental in carbon cycling and atmospheric carbon dioxide (CO2) regulation. One group, coccolithophores, uses carbon to photosynthesize and to calcify, covering their cells with chalk platelets (coccoliths). How ocean acidification influences coccolithophore calcification is strongly debated, and the effects of carbonate chemistry changes in the geological past are poorly understood. This paper relates degree of coccolith calcification to cellular calcification, and presents the first records of size-normalized coccolith thickness spanning the last 14 Myr from tropical oceans. Degree of calcification was highest in the low-pH, high-CO2 Miocene ocean, but decreased significantly between 6 and 4 Myr ago. Based on this and concurrent trends in a new alkenone εp record, we propose that decreasing CO2 partly drove the observed trend via reduced cellular bicarbonate allocation to calcification. This trend reversed in the late Pleistocene despite low CO2, suggesting an additional regulator of calcification such as alkalinity

Targeting cells with single vectors using multiple-feature Boolean logic

Precisely defining the roles of specific cell types is an intriguing frontier in the study of intact biological systems and has stimulated the rapid development of genetically encoded tools for observation and control. However, targeting these tools with adequate specificity remains challenging: most cell types are best defined by the intersection of two or more features such as active promoter elements, location and connectivity. Here we have combined engineered introns with specific recombinases to achieve expression of genetically encoded tools that is conditional upon multiple cell-type features, using Boolean logical operations all governed by a single versatile vector. We used this approach to target intersectionally specified populations of inhibitory interneurons in mammalian hippocampus and neurons of the ventral tegmental area defined by both genetic and wiring properties. This flexible and modular approach may expand the application of genetically encoded interventional and observational tools for intact-systems biology

Breathing more deeply: Deep ocean carbon storage during the mid Pleistocene Transition

The ~100 k.y. cyclicity of the late Pleistocene ice ages started during the mid-Pleistocene transition (MPT), as ice sheets became larger and persisted for longer. The climate system feedbacks responsible for introducing this nonlinear ice sheet response to orbital variations in insolation remain uncertain. Here we present benthic foraminiferal stable isotope (δ18O, δ13C) and trace metal records (Cd/Ca, B/Ca, U/Ca) from Deep Sea Drilling Project Site 607 in the North Atlantic. During the onset of the MPT, glacial-interglacial changes in δ13C values are associated with changes in nutrient content and carbonate saturation state, consistent with a change in water mass at our site from a nutrient-poor northern source during interglacial intervals to a nutrient-rich, corrosive southern source during glacial intervals. The respired carbon content of glacial Atlantic deep water increased across the MPT. Increased dominance of corrosive bottom waters during glacial intervals would have raised mean ocean alkalinity and lowered atmospheric pCO2. The amplitude of glacial-interglacial changes in δ13C increased across the MPT, but this was not mirrored by changes in nutrient content. We interpret this in terms of air-sea CO2 exchange effects, which changed the δ13C signature of dissolved inorganic carbon in the deep water mass source regions. Increased sea ice cover or ocean stratification during glacial times may have reduced CO2 outgassing in the Southern Ocean, providing an additional mechanism for reducing glacial atmospheric pCO2. Conversely, following the establishment of the ~100 k.y. glacial cycles, δ13C of interglacial northern-sourced waters increased, perhaps reflecting reduced invasion of CO2 into the North Atlantic following the MPT

Breathing more deeply: Deep ocean carbon storage during the mid Pleistocene Transition

The ~100 k.y. cyclicity of the late Pleistocene ice ages started during the mid-Pleistocene transition (MPT), as ice sheets became larger and persisted for longer. The climate system feedbacks responsible for introducing this nonlinear ice sheet response to orbital variations in insolation remain uncertain. Here we present benthic foraminiferal stable isotope (δ18O, δ13C) and trace metal records (Cd/Ca, B/Ca, U/Ca) from Deep Sea Drilling Project Site 607 in the North Atlantic. During the onset of the MPT, glacial-interglacial changes in δ13C values are associated with changes in nutrient content and carbonate saturation state, consistent with a change in water mass at our site from a nutrient-poor northern source during interglacial intervals to a nutrient-rich, corrosive southern source during glacial intervals. The respired carbon content of glacial Atlantic deep water increased across the MPT. Increased dominance of corrosive bottom waters during glacial intervals would have raised mean ocean alkalinity and lowered atmospheric pCO2. The amplitude of glacial-interglacial changes in δ13C increased across the MPT, but this was not mirrored by changes in nutrient content. We interpret this in terms of air-sea CO2 exchange effects, which changed the δ13C signature of dissolved inorganic carbon in the deep water mass source regions. Increased sea ice cover or ocean stratification during glacial times may have reduced CO2 outgassing in the Southern Ocean, providing an additional mechanism for reducing glacial atmospheric pCO2. Conversely, following the establishment of the ~100 k.y. glacial cycles, δ13C of interglacial northern-sourced waters increased, perhaps reflecting reduced invasion of CO2 into the North Atlantic following the MPT