Experience dependent contextual codes in the hippocampus, bioRxiv, 2019-12-04
AbstractThe hippocampus is a medial temporal lobe brain structure that contains circuitry and neural representations capable of supporting declarative memory. Hippocampal place cells fire in one or few restricted spatial locations in a given environment. Between environmental contexts, place cell firing fields remap (turning onoff or moving to a new spatial location), providing a unique population-wide neural code for context specificity. However, the manner by which features associated with a given context combine to drive place cell remapping remains a matter of debate. Here we show that remapping of neural representations in region CA1 of the hippocampus is strongly driven by prior beliefs about the frequency of certain contexts, and that remapping is equivalent to an optimal estimate of the identity of the current context under that prior. This prior-driven remapping is learned early in training and remains robust to changes in behavioral task-demands. Furthermore, a simple associative learning mechanism is sufficient to reproduce these results. Our findings demonstrate that place cell remapping is a generalization of representing an animal’s location. Rather than simply representing location in physical space, the hippocampus represents an optimal estimate of location in a multi-dimensional stimulus space.
biorxiv neuroscience 100-200-users 2019Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria, bioRxiv, 2019-12-04
AbstractMobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium and, as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. Moreover, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalogue of genes encoded on MGEs, dictating bacterial evolution through HGT.
biorxiv microbiology 100-200-users 2019Late life metformin treatment limits cell survival and shortens lifespan by triggering an aging-associated failure of energy metabolism, bioRxiv, 2019-12-04
SummaryThe diabetes drug metformin is to be clinically tested in aged humans to achieve health span extension, but little is known about responses of old non-diabetic individuals to this drug. By in vitro and in vivo tests we found that metformin shortens life span and limits cell survival when provided in late life, contrary to its positive early life effects. Mechanistically, metformin exacerbates aging-associated mitochondrial dysfunction towards respiratory failure, aggravated by the inability of old cells to upregulate glycolysis in response to metformin, leading to ATP exhaustion. The beneficial dietary restriction effect of metformin on lipid reserves is abrogated in old animals, contributing to metabolic failure, while ectopic stabilization of cellular ATP levels alleviates late life metformin toxicity in vitro and in vivo. The toxicity is also suspended in nematodes carrying diabetes-like insulin receptor insufficiency and showing prolonged resilience to metabolic stress induced by metformin. In sum, we uncovered an alarming metabolic decay triggered by metformin in late life which may limit its benefits for non-diabetic elderly patients. Novel regulators of life extension by metformin are also presented.Highlights<jatslist list-type=bullet><jatslist-item>Late life metformin treatment limits cell survival and shortens lifespan.<jatslist-item><jatslist-item>Metformin exacerbates aging-associated mitochondrial dysfunction causing fatal ATP exhaustion.<jatslist-item><jatslist-item>Old cells fail to upregulate glycolysis as a compensatory response to metformin.<jatslist-item><jatslist-item>The dietary restriction (DR) mimetic response to metformin is abrogated in old animals.<jatslist-item><jatslist-item>PKA and not AMPK pathway instigates the early life DR response to metformin.<jatslist-item><jatslist-item>Stabilization of cellular ATP levels alleviates late life metformin toxicity in vitro and in vivo.<jatslist-item>
biorxiv physiology 200-500-users 2019Plant Small RNA Species Direct Gene Silencing in Pathogenic Bacteria as well as Disease Protection, bioRxiv, 2019-12-04
AbstractPlant small RNAs (sRNAs) andor double-stranded RNAs (dsRNAs) trigger RNA interference (RNAi) in interacting eukaryotic pathogens or parasites. However, it is unknown whether this phenomenon could operate in bacterial phytopathogens, which lack a eukaryotic-like RNAi machinery. Here, we first show that Arabidopsis-encoded inverted repeat transgenes trigger silencing of Pseudomonas syringae heterologous reporter and endogenous virulence-associated genes during infection. Antibacterial Gene Silencing (AGS) of the latter was associated with a reduced pathogenesis, which was also observed upon application of corresponding plant-derived RNAs onto wild-type plants prior to infection. We additionally demonstrate that sRNAs directed against virulence factor transcripts were causal for silencing and pathogenesis reduction, while cognate long dsRNAs were inactive. Overall, this study provides the first evidence that plant sRNAs can directly reprogram gene expression in a phytopathogenic bacterium and may have wider implications in the understanding of how plants regulate transcriptome, community composition and genome evolution of associated bacteria.
biorxiv plant-biology 100-200-users 2019A minimal CRISPR-Cas3 system for genome engineering, bioRxiv, 2019-12-03
AbstractCRISPR-Cas technologies have provided programmable gene editing tools that have revolutionized research. The leading CRISPR-Cas9 and Cas12a enzymes are ideal for programmed genetic manipulation, however, they are limited for genome-scale interventions. Here, we utilized a Cas3-based system featuring a processive nuclease, expressed endogenously or heterologously, for genome engineering purposes. Using an optimized and minimal CRISPR-Cas3 system (Type I-C) programmed with a single crRNA, large deletions ranging from 7 - 424 kb were generated in Pseudomonas aeruginosa with high efficiency and speed. By comparison, Cas9 yielded small deletions and point mutations. Cas3-generated deletion boundaries were variable in the absence of a homology-directed repair (HDR) template, and successfully and efficiently specified when present. The minimal Cas3 system is also portable; large deletions were induced with high efficiency in Pseudomonas syringae and Escherichia coli using an “all-in-one” vector. Notably, Cas3 generated bi-directional deletions originating from the programmed cut site, which was exploited to iteratively reduce a P. aeruginosa genome by 837 kb (13.5%) using 10 distinct crRNAs. We also demonstrate the utility of endogenous Cas3 systems (Type I-C and I-F) and develop an “anti-anti-CRISPR” strategy to circumvent endogenous CRISPR-Cas inhibitor proteins. CRISPR-Cas3 could facilitate rapid strain manipulation for synthetic biological and metabolic engineering purposes, genome minimization, and the analysis of large regions of unknown function.
biorxiv molecular-biology 0-100-users 2019A synthetic Calvin cycle enables autotrophic growth in yeast, bioRxiv, 2019-12-03
AbstractThe methylotrophic yeast Pichia pastoris is frequently used for heterologous protein production and it assimilates methanol efficiently via the xylulose-5-phosphate pathway. This pathway is entirely localized in the peroxisomes and has striking similarities to the Calvin-Benson-Bassham (CBB) cycle, which is used by a plethora of organisms like plants to assimilate CO2 and is likewise compartmentalized in chloroplasts. By metabolic engineering the methanol assimilation pathway of P. pastoris was re-wired to a CO2 fixation pathway resembling the CBB cycle. This new yeast strain efficiently assimilates CO2 into biomass and utilizes it as its sole carbon source, which changes the lifestyle from heterotrophic to autotrophic.In total eight genes, including genes encoding for RuBisCO and phosphoribulokinase, were integrated into the genome of P. pastoris, while three endogenous genes were deleted to block methanol assimilation. The enzymes necessary for the synthetic CBB cycle were targeted to the peroxisome. Methanol oxidation, which yields NADH, is employed for energy generation defining the lifestyle as chemoorganoautotrophic. This work demonstrates that the lifestyle of an organism can be changed from chemoorganoheterotrophic to chemoorganoautotrophic by metabolic engineering. The resulting strain can grow exponentially and perform multiple cell doublings on CO2 as sole carbon source with a µmax of 0.008 h−1.Graphical Abstract<jatsfig id=ufig1 position=float fig-type=figure orientation=portrait><jatsgraphic xmlnsxlink=httpwww.w3.org1999xlink xlinkhref=862599v1_ufig1 position=float orientation=portrait >
biorxiv synthetic-biology 100-200-users 2019