Spatial information enhanced by non-spatial information in hippocampal granule cells

The hippocampus organizes sequential memory composed of non-spatial information (such as objects and odors) and spatial information (places). The dentate gyrus (DG) in the hippocampus receives two types of information from the lateral and medial entorhinal cortices. Non-spatial and spatial information is delivered respectively to distal and medial dendrites (MDs) of granule cells (GCs) within the molecular layer in the DG. To investigate the role of the association of those two inputs, we measured the response characteristics of distal and MDs of a GC in a rat hippocampal slice and developed a multi-compartment GC model with dynamic synapses; this model reproduces the response characteristics of the dendrites. Upon applying random inputs or input sequences generated by a Markov process to the computational model, it was found that a high-frequency random pulse input to distal dendrites (DDs) and, separately, regular burst inputs to MDs were effective for inducing GC activation. Furthermore, when the random and theta burst inputs were simultaneously applied to the respective dendrites, the pattern discrimination for theta burst input to MDs that caused slight GC activation was enhanced in the presence of random input to DDs. These results suggest that the temporal pattern discrimination of spatial information is originally involved in a synaptic characteristic in GCs and is enhanced by non-spatial information input to DDs. Consequently, the co-activation of two separate inputs may play a crucial role in the information processing on dendrites of GCs by usefully combing each temporal sequence.     

Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering

Replication initiator proteins (Reps) from the HUH-endonuclease superfamily process specific single-stranded DNA (ssDNA) sequences to initiate rolling circle/hairpin replication in viruses, such as crop ravaging geminiviruses and human disease causing parvoviruses. In biotechnology contexts, Reps are the basis for HUH-tag bioconjugation and a critical adeno-associated virus genome integration tool. We solved the first co-crystal structures of Reps complexed to ssDNA, revealing a key motif for conferring sequence specificity and for anchoring a bent DNA architecture. In combination, we developed a deep sequencing cleavage assay, termed HUH-seq, to interrogate subtleties in Rep specificity and demonstrate how differences can be exploited for multiplexed HUH-tagging. Together, our insights allowed engineering of only four amino acids in a Rep chimera to predictably alter sequence specificity. These results have important implications for modulating viral infections, developing Rep-based genomic integration tools, and enabling massively parallel HUH-tag barcoding and bioconjugation applications.     

Involvement of singlet oxygen in the fungal degradation of lignin

The possible involvement of singlet oxygen (¹O₂) in the degradation of lignin by $\text{Phanerochaete}\text{chrysosporium}$ was examined. Ligninolytic cultures and photochemically generated ¹O₂ gave the same oxidation products from the lignin substructure model compound 1,2-bis(3-methoxy-4-alkoxyphenyl)propan-1,3-diol. Fluorescence and near UV absorbance of the specific ¹O₂ trapping agent anthracene-9,10-bisethanesulfonic acid (AES) disappeared in ligninolytic cultures, indicating that ¹O₂ was produced. AES strongly inhibited oxidation of ¹⁴C-lignin, but not ¹⁴C-glucose, to ¹⁴CO₂ in cultures, and also strongly suppressed oxidation of the model compound. These results indicate the ¹O₂ plays an integral role in lignin biodegradation.     

Differentiation of mitochondrial DNA types inMacaca fascicularis

Restriction fragment length polymorphism in the mitochondrial DNA ofMacaca fascicularis from four geographical regions, Indonesia, the Philippines, Malaysia, and Indochina, was analyzed. In total, 21 types of mitochondrial DNA were detected using five restriction enzymes. These types were divided into two main groups based on phylogenetic analyses, one of which corresponded to the types of continental (Malaysia/Indochina) populations and the other to the types of a insular (Philippine) population. The types in the Indonesian population belonged to both groups. In the phylogenetic tree for the four populations, two clusters were constructed, one for the continental populations and the other for the insular ones.     

Improving noise resistance of intrinsic rhythms in a square-wave burster model

The square-wave burster (Wang and Rinzel, 2003) is a class of autonomous bursting cells that share a bifurcation structure. It is known that this class of cells is involved in the generation of various life-supporting rhythms. In our research to realize an electronic circuit that mimics the rhythm generating mechanism in the square-wave burster, our circuit experimentally exhibited severe fluctuations in its rhythmic activity. We have found a noise-sensitive region in the phase portrait of the ideal model and have proposed modifications of the model that can reduce this fluctuation. A possible modification to ionic-conductance neuron models (Kohno and Aihara, 2011) was inspired by them. This modification, however, cannot be applied to a group of square-wave bursters, including the Butera–Rinzel–Smith model (0010 and 0050), which is a model of the pre-Bötzinger complex bursting neuron that plays a crucial role in the generation of respiration rhythms, because this modification premises that the slow dynamics originates from an activation gate variable of a hyperpolarizing ionic current. However, in some square-wave bursters, they are controlled by an inactivation gate variable of a depolarizing ionic current. In this study, we proposed a similar modification with a completely different mechanism that can be applied to this group of square-wave bursters. In the presence of noises, the modified Butera–Rinzel–Smith model can generate rhythmic activity that is more stable and similar to biological observations than the original model. The mechanisms underlying this modification are explained with noisy bifurcation diagrams.