Migration, early axonogenesis, and Reelin-dependent layer-forming behavior of early/posterior-born Purkinje cells in the developing mouse lateral cerebellum

<p>Abstract</p> <p>Background</p> <p>Cerebellar corticogenesis begins with the assembly of Purkinje cells into the Purkinje plate (PP) by embryonic day 14.5 (E14.5) in mice. Although the dependence of PP formation on the secreted protein Reelin is well known and a prevailing model suggests that Purkinje cells migrate along the 'radial glial' fibers connecting the ventricular and pial surfaces, it is not clear how Purkinje cells behave in response to Reelin to initiate the PP. Furthermore, it is not known what nascent Purkinje cells look like <it>in vivo</it>. When and how Purkinje cells start axonogenesis must also be elucidated.</p> <p>Results</p> <p>We show that Purkinje cells generated on E10.5 in the posterior periventricular region of the lateral cerebellum migrate tangentially, after only transiently migrating radially, towards the anterior, exhibiting an elongated morphology consistent with axonogenesis at E12.5. After their somata reach the outer/dorsal region by E13.5, they change 'posture' by E14.5 through remodeling of non-axon (dendrite-like) processes and a switchback-like mode of somal movement towards a superficial Reelin-rich zone, while their axon-like fibers remain relatively deep, which demarcates the somata-packed portion as a plate. In <it>reeler </it>cerebella, the early born posterior lateral Purkinje cells are initially normal during migration with anteriorly extended axon-like fibers until E13.5, but then fail to form the PP due to lack of the posture-change step.</p> <p>Conclusions</p> <p>Previously unknown behaviors are revealed for a subset of Purkinje cells born early in the posteior lateral cerebellum: tangential migration; early axonogenesis; and Reelin-dependent reorientation initiating PP formation. This study provides a solid basis for further elucidation of Reelin's function and the mechanisms underlying the cerebellar corticogenesis, and will contribute to the understanding of how polarization of individual cells drives overall brain morphogenesis.</p

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.

De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and it has a function in the production of the traditional Japanese fermented food "natto." The B. subtilis natto BEST195 genome was previously sequenced with short reads, but it included some incomplete regions. We resequenced the BEST195 genome using a PacBio RS sequencer, and we successfully obtained a complete genome sequence from one scaffold without any gaps, and we also applied Illumina MiSeq short reads to enhance quality. Compared with the previous BEST195 draft genome and Marburg 168 genome, we found that incomplete regions in the previous genome sequence were attributed to GC-bias and repetitive sequences, and we also identified some novel genes that are found only in the new genome

Example of one previous gap region.

<p>The region correspond to 4,003,725 bp to 4,007,944 bp in the previous genome. The upper part of this figure shows the mapping results of Illumina GAII reads, MiSeq reads, and PacBio reads. The bottom part displays an anchor alignment within the new genome using Murasaki, a multiple genome comparison program <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109999#pone.0109999-Popendorf1" target="_blank">[33]</a>. For the anchor alignment, blue regions represent aligned anchors, which means that the same subsequences are present in other positions of the genome. For the mapping results, reads coloured with white were mapped with mapping quality zero; that is, each read is not uniquely mapped to one position. Compared with the mapping results of Illumina reads, blue regions in the anchor alignment corresponded to positions where white reads were mapped. Additionally, both ends of the gap region include transposases with repetitive sequences.</p

Assembly results with PacBio subreads and Illumina MiSeq reads.

<p>Assembly results with PacBio subreads and Illumina MiSeq reads.</p

The improvable gene in the Marburg 168 genome by the complete BEST195 genome.

<p>The upper part of this figure displays an anchor alignment between the Marburg 168 genome sequence and the complete BEST195 genome sequence using Murasaki. The bottom part shows the alignment results of sequences of Marburg 168 genome, BEST195, and three relative species, <i>B. amyloliquefaciens</i>, <i>B. licheniformis</i>, and <i>B. pumilus</i>, using CLC Sequence Viewer. The substitution of C for T and deletions of C and A in the Marburg 168 genome sequence in red dash line box were thought to be the cause of separated genes, BSU16890 and BSU16900.</p

Detail of corrected positions via MiSeq.

<p>Detail of corrected positions via MiSeq.</p