AFM Imaging Reveals MicroRNA-132 to be a Positive Regulator of Synaptic Functions.

The modification of synaptic and neural connections in adults, including the formation and removal of synapses, depends on activity-dependent synaptic and structural plasticity. MicroRNAs (miRNAs) play crucial roles in regulating these changes by targeting specific genes and regulating their expression. The fact that somatic and dendritic activity in neurons often occurs asynchronously highlights the need for spatial and dynamic regulation of protein synthesis in specific milieu and cellular loci. MicroRNAs, which can show distinct patterns of enrichment, help to establish the localized distribution of plasticity-related proteins. The recent study using atomic force microscopy (AFM)-based nanoscale imaging reveals that the abundance of miRNA(miR)-134 is inversely correlated with the functional activity of dendritic spine structures. However, the miRNAs that are selectively upregulated in potentiated synapses, and which can thereby support prospective changes in synaptic efficacy, remain largely unknown. Using AFM force imaging, significant increases in miR-132 in the dendritic regions abutting functionally-active spines is discovered. This study provides evidence for miR-132 as a novel positive miRNA regulator residing in dendritic shafts, and also suggests that activity-dependent miRNAs localized in distinct sub-compartments of neurons play bi-directional roles in controlling synaptic transmission and synaptic plasticity.

Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures.

Telomeres are composed of tandem arrays of telomeric-repeat motifs (TRMs) and telomere-binding proteins (TBPs), which are responsible for ensuring end-protection and end-replication of chromosomes. TRMs are highly conserved owing to the sequence specificity of TBPs, although significant alterations in TRM have been observed in several taxa, except Nematoda. We used public whole-genome sequencing data sets to analyze putative TRMs of 100 nematode species and determined that three distinct branches included specific novel TRMs, suggesting that evolutionary alterations in TRMs occurred in Nematoda. We focused on one of the three branches, the Panagrolaimidae family, and performed a de novo assembly of four high-quality draft genomes of the canonical (TTAGGC) and novel TRM (TTAGAC) isolates; the latter genomes revealed densely clustered arrays of the novel TRM. We then comprehensively analyzed the subtelomeric regions of the genomes to infer how the novel TRM evolved. We identified DNA damage-repair signatures in subtelomeric sequences that were representative of consequences of telomere maintenance mechanisms by alternative lengthening of telomeres. We propose a hypothetical scenario in which TTAGAC-containing units are clustered in subtelomeric regions and pre-existing TBPs capable of binding both canonical and novel TRMs aided the evolution of the novel TRM in the Panagrolaimidae family.

Quantification of a Neurological Protein in a Single Cell Without Amplification.

Proteins are key biomolecules that not only play various roles in the living body but also are used as biomarkers. If these proteins can be quantified at the level of a single cell, understanding the role of proteins will be deepened and diagnosing diseases and abnormality will be further upgraded. In this study, we quantified a neurological protein in a single cell using atomic force microscopy (AFM). After capturing specifically disrupted-in-schizophrenia 1 (DISC1) in a single cell onto a microspot immobilizing the corresponding antibody on the surface, force mapping with AFM was followed to visualize individual DISC1. Although a large variation of the number of DISC1 in a cell was observed, the average number is 4.38 × 103, and the number agrees with the ensemble-averaged value. The current AFM approach for the quantitative analysis of proteins in a single cell should be useful to study molecular behavior of proteins in depth and to follow physiological change of individual cells in response to external stimuli.

Force Mapping Reveals the Spatial Distribution of Individual Proteins in a Neuron.

Conventional methods for studying the spatial distribution and expression level of proteins within neurons have primarily relied on immunolabeling and/or signal amplification. Here, we present an atomic force microscopy (AFM)-based nanoscale force mapping method, where Anti-LIMK1-tethered AFM probes were used to visualize individual LIMK1 proteins in cultured neurons directly through force measurements. We observed that the number density of LIMK1 decreased in neuronal somas after the cells were depolarized. We also elucidated the spatial distribution of LIMK1 in single spine areas and found that the protein predominantly locates at heads of spines rather than dendritic shafts. The study demonstrates that our method enables unveiling of the abundance and spatial distribution of a protein of interest in neurons without signal amplification or labeling. We expected that this approach should facilitate the studies of protein expression phenomena in depth in a wide range of biological systems.

Natural variation in reproductive timing and X-chromosome nondisjunction in Caenorhabditis elegans.

Caenorhabditis elegans hermaphrodites first produce a limited number of sperm cells, before their germline switches to oogenesis. Production of progeny then ensues until sperm is depleted. Male production in the self-progeny of hermaphrodites occurs following X-chromosome nondisjunction during gametogenesis, and in the reference strain increases with age of the hermaphrodite parent. To enhance our understanding of the reproductive timecourse in C. elegans, we measured and compared progeny production and male proportion during the early and late reproductive periods of hermaphrodites for 96 wild C. elegans strains. We found that the two traits exhibited natural phenotypic variation with few outliers and a similar reproductive timing pattern as previous reports. Progeny number and male proportion were not correlated in the wild strains, implying that wild strains with a large brood size did not produce males at a higher rate. We also identified loci and candidate genetic variants significantly associated with male-production rate in the late and total reproductive periods. Our results provide an insight into life-history traits in wild C. elegans strains.

Brain MRI radiomics analysis may predict poor psychomotor outcome in preterm neonates.

OBJECTIVES: This study aimed to apply a radiomics approach to predict poor psychomotor development in preterm neonates using brain MRI. METHODS: Prospectively enrolled preterm neonates underwent brain MRI near or at term-equivalent age and neurodevelopment was assessed at a corrected age of 12 months. Two radiologists visually assessed the degree of white matter injury. The radiomics analysis on white matter was performed using T1-weighted images (T1WI) and T2-weighted images (T2WI). A total of 1906 features were extracted from the images and the minimum redundancy maximum relevance algorithm was used to select features. A prediction model for the binary classification of the psychomotor developmental index was developed and eightfold cross-validation was performed. The diagnostic performance of the model was evaluated using the AUC with and without including significant clinical and DTI parameters. RESULTS: A total of 46 preterm neonates (median gestational age, 29 weeks; 26 males) underwent brain MRI (median corrected gestational age, 37 weeks). Thirteen of 46 (28.3%) neonates showed poor psychomotor outcomes. There was one neonate among 46 with moderate to severe white matter injury on visual assessment. For the radiomics analysis, twenty features were selected for each analysis. The AUCs of prediction models based on T1WI, T2WI, and both T1WI and T2WI were 0.925, 0.834, and 0.902. Including gestational age or DTI parameters did not improve the prediction performance of T1WI. CONCLUSIONS: A radiomics analysis of white matter using early T1WI or T2WI could predict poor psychomotor outcomes in preterm neonates. KEY POINTS: • Radiomics analysis on T1-weighted images of preterm neonates showed the highest diagnostic performance (AUC, 0.925) for predicting poor psychomotor outcomes. • In spite of 45 of 46 neonates having no significant white matter injury on visual assessment, the radiomics analysis of early brain MRI showed good diagnostic performance (sensitivity, 84.6%; specificity, 78.8%) for predicting poor psychomotor outcomes. • Radiomics analysis on early brain MRI can help to predict poor neurodevelopmental outcomes in preterm neonates.