Biology subjects

Yamazaki, M.

Publications and source records attributed to Yamazaki, M..

25 records · Page 2Linked to original sources

bioRxiv2019

Coupling Day Length Data and Genomic Prediction tools for Predicting Time-Related Traits under Complex Scenarios

Genomic selection (GS) has proven to be an efficient tool for predicting crop-rank performance of untested genotypes; however, when the traits have intermediate optima (phenology stages) this implementation might not be the most convenient. GS might deliver high rank correlations but incurring in serious bias. Days to heading (DTH) is a crucial development stage in rice for regional adaptability with significant impact in yield potential. The objectives of this research consisted in the development of a method that accurately predicts time related traits like DTH in unobserved environments. For this, we developed an implementation that incorporate day length information (DL) in the prediction process for two relevant scenarios: CV0, predicting tested genotypes in unobserved environments (C method); and CV00, predicting untested genotypes in unobserved environments (CB method). The use of DL has advantages over weather data since it can be determined in advance just by knowing the location and planting date. The proposed methods showed that DL information significantly helps to improve the predictive ability of DTH in unobserved environments. Under CV0, the C method returned an root-mean-square-error (RMSE) of 3.9 days, a Pearson Correlation (PC) of 0.98 and the differences between the predicted and observed environmental means (EMD) ranged between -4.95 and 4.67 days. For CV00, the CB method returned an RMSE of 7.3 days, a PC of 0.93 and the EMD ranged between -6.4 and 4.1 days while the conventional GS implementation produced an RMSE of 18.1 days, a PC of 0.41 and the EMD ranged between -31.5 and 28.7 days.

genomics↗

bioRxiv2019

Transcriptional variation in glucosinolate biosynthetic genes and inducible responses to aphid herbivory on field-grown Arabidopsis thaliana

Recently, increasing attempts have been made to understand how plant genes function in natura studies. To determine whether plant defense genes are activated under multiple biotic stimuli, we combined a high-throughput RNA-Seq with insect survey data on 19 accessions of Arabidopsis thaliana growing on the field site of Switzerland. We found that genes with GO annotations "glucosinolate biosynthetic process" and "response to insects" were the most significantly enriched, exhibiting largely variable expression among plant accessions. Nearly half of the total expression variation in glucosinolate biosynthetic genes, AOPs, ESM1, ESP, and TGG1, was explained by among-accession variance. Combined with the field RNA-Seq data, bioassays confirmed that AOP3 was up-regulated in response to the mustard aphid Lipaphis erysimi. In addition, we also found that the expression of a major cis-jasmone activated gene CYP81D11 was positively correlated with the number of the flea beetles Phyllotreta spp. The combined results from RNA-Seq and insect surveys suggested that plants can activate their defenses even when they are exposed to multiple biotic stimuli in natura.

plant biology↗

bioRxiv2018

Cerebral amyloid angiopathy and comparative analysis of amyloid-β protein in birds

Senile plaques and cerebral amyloid angiopathy (CAA) are well-documented in various mammals, and several species even exhibit neurofibrillary tangle (NFT). However, we know far less about whether such symptoms are present in birds. Therefore, here we clarified the occurrence and pathogenesis of avian a{beta}-related lesions, analyzing the a{beta} amino-acid sequence across 28 birds at multiple life stages, representing 15 species, 14 genera, and 9 nine families. We also determined the expected a{beta} amino-acid sequence after comparing data from the brains of nine birds (seven species) with publicly available NCBI data. We observed CAA and senile plaque-like deposition only in a female Amazon parrot, estimated to be around 30-40 years old. We identified two A{beta} depositions (40 and 42) in the same location that correspond to A{beta} 6-42. Additionally, we observed severe A{beta} deposition, accompanied by severe hemorrhaging, in blood vessels of the superficial and deep portions of the brain. These lesions were directly related to the cause of death. Of 40 bird species, 36 exhibited type 1 A{beta} amino-acid sequences, similar to humans. Given that all of these birds were old, our results suggest that A{beta} is deposited primarily as CAA as the animals age. This report is the first clinically based description of CAA in birds. Interspecific variation likely exists because we identified species that did not exhibit A{beta} deposition even when the birds are old enough. However, even birds of the same taxonomic status differed in whether they possessed or lacked A{beta} deposition. Thus, other factors besides A{beta} amino-acid sequence could influence this symptom.

pathology↗

bioRxiv2018

Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana

Background: Genetic variation in plants alters insect abundance and community structure in the field; however, little is known about the importance of a single gene among diverse plant genotypes. In this context, Arabidopsis trichomes provide an excellent system to discern the roles of natural variation and a key gene, GLABRA1, in shaping insect communities. In this study, we transplanted two independent glabrous mutants (gl1-1 and gl1-2) and 17 natural accessions of Arabidopsis thaliana to two localities in Switzerland and Japan.\n\nResults: Fifteen insect species inhabited plant accessions, with 10-30% broad-sense heritability of community indices being detected, such as species richness and diversity. The total abundance of leaf-chewing herbivores was negatively correlated with trichome density at both the field sites, while glucosinolates had variable effects on leaf chewers between the two sites. Interestingly, there was a parallel tendency for the abundance of leaf chewers to be higher on gl1-1 and gl1-2 than for their different parental accessions, Ler-1 and Col-0, respectively. Furthermore, the loss of function in the GLABRA1 gene significantly decreased the resistance of plants to the two predominant chewers, flea beetles and turnip sawflies.\n\nConclusions: Overall, our results indicate that insect community composition on A. thaliana is heritable across two distant field sites, with GLABRA1 playing a key role in altering the abundance of leaf-chewing herbivores. Given that such a trichome variation is widely observed in Brassicaceae plants, the present study exemplifies the community-wide impact of a single plant gene on crucifer-feeding insects in the field.

plant biology↗

bioRxiv2018

Adaptive Reduction of Male Gamete Number in a Selfing Species

The number of male gametes produced is critical for reproductive success and varies greatly between and within species1-3. Evolutionary reduction of male gamete production has been widely reported in plants as a hallmark of the selfing syndrome, as well as in humans. Such a reduction may simply represent deleterious decay4-7, but evolutionary theory predicts that breeding systems could act as a major selective force on male gamete number: while large numbers of sperm should be produced in highly promiscuous species because of male-male gamete competition1, reduced sperm numbers may be advantageous at lower outcrossing rates because of the cost of gamete production. Here we used genome-wide association study (GWAS) to show a signature of polygenic selection on pollen number in the predominantly selfing plant Arabidopsis thaliana. The top associations with pollen number were significantly more strongly enriched for signatures of selection than those for ovule number and 107 phenotypes analyzed previously, indicating polygenic selection8. Underlying the strongest association, responsible for 20% of total pollen number variation, we identified the gene REDUCED POLLEN NUMBER 1 affecting cell proliferation in the male germ line. We validated its subtle but causal allelic effects using a quantitative complementation test with CRISPR-Cas9-generated null mutants in a nonstandard wild accession. Our results support polygenic adaptation underlying reduced male gamete numbers.

evolutionary biology↗

bioRxiv2018

Genome-wide association study of 1 million people identifies 111 loci for atrial fibrillation

To understand the genetic variation underlying atrial fibrillation (AF), the most common cardiac arrhythmia, we performed a genome-wide association study (GWAS) of > 1 million people, including 60,620 AF cases and 970,216 controls. We identified 163 independent risk variants at 111 loci and prioritized 165 candidate genes likely to be involved in AF. Many of the identified risk variants fall near genes where more deleterious mutations have been reported to cause serious heart defects in humans or mice (MYH6, NKX2-5, PITX2, TBC1D32, TBX5),1,2 or near genes important for striated muscle function and integrity (e.g. MYH7, PKP2, SSPN, SGCA). Experiments in rabbits with heart failure and left atrial dilation identified a heterogeneous distributed molecular switch from MYH6 to MYH7 in the left atrium, which resulted in contractile and functional heterogeneity and may predispose to initiation and maintenance of atrial arrhythmia.

genetics↗

bioRxiv2017

Input-specific NMDAR-dependent potentiation of dendritic GABAergic inhibition

Preservation of a balance between synaptic excitation and inhibition is critical for normal brain function. A number of homeostatic cellular mechanisms have been suggested to play a role in maintaining this balance, including long-term plasticity of GABAergic inhibitory synapses. Many previous studies have demonstrated a coupling of postsynaptic spiking with modification of perisomatic inhibition. Here, we demonstrate that activation of NMDA-type glutamate receptors leads to input-specific long-term potentiation of dendritic inhibition mediated by somatostatin-expressing interneurons. This form of plasticity is expressed postsynaptically and requires both CaMKII and the {beta}2-subunit of the GABA-A receptor. Importantly, this process may function to preserve dendritic inhibition, as in vivo loss of NMDAR signaling results in a selective weakening of dendritic inhibition. Overall, our results reveal a new mechanism for linking excitatory and inhibitory input in neuronal dendrites and provide novel insight into the homeostatic regulation of synaptic transmission in cortical circuits.

neuroscience↗