Biology subjects

Nakagawa, S.

Publications and source records attributed to Nakagawa, S..

At least 91 records · Page 5Linked to original sources

bioRxiv2020

Conditional repeatability and the variance explained by reaction norm variation in random slope models

Individuals differ in average phenotypes and in sensitivity to environmental variation. Such context-sensitivity can be modelled as random-slope variation. Random-slope variation implies that the proportion of between-individual variation varies across the range of a covariate (environment/context/time/age) and has thus been called conditional repeatability. We propose to put conditional repeatabilities in perspective of the total phenotypic variance and suggest a way of standardization using the random-slope coefficient of determination [Formula]. Furthermore, we illustrate that the marginalized repeatability Rmar averaged across an environmental gradient offers a biologically relevant description of between-individual variation. We provide simple equations for calculating key descriptors of conditional repeatabilities, clarify the difference between random-intercept variation and average between-individual variation and make recommendations for comprehensive reporting. While we introduce the concept with individual variation in mind, the framework is equally applicable to other type of between-group/cluster variation that varies across some (environmental) gradient.

animal behavior and cognition↗

bioRxiv2020

Revisiting and expanding the meta-analysis of variation: The log coefficient of variation ratio, lnCVR

Meta-analyses are frequently used to quantify the difference in the average values of two groups (e.g., control and experimental treatment groups), but examine the difference in the variability (variance) of two groups. For such comparisons, the two relatively new effect size statistics, namely the log-transformed variability ratio (the ratio of two standard deviations; lnVR) and the log-transformed CV ratio (the ratio of two coefficients of variation; lnCVR) are useful. In practice, lnCVR may be of most use because a treatment may affect the mean and the variance simultaneously. We review current, and propose new, estimators for lnCVR and lnVR. We also present methods for use when the two groups are dependent (e.g., for cross-over and pre-test-post-test designs). A simulation study evaluated the performance of these estimators and we make recommendations about which estimators one should use to minimise bias. We also present two worked examples that illustrate the importance of accounting for the dependence of the two groups. We found that the degree to which dependence is accounted for in the sampling variance estimates can impact heterogeneity parameters such as{tau} 2 (i.e., the between-study variance) and I2 (i.e., the proportion of the total variability due to between-study variance), and even the overall effect, and in turn qualitative interpretations. Meta-analytic comparison of the variability between two groups enables us to ask completely new questions and to gain fresh insights from existing datasets. We encourage researchers to take advantage of these convenient new effect size measures for the meta-analysis of variation.

bioinformatics↗

bioRxiv2019

Sexual conflict explains diverse patterns of transgenerational plasticity

Transgenerational plasticity (TGP) occurs when the environment experienced by parents induces changes in traits of offspring and/or subsequent generations. Such effects can be adaptive or non-adaptive and are increasingly recognised as key determinants of health, cognition, development and performance across a wide range of taxa, including humans. While the conditions that favour maternal TGP are well understood, rapidly accumulating evidence indicates that TGP can be maternal or paternal, and offspring responses can be sex-specific. However, the evolutionary mechanisms that drive this diversity are unknown. We used an individual-based model to investigate the evolution of TGP when the sexes experience different ecologies. We find that adaptive TGP rarely evolves when alleles at loci that determine offspring responses to environmental information originating from the mother and father are subject to sexually antagonistic selection. By contrast, duplication and sex-limitation of such loci can allow for the evolution of a variety of sex-specific responses, including non-adaptive sex-specific TGP when sexual selection is strong. Sexual conflict could therefore help to explain why adaptive TGP evolves in some species but not others, why sons and daughters respond to parental signals in different ways, and why complex patterns of sex-specific TGP may often be non-adaptive.

evolutionary biology↗

bioRxiv2019

Long non-coding RNA Neat1 regulates adaptive behavioural response to stress in mice

AbstractNEAT1 is a highly and ubiquitously expressed long non-coding RNA (lncRNA) which serves as an important regulator of cellular stress response. However, the physiological role of NEAT1 in the central nervous system (CNS) is still poorly understood. In the current study, we addressed this by characterising the CNS function in the Neat1 knockout mouse model (Neat1-/- mice), using a combination of behavioural phenotyping, electrophysiology and expression analysis. RNAscope(R) in situ hybridisation revealed that in wild-type mice, Neat1 is expressed evenly across the CNS, with high expression in glial cells and low expression in neurons. Loss of Neat1 in mice results in an inadequate reaction to physiological stress manifested as hyperlocomotion and panic escape response. In addition, Neat1-/- mice display deficits in social interaction and rhythmic patterns of activity but retain normal motor function and memory. Neat1-/- mice do not present with neuronal loss, overt neuroinflammation or gross synaptic dysfunction in the brain. However, cultured Neat1-/- neurons are characterised by hyperexcitability and dysregulated calcium homeostasis, and stress-induced neuronal activity is also augmented in Neat1-/- mice in vivo. Gene expression analysis showed that Neat1 may act as a weak positive regulator of multiple genes in the brain. Furthermore, loss of Neat1 affects alternative splicing of genes important for the CNS function and implicated in neurological diseases. Overall, our data suggest that Neat1 is involved in stress signaling in the brain and fine-tunes the CNS functions to enable adaptive behaviour in response to physiological stress.

neuroscience↗

bioRxiv2019

Forced isoform switching of Neat1_1 to Neat1_2 leads to the hyperformation of paraspeckles but does not affect the development and growth of mice

Neat1 is a long noncoding RNA (lncRNA) that serves as an architectural component of the nuclear bodies known as paraspeckles. Two isoforms of Neat1, the short isoform Neat1_1 and the long isoform Neat1_2, are generated from the same gene locus by alternative 3 processing. Neat1_1 is the most abundant and the best conserved isoform expressed in various cell types, whereas Neat1_2 is expressed in a small population of particular cell types, including the tip cells of the intestinal epithelium. To investigate the physiological significance of isoform switching, we created mutant mice that solely expressed Neat1_2 by deleting the upstream polyadenylation (poly-A) signal (PAS) required for the production of Neat1_1. We observed the loss of Neat1_1 and strong upregulation of Neat1_2 in various tissues and cells and the subsequent hyperformation of paraspeckles, especially in cells that normally express Neat1_2. However, the mutant mice were born at the expected Mendelian ratios and did not exhibit obvious external and histological abnormalities. These observations suggested that the hyperformation of paraspeckles does not interfere with the development and growth of these animals under normal laboratory conditions.

molecular biology↗

bioRxiv2019

Efficient differentiation and polarization of primary cultured neurons on poly(lactic acid) scaffolds with microgrooved structures

Synthetic biodegradable polymers including poly(lactic acid) (PLA) are attractive cell culture substrates because their surfaces can be micropatterned to support cell adhesion. The cell adhesion properties of a scaffold mainly depend on its surface chemical and structural features; however, it remains unclear how these characteristics affect the growth and differentiation of cultured cells or their gene expression. In this study, we fabricated two differently structured PLA nanosheets: flat and microgrooved. We assessed the growth and differentiation of mouse primary cultured cortical neurons on these two types of nanosheets after pre-coating with poly-D-lysine and vitronectin. Interestingly, prominent neurite bundles were formed along the grooves on the microgrooved nanosheets, whereas thin and randomly extended neurites were only observed on the flat nanosheets. Comparative RNA sequencing analyses revealed that the expression of genes related to postsynaptic density, dendritic shafts, and asymmetric synapses was significantly and consistently up-regulated in cells cultured on the microgrooved nanosheets when compared with those cultured on the flat nanosheets. These results indicate that microgrooved PLA nanosheets can provide a powerful means of establishing a culture system for the efficient and reproducible differentiation of neurons, which will facilitate future investigations of the molecular mechanisms underlying the pathogenesis of neurological disorders.

molecular biology↗

bioRxiv2019

Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases

BackgroundNearly all molecular sequence databases currently use gzip for data compression. Ongoing rapid accumulation of stored data calls for more efficient compression tool. Although numerous compressors exist, both specialized and general-purpose, choosing one of them was difficult because no comprehensive analysis of their comparative advantages for sequence compression was available. FindingsWe systematically benchmarked 410 settings of 44 compressors (including 26 specialized sequence compressors and 18 general-purpose compressors) on representative FASTA-formatted datasets of DNA, RNA and protein sequences. Each compressor was evaluated on 17 performance measures, including compression strength, as well as time and memory required for compression and decompression. We used 25 test datasets including individual genomes of various sizes, DNA and RNA datasets, and standard protein datasets. We summarized the results as the Sequence Compression Benchmark database (SCB database, http://kirr.dyndns.org/sequence-compression-benchmark/) that allows building custom visualizations for selected subsets of benchmark results. ConclusionWe found that modern compressors offer large improvement in compactness and speed compared to gzip. Our benchmark allows comparing compressors and their settings using a variety of performance measures, offering the opportunity to select the optimal compressor based on the data type and usage scenario specific to particular application.

bioinformatics↗

bioRxiv2019

Comprehensive genomic analysis reveals dynamic evolution of mammalian transposable elements that code for viral-like protein domains

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of mammalian germline cells. A large proportion of ERVs lose their open reading frames (ORFs), while others retain them and become exapted by the host species. However, it remains unclear what proportion of ERVs possess ORFs (ERV-ORFs), become transcribed, and serve as candidates for co-opted genes. Hence, we investigated characteristics of 176,401 ERV-ORFs containing retroviral-like protein domains (gag, pro, pol, and env) in 19 mammalian genomes. The fractions of ERVs possessing ORFs were overall small ([~]0.15%) although they varied depending on domain types as well as species. The observed divergence of ERV-ORF from their consensus sequences suggested that a large proportion of ERV-ORFs either recently or anciently inserted themselves into mammalian genomes. Alternatively, very few ERVs lacking ORFs were found to exhibit similar divergence patterns. To identify ERV-ORFs transcribed as proteins, we compared ERV-ORFs with various multi-omics data including transcriptome data, trimethylation at histone H3 lysine 36, and transcription initiation sites from 2,834 cell types, and found 408 and 752 ERV-ORFs, accounting for 2-3% of all ERV-ORFs, with high transcriptional potential in humans and mice, respectively. Moreover, many of these ERV-ORFs with transcriptional potential were lineage-specific sequences exhibiting tissue-specific expression. These results suggest a possibility for the expression of uncharacterized functional genes containing ERV-ORFs hidden within mammalian genomes. Together, our analyses suggest that more ERV-ORFs may be co-opted in a host-species specific manner than we currently know, which are likely to have contributed to mammalian evolution and diversification.

genomics↗

bioRxiv2019

Mammalian NSUN2 introduces 5-methylcytidines into mitochondrial tRNAs

Post-transcriptional modifications in mitochondrial tRNAs (mt-tRNAs) play critical roles in mitochondrial protein synthesis, which produces respiratory chain complexes. In this study, we used mass spectrometric analysis to map 5-methylcytidine (m5C) at positions 48-50 in eight mouse and six human mt-tRNAs. We also confirmed the absence of m5C in mt-tRNAs isolated from Nsun2 knockout (KO) mice, as well as from NSUN2 KO human culture cells. In addition, we successfully reconstituted m5C at positions 48-50 of mt-tRNA in vitro with NSUN2 protein in the presence of S-adenosylmethionine (SAM). Although NSUN2 is predominantly localized to the nucleus and introduces m5C into cytoplasmic tRNAs and mRNAs, structured illumination microscopy (SIM) clearly revealed NSUN2 foci inside mitochondria. These observations provide novel insights into the role of NSUN2 in the physiology and pathology of mitochondrial functions.

molecular biology↗

bioRxiv2019

Meta-analysis reveals that the provision of multiple ecosystem services requires a diversity of land covers

Sustaining multiple ecosystem services across a landscape requires an understanding of how consistently services are shaped by different categories of land uses. Yet, this understanding is generally constrained by the availability of fine-resolution data for multiple services across large areas and the spatial variability of land-use effects on services. We systematically surveyed published literature for New Zealand (1970 - 2015) to quantify the supply of 17 services across 25 land covers (as a proxy for land use). We found a consistent trade-off in the services supplied by anthropogenic land covers with a high production intensity (e.g., cropping) versus those with extensive or no production. In contrast, forest cover was not associated with any distinct patterns of service supply. By drawing on existing research findings we reveal complementarity and redundancy (potentially influencing resilience) in service supply from different land covers. This can guide practitioners in shaping land systems that sustainably support human well-being.

ecology↗

bioRxiv2019

Pharmacological manipulations of judgement bias: a systematic review and meta-analysis

Validated measures of animal affect are crucial to research spanning a number of disciplines including neuroscience, psychopharmacology, and animal welfare science. Judgement bias, which assesses decision-making under ambiguity, is a promising measure of animal affect. One way of validating this measure is to induce affective states using pharmacological manipulations and determine whether the predicted judgement biases are observed. Here, we conducted a systematic review and meta-analysis using data from 19 published research articles that use this approach from which 440 effect sizes were extracted. The results of the meta-analysis suggest that pharmacological manipulations overall altered judgement bias as predicted. However, there were several moderating factors including the neurobiological target of the drug, whether the drug was hypothesised to induce a relatively positive or negative affective state, dosage, and the presented cue. This may partially reflect interference from adverse effects of the drug, such as sedation. Thus, while judgement bias can be used to measure pharmacologically-induced affective states, potential adverse effects of the drug should be considered when interpreting results.

animal behavior and cognition↗

bioRxiv2019

Ageing in house sparrows is insensitive to environmental effects

Variation in individual life histories, and physiology, determines the rates at which new life is generated (reproduction) and lost (death) in a population. Studying the demography of deaths thus reveals fundamental aspects of the biology of individuals within a population. We studied mortality senescence - the increase in mortality rate with age - in wild and captive house sparrows (Passer domesticus), and demonstrate highly similar mortality senescence in both, but markedly lower vulnerability to death (frailty) in captivity. This suggests that house sparrows have a species-specific rate of ageing that is insensitive to environmental effects. Unexpectedly, juvenile and adult mortality co-varied positively across years in the wild, indicating that mortality is not strongly density-dependent. Mortality also varied widely among years, suggesting a strong environmental effect, and we explain the observed patterns using temperature data and predation by birds of prey. We discuss how stochastic environmental effects can affect the evolution of ageing.

evolutionary biology↗

bioRxiv2019

The lncRNA NEAT1_1 is dispensable for normal tissue homeostasis and cancer cell growth

NEAT1 is one of the most studied lncRNAs, in part because its silencing in mice causes defects in mammary gland development and corpus luteum formation, and protects them from skin cancer development. Moreover, depleting NEAT1 in established cancer cell lines reduces growth and sensitizes cells to DNA damaging agents. However, NEAT1 produces two isoforms and because the short isoform, NEAT1_1, completely overlaps the 5 part of the long NEAT1_2 isoform, the respective contributions of each of the isoforms to these phenotypes has remained unclear. Whereas NEAT1_1 is highly expressed in most tissues, NEAT1_2 is the central architectural component of paraspeckles, which are nuclear bodies that assemble in specific tissues and cells exposed to various forms of stress. Using dual RNA-FISH to detect both NEAT1_1 outside of paraspeckles and NEAT1_2/NEAT1 inside this nuclear body, we report herein that NEAT1_1 levels are dynamically regulated during the cell cycle and targeted for degradation by the nuclear RNA exosome. Unexpectedly, however, cancer cells engineered to lack NEAT1_1, but not NEAT1_2, do not exhibit cell cycle defects. Moreover, Neat1_1-specific knockout mice do not exhibit the phenotypes observed in Neat1-deficient mice. We propose that NEAT1 functions are mainly, if not exclusively, attributable to NEAT1_2 and, by extension, to paraspeckles.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/574582_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (54K):\norg.highwire.dtl.DTLVardef@1ceaf78org.highwire.dtl.DTLVardef@6203b2org.highwire.dtl.DTLVardef@e0d5c9org.highwire.dtl.DTLVardef@f37f92_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

molecular biology↗

bioRxiv2019

No evidence for kin recognition in a passerine bird.

Theory predicts that individuals behave altruistically towards their relatives. Hence, some form of kin recognition is useful for individuals to optimize their behaviour. In species displaying bi-parental care and subject to extra-pair matings, kin recognition theoretically allows cuckolded fathers to reduce their parental investment, and thus optimize their fitness, but whether this is possible remains unclear in birds. This study investigates the ability of male sparrows to recognize their own chicks, using a large cross-foster experiment, parental care as an indicator and House Sparrows (Passer domesticus) as a model organism. We cross-fostered chicks after hatching, and then expected that fathers would show a decrease in their parental efforts when tending to a clutch of unrelated offspring. However, there was no significant effect of relatedness on provisioning rates. This suggests that sparrows may not be capable of kin recognition, or at least do not display kin discrimination despite its apparent evolutionary advantage.

animal behavior and cognition↗

bioRxiv2018

Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences

SummaryDNA sequence databases use compression such as gzip to reduce the required storage space and network transmission time. We describe Nucleotide Archival Format (NAF) - a new file format for lossless reference-free compression of FASTA and FASTQ-formatted nucleotide sequences. NAF compression ratio is comparable to the best DNA compressors, while providing dramatically faster decompression. We compared our format with DNA compressors: DELIMINATE and MFCompress, and with general purpose compressors: gzip, bzip2, xz, brotli, and zstd. AvailabilityNAF compressor and decompressor, as well as format specification are available at https://github.com/KirillKryukov/naf. Format specification is in public domain. Compressor and decompressor are open source under the zlib/libpng license, free for nearly any use. Contactkkryukov@gmail.com

bioinformatics↗

bioRxiv2018

Direct PCR amplification of 16S rRNA genes offers accelerated bacterial identification using the MinION™ nanopore sequencer

Rapid identification of bacterial pathogens is crucial for appropriate and adequate antibiotic treatment, which significantly improves patient outcomes. 16S ribosomal RNA (rRNA) gene amplicon sequencing has proven to be a powerful strategy for diagnosing bacterial infections. We have recently established a sequencing method and bioinformatics pipeline for 16S rRNA gene analysis utilizing the Oxford Nanopore Technologies MinION sequencer. In combination with our taxonomy annotation analysis pipeline, the system enabled the molecular detection of bacterial DNA in a reasonable timeframe for diagnostic purposes. However, purification of bacterial DNA from specimens remains a rate-limiting step in the workflow. To further accelerate the process of sample preparation, we adopted a direct PCR strategy that amplifies 16S rRNA genes from bacterial cell suspensions without DNA purification. Our results indicate that differences in cell wall morphology significantly affect direct PCR efficiency and sequencing data. Notably, mechanical cell disruption preceding direct PCR was indispensable for obtaining an accurate representation of the specimen bacterial composition. Furthermore, 16S rRNA gene analysis of mock polymicrobial samples indicated that primer sequence optimization is required to avoid preferential detection of particular taxa and to cover a broad range of bacterial species. This study establishes a relatively simple workflow for rapid bacterial identification via MinIONTM sequencing, which reduces the turnaround time from sample to result, and provides a reliable method that may be applicable to clinical settings.

microbiology↗

bioRxiv2018

UPA-Seq: Prediction of Functional LncRNAs Using Differential Sensitivity to UV Crosslinking

While a large number of long noncoding RNAs (lncRNAs) are transcribed from the genome of higher eukaryotes, systematic prediction of their functionality has been challenging due to the lack of conserved sequence motifs or structures. Assuming that lncRNAs function as large ribonucleoprotein complexes and thus are easily crosslinked to proteins upon UV irradiation, we performed RNA-Seq analyses of RNAs recovered from the aqueous phase after UV irradiation and phenol-chloroform extraction (UPA-Seq). As expected, the numbers of UPA-Seq reads mapped to known functional lncRNAs were remarkably reduced upon UV irradiation. Comparison with ENCODE eCLIP data revealed that lncRNAs that exhibited greater decreases upon UV irradiation preferentially associated with proteins containing prion-like domains (PrLDs). Fluorescent in situ hybridization (FISH) analyses revealed the nuclear localization of novel functional lncRNA candidates, including one that accumulated at the site of transcription. We propose that UPA-Seq provides a useful tool for the selection of lncRNA candidates to be analyzed in depth in subsequent functional studies.

molecular biology↗

bioRxiv2018

Alopecia areata susceptibility variant identified by MHC risk haplotype sequencing reproduces symptomatic patched hair loss in mice

BackgroundAlopecia areata (AA) is a highly heritable multifactorial and complex disease. However, no convincing susceptibility gene has yet been pinpointed in the major histocompatibility complex (MHC), a region in the human genome known to be associated with AA as compared to other regions.\n\nResultsBy sequencing MHC risk haplotypes, we identified a variant (rs142986308, p.Arg587Trp) in the coiled-coil alpha-helical rod protein 1 (CCHCR1) gene as the only non-synonymous variant in the AA risk haplotype. Using CRISPR/Cas9 for allele-specific genome editing, we then phenocopied AA symptomatic patched hair loss in mice engineered to carry the Cchcr1 risk allele. Skin biopsies of these alopecic mice showed strong up-regulation of hair-related genes, including hair keratin and keratin-associated proteins (KRTAPs). Using transcriptomics findings, we further identified CCHCR1 as a novel component of hair shafts and cuticles in areas where the engineered alopecic mice displayed fragile and impaired hair.\n\nConclusionsThese results suggest an alternative mechanism for the aetiology of AA based on aberrant keratinization, in addition to generally well-known autoimmune events.

genomics↗