Biology subjects

Yamada, Y.

Publications and source records attributed to Yamada, Y..

48 records · Page 3Linked to original sources

bioRxiv2020

MS-DIAL 4: accelerating lipidomics using an MS/MS, CCS, and retention time atlas

To the EditorWe formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry (MS/MS) to provide a comprehensive lipidome atlas with retention time, collision cross section, and MS/MS information. The all-in-one solution from import of raw MS data to export of a common output format (mztab-M) was packaged in MS-DIAL 4 (http://prime.psc.riken.jp/) providing an enhanced standardized untargeted lipidomics procedure following lipidomics standards initiative (LSI) semi-quantitative definitions and shorthand notation system of lipid structures with a 1-2% estimated false discovery rate, which will contribute to harmonizing lipidomics data across laboratories to accelerate lipids research.

bioinformatics↗

bioRxiv2019

Self-body recognition through a mirror: Easing spatial-consistency requirements for rubber hand illusion

Typical experiments to induce the rubber hand illusion (RHI) require experimental participants to gaze at a fake hand while tactile stimuli are provided to both the fake and hidden actual hands in a synchronous manner. However, under such conditions, postural and apparent disagreement between a seen fake hand and hidden actual hand prevents illusory body ownership. Provided that humans recognize mirror images as copies of the real world in spite of their spatial uncertainties or incongruence, the sensory disagreement may be accepted in RHI settings if using a mirror to show a fake hand. The present study performed two experiments to reveal how self-body recognition of a fake hand feature via mirror affects the RHI. These experiments were conducted in an RHI environment involving voluntary hand movements to investigate not only body ownership but also agency. The first experiment (Experiment 1) examined whether illusory ownership of a fake hand seen in a mirror could be induced. Then, we examined whether the RHI using a mirror image allows disagreement in orientation between the rubber and actual hands (Experiment 2). Subjective evaluations using a RHI questionnaire demonstrated that evoked embodiment of the rubber hand was stronger in the presence of a mirror than in the absence of it (Experiment 1) and that participants experienced the RHI even if the actual and rubber hands were incongruent in terms of orientation (45 {degrees}; Experiment 2). No significant difference was found in the change of perceived finger location (proprioceptive drift) between these experiments. These findings suggest that the use of a mirror masks subtle spatial incongruency or degrades the contribution of visual cues for spatial recognition and facilitates multisensory integration for bodily illusions.

neuroscience↗

bioRxiv2019

Generation of human hepatic progenitor cells with regenerative and metabolic capacities from primary hepatocytes

Hepatocytes are regarded as the only effective cell source for cell transplantation to treat liver diseases; however, their availability is limited due to a donor shortage. Thus, a novel cell source must be developed. We recently reported that mature rodent hepatocytes can be reprogrammed into progenitor-like cells with a repopulative capacity using small molecule inhibitors. Here, we demonstrate that hepatic progenitor cells can be obtained from human infant hepatocytes using the same strategy. These cells, named human chemically induced liver progenitors (hCLiPs), had a significant repopulative capacity in injured mouse livers following transplantation. hCLiPs redifferentiated into mature hepatocytes in vitro upon treatment with hepatic maturation-inducing factors. These redifferentiated cells exhibited cytochrome P450 (CYP) enzymatic activities in response to CYP-inducing molecules and these activities were comparable with those in primary human hepatocytes. These findings will facilitate liver cell transplantation therapy and drug discovery studies.

cell biology↗

bioRxiv2019

Jomon genome sheds light on East Asian population history

Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

genomics↗

bioRxiv2019

Relationship between ocean area and incidence of anthropogenic debris ingested by longnose lancetfish (Alepisaurus ferox)

Longnose lancetfish (Alepisaurus ferox) may has been studied as an indicator of marine pollution caused by marine litter. The objectives of this study were to determine the difference in frequency of occurrence of plastics ingested by longnose lancetfish in different ocean area. In this study, we compared the incidence and characteristics of anthropogenic debris in the stomachs of longnose lancetfish. We examined 91 longnose lancetfish caught by pelagic longline fishing in Sagami Bay, the North Pacific Ocean, approximately 200 km south of Shikoku, and in the Indian Ocean. Broken down by ocean area, the incidence of anthropogenic debris ingestion was highest in Sagami Bay (23 of 34 specimens, 68%), followed by the North Pacific Ocean (1 of 9, 11%), and the Indian Ocean (8 of 48, 17%). The frequency of occurrence increased in area close to the sphere of human habitation. The anthropogenic debris collected in this study were more than 70% classified as plastic sheeting. Stomach content analysis revealed that more than 90% of the plastic fragments were composed of PP and PE, which have specific gravities that are less than that of seawater. The results of this study show that some of the plastics flowing from the land into the sea are spreading through under the water surface of the ocean.

ecology↗

bioRxiv2018

Development of oocytes in a post-spawning Japanese eel Anguilla japonica Temminck & Schlegel in captivity

It is generally believed that parent freshwater eels (Anguilla sp.) die soon after spawning on the assumption that eels are a semelparous (or monocyclic) fish (spawn once at the last stage of life) like Pacific salmonids. However, we observed for the first time a post-spawning female Anguilla japonica again possessed developing oocytes reaching the final maturation stage in captivity five months after the last spawning even without hormonal treatment. Here we describe information on this female about its biological characteristics including gonadal histology and endocrine profiles. The data suggest that lowering water temperature for a period of time is one of the important factors influencing spontaneous gonadal development in this specimen. We also discuss the possibility of induced multiple spawning of this species in captivity.

zoology↗

bioRxiv2018

Adenosine Deaminase Acting on RNA 1 Associates with Orf Virus OV20.0 and Enhances Viral Replication

Orf virus (ORFV) infects sheep and goats and is also an important zoonotic pathogen. The viral protein OV20.0 has been shown to suppress innate immunity by targeting the double-stranded RNA (dsRNA)-activated protein kinase (PKR) by multiple mechanisms. These mechanisms include a direct interaction with PKR and binding with two PKR activators, dsRNA and the cellular PKR activator (PACT), which ultimately leads to the inhibition of PKR activation. In the present study, we identified a novel association between OV20.0 and adenosine deaminase acting on RNA 1 (ADAR1). OV20.0 bound directly to the dsRNA binding domains (RBDs) of ADAR1 in the absence of dsRNA. Additionally, OV20.0 preferentially interacted with RBD1 of ADAR1, which was essential for its dsRNA binding ability and for the homodimerization that is critical for intact adenosine (A)-to-inosine (I) editing activity. Finally, the association with OV20.0 suppressed the A-to-I editing ability of ADAR1, while ADAR1 played a proviral role during ORFV infection by inhibiting PKR phosphorylation. These observations revealed a new strategy used by OV20.0 to evade antiviral responses via PKR.\n\nImportanceViruses evolve specific strategies to counteract host innate immunity. ORFV, an important zoonotic pathogen, encodes OV20.0 to suppress PKR activation via multiple mechanisms, including interactions with PKR and two PKR activators. In this study, we demonstrated that OV20.0 interacts with ADAR1, a cellular enzyme responsible for converting adenosine (A) to inosine (I) in RNA. The RNA binding domains, but not the catalytic domain, of ADAR1 are required for this interaction. The OV20.0-ADAR1 association affects the functions of both proteins; OV20.0 suppressed the A-to-I editing of ADAR1, while ADAR1 elevated OV20.0 expression. The proviral role of ADAR1 is likely due to the inhibition of PKR phosphorylation. As RNA editing by ADAR1 contributes to the stability of the genetic code and the structure of RNA, these observations suggest that in addition to serving as a PKR inhibitor, OV20.0 might modulate ADAR1-dependent gene expression to combat antiviral responses or achieve efficient viral infection.

microbiology↗

bioRxiv2018

Suppressor analysis uncovers that MAPs and microtubule dynamics balance with the Cut7/Kinesin-5 motor for mitotic spindle assembly in Schizosaccharomyces pombe

The Kinesin-5 motor Cut7 in Schizosaccharomyces pombe plays essential roles in spindle pole separation, leading to the assembly of bipolar spindle. In many organisms, simultaneous inactivation of Kinesin-14s neutralizes Kinesin-5 deficiency. To uncover the molecular network that counteracts Kinesin-5, we have conducted a genetic screening for suppressors that rescue the cut7-22 temperature sensitive mutation, and identified 10 loci. Next generation sequencing analysis reveals that causative mutations are mapped in genes encoding -, {beta}-tubulins and the microtubule plus-end tracking protein Mal3/EB1, in addition to the components of the Pkl1/Kinesin-14 complex. Moreover, the deletion of various genes required for microtubule nucleation/polymerization also suppresses the cut7 mutant. Intriguingly, Klp2/Kinesin-14 levels on the spindles are significantly increased in cut7 mutants, whereas these increases are negated by suppressors, which may explain the suppression by these mutations/deletions. Consistent with this notion, mild overproduction of Klp2 confers temperature sensitivity. Surprisingly, treatment with a microtubule-destabilizing drug not only suppresses cut7 temperature sensitivity but also rescues the lethality resulting from the deletion of cut7, though a single klp2 deletion per se cannot compensate for the loss of Cut7. We propose that microtubule assembly and/or dynamics antagonize Cut7 functions, and that the orchestration between these two factors is crucial for bipolar spindle assembly.

genetics↗

bioRxiv2017

Two spatially distinct Kinesin-14 Pkl1 and Klp2 generate collaborative inward forces against Kinesin-5 Cut7 in S. pombe

Kinesin motors play central roles in bipolar spindle assembly. In many eukaryotes, spindle pole separation is driven by Kinesin-5 that generates outward force. This outward force is balanced by antagonistic inward force elicited by Kinesin-14 and/or Dynein. In fission yeast, two Kinesin-14s, Pkl1 and Klp2, play an opposing role against Kinesin-5/Cut7. However, how these two Kinesin-14s coordinate individual activities remains elusive. Here we show that while deletion of either pkl1 or klp2 rescues temperature sensitive cut7 mutants, only pkl1 deletion can bypass the lethality caused by cut7 deletion. Pkl1 is tethered to the spindle pole body, while Klp2 is localized along the spindle microtubule. Forced targeting of Klp2 to the spindle pole body, however, compensates for Pkl1 functions, indicating that cellular localizations, rather than individual motor specificities, differentiate between the two Kinesin-14s. Interestingly, human Kinesin-14/HSET can replace either Pkl1 or Klp2. Moreover, overproducing HSET induces monopolar spindles, reminiscent of the phenotype of Cut7 inactivation. Taken together, this study has uncovered the biological mechanism of how two different Kinesin-14s exert their antagonistic roles against Kinesin-5 in a spatially distinct manner.\n\nSUMMARY STATEMENTProper force-balance generated by Kinesin-5 and Kinesin-14 is crucial for spindle bipolarity. Two fission yeast Kinesin-14s localize to different structures, thereby collaboratively producing inward forces against Kinesin-5-mediated outward force.\n\nAbbreviations used

cell biology↗

bioRxiv2017

Experience-dependent modulation of behavioral features in sensory navigation of nematodes and bats revealed by machine learning

Animal behavior is the final and integrated output of the brain activity. Thus, recording and analyzing behavior is critical to understand the underlying brain function. While recording animal behavior has become easier than ever with the development of compact and inexpensive devices, detailed behavioral data analysis requires sufficient previous knowledge and/or high content data such as video images of animal postures, which makes it difficult for most of the animal behavioral data to be efficiently analyzed to understand brain function. Here, we report a versatile method using a hybrid supervised/unsupervised machine learning approach to efficiently estimate behavioral states and to extract important behavioral features only from low-content animal trajectory data. As proof of principle experiments, we analyzed trajectory data of worms, fruit flies, rats, and bats in the laboratories, and penguins and flying seabirds in the wild, which were recorded with various methods and span a wide range of spatiotemporal scales--from mm to 1000 km in space and from sub-seconds to days in time. We estimated several states during behavior and comprehensively extracted characteristic features from a behavioral state and/or a specific experimental condition. Physiological and genetic experiments in worms revealed that the extracted behavioral features reflected specific neural or gene activities. Thus, our method provides a versatile and unbiased way to extract behavioral features from simple trajectory data to understand brain function.

neuroscience↗

bioRxiv2017

Sequential interactions with Mre11-Rad50-Nbs1 activate ATM/Tel1 at DNA double-strand breaks and telomeres

The Mre11-Rad50-Nbs1 (MRN) protein complex, CtIP/Ctp1/Sae2 and ATM/Tel1 kinase protect genome integrity through their functions in DNA double-strand break (DSB) repair, checkpoint signaling, and telomere maintenance. Nbs1 has a conserved C-terminal motif that binds ATM, but the full extent of ATM interactions with MRN are unknown. Here, we show that Tel1 overexpression in Schizosaccharomyces pombe restores Tel1 activity at DSBs and telomeres in the absence of Nbs1. This activity requires Mre11, indicating that Tel1 overexpression drives low affinity binding to the Mre11-Rad50 subcomplex. Mre11-Rad50 binds DSBs in nbs1{Delta} cells, and fusing the Tel1-binding motif of Nbs1 to Mre11 fully restores Tel1 signaling in these cells. Tel1 overexpression does not restore Tel1 signaling in cells carrying the rad50-I1192W mutation, which impairs the ability of Mre11-Rad50 to form the ATP-bound closed conformation. From these findings, we propose that Tel1 activation at DNA ends proceeds by a sequential mechanism initiated by high affinity binding to Nbs1 which recruits Tel1, followed by a low affinity interaction with Mre11-Rad50 in the closed conformation to activate Tel1.

cell biology↗

bioRxiv2017

Serial Crystallography with Multi-stage Merging of 1000’s of Images

KAMO and Blend provide particularly effective tools to manage automatically the merging of large numbers of datasets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending Blend to support additional clustering options such as use of more accurate cell distance metrics and use of reflection-intensity correlation coefficients to infer "distances" among sets of reflec- tions. This increases the sensitivity to differences in unit cell parameters and allows for clustering to assemble nearly complete datasets on the basis of intensity or ampli- tude differences. If datasets are already sufficiently complete to permit it, one applies KAMO once and clusters the data using intensities only. If starting from incomplete datasets, one applies KAMO twice, first using cell parameters. In this step we use either the simple cell vector distance of the original Blend, or we use the more sensi- tive NCDist. This step tends to find clusters of sufficient size so that, when merged, each cluster is sufficiently complete to allow reflection intensities or amplitudes to be compared. One then uses KAMO again using the correlation between the reflections having a common hkl to merge clusters in a way sensitive to structural differences that may not have perturbed the cell parameters sufficiently to make meaningful clusters. Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into cate- gories which then can be merged, one hopes, to yield the electron density from a single protein form. Since these physical parameters are often largely independent from one another, it should be possible to greatly improve the efficacy of data clustering software by using a multi-stage partitioning strategy. Here, we have demonstrated one possible approach to multi-stage data clustering. Our strategy is to use unit-cell clustering until merged data is sufficiently complete then to use intensity-based clustering. We have demonstrated that, using this strategy, we are able to accurately cluster datasets from crystals that have subtle differences.

bioinformatics↗