Biology subjects

Seki, K.

Publications and source records attributed to Seki, K..

27 records · Page 2Linked to original sources

bioRxiv2023

LsTT2 encoding R2R3-MYB transcription factor is responsible for a shift from black to white in lettuce seed

Prickly lettuce (Lactuca serriola), which is considered the wild ancestor of lettuce, has black seeds, whereas the major seed color of domesticated lettuce is black or white. The successfully-selected white seed trait is a key domestication trait for lettuce cultivation and breeding; however, the mechanism underlying the shift from black to white seeds remains to be clarified. We aimed to identify the gene/s responsible for white seed trait in lettuce. Genetic mapping of a candidate gene was performed with double-digest RAD sequencing using an F2 population derived from a cross between ShinanoPower (white seed) and Escort (black seed). The white seed trait was controlled by a single recessive locus (48.055-50.197 Mbp) in linkage group 7. Narrowing down using five PCR-based markers and 84 cultivars, eight candidate genes were mapped in the locus. Only the LG7_v8_49.251Mbp_HinfI marker, which employs a single nucleotide mutation in the stop codon of Lsat_1_v5_gn_7_35020.1 was completely linked to the seed color phenotype. In addition, the sequences of the coding region for candidate genes except for Lsat_1_v5_gn_7_35020.1 were identical in the resequence analysis of ShinanoPower (white seed) and Escort (black seed). Therefore, we proposed Lsat_1_v5_gn_7_35020.1, a gene located in the locus, as the candidate gene and designated it as LsTT2, an ortholog encoding the R2R3 MYB transcription factor in Arabidopsis. When we validated the role of LsTT2 in seed color through genome editing, LsTT2 knockout mutants harboring an early termination codon showed a change in seed color from black to white. White seeds accumulated less proanthocyanidins than black seeds, which was similar to the phenotype observed in Arabidopsis TRANSPARENT TESTA 2 (TT2) mutants. Therefore, LsTT2 was the allele responsible for the shift in seed color from black to white. The development of a robust marker for marker-assisted selection and identification of the gene responsible for white seeds has implications for future breeding technology and physiological analysis.

genetics↗

bioRxiv2023

Modulation of somatosensory signal transmission in the primate cuneate nucleus during voluntary hand movement

Successful extraction of tactile and kinematic information is crucial for appropriate motor actions in daily life. To achieve this objective, sensory signals should be effectively regulated during motor actions. This regulation is understood both empirically and conceptually, but it is not well known where and how it is implemented in the central nervous system. Here, we show that, during voluntary movement, sensory signals are already attenuated in the primate cuneate nucleus, an early processing site in the ascending lemniscus pathway. The degree of suppression was comparable with the one reported in the cortex, suggesting that psychological attenuation of somatosensation could be ascribed to the cuneate. The results also revealed that this sensory attenuation was of descending origin, suggesting that cortical sensory prediction signals could regulate cuneate sensory transmission for extracting meaningful, and attenuate unnecessary, signals for movement regulation. This recurrent sensory modulation mechanism between cortical and subcortical areas may generalize to other sensory modalities and cognitive processes.

neuroscience↗

bioRxiv2022

Orthogonal tRNA Expression using Endogenous Machinery in Cell-Free Systems

A wide variety of non-canonical amino acids (ncAAs) can be incorporated into proteins through the coordinated action of a stop codon suppressing tRNA and aminoacyl-tRNA synthetase. However, methods to discover and characterize suppressor tRNAs are generally lacking. In this work, we show that cell-free systems can express functional suppressor tRNAs using endogenous machinery and characterize their activity. This method is compatible with widely used orthogonal tRNAs, such as the Methanocaldococus jannaschii tyrosyl tRNA, the Methanosarcina barkeri pyrrolysyl tRNA, the Methanomethylophilus Alvus pyrrolysyl tRNA, and an engineered Int pyrroysyl tRNA. Modifying the workflow to evaluate TAA suppression revealed that the M. jannaschii and M. alvus are highly functional TAA suppressors in cell-free systems. Finally, we show that we can express two distinct tRNAs simultaneously, enabling the incorporation of multiple, distinct ncAAs. In total, our work shows that cell-free systems are useful platforms to express and characterize tRNAs.

synthetic biology↗

bioRxiv2022

QTL mapping for seed morphology using the instance segmentation neural network in Lactuca spp.

Wild species of lettuce (Lactuca sp.) are thought to have first been domesticated for oilseed contents to provide seed oil for human consumption. Although seed morphology is an important trait contributing to oilseed in lettuce, the underlying genetic mechanisms remain elusive. Since lettuce seeds are small, a manual phenotypic determination required for a genetic dissection of such traits is challenging. In this study, we built and applied an instance segmentation-based seed morphology quantification pipeline to measure traits in seeds generated from a cross between the domesticated oilseed type cultivar Oilseed and the wild species UenoyamaMaruba in an automated manner. Quantitative trait locus (QTL) mapping following ddRAD-seq revealed 11 QTLs linked to 7 seed traits (area, width, length, length-to-width ratio, eccentricity, perimeter length, and circularity). Remarkably, the three QTLs with the highest LOD scores, qLWR-3.1, qECC-3.1, and qCIR-3.1, for length-to-width ratio, eccentricity, and circularity, respectively, mapped to linkage group 3 (LG3) around 161.5 to 214.6 Mb, a region previously reported to be associated with domestication traits from wild species. These results suggest that the oilseed cultivar harbors genes acquired during domestication to control seed shape in this genomic region. This study also provides genetic evidence that domestication arose, at least in part, by selection for the oilseed type from wild species and demonstrates the effectiveness of image-based phenotyping to accelerate discoveries of the genetic basis for small morphological features such as seed size and shape.

plant biology↗

bioRxiv2021

Improving genomically recoded Escherichia coli for the production of proteins containing non-canonical amino acids

A genomically recoded Escherichia coli strain that lacks all amber codons and release factor 1 (C321.{Delta}A) enables efficient genetic encoding of chemically diverse, non-canonical amino acids (ncAAs) into proteins. While C321.{Delta}A has opened new opportunities in chemical and synthetic biology, this strain has not been optimized for protein production, limiting its utility in widespread industrial and academic applications. To address this limitation, we describe the construction of a series of genomically recoded organisms that are optimized for cellular protein production. We demonstrate that the functional deactivation of nucleases (e.g., rne, endA) and proteases (e.g., lon) increases production of wild-type superfolder green fluorescent protein (sfGFP) and sfGFP containing two ncAAs up to [~]5-fold. Additionally, we introduce a genomic IPTG-inducible T7 RNA polymerase (T7RNAP) cassette into these strains. Using an optimized platform, we demonstrated the ability to introduce 2 identical N6-(propargyloxycarbonyl)-L-Lysine residues site specifically into sfGFP with a 17-fold improvement in production relative to the parent. We envision that our library of organisms will provide the community with multiple options for increased expression of proteins with new and diverse chemistries.

synthetic biology↗

bioRxiv2021

Comparison of subjective peripheral sensation, F-waves, and somatosensory evoked potentials in response to a unilateral pinch task measured on the contractile and non-contractile sides

Depression of sensory input during voluntary muscle contractions has been demonstrated using electrophysiological methods in both animals and humans. However, the association between electrophysiological responses of the sensory system and subjective peripheral sensation (SPS) during a voluntary muscle contraction remains unclear. Our aim in this study was to describe the changes in SPS, spinal -motoneuron excitability (F-wave to M-wave amplitude), and somatosensory evoked potentials (SEPs) during a unilateral pinch-grip task. Outcome variables were measured on the side ipsilateral and contralateral to the muscle contraction, and at rest (control). Participants were 8 healthy men, 20.9{+/-}0.8 years of age. The isometric pinch-grip task was performed at 30% of the maximum voluntary isometric force measured for the right and left hand separately. The appearance rate of the F-wave during the task was significantly higher for the ipsilateral (right) hand than for the contralateral (left) hand and control condition. Although there was no difference in F-wave latency between hands and the control condition, the amplitude of the F-wave was significantly higher for the ipsilateral (right) hand than for the contralateral (left) hand and the control condition. There was no difference in the amplitude of the SEP at N20. However, the amplitude at P25 was significantly lower for the ipsilateral (right) hand than for the contralateral (left) hand and the control condition. The accuracy rate of detecting tactile stimulation, evaluated for 20 repetitions using a Semmes-Weinstein monofilament at the sensory threshold for each participant, was significantly lower during the pinch-grip task for both the ipsilateral (right) and contralateral (left) hand compared to the control condition. Overall, our findings show that SPS and neurophysiological parameters were not modulated in parallel during the task, with changes in subjective sensation preceding changes in electrophysiological indices during the motor task. Our findings provide basic information on sensory-motor coordination.

neuroscience↗

bioRxiv2019

PATTIE: Publication access through tiered interaction & exploration

In this work we present Publication Access Through Tiered Interaction & Exploration (PATTIE) - an information foraging, sense-making, and exploratory spatial-semantic information retrieval (IR) system (http://pattie.unc.edu/plos). Non-spatial, spatial IR systems, and some recent studies focused on their principal functions are discussed and compared. To interactively work through a use-case from the biomedical domain, instructions are provided for readers to conduct exploratory searches directly on the PLOS archive based on the software embedded in the online version of this paper (http://vzlib.unc.edu/software/). To carefully evaluate some of the critical parameters of the PATTIE algorithm, and the core functions of the implemented system, a set of experiments were conducted. Along with details on the experimental methods and their rationale, key findings from the experiments are analyzed and presented. Finally, with an eye toward the future of software-embedded scientific papers, their potential benefits for supporting direct engagement with scientific content, replication, and validation are discussed.

scientific communication and education↗

bioRxiv2019

Distinct sensorimotor feedback loops for dynamic and static control of primate precision grip

Volitional limb motor control involves dynamic and static muscle actions. It remains elusive how such distinct actions are controlled through separated or shared neural circuits. Here we explored the potential separation for dynamic and static controls in the primate hand actions, by investigating the neuronal coherence between local 1eld potentials (LFPs) of the spinal cord and the forelimb electromyographic activity (EMGs), and LFPs of the motor cortex and the EMGs during the performance of a precision grip in macaque monkeys. We observed the emergence of beta-range coherence with EMGs at spinal cord and motor cortex in the separated phases; spinal coherence during the grip phase and cortical coherence during the hold phase. Further, both of the coherence were influenced by bidirectional interactions with reasonable latencies as beta oscillatory cycles. These results indicate that dedicated feedback circuits comprising spinal and cortical structures underlie dynamic and static controls of dexterous hand actions.

neuroscience↗

bioRxiv2018

Two distinct proprioceptive representations of voluntary movements in primate spinal neurons

When willingly setting our body in motion, we simultaneously know where and how our limbs are moving. While this indicates that proprioceptive information is readily represented in the neurons of the central nervous system, it is still unclear how. We recorded the activity of spinal neurons with direct projections from muscle spindle afferents in four monkeys, while they performed simple wrist movements. Against the assumption that these spinal neurons act as a simple relay of afferent input, we found the majority (56%) of neurons had firing patterns incongruent with a simple representation of spindle activity, and the minority had congruent patterns. Two groups of neurons showed distinct intrinsic characteristics (spike width, base firing rate and firing irregularity), and distinct control of their input-output gain. These results are the first demonstration that proprioceptive representation is achieved by the coordinated activity of distinct groups of neurons during volitional movement.

neuroscience↗