Comparison of the effects of perfluoroalkyl and alkyl groups on cellular uptake in short peptides.

The differences in the effects of perfluoroalkyl (R) and alkyl (R) groups on the cellular uptake of short peptides were evaluated. A facile synthetic method was established to produce Fmoc-protected amino acids bearing R and R groups on their side chains. The synthesized Fmoc-protected amino acids were successfully incorporated into peptides using solid-phase peptide synthesis.

MBCdeg4: A modified clustering-based method for identifying differentially expressed genes from RNA-seq data.

RNA-seq is a commonly employed methodology for the measurement of transcriptomes, particularly for the identification of differentially expressed genes (DEGs) between different conditions or groups. In a previous report, we described a clustering-based method for identifying DEGs, designated MBCdeg1 and MBCdeg2. and a modified version, MBCdeg3.

Enhanced clustering-based differential expression analysis method for RNA-seq data.

RNA-seq is a tool for measuring gene expression and is commonly used to identify differentially expressed genes (DEGs). Gene clustering has been widely used to classify DEGs with similar expression patterns, but rarely used to identify DEGs themselves. We recently reported that the clustering-based method (called MBCdeg1 and 2) for identifying DEGs has great potential.

Synthesis of Short Peptides with Perfluoroalkyl Side Chains and Evaluation of Their Cellular Uptake Efficiency.

With an increasing demand for macromolecular biotherapeutics, the issue of their poor cell-penetrating abilities requires viable and relevant solutions. Herein, we report tripeptides bearing an amino acid with a perfluoroalkyl (R ) group adjacent to the α-carbon. R -containing tripeptides were synthesized and evaluated for their ability to transport a conjugated hydrophilic dye (Alexa Fluor 647) into the cells.

Spatial Accuracy of Predictive Saccades Determines the Performance of Continuous Visuomotor Action.

In a table tennis rally, players perform interceptive actions on a moving ball continuously in a short time, such that the acquisition process of visual information is an important determinant of the performance of the action. However, because it is technically hard to measure gaze movement in a real game, little is known about how gaze behavior is conducted during the continuous visuomotor actions and contributes to the performance. To examine these points, we constructed a novel psychophysical experiment model enabling a continuous visuomotor task without spatial movement of any body parts, including the arm and head, and recorded the movement of the gaze and effector simultaneously at high spatiotemporal resolution.

Differential expression analysis using a model-based gene clustering algorithm for RNA-seq data.

Background: RNA-seq is a tool for measuring gene expression and is commonly used to identify differentially expressed genes (DEGs). Gene clustering is used to classify DEGs with similar expression patterns for the subsequent analyses of data from experiments such as time-courses or multi-group comparisons. However, gene clustering has rarely been used for analyzing simple two-group data or differential expression (DE).

Effects of Daily Hand Activities on Age-Related Declines of Dynamic Motor Function in Individual Fingers.

The present study examined the effects of daily activities of the hands on finger motor function in older adults. Maximum tapping frequency with each finger during single-finger tapping and alternate movements of index-middle, middle-ring, and ring-little finger pairs during double-finger tapping were compared between older adults who used their hands actively in their daily lives and those who did not. The active participants had significantly faster tapping rates for the ring finger in the single-finger tapping and the middle-ring finger pair in the double-finger tapping than did the inactive participants.

Gene regulatory network and its constituent transcription factors that control nitrogen-deficiency responses in rice.

Increase in the nitrogen (N)-use efficiency and optimization of N response in crop species are urgently needed. Although transcription factor-based genetic engineering is a promising approach for achieving these goals, transcription factors that play key roles in the response to N deficiency have not been studied extensively. Here, we performed RNA-seq analysis of root samples of 20 Asian rice (Oryza sativa) accessions with differential nutrient uptake.

Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data.

Empirical Bayes is a choice framework for differential expression (DE) analysis for multi-group RNA-seq count data. Its characteristic ability to compute posterior probabilities for predefined expression patterns allows users to assign the pattern with the highest value to the gene under consideration. However, current Bayesian methods such as baySeq and EBSeq can be improved, especially with respect to normalization.

TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data.

Objective: Differential expression (DE) is a fundamental step in the analysis of RNA-Seq count data. We had previously developed an R/Bioconductor package (called TCC) for this purpose. While this package has the unique feature of an in-built robust normalization method, its use has so far been limited to R users only.

Rhinoceros beetle horn development reveals deep parallels with dung beetles.

Beetle horns are attractive models for studying the evolution of novel traits, as they display diverse shapes, sizes, and numbers among closely related species within the family Scarabaeidae. Horns radiated prolifically and independently in two distant subfamilies of scarabs, the dung beetles (Scarabaeinae), and the rhinoceros beetles (Dynastinae). However, current knowledge of the mechanisms underlying horn diversification remains limited to a single genus of dung beetles, Onthophagus.

Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results.

Background: Hierarchical Sample clustering (HSC) is widely performed to examine associations within expression data obtained from microarrays and RNA sequencing (RNA-seq). Researchers have investigated the HSC results with several possible criteria for grouping (e.g.

Finger forces in fastball baseball pitching.

Forces imparted by the fingers onto a baseball are the final, critical aspects for pitching, however these forces have not been quantified previously as no biomechanical technology was available. In this study, an instrumented baseball was developed for direct measurement of ball reaction force by individual fingers and used to provide fundamental information on the forces during a fastball pitch. A tri-axial force transducer with a cable having an easily-detachable connector were installed in an official baseball.

Comparative analysis of the brain transcriptome in a hyper-aggressive fruit fly, Drosophila prolongata.

Aggressive behavior is observed in many animals, but its intensity differs between species. In a model animal of genetics, Drosophila melanogaster, genetic basis of aggressive behavior has been studied intensively, including transcriptome analyses to identify genes whose expression level was associated with intra-species variation in aggressiveness. However, whether these genes are also involved in the evolution of aggressiveness among different species has not been examined.

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data.

Background: RNA-seq is a powerful tool for measuring transcriptomes, especially for identifying differentially expressed genes or transcripts (DEGs) between sample groups. A number of methods have been developed for this task, and several evaluation studies have also been reported. However, those evaluations so far have been restricted to two-group comparisons.

The impact of aging on the spatial accuracy of quick corrective arm movements in response to sudden target displacement during reaching.

Age-related declines in visuomotor processing speed can have a large impact on motor performance in elderly individuals. Contrary to previous findings, however, recent studies revealed that elderly individuals are able to quickly react to displacement of a visual target during reaching. Here, we investigated the influence of aging on quick, corrective responses to perturbations during reaching in the terms of their functional contribution to accuracy.

Control of Precision Grip Force in Lifting and Holding of Low-Mass Objects.

Few studies have investigated the control of grip force when manipulating an object with an extremely small mass using a precision grip, although some related information has been provided by studies conducted in an unusual microgravity environment. Grip-load force coordination was examined while healthy adults (N = 17) held a moveable instrumented apparatus with its mass changed between 6 g and 200 g in 14 steps, with its grip surface set as either sandpaper or rayon. Additional measurements of grip-force-dependent finger-surface contact area and finger skin indentation, as well as a test of weight discrimination, were also performed.

Impact of denervation-induced muscle atrophy on housekeeping gene expression in mice.

Introduction: Immobilization induced by experimental denervation leads to rapid and progressive alterations in structural and biochemical properties of skeletal muscle. Real-time reverse transcription-polymerase chain reaction (RT-PCR) is a popular method of elucidating the molecular mechanisms involved in muscle atrophy. Identification of suitable reference genes that are not affected by experimental conditions is a critical step in accurate normalization of real-time RT-PCR.

Two types of motor strategy for accurate dart throwing.

This study investigated whether expert dart players utilize hand trajectory patterns that can compensate for the inherent variability in their release timing. In this study, we compared the timing error and hand trajectory patterns of expert players with those of novices. Eight experts and eight novices each made 60 dart throws, aiming at the bull's-eye.

Joint action syntax in Japanese martial arts.

Participation in interpersonal competitions, such as fencing or Japanese martial arts, requires players to make instantaneous decisions and execute appropriate motor behaviors in response to various situations. Such actions can be understood as complex phenomena emerging from simple principles. We examined the intentional switching dynamics associated with continuous movement during interpersonal competition in terms of their emergence from a simple syntax.

TCC: an R package for comparing tag count data with robust normalization strategies.

Background: Differential expression analysis based on "next-generation" sequencing technologies is a fundamental means of studying RNA expression. We recently developed a multi-step normalization method (called TbT) for two-group RNA-seq data with replicates and demonstrated that the statistical methods available in four R packages (edgeR, DESeq, baySeq, and NBPSeq) together with TbT can produce a well-ranked gene list in which true differentially expressed genes (DEGs) are top-ranked and non-DEGs are bottom ranked. However, the advantages of the current TbT method come at the cost of a huge computation time.

Continuous exposure to a novel stressor based on water aversion induces abnormal circadian locomotor rhythms and sleep-wake cycles in mice.

Psychological stressors prominently affect diurnal rhythms, including locomotor activity, sleep, blood pressure, and body temperature, in humans. Here, we found that a novel continuous stress imposed by the perpetual avoidance of water on a wheel (PAWW) affected several physiological diurnal rhythms in mice. One week of PAWW stress decayed robust circadian locomotor rhythmicity, while locomotor activity was evident even during the light period when the mice are normally asleep.

A critical interpersonal distance switches between two coordination modes in kendo matches.

In many competitive sports, players need to quickly and continuously execute movements that co-adapt to various movements executed by their opponents and physical objects. In a martial art such as kendo, players must be able to skillfully change interpersonal distance in order to win. However, very little information about the task and expertise properties of the maneuvers affecting interpersonal distance is available.

Switching dynamics in an interpersonal competition brings about "deadlock" synchronization of players.

In competitive sport game behavior, certain interpersonal patterns of movement coordination evolve even though each individual player only intends to exert their own strategy to win. To investigate this interpersonal pattern formation process, we asked pairs of naïve participants to engage in a play-tag game in which they had to remove a tag fastened to their partner's hip. Relative phase analysis of the players' step towards-away velocities indicated that anti-phase synchronization evolved across 10 repetitions of the game.