DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes.

Background: Accurate taxonomic classification in genome databases is essential for reliable biological research and effective data sharing. Mislabeling or inaccuracies in genome annotations can lead to incorrect scientific conclusions and hinder the reproducibility of research findings. Despite advances in genome analysis techniques, challenges persist in ensuring precise and reliable taxonomic assignments.

Physcomitrium LATERAL SUPPRESSOR genes promote formative cell divisions to produce germ cell lineages in both male and female gametangia.

The evolution of green plants from aquatic to terrestrial environments is thought to have been facilitated by the acquisition of gametangia, specialized multicellular organs housing gametes. Antheridia and archegonia, responsible for producing and protecting sperm and egg cells, undergo formative cell divisions to produce a cell to differentiate into germ cell lineages and the other cell to give rise to surrounding structures. However, the genes governing this process remain unidentified.

Bayesian Latent Class Models for Evaluating the Validity of Claim-based Definitions of Disease Outcomes.

Background: Large electronic databases have been widely used in recent years; however, they can be susceptible to bias due to incomplete information. To address this, validation studies have been conducted to assess the accuracy of disease diagnoses defined in databases. However, such studies may be constrained by potential misclassification in references and the interdependence between diagnoses from the same data source.

Temporal dynamics in a red alga dominated geothermal feature in Yellowstone National Park.

Alga-dominated geothermal spring communities in Yellowstone National Park (YNP), USA, have been the focus of many studies, however, relatively little is known about the composition and community interactions which underpin these ecosystems. Our goal was to determine, in three neighboring yet distinct environments in Lemonade Creek, YNP, how cells cope with abiotic stressors over the diurnal cycle. All three environments are colonized by two photosynthetic lineages, and , both of which are extremophilic Cyanidiophyceae red algae.

Development of Molecular Dynamics Parameters and Theoretical Analysis of Excitonic and Optical Properties in the Light-Harvesting Complex II.

The light-harvesting complex II (LHCII) in green plants exhibits highly efficient excitation energy transfer (EET). A comprehensive understanding of the EET mechanism in LHCII requires quantum chemical, molecular dynamics (MD), and statistical mechanics calculations that can adequately describe pigment molecules in heterogeneous environments. Herein, we develop MD simulation parameters that accurately reproduce the quantum mechanical/molecular mechanical energies of both the ground and excited states of all chlorophyll (Chl) molecules in membrane embedded LHCII.

Future spinal reflex is embedded in primary motor cortex output.

Mammals can execute intended limb movements despite the fact that spinal reflexes involuntarily modulate muscle activity. To generate appropriate muscle activity, the cortical descending motor output must coordinate with spinal reflexes, yet the underlying neural mechanism remains unclear. We simultaneously recorded activities in motor-related cortical areas, afferent neurons, and forelimb muscles of monkeys performing reaching movements.

Nanoscale Visualization of Drosophila E-cadherin Ectodomain Fragments and Their Interactions Using DNA Origami Nanoblocks.

The adhesive function of cell surface proteins can be visually assessed through direct observation; however, the underlying structures that mediate adhesion typically remain invisible at the nanoscale level. This hinders knowledge on the diversity of molecular architectures responsible for cell-cell adhesion. Drosophila E-cadherin (DE-cadherin), a classical cadherin with a unique domain structure, demonstrates adhesive function; however, it lacks a structural model that explains its adhesion mechanism.

Transport-of-intensity phase imaging using commercially available confocal microscope.

Significance: Confocal microscopy is an indispensable tool for biologists to observe samples and is useful for fluorescence imaging of living cells with high spatial resolution. Recently, phase information induced by the sample has been attracting attention because of its applicability such as the measurability of physical parameters and wavefront compensation. However, commercially available confocal microscopy has no phase imaging function.

Infrared laser-induced gene expression in single cells characterized by quantitative imaging in Physcomitrium patens.

A spatiotemporal understanding of gene function requires the precise control of gene expression in each cell. Here, we use an infrared laser-evoked gene operator (IR-LEGO) system to induce gene expression at the single-cell level in the moss Physcomitrium patens by heating a living cell with an IR laser and thereby activating the heat shock response. We identify the laser irradiation conditions that provide higher inducibility with lower invasiveness by changing the laser power and irradiation duration.

Profiling of 24-nt phasiRNAs in Rice Anther by Massively Parallel Sequencing and Stem-Loop Reverse Transcription PCR.

Small RNAs are highly abundant and play important roles in plant reproduction. Profiling of small RNAs in reproductive tissues is a critical step in understanding their biology. Here, we describe a protocol for small RNA profiling in rice anthers, with a focus on an abundantly expressed but little-understood reproductive small RNA class named 24-nucleotide phased secondary small interfering RNAs (24-nt phasiRNAs).

Experimental evidence of phase transition of silica polymorphs in basaltic eucrites: implications for thermal history of protoplanetary crust.

Silica polymorphs occur under various pressures and temperature conditions, and their characteristics can be used to better understand the complex metamorphic history of planetary materials. Here, we conducted isothermal heating experiments of silica polymorphs in basaltic eucrites to assess their formation and stability. We revealed that each silica polymorph exhibits different metamorphic responses: (1) Quartz recrystallizes into cristobalite when heated at ≥ 1040 °C.

Axial heterogeneity of superficial proximal tubule paracellular transport in mice.

A considerable amount of NaCl reabsorption in proximal tubules (PTs) occurs via the paracellular transport regulated by the tight junction proteins claudins (Cldns). However, the paracellular transport properties in mouse superficial PTs remain unclear. We characterized these properties in superficial PT S1-S3 segments from mice expressing [wild-type (WT, WTS1-WTS3)] or lacking [knockout (KO, KOS1-KOS3)] claudin-2.

An Indirect Pathway from the Rat Interstitial Nucleus of Cajal to the Vestibulocerebellum Involved in Vertical Gaze Holding.

The neural network, including the interstitial nucleus of Cajal (INC), functions as an oculomotor neural integrator involved in the control of vertical gaze holding. Impairment of the vestibulocerebellum (VC), including the flocculus (FL), has been shown to affect vertical gaze holding, indicating that the INC cooperates with the VC in controlling this function. However, a network between the INC and VC has not been identified.

Bonobo geophagy at Wamba.

Geophagy, the deliberate consumption of earth materials, is widely observed in animals. While anecdotal evidence exists of bonobos (Pan paniscus) consuming soil from Cubitermes termite mounds, the functions of their geophagic behavior remains unexplored. This study aims to examine a preliminary hypothesis that termite mound geophagy of free-ranging bonobos at Wamba are helpful for iron supplementation.

Tracing early pastoralism in Central Europe using sedimentary ancient DNA.

Central European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic (∼7.5-6.0 ka before present [BP]).

Thermosensation and TRP Channels.

Somatosensory neurons can sense external temperature by converting sensation of temperature information to neural activity via afferent input to the central nervous system. Various populations of somatosensory neurons have specialized gene expression, including expression of thermosensitive transient receptor potential (TRP) ion channels. Thermosensitive TRP channels are responsible for thermal transduction at the peripheral ends of somatosensory neurons and can sense a wide range of temperatures.

A primordial noble gas component discovered in the Ryugu asteroid and its implications.

Ryugu is the C-type asteroid from which material was brought to Earth by the Hayabusa2 mission. A number of individual grains and fine-grained samples analysed so far for noble gases have indicated that solar wind and planetary (known as P1) noble gases are present in Ryugu samples with concentrations higher than those observed in CIs, suggesting the former to be more primitive compared to the latter. Here we present results of analyses of three fine-grained samples from Ryugu, in one of which Xe concentration is an order of magnitude higher than determined so far in other samples from Ryugu.

Selective consistency of recurrent neural networks induced by plasticity as a mechanism of unsupervised perceptual learning.

Understanding the mechanism by which the brain achieves relatively consistent information processing contrary to its inherent inconsistency in activity is one of the major challenges in neuroscience. Recently, it has been reported that the consistency of neural responses to stimuli that are presented repeatedly is enhanced implicitly in an unsupervised way, and results in improved perceptual consistency. Here, we propose the term "selective consistency" to describe this input-dependent consistency and hypothesize that it will be acquired in a self-organizing manner by plasticity within the neural system.

Subnanometer structure of medusavirus capsid during maturation using cryo-electron microscopy.

Medusavirus is a giant virus classified into an independent family of . Amoebae infected with medusavirus release immature particles in addition to virions. These particles were suggested to exhibit the maturation process of this virus, but the structure of these capsids during maturation remains unknown.