Transcriptomic landscape of seedstick in Arabidopsis thaliana funiculus after fertilisation.

Background: In Angiosperms, the continuation of plant species is intricately dependent on the funiculus multifaceted role in nutrient transport, mechanical support, and dehiscence of seeds. SEEDSTICK (STK) is a MADS-box transcription factor involved in seed size and abscission, and one of the few genes identified as affecting funiculus growth. Given the importance of the funiculus to a correct seed development, allied with previous phenotypic observations of stk mutants, we performed a transcriptomic analysis of stk funiculi from floral stage 17, using RNA-sequencing, to infer on the deregulated networks of genes.

Identification of APBB1 as a substrate for anaplastic lymphoma kinase.

Anaplastic lymphoma kinase (ALK) is a well-known oncogene involved in various malignancies such as anaplastic large cell lymphoma, lung cancer and neuroblastoma. Several substrates for fused ALK have been identified and their biological functions have been described. However, the lack of a comprehensive identification of ALK substrates limits our understanding of the biological roles of receptor ALK.

Synthesis and preclinical testing of a selective beta-subtype agonist of thyroid hormone receptor ZTA-261.

Background: Thyroid hormones (TH) regulate the basal metabolic rate through their receptors THRα and THRβ. TH activates lipid metabolism via THRβ, however, an excess amount of TH can lead to tachycardia, bone loss, and muscle wasting through THRα. In recent years, TH analogs that selectively bind to THRβ have gained attention as new agents for treating dyslipidemia and obesity, which continue to pose major challenges to public health worldwide.

The dopaminergic system promotes neprilysin-mediated degradation of amyloid-β in the brain.

Deposition of amyloid-β (Aβ) in the brain can impair neuronal function and contribute to cognitive decline in Alzheimer's disease (AD). Here, we found that dopamine and the dopamine precursor levodopa (also called l-DOPA) induced Aβ degradation in the brain. Chemogenetic approaches in mice revealed that the activation of dopamine release from ventral tegmental area (VTA) neurons increased the abundance and activity of the Aβ-degrading enzyme neprilysin and reduced the amount of Aβ deposits in the prefrontal cortex in a neprilysin-dependent manner.

Deciphering the spectrum of astrocyte diversity: Insights into molecular, morphological, and functional dimensions in health and neurodegenerative diseases.

Astrocytes are the most abundant and morphologically complex glial cells that play active roles in the central nervous system (CNS). Recent research has identified shared and region-specific astrocytic genes and functions, elucidated the cellular origins of their regional diversity, and uncovered the molecular networks for astrocyte morphology, which are essential for their functional complexity. Reactive astrocytes exhibit a wide range of functional diversity in a context-specific manner in CNS disorders.

α-Mannosylated HLA-II glycopeptide antigens dominate the immunopeptidome of immortalised cells and tumour tissues.

Immunopeptides are cell surface-located protein fragments that aid our immune system to recognise and respond to pathogenic insult and malignant transformation. In this two-part communication, we firstly summarise and reflect on our recent discovery documenting that MHC-II-bound immunopeptides from immortalised cell lines prevalently carry N-glycans that differ from the cellular glycoproteome (Goodson, Front Immunol, 2023). These findings are important as immunopeptide glycosylation remains poorly understood in immunosurveillance.

Feed Components and Timing to Improve the Feed Conversion Ratio for Sustainable Aquaculture Using Starch.

Aquaculture contributes to the sustainable development of food security, marine resource conservation, and economy. Shifting aquaculture feed from fish meal and oil to terrestrial plant derivatives may result in cost savings. However, many carnivorous fish cannot be sustained on plant-derived materials, necessitating the need for the identification of important factors for farmed fish growth and the identification of whether components derived from terrestrial plants can be used in feed.

Crystalline organic monoliths with bicontinuous porosity.

Organic crystals are a promising class of materials for various optical applications. However, it has been challenging to make macroscopic organic crystals with bicontinuous porosity that are applicable to flow chemistry. In this study, a new class of porous materials, cm-scale crystalline organic monoliths (COMs) with bicontinuous porosity, are synthesized by replicating the porous structure of silica monolith templates.

Transcriptionally Conditional Recurrent Neural Network for De Novo Drug Design.

Computational molecular generation methods that generate chemical structures from gene expression profiles have been actively developed for de novo drug design. However, most omics-based methods involve complex models consisting of multiple neural networks, which require pretraining. In this study, we propose a straightforward molecular generation method called GxRNN (gene expression profile-based recurrent neural network), employing a single recurrent neural network (RNN) that necessitates no pretraining for omics-based drug design.

Glutamatergic signaling from melanin-concentrating hormone-producing neurons: A requirement for memory regulation, but not for metabolism control.

Melanin-concentrating hormone-producing neurons (MCH neurons), found mainly in the lateral hypothalamus and surrounding areas, play essential roles in various brain functions, including sleep and wakefulness, reward, metabolism, learning, and memory. These neurons coexpress several neurotransmitters and act as glutamatergic neurons. The contribution of glutamate from MCH neurons to memory- and metabolism-related functions has not been fully investigated.

Periodic cytokinin responses in rhizobium infection and nodule development.

Host plants benefit from legume root nodule symbiosis with nitrogen-fixing bacteria under nitrogen-limiting conditions. In this interaction, the hosts must regulate nodule numbers and distribution patterns to control the degree of symbiosis and maintain root growth functions. The host response to symbiotic bacteria occurs discontinuously but repeatedly at the region behind the tip of the growing roots.

Carnosine supplementation in cryopreservation solution improved frozen-thawed bovine embryo viability.

Cryopreservation adversely affects embryo quality and viability in vitro. We investigated the effects of cryopreservation solutions supplemented with the antioxidant carnosine on frozen-thawed bovine embryo viability. Bovine blastocysts were produced in vitro and cryopreserved using slow freezing.

Visible-light-induced direct C-H alkylation of polycyclic aromatic hydrocarbons with alkylsulfones.

Polycyclic aromatic hydrocarbons (PAHs) are fragments of graphene that have attracted considerable attention as a new class of carbon-based materials. The functionalization of edge positions in PAHs is important to enable the modulation of physical and chemical properties essential for various applications. However, straightforward methods that combine functional group tolerance and regioselectivity remain sought after.

Electrical resistivity tomography combined with seismic data estimates heterogeneous distribution of near-seafloor concentrated gas hydrates within gas chimneys.

Near-seafloor concentrated gas hydrates (GHs) containing large amounts of methane have been identified at various gas chimney sites. Although understanding the spatial distribution of GHs is fundamental for assessing their dissociation impact on aggravating global warming and resource potential, the spatial distribution of GHs within gas chimneys remains unclear. Here, we estimate the subseafloor distribution of GHs at a gas chimney site in the Japan Sea using marine electrical resistivity tomography data.

Revealing Comprehensive Food Functionalities and Mechanisms of Action through Machine Learning.

Foods possess a range of unexplored functionalities; however, fully identifying these functions through empirical means presents significant challenges. In this study, we have proposed an approach to comprehensively predict the functionalities of foods, encompassing even processed foods. This prediction is accomplished through the utilization of machine learning on biomedical big data.

Socially activated neurons in the anterior cingulate cortex are essential for social behavior in mice.

Social behavior, defined as any mode of communication between conspecifics is regulated by a widespread network comprising multiple brain structures. The anterior cingulate cortex (ACC) serves as a hub region interconnected with several brain regions involved in social behavior. Because the ACC coordinates various behaviors, it is important to focus on a subpopulation of neurons that are potentially involved in social behavior to clarify the precise role of the ACC in social behavior.

Attempting to Create a Pathway to 15-Deacetylcalonectrin with Limited Accumulation in Cultures of Mutants: Insight into Trichothecene Biosynthesis Machinery.

The compound 15-deacetylcalonectrin (15-deCAL) is a common pathway intermediate in the biosynthesis of trichothecenes. This tricyclic intermediate is metabolized to calonectrin (CAL) by trichothecene 15--acetyltransferase encoded by . Unlike other trichothecene pathway gene mutants, the Δ mutant produces lower amounts of the knocked-out enzyme's substrate 15-deCAL, and instead, accumulates higher quantities of earlier bicyclic intermediate and shunt metabolites.

Internally Formed Preferences for Options only Influence Initial Decisions in Gambling Tasks, while the Gambling Outcomes do not Alter these Preferences.

All humans must engage in decision-making. Decision-making processes can be broadly classified into internally guided decision-making (IDM), which is determined by individuals' internal value criteria, such as preference, or externally guided decision-making (EDM), which is determined by environmental external value criteria, such as monetary rewards. However, real-life decisions are never made simply using one kind of decision-making, and the relationship between IDM and EDM remains unclear.

Turbulence Transition in Magnetically Confined Hydrogen and Deuterium Plasmas.

In this study, we discovered a turbulence transition in a large helical device. The turbulence level and turbulence-driven energy transport decrease to a specific transition density and increase above it. The ruling turbulences below and above the transition density were ion-temperature gradient (ITG) and resistive-interchange (RI) turbulences, consistent with the predictions of gyrokinetic theory and two-fluid MHD model, respectively.

Phase-separated super-enhancers confer an innate radioresistance on genomic DNA.

Recently, biomolecular condensates formed through liquid-liquid phase separation have been widely reported to regulate key intracellular processes involved in cell biology and pathogenesis. BRD4 is a nuclear protein instrumental to the establishment of phase-separated super-enhancers (SEs) to direct the transcription of important genes. We previously observed that protein droplets of BRD4 became hydrophobic as their size increase, implying an ability of SEs to limit the ionization of water molecules by irradiation.

Efficient activation of hundreds of LTR12C elements reveals cis-regulatory function determined by distinct epigenetic mechanisms.

Long terminal repeats (LTRs), which often contain promoter and enhancer sequences of intact endogenous retroviruses (ERVs), are known to be co-opted as cis-regulatory elements for fine-tuning host-coding gene expression. Since LTRs are mainly silenced by the deposition of repressive epigenetic marks, substantial activation of LTRs has been found in human cells after treatment with epigenetic inhibitors. Although the LTR12C family makes up the majority of ERVs activated by epigenetic inhibitors, how these epigenetically and transcriptionally activated LTR12C elements can regulate the host-coding gene expression remains unclear due to genome-wide alteration of transcriptional changes after epigenetic inhibitor treatments.