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Breeding cool-season (C3) grasses with higher magnesium (Mg) content is a promising attempt for reducing grass tetany hazard in ruminants. Faster methods for plant mineral analyses could increase the number of individual plants screened for higher Mg content (High-Mg). This study evaluates the effectiveness of energy dispersive X-ray microanalysis (EDX) as well as energy reflectance X-ray spectrometry (XRF) for screening high-Mg grass genotypes. The approach was verified by using two tall fescue cultivars having known differences in magnesium (Mg) content, viz. HiMag (high-Mg cultivar) and Ky-31 (control cultivar). We assumed that cultivars with known variation in Mg concentrations could provide a test for the applicability of the new methodology in finding naturally occurring high and low Mg containing grass genotypes. Plants samples included a population of 8 plants consisting of four harvests for three years and were analyzed for Mg, calcium (Ca), and potassium (K) by EDX and ERF, and data were verified with atomic absorption spectrometry wet (AAS). While observing the frequency distribution for different nutrient concentrations, HiMag tall fescue showed higher Mg and lower K concentrations than that of Ky-31. There was positive linear relationship between AAS and EDX estimated Mg, Ca and K (r = 0.88, 0.62 and 0.89, respectively), indicating close agreement between AAS and EDX estimation. Also, there was a positive linear relationship between AAS and XRF, as the r values were 0.87, 0.65 and 0.88 for Mg, Ca, and K, respectively. The tetany ration was established for EDX and XRF and the results were dependable with wet chemistry. [ABSTRACT FROM AUTHOR]

DNA markers serve as essential tools in breeding selection and genetic analysis. However, developing DNA markers can be time-consuming and labor-intensive due to the need to identify polymorphisms between cultivars/lines and to design suitable primers. To address these challenges, we have developed DNAMarkMaker, a tool designed to automate the process of primer design for Amplification Refractory Mutation System (ARMS) and Cleaved Amplified Polymorphic Sequences (CAPS) markers, utilizing resequencing data. One key feature of DNAMarkMaker is its user-friendly graphical user interface (GUI), ensuring its accessibility and ease of use, even for researchers not well-versed in bioinformatics. We confirmed DNAMarkMaker's applicability by developing DNA markers for rice, potato, and turnip-each representing distinct genome structures: homozygous diploid, heterozygous autotetraploid, and heterozygous diploid, respectively. DNAMarkMaker will contribute to the rapid and efficient development of DNA markers, accelerating breeding and genetic analysis in various crops., (Copyright © 2024 by JAPANESE SOCIETY OF BREEDING.)

Galacto- N -biose (GNB) is an important core structure of glycan of mucin glycoproteins in the gastrointestinal (GI) mucosa. Because certain beneficial bacteria inhabiting the GI tract, such as bifidobacteria and lactic acid bacteria, harbor highly specialized GNB metabolic capabilities, GNB is considered a promising prebiotic for nourishing and manipulating beneficial bacteria in the GI tract. However, the precise interactions between GNB and beneficial bacteria and their accompanying health-promoting effects remain elusive. First, we evaluated the proliferative tendency of beneficial bacteria and their production of beneficial metabolites using gut bacterial strains. By comparing the use of GNB, glucose, and inulin as carbon sources, we found that GNB enhanced acetate production in Lacticaseibacillus casei , Lacticaseibacillus rhamnosus , Lactobacillus gasseri , and Lactobacillus johnsonii . The ability of GNB to promote acetate production was also confirmed by RNA-seq analysis, which indicated the upregulation of gene clusters that catalyze the deacetylation of N -acetylgalactosamine-6P and biosynthesize acetyl-CoA from pyruvate, both of which result in acetate production. To explore the in vivo effect of GNB in promoting acetate production, antibiotic-treated BALB/cA mice were administered with GNB with L. rhamnosus , resulting in a fecal acetate content that was 2.7-fold higher than that in mice administered with only L. rhamnosus . Moreover, 2 days after the last administration, a 3.7-fold higher amount of L. rhamnosus was detected in feces administered with GNB with L. rhamnosus than in feces administered with only L. rhamnosus . These findings strongly suggest the prebiotic potential of GNB in enhancing L. rhamnosus colonization and converting L. rhamnosus into higher acetate producers in the GI tract., Importance: Specific members of lactic acid bacteria, which are commonly used as probiotics, possess therapeutic properties that are vital for human health enhancement by producing immunomodulatory metabolites such as exopolysaccharides, short-chain fatty acids, and bacteriocins. The long residence time of probiotic lactic acid bacteria in the GI tract prolongs their beneficial health effects. Moreover, the colonization property is also desirable for the application of probiotics in mucosal vaccination to provoke a local immune response. In this study, we found that GNB could enhance the beneficial properties of intestinal lactic acid bacteria that inhabit the human GI tract, stimulating acetate production and promoting intestinal colonization. Our findings provide a rationale for the addition of GNB to lactic acid bacteria-based functional foods. This has also led to the development of therapeutics supported by more rational prebiotic and probiotic selection, leading to an improved healthy lifestyle for humans., Competing Interests: The authors declare no conflict of interest.

Key Message: We identified and characterized a dominant FT allele for flowering without vernalization in Brassica rapa, while demonstrating its potential for deployment in breeding to accelerate flowering in various Brassicaceae crops. Controlling the timing of flowering is key to improving yield and quality of several agricultural crops including the Brassicas. Many Brassicaceae crops possess a conserved flowering mechanism in which FLOWERING LOCUS C (FLC) represses the transcription of flowering activators such as FLOWERING LOCUS T (FT) during vernalization. Here, we employed genetic analysis based on next-generation sequencing to identify a dominant FT allele, BraA.FT.2-C, for flowering in the absence of vernalization in the Brassica rapa cultivar 'CHOY SUM EX CHINA 3'. BraA.FT.2-C harbors two large insertions upstream of its coding region and is expressed without vernalization, despite FLC expression. We show that BraA.FT.2-C offers an opportunity to introduce flowering without vernalization requirement into winter-type brassica crops, including B. napus, which have many functional FLC paralogs. Furthermore, we demonstrated the feasibility of using B. rapa harboring BraA.FT.2-C as rootstock for grafting to induce flowering in radish (Raphanus sativus), which requires vernalization for flowering. We believe that the ability of BraA.FT.2-C to overcome repression by FLC can have significant applications in brassica crops breeding to increase yields by accelerating or delaying flowering., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Youth become psychologically independent by emotionally separating from their parents and simultaneously developing a sense of trust in them. While these relational components have been addressed separately, studies focusing on the change in dynamics of these components are lacking. This study examined profiles of parent-youth relationship quality based on emotional separation and parental trust, age differences in the prevalence of these profiles, and age differences in the associations between the profiles, identity, and life satisfaction. Participants included 14,428 youth living in Japan from five age groups (44.8% girls/women; M age  = 20.6 years; range = 12-25 years). Six profiles were identified: healthy-independent, unhealthy-independent, balanced, moderate/ambivalent, connected, and distant. The connected profile was predominant among early adolescents, while the healthy-independent profile was predominant among late adolescents and early and middle emerging adults. Among all age groups, identity synthesis was the highest in the healthy-independent profile, and life satisfaction was the highest and identity confusion was the lowest in the healthy-independent and connected profiles. These findings indicate that young people navigate the process of becoming independent from their parents by balancing emotional separation and parental trust, and this balance relates to identity development and life satisfaction., (© 2022. The Author(s).)

Developing identities that are well-aligned with sociocultural expectations is a key psychosocial developmental task for adolescents and emerging adults. Most studies have examined identity development focusing on how individuals develop their identities (identity process), such as identity exploration and commitment. Meanwhile, researchers have emphasized incorporating the what of identity development (identity content) with identity processes to further the understanding of identity development in sociocultural contexts. This study focuses on the positive and negative valences of identity defined by desirable and undesirable images shared in sociocultural contexts. We investigated the bidirectional associations of identity exploration and commitment processes with positive and negative identity elements using longitudinal data over three measurement waves. Participants were 2,313 Japanese emerging adults enrolled in higher education (70.95% women; Mage = 20.43). The cross-lagged panel analysis and random-intercept cross-lagged panel analysis were used to estimate associations at both between- and within-person levels. Results indicated that commitment making negatively predicted negative identity elements, whereas identification with commitment positively predicted positive identity elements. Meanwhile, positive identity elements positively predicted identification with commitment only for participants with low levels of negative identity elements, while negative identity elements negatively predicted commitment making and identification with commitment. These associations were found only at the between-person level. The findings highlight that emerging adults develop identities through close interactions in which they engage in identity exploration and commitment processes, as well as construct identity content valences. Developmental sequences of identity, along with their sociocultural contexts and practical implications, are discussed. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1-3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical-basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain.

In the version of this Resource originally published, the author information was incorrect. Jos R. Wendrich should have had a present address: Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, 9052 Ghent, Belgium. Mark Boekschoten and Guido J. Hooiveld should have been affiliated to the Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE Wageningen, The Netherlands. In addition, the version of Supplementary Table 5 originally published with this Resource was not the intended final version and included inaccurate citations to the display items of the Resource, and the file format and extension did not match. These errors have now been corrected in all versions of the Resource.

Many developmental processes involve transitions between different cell identities as cells differentiate or undergo reprogramming. Cell identity specifications are generally associated with the activation and suppression of specific sets of genes mediated by transcription factors. Therefore, transcriptional reporters, such as promoters of cell-type-specific genes, are broadly used as cell identity markers in developmental biology. In Arabidopsis (Arabidopsis thaliana), a collection of GAL4/UAS enhancer trap lines is an established standard for inferring cell identity. However, only a few of these enhancer trap lines have been molecularly characterized, which limits their potential. Here, we describe an approach for a detailed characterization of expression and mapping of T-DNA insert location of GAL4/UAS enhancer trap lines. Additionally, we demonstrate how the acquired information can be further used for the generation of novel cell-type-specific promoters as well as for genotyping of enhancer trap lines.

During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered-in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, probably signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue- and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.

In plants, apical meristems allow continuous growth along the body axis. Within the root apical meristem, a group of slowly dividing quiescent center cells is thought to limit stem cell activity to directly neighboring cells, thus endowing them with unique properties, distinct from displaced daughters. This binary identity of the stem cells stands in apparent contradiction to the more gradual changes in cell division potential and differentiation that occur as cells move further away from the quiescent center. To address this paradox and to infer molecular organization of the root meristem, we used a whole-genome approach to determine dominant transcriptional patterns along root ontogeny zones. We found that the prevalent patterns are expressed in two opposing gradients. One is characterized by genes associated with development, the other enriched in differentiation genes. We confirmed these transcript gradients, and demonstrate that these translate to gradients in protein accumulation and gradual changes in cellular properties. We also show that gradients are genetically controlled through multiple pathways. Based on these findings, we propose that cells in the Arabidopsis root meristem gradually transition from stem cell activity toward differentiation., Competing Interests: The authors declare no conflict of interest., (Published under the PNAS license.)

The incidence of breast cancer in female-to-male (FTM) transsexuals who received mastectomy and sex reassignment surgery is very rare. In fact, there is only one previous medical report of such a case. We experienced a case of an FTM transsexual who developed breast cancer 12 years after mastectomy and hysterectomy with bilateral salpingo-oophorectomy. Because he had been continuously receiving testosterone during the last 15 years and because histopathological examination revealed positive estrogen receptor and androgen receptor expression, we suggest that exogenous testosterone may have initiated the development of breast cancer via two distinct pathways. We describe the clinical course and condition of the patient and recommend that medical personnel consider the possibility of hormone-related cancer in FTM transsexuals receiving cross-sex hormones.

Cell-type-specific gene expression is essential to distinguish between the numerous cell types of multicellular organism. Therefore, cell-type-specific gene expression is tightly regulated and for most genes RNA transcription is the central point of control. Thus, transcriptional reporters are broadly used markers for cell identity. In Arabidopsis (Arabidopsis thaliana), a recognized standard for cell identities is a collection of GAL4/UAS enhancer trap lines. Yet, while greatly used, very few of them have been molecularly characterized. Here, we have selected a set of 21 frequently used GAL4/UAS enhancer trap lines for detailed characterization of expression pattern and genomic insertion position. We studied their embryonic and postembryonic expression domains and grouped them into three groups (early embryo development, late embryo development, and embryonic root apical meristem lines) based on their dominant expression. We show that some of the analyzed lines are expressed in a domain often broader than the one that is reported. Additionally, we present an overview of the location of the T-DNA inserts of all lines, with one exception. Finally, we demonstrate how the obtained information can be used for generating novel cell-type-specific marker lines and for genotyping enhancer trap lines. The knowledge could therefore support the extensive use of these valuable lines., (© 2016 American Society of Plant Biologists. All Rights Reserved.)

The stem cells in the shoot apical meristem (SAM) are the origin of all above ground tissues in plants. In Arabidopsis thaliana, shoot meristem stem cells are maintained by the homeobox transcription factor gene WUS (WUSCHEL) that is expressed in cells of the organizing center underneath the stem cells. In order to identify factors that operate together with WUS in stem cell maintenance, we performed an EMS mutant screen for modifiers of the hypomorphic wus-6 allele. We isolated the oberon3-2 (obe3-2) mutant that enhances stem cell defects in wus-6, but does not affect the putative null allele wus-1. The OBE3 gene encodes a PHD (Plant Homeo Domain) protein that is thought to function in chromatin regulation. Single mutants of OBE3 or its closest homolog OBE4 do not display any defects, whereas the obe3-2 obe4-2 double mutant displays broad growth defects and developmental arrest of seedlings. Transcript levels of WUS and its target gene in the stem cells, CLAVATA3, are reduced in obe3-2. On the other hand, OBE3 and OBE4 transcripts are both indirectly upregulated by ectopic WUS expression. Our results suggest a positive feedback regulation between WUS and OBE3 that contributes to shoot meristem homeostasis.

Early plant embryogenesis condenses the fundamental processes underlying plant development into a short sequence of predictable steps. The main tissues, as well as stem cells for their post-embryonic maintenance, are specified through genetic control networks. A key question is how cell fates are instructed by unique cellular transcriptomes, and important insights have recently been gained through cell type-specific transcriptomics during post-embryonic development. However, the poor accessibility and small size of Arabidopsis (Arabidopsis thaliana) embryos have obstructed similar progress during embryogenesis. Here, we review the current situation in plant embryo transcriptomics, and discuss how the recent development of novel cell-specific analysis technologies will enable the identification of cellular transcriptomes in the early Arabidopsis embryo., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

The plant hormone auxin was initially identified as the bioactive substance that induces roots in plant tissue culture. In the past decades, mechanisms for auxin action, including its transport and response, have been described in detail. However, a molecular and cellular description of its role in root initiation is far from complete. In this review, we discuss recent advances in our understanding of auxin-dependent embryonic root formation. During this process, a root meristem is initiated in a precise and predictable position, and at a stage when the organism consists of relatively few cells. Recent studies have revealed mechanisms for local control of auxin transport, for cellular differences in auxin response components and cell type-specific chromatin regulation. The recent identification of biologically relevant target genes for auxin regulation during embryonic root initiation now also allows dissection of auxin-activated cellular processes. Finally, we discuss the potential for hormonal cross-regulation in embryonic root formation.

Plant growth is directed by the activity of stem cells within meristems. The first meristems are established during early embryogenesis, and this process involves the specification of both stem cells and their organizer cells. One of the earliest events in root meristem initiation is marked by re-specification of the uppermost suspensor cell as hypophysis, the precursor of the organizer. The transcription factor MONOPTEROS (MP) is a key regulator of hypophysis specification, and does so in part by promoting the transport of the plant hormone auxin and by activating the expression of TARGET OF MP (TMO) transcription factors, both of which are required for hypophysis specification. The mechanisms leading to the activation of these genes by MP in a chromatin context are not understood. Here, we show that the PHD-finger proteins OBERON (OBE) and TITANIA (TTA) are essential for MP-dependent embryonic root meristem initiation. TTA1 and TTA2 are functionally redundant and function in the same pathway as OBE1 and OBE2. These PHD-finger proteins interact with each other, and genetic analysis shows that OBE-TTA heterotypic protein complexes promote embryonic root meristem initiation. Furthermore, while MP expression is unaffected by mutations in OBE/TTA genes, expression of MP targets TMO5 and TMO7 is locally lost in obe1 obe2 embryos. PHD-finger proteins have been shown to act in initiation of transcription by interacting with nucleosomes. Indeed, we found that OBE1 binds to chromatin at the TMO7 locus, suggesting a role in its MP-dependent activation. Our data indicate that PHD-finger protein complexes are crucial for the activation of MP-dependent gene expression during embryonic root meristem initiation, and provide a starting point for studying the mechanisms of developmental gene activation within a chromatin context in plants.

Our purpose in this study was to evaluate the fundamental accuracy of reconstructed dose distributions from the COMPASS system using specific MLC test patterns and complicated IMRT neck plans. The COMPASS-reconstructed dose distributions were compared with those measured with EPID, MapCHECK, and EDR2 film and as well as Monte Carlo-calculated dose profiles with use of square-wave chart patterns of 20-, 10-, and 5-mm gaps and step and pyramid patterns. Additionally, the COMPASS dose distributions for clinical IMRT neck plans were tested. The COMPASS dose profiles were almost in agreement with the Monte Carlo-calculated dose profiles and point doses measured with MapCHECK for 20- and 10-mm gap patterns. The dose profile for a 5-mm gap pattern showed a narrow width due to the detector size in the penumbra region. For step and pyramid patterns, COMPASS agreed with MapCHECK and Monte Carlo calculation, except for EDR2 film. The COMPASS and MapCHECK dose distributions agreed with that of a treatment planning system by gamma analysis (criteria; 3 mm/3%). In comparisons of clinical IMRT neck dose distributions, COMPASS was measured with almost the same accuracy as MapCHECK, but slight deviations were found for large IMRT fields. These deviations could be minimized by improvement of the beam model of the COMPASS system. The COMPASS system can be expected to be used for traditional QA methods in clinical routine with the same accuracy as a MapCHECK diode detector.

The dosimetric properties between various 2D array detectors were compared and were evaluated with regard to the accuracy in absolute dose and dose distributions for clinical treatment fields. We used to check the dose accuracy: 2D array detectors; MapCHECK (Sun Nuclear), EPID (Varian Medical Systems), EPID-based dosimetry (EPIDose, Sun Nuclear), COMPASS (IBA) and conventional system; EDR2 film (Eastman Kodak), Exradin A-14SL ion chamber (0.016 cc, Standard Imaging). First, we compared the dose linearity, dose rate dependence, and output factor between the 2D array detectors. Next, the accuracy of the absolute dose and dose distributions were evaluated for clinical fields. All detector responses for the dose linear were in agreement within 1%, and the dose rate dependence and output factor agreed within a standard deviation of ±1.2%, except for EPID. This is because EPID is fluence distributions. In all the 2D array detectors, the point dose agreed within 5% with treatment planning system (TPS). Pass rates of each detector for TPS were more than 97% in the gamma analysis (3 mm/3%). EPIDose was in a good agreement with TPS. All 2D array detectors used in this study showed almost the same accuracy for clinical fields. EPIDose has better resolution than other 2D array detectors and thus this is expected for dose distributions with a small field.

Maintenance of the stem cell population located at the apical meristems is essential for repetitive organ initiation during the development of higher plants. Here, we have characterized the roles of OBERON1 (OBE1) and its paralog OBERON2 (OBE2), which encode plant homeodomain finger proteins, in the maintenance and/or establishment of the meristems in Arabidopsis. Although the obe1 and obe2 single mutants were indistinguishable from wild-type plants, the obe1 obe2 double mutant displayed premature termination of the shoot meristem, suggesting that OBE1 and OBE2 function redundantly. Further analyses revealed that OBE1 and OBE2 allow the plant cells to acquire meristematic activity via the WUSCHEL-CLAVATA pathway, which is required for the maintenance of the stem cell population, and they function parallel to the SHOOT MERISTEMLESS gene, which is required for preventing cell differentiation in the shoot meristem. In addition, obe1 obe2 mutants failed to establish the root apical meristem, lacking both the initial cells and the quiescent center. In situ hybridization revealed that expression of PLETHORA and SCARECROW, which are required for stem cell specification and maintenance in the root meristem, was lost from obe1 obe2 mutant embryos. Taken together, these data suggest that the OBE1 and OBE2 genes are functionally redundant and crucial for the maintenance and/or establishment of both the shoot and root meristems.