CRWN nuclear lamina components maintain the H3K27me3 landscape and promote successful reproduction in Arabidopsis.

Arabidopsis lamin analogs CROWDED NUCLEIs (CRWNs) are necessary to maintain nuclear structure, genome function, and proper plant growth. However, whether and how CRWNs impact reproduction and genome-wide epigenetic modifications is unknown. Here, we investigate the role of CRWNs during the development of gametophytes, seeds, and endosperm, using genomic and epigenomic profiling methods. We observed defects in crwn mutant seeds including seed abortion and reduced germination rate. Quadruple crwn null genotypes were rarely transmitted through gametophytes. Because defects in seeds often stem from abnormal endosperm development, we focused on crwn1 crwn2 (crwn1/2) endosperm. These mutant seeds exhibited enlarged chalazal endosperm cysts and increased expression of stress-related genes and the MADS-box transcription factor PHERES1 and its targets. Previously, it was shown that PHERES1 expression is regulated by H3K27me3 and that CRWN1 interacts with the PRC2 interactor PWO1. Thus, we tested whether crwn1/2 alters H3K27me3 patterns. We observed a mild loss of H3K27me3 at several hundred loci, which differed between endosperm and leaves. These data indicate that CRWNs are necessary to maintain the H3K27me3 landscape, with tissue-specific chromatin and transcriptional consequences.

In situ Synthesis of Single Layered Metal-Organic Frameworks via Inkjet Printing on a Cellulose Nanofiber Film.

The inkjet printing is a simple method to develop pattern-controlled 2D metal-organic frameworks (MOFs) due to its cost-effectiveness and ease of operation. Despite the sophisticated structures of MOF crystals, the MOF surfaces are easily contaminated by the adsorption of an ink solution, and the printing nozzle can be clogged by the aggregates of MOFs during printing. Unlike the mixture inks of MOFs and a carrier medium, the surface-specific patterning by in situ synthesis provides the film surface with the controlled patterns of an MOF single layer having different morphologies of MOFs without changing the ink cartridges. It enables facile printing due to the low viscosity of inks and escapes the risk of nozzle clogging because MOFs are synthesized at the printed patterns on the substrates. The ion-exchanged cellulose nanofiber (CNF) films form strong coordination with metal ions enhancing the stability of the MOFs on the film surface. It also demonstrates the controlled coverage of the MOFs by the printing pass number and the carboxylate content of CNF and the tunable adsorption of the guest molecules for different loading capacities of the printed patterns.

Hydrochromic film for dynamic information storage using cellulose nanofibers and silica nanoparticles.

A hydrochromic composite film was fabricated by incorporating silica nanoparticles (SiNPs) with cellulose nanofibers (CNFs). The CNF/SiNP composite film underwent a reversible change in transparency in response to external moisture variation. The CNFs improved the dimensional stability of the CNF/SiNP composite film and induced morphological differences in SiNP agglomerates, which control the water vapor condensation in a porous film. The condensed water in the pores reduced the difference in refractive index over the CNF/SiNP film, enhancing its transparency. The selective transparency of the composite film was challenged by printing CNF/SiNP inks at different composition ratios. The differing susceptibility of the printed patterns to moisture provided selective transparency at specific patterns, which can store dynamic information such as QR or numerical codes by simple water vapor adsorption and desorption.

CRWN nuclear lamina components maintain the H3K27me3 landscape and promote successful reproduction in Arabidopsis.

The nuclear lamina, a sub-nuclear protein matrix, maintains nuclear structure and genome function. Here, we investigate the role of Arabidopsis lamin analogs CROWDED NUCLEIs during gametophyte and seed development. We observed defects in crwn mutant seeds, including seed abortion and reduced germination rate. Quadruple crwn null genotypes were rarely transmitted through gametophytes. We focused on the crwn1 crwn2 (crwn1/2) endosperm, which exhibited enlarged chalazal cysts and increased expression of stress-related genes and the MADS-box transcription factor PHERES1 and its targets. Previously, it was shown that PHERES1 is regulated by H3K27me3 and that CRWN1 interacts with the PRC2 interactor PWO1. Thus, we tested whether crwn1/2 alters H3K27me3 patterns. We observed a mild loss of H3K27me3 at several hundred loci, which differed between endosperm and leaves. These data indicate that CRWNs are necessary to maintain the H3K27me3 landscape, with tissue-specific chromatin and transcriptional consequences.

The nuclear lamina is required for proper development and nuclear shape distortion in tomato.

The nuclear lamina in plant cells is composed of plant-specific proteins, including nuclear matrix constituent proteins (NMCPs), which have been postulated to be functional analogs of lamin proteins that provide structural integrity to the organelle and help stabilize the three-dimensional organization of the genome. Using genomic editing, we generated alleles for the three genes encoding NMCPs in cultivated tomato (Solanum lycopersicum) to determine if the consequences of perturbing the nuclear lamina in this crop species were similar to or distinct from those observed in the model Arabidopsis thaliana. Loss of the sole NMCP2-class protein was lethal in tomato but is tolerated in Arabidopsis. Moreover, depletion of NMCP1-type nuclear lamina proteins leads to distinct developmental phenotypes in tomato, including leaf morphology defects and reduced root growth rate (in nmcp1b mutants), compared with cognate mutants in Arabidopsis. These findings suggest that the nuclear lamina interfaces with different developmental and signaling pathways in tomato compared with Arabidopsis. At the subcellular level, however, tomato nmcp mutants resembled their Arabidopsis counterparts in displaying smaller and more spherical nuclei in differentiated cells. This result argues that the plant nuclear lamina facilitates nuclear shape distortion in response to forces exerted on the organelle within the cell.

Free-form three-dimensional nanocellulose structure reinforced with poly(vinyl alcohol) using freeze-thaw process.

The free-form fabrication of networked bacterial cellulose (BC) structures was available using a particle matrix and a bioink embedding bacteria. However, the mechanical strength of such BC hydrogel structures does not satisfy the requirements for biomedical applications that require high toughness and elasticity. Here, we adopt the freeze-thaw process with a water-soluble polymer to form a crystalline structure around the BC nanofibers. The crystallization of polymer chains such as poly(vinyl alcohol) (PVA) occurs spontaneously during this process, which results in the unique and environment-friendly methodology of the composition. Crystallization enhances the mechanical strength of free-form BC hydrogels by filling the space between the nanofiber networks with crystalline polymeric fillers. Uniquely, a simple morphological variation can improve the mechanical strengths of BC/PVA cryogels, and this process may be broadly applicable as a tool for biomaterial design and fabrication.

The edge of the nucleus: Variations on a theme.

The plant nuclear lamina utilizes distinct and highly divergent proteins to mediate chromatin interactions at the nuclear edge. In this issue of Developmental Cell, Tang et al. show that members of PNET2, a family of inner nuclear membrane proteins in Arabidopsis, are capable of binding histones and are involved in large-scale genome organization.

The role of CRWN nuclear proteins in chromatin-based regulation of stress response genes.

The periphery in animal nuclei is generally considered to be a transcriptionally repressive environment. Recent studies indicate that chromatin-based mechanisms establish a similar situation in plant nuclei. We demonstrated recently that the loss of CRWN nuclear lamina proteins in Arabidopsis leads to the misregulation of a group of genes involved in plant defense. How this defense response is triggered is largely unknown. Here, we briefly review recent findings that identify several layers of chromatin-based regulation responsible for this response. Further, we introduce new data suggesting that histone H3 lysine 27 tri-methylation levels are reduced in the absence of CRWNs near genes encoding transcription factors regulating SA biosynthesis, providing an explanation for SA induction. These discoveries begin to uncover the interplay between nuclear architecture and stress response in plants.

Toward an interpretable Alzheimer's disease diagnostic model with regional abnormality representation via deep learning.

In this paper, we propose a novel method for magnetic resonance imaging based Alzheimer's disease (AD) or mild cognitive impairment (MCI) diagnosis that systematically integrates voxel-based, region-based, and patch-based approaches into a unified framework. Specifically, we parcellate the brain into predefined regions based on anatomical knowledge (i.e., templates) and derive complex nonlinear relationships among voxels, whose intensities denote volumetric measurements, within each region. Unlike existing methods that use cubical or rectangular shapes, we consider the anatomical shapes of regions as atypical patches. Using complex nonlinear relationships among voxels in each region learned by deep neural networks, we extract a "regional abnormality representation." We then make a final clinical decision by integrating the regional abnormality representations over the entire brain. It is noteworthy that the regional abnormality representations allow us to interpret and understand the symptomatic observations of a subject with AD or MCI by mapping and visualizing these observations in the brain space. On the baseline MRI dataset from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort, our method achieves state-of-the-art performance for four binary classification tasks and one three-class classification task. Additionally, we conducted exhaustive experiments and analysis to validate the efficacy and potential of our method.

Commercial Silk-Based Electronic Yarns Fabricated Using Microwave Irradiation.

Electronic textiles (e-textiles) are being developed because of their potential applications in wearable and flexible electronics. However, complex procedures and chemical agents are required to synthesize carbon-based e-textiles. Pyroprotein-based e-textiles, obtained by the pyrolysis of silk proteins, consume large amounts of time and energy due to the high-temperature process (from 800 to 2800 °C). In this study, we report a novel method of fabricating pyroprotein-based electronic yarns (e-yarns) using microwave irradiation. Microwaves were applied to pyroprotein treated at 650 °C to remove numerous heteroatoms in a short time without the high-temperature process and chemical agents. The structural modulation was confirmed by Raman spectroscopy and X-ray photoelectron spectroscopy. We found a reduction in heteroatoms and enlargement of the carbon region. The temperature-dependent resistance was well explained by the fluctuation-induced tunneling model, which also showed structural modification. The electrical conductivity of the fabricated e-yarns was comparable to that of pyroprotein-based e-textiles heat-treated at 1000 °C (order of 102 S/cm) and showed electrical stability under bending.

In Vivo Trapping of Proteins Interacting with the Chloroplast CLPC1 Chaperone: Potential Substrates and Adaptors.

The chloroplast stromal CLP protease system is essential for growth and development. It consists of a proteolytic CLP core complex that likely dynamically interacts with oligomeric rings of CLPC1, CLPC2, or CLPD AAA+ chaperones. These ATP-dependent chaperones are predicted to bind and unfold CLP protease substrates, frequently aided by adaptors (recognins), and feed them into the proteolytic CLP core for degradation. To identify new substrates and possibly also new adaptors for the chloroplast CLP protease system, we generated an in vivo CLPC1 substrate trap with a C-terminal STREPII affinity tag in Arabidopsis thaliana by mutating critical glutamate residues (E374A and E718A) in the two Walker B domains of CLPC1 required for the hydrolysis of ATP (CLPC1-TRAP). On the basis of homology to nonplant CLPB/C chaperones, it is predicted that interacting substrates are unable to be released; that is, they are trapped. When expressed in the wild type, this CLPC1-TRAP induced a dominant visible phenotype, whereas no viable mutants that express CLPC1-TRAP in the clpc1-1 null mutant could be recovered. Affinity purification of the CLPC1-TRAP resulted in a dozen proteins highly enriched compared with affinity-purified CLPC1 with a C-terminal STREPII affinity tag (CLPC1-WT). These enriched proteins likely represent CLP protease substrates or new adaptors. Several of these trapped proteins overaccumulated in clp mutants or were found as interactors for the adaptor CLPS1, supporting their functional relationship to CLP function. Importantly, the affinity purification of this CLPC1-TRAP also showed high enrichment of all CLPP, CLPR, and CLPT subunits, indicating the stabilization of the CLPC to CLP core interaction and providing direct support for their physical and functional interaction.

Multi-scale gradual integration CNN for false positive reduction in pulmonary nodule detection.

Lung cancer is a global and dangerous disease, and its early detection is crucial for reducing the risks of mortality. In this regard, it has been of great interest in developing a computer-aided system for pulmonary nodules detection as early as possible on thoracic CT scans. In general, a nodule detection system involves two steps: (i) candidate nodule detection at a high sensitivity, which captures many false positives and (ii) false positive reduction from candidates. However, due to the high variation of nodule morphological characteristics and the possibility of mistaking them for neighboring organs, candidate nodule detection remains a challenge. In this study, we propose a novel Multi-scale Gradual Integration Convolutional Neural Network (MGI-CNN), designed with three main strategies: (1) to use multi-scale inputs with different levels of contextual information, (2) to use abstract information inherent in different input scales with gradual integration, and (3) to learn multi-stream feature integration in an end-to-end manner. To verify the efficacy of the proposed network, we conducted exhaustive experiments on the LUNA16 challenge datasets by comparing the performance of the proposed method with state-of-the-art methods in the literature. On two candidate subsets of the LUNA16 dataset, i.e., V1 and V2, our method achieved an average CPM of 0.908 (V1) and 0.942 (V2), outperforming comparable methods by a large margin. Our MGI-CNN is implemented in Python using TensorFlow and the source code is available from https://github.com/ku-milab/MGICNN.

Loss of CRWN Nuclear Proteins Induces Cell Death and Salicylic Acid Defense Signaling.

Defects in the nuclear lamina of animal cell nuclei have dramatic effects on nuclear structure and gene expression as well as diverse physiological manifestations. We report that deficiencies in CROWDED NUCLEI (CRWN), which are candidate nuclear lamina proteins in Arabidopsis (Arabidopsis thaliana), trigger widespread changes in transcript levels and whole-plant phenotypes, including dwarfing and spontaneous cell death lesions. These phenotypes are caused in part by ectopic induction of plant defense responses via the salicylic acid pathway. Loss of CRWN proteins induces the expression of the salicylic acid biosynthetic gene ISOCHORISMATE SYNTHASE1, which leads to spontaneous defense responses in crwn1 crwn2 and crwn1 crwn4 mutants, which are deficient in two of the four CRWN paralogs. The symptoms of ectopic defense response, including pathogenesis marker gene expression and cell death, increase in older crwn double mutants. These age-dependent effects are postulated to reflect an increase in nuclear dysfunction or damage over time, a phenomenon reminiscent of aging effects seen in animal nuclei and in some human laminopathy patients.