Exploring protein natural diversity in environmental microbiomes with DeepMetagenome.

Protein natural diversity offers a vast sequence space for protein engineering, and deep learning enables its detection from metagenomes/proteomes without prior assumptions. DeepMetagenome, a Python-based method, explores protein diversity through modules for training and analyzing sequence datasets. The deep learning model includes Embedding, Conv1D, LSTM, and Dense layers, with sequence feature analysis for data cleaning.

Non-invasive lipid panel of MASLD fibrosis transition underscores the role of lipoprotein sulfatides in hepatic immunomodulation.

There exists a pressing need for a non-invasive panel that differentiates mild fibrosis from non-fibrosis in metabolic dysfunction-associated steatotic liver disease (MASLD). In this work, we applied quantitative lipidomics and sterolomics on sera from the PERSONS cohort with biopsy-based histological assessment of liver pathology. We trained a lasso regression model using quantitative omics data and clinical variables, deriving a combinatorial panel of lipids and clinical indices that differentiates mild fibrosis (>F1, n = 324) from non-fibrosis (F0, n = 195), with an area under receiver operating characteristic curve (AUROC) at 0.

Regulatory mechanisms of strigolactone perception in rice.

Strigolactones (SLs) are hormones essential for plant development and environmental responses. SL perception requires the formation of the complex composed of an SL receptor DWARF14 (D14), F-box protein D3, and transcriptional repressor D53, triggering ubiquitination and degradation of D53 to activate signal transduction. However, mechanisms of SL perception and their influence on plant architecture and environmental responses remain elusive and controversial.

Mutation of GLR2 confers enhanced glufosinate resistance and salt tolerance in rice.

The GLR2 transcription factor regulates glufosinate resistance and enhances abiotic stress tolerance in rice through interaction with the GLR1 transcription factor and modulation of gene expression.

The Arabidopsis E3 ubiquitin ligase DOA10A promotes localization of abscisic acid (ABA) receptors to the membrane through mono-ubiquitination in ABA signaling.

The endoplasmic reticulum-associated degradation (ERAD) system eliminates misfolded and short-lived proteins to maintain physiological homeostasis in the cell. We have previously reported that ERAD is involved in salt tolerance in Arabidopsis. Given the central role of the phytohormone abscisic acid (ABA) in plant stress responses, we sought to identify potential intersections between the ABA and the ERAD pathways in plant stress response.

Transfer of mitochondrial DNA into the nuclear genome during induced DNA breaks.

Mitochondria serve as the cellular powerhouse, and their distinct DNA makes them a prospective target for gene editing to treat genetic disorders. However, the impact of genome editing on mitochondrial DNA (mtDNA) stability remains a mystery. Our study reveals previously unknown risks of genome editing that both nuclear and mitochondrial editing cause discernible transfer of mitochondrial DNA segments into the nuclear genome in various cell types including human cell lines, primary T cells, and mouse embryos.

Wild rice GL12 synergistically improves grain length and salt tolerance in cultivated rice.

The abounding variations in wild rice provided potential reservoirs of beneficial genes for rice breeding. Maintaining stable and high yields under environmental stresses is a long-standing goal of rice breeding but is challenging due to internal trade-off mechanisms. Here, we report wild rice GL12 improves grain length and salt tolerance in both indica and japonica genetic backgrounds.

Spatial organization of PI3K-PI(3,4,5)P-AKT signaling by focal adhesions.

The class I phosphatidylinositol 3-kinase (PI3K)-AKT signaling pathway is a key regulator of cell survival, growth, and proliferation and is among the most frequently mutated pathways in cancer. However, where and how PI3K-AKT signaling is spatially activated and organized in mammalian cells remains poorly understood. Here, we identify focal adhesions (FAs) as subcellular signaling hubs organizing the activation of PI3K-PI(3,4,5)P-AKT signaling in human cancer cells containing p110α mutations under basal conditions.

A Pvr-AP-1-Mmp1 signaling pathway is activated in astrocytes upon traumatic brain injury.

Traumatic brain injury (TBI) caused by external mechanical forces is a major health burden worldwide, but the underlying mechanism in glia remains largely unclear. We report herein that adults exhibit a defective blood-brain barrier, elevated innate immune responses, and astrocyte swelling upon consecutive strikes with a high-impact trauma device. RNA sequencing (RNA-seq) analysis of these astrocytes revealed upregulated expression of genes encoding PDGF and VEGF receptor-related (Pvr, a receptor tyrosine kinase), adaptor protein complex 1 (AP-1 a transcription factor complex of the c-Jun N-terminal kinase pathway) composed of Jun-related antigen (Jra) and kayak (kay), and matrix metalloproteinase 1 (Mmp1) following TBI.

Combinatorial lipidomics and proteomics underscore erythrocyte lipid membrane aberrations in the development of adverse cardio-cerebrovascular complications in maintenance hemodialysis patients.

Patients on maintenance hemodialysis exhibit a notably higher risk of cardio-cerebrovascular complications that constitute the major cause of death. Preceding studies have reported conflicting associations between traditional lipid measures and clinical outcome in dialysis patients. In this prospective longitudinal study, we utilized quantitative lipidomics to elucidate, at molecular resolution, changes in lipidome profiles of erythrocyte and plasma samples collected from maintenance hemodialysis patients followed up for 86 months (≈7 years).

Mutation of rice SM1 enhances solid leaf midrib formation and increases methane emissions.

The leaf midrib system is essential for plant growth and development, facilitating nutrient transport, providing structural support, enabling gas exchange, and enhancing resilience to environmental stresses. However, the molecular mechanism regulating leaf midrib development is still unclear.In this study, we reported a rice solid midrib 1 (sm1) mutant, exhibiting solid leaf aerenchyma and abaxial rolling leaves due to abnormal development of parenchyma and bulliform cells.

CAMSAP3 forms dimers via its α-helix domain that directly stabilize non-centrosomal microtubule minus ends.

Microtubules are vital components of the cytoskeleton. Their plus ends are dynamic and respond to changes in cell morphology, whereas the minus ends are stable and serve a crucial role in microtubule seeding and maintaining spatial organization. In mammalian cells, the calmodulin-regulated spectrin-associated proteins (CAMSAPs), play a key role in directly regulating the dynamics of non-centrosomal microtubules minus ends.

Three RLKs integrate SHR-SCR and gibberellins to regulate root ground tissue patterning in Arabidopsis thaliana.

Precise regulation of cell division is essential for proper tissue patterning in multicellular organisms. In Arabidopsis, the ground tissue (GT) comprises cortex and endodermis in the early stages of root development. During GT maturation, additional periclinal cell divisions (PCDs) occasionally occur of the endodermis, generating a middle cortex (MC) layer between the cortex and endodermis.

VDGE: a data repository of variation database for gene-edited animals across multiple species.

Gene-edited animals are crucial for addressing fundamental questions in biology and medicine and hold promise for practical applications. In light of the rapid advancement of gene editing technologies over the past decade, a dramatically increased number of gene-edited animals have been generated. Genome editing at off-target sites can, however, introduce genomic variations, potentially leading to unintended functional consequences in these animals.

Glut3 promotes cellular O-GlcNAcylation as a distinctive tumor-supportive feature in Treg cells.

Regulatory T cells (Tregs) establish dominant immune tolerance but obstruct tumor immune surveillance, warranting context-specific mechanistic insights into the functions of tumor-infiltrating Tregs (TIL-Tregs). We show that enhanced posttranslational O-linked N-acetylglucosamine modification (O-GlcNAcylation) of cellular factors is a molecular feature that promotes a tumor-specific gene expression signature and distinguishes TIL-Tregs from their systemic counterparts. We found that altered glucose utilization through the glucose transporter Glut3 is a major facilitator of this process.

Dual modes of ZFC3H1 confer selectivity in nuclear RNA sorting.

The export and degradation pathways compete to sort nuclear RNAs, yet the default pathway remains unclear. Sorting of mature RNAs to degradation, facilitated by the exosome co-factor poly(A) exosome targeting (PAXT), is particularly challenging for their resemblance to mRNAs intended for translation. Here, we unveil that ZFC3H1, a core PAXT component, is co-transcriptionally loaded onto the first exon/intron of RNA precursors (pre-RNAs).

ZmKTF1 promotes salt tolerance by mediating RNA-directed DNA methylation in maize.

The epigenetic process of RNA-directed DNA methylation (RdDM) regulates the expression of genes and transposons. However, little is known about the involvement of RdDM in the response of maize (Zea mays) to salt stress. Here, we isolated a salt-sensitive maize mutant and cloned the underlying gene, which encodes KOW DOMAIN-CONTAINING TRANSCRIPTION FACTOR1 (KTF1), an essential component of the RdDM pathway.

Sugar transporter modulates nitrogen-determined tillering and yield formation in rice.

Nitrogen (N) fertilizer application ensures crop production and food security worldwide. N-controlled boosting of shoot branching that is also referred as tillering can improve planting density for increasing grain yield of cereals. Here, we report that Sugar Transporter Protein 28 (OsSTP28) as a key regulator of N-responsive tillering and yield formation in rice.

The thylakoid phosphatase TEF8 is involved in state transition and high light stress resistance in Chlamydomonas.

The sophisticated regulation of state transition is required to maintain optimal photosynthetic performance under fluctuating light condition, through balancing the absorbed light energy between photosystem II and photosystem I. This exquisite process incorporates phosphorylation and dephosphorylation of light-harvesting complexes and PSII core subunits, accomplished by thylakoid membrane-localized kinases and phosphatases that have not been fully identified. In this study, one Chlamydomonas high light response gene, THYLAKOID ENRICHED FRACTION 8 (TEF8), was characterized.

Characterization and fine mapping of () mutant in sorghum [ (L.) Moench].

Unlabelled: The sorghum inflorescence is consisted of sessile (SS) and pedicellate spikelets (PS). Commonly, only SS could produce seeds and each spikelet produces one single seed. Here, we identified a sorghum mutant, named (), which can produce twin seeds in each pair of glumes.