Individual leaf microbiota tunes a genetic regulatory network to promote leaf growth.

In natural ecosystems, microbes have the ability to stably colonize plant leaves, overcoming the fluctuating environmental conditions that the leaves represent. How the phyllosphere microbiota influences the growth of individual leaves remains poorly understood. Here, we investigate the growth of Zea mays (maize/corn) leaves in plants grown in three soils with differing amounts of nutrients and water and identify a leaf-growth-promoting effect driven by the leaf microbiota, which we also validate in field studies.

Engineering Titanium Dioxide/Titanocene-Polysulfide Interface for Flexible, Optical-Modulated, and Thermal-Tolerant Multilevel Memristor.

Multifunctional memristors with a high memory density, low power consumption, flexibility, programmability, and environmental robustness are essential for next-generation memories. In this work, a titanocene-polysulfide complex (CpTiS) with strong S···S interactions and hydrogen bonds was synthesized and integrated with TiO to create a novel Cu/TiO/CpTiS/Ag memristor. This device shows bipolar nonvolatile memory performance with a remarkable ON/OFF ratio (10), low switching voltages (, -0.

Soil compaction sensing mechanisms and root responses.

Soil compaction is an agricultural challenge with profound influence on the physical, chemical, and biological properties of the soil. It causes drastic changes by increasing mechanical impedance, reducing water infiltration, gaseous exchange, and biological activities. Soil compaction hinders root growth, limiting nutrient and water foraging abilities of plants.

Regulation of Glandular Size and Phytoalexin Biosynthesis by a Negative Feedback Loop in Cotton.

Plants have evolved diverse defense mechanisms encompassing physical and chemical barriers. Cotton pigment glands are known for containing various defense metabolites, but the precise regulation of gland size to modulate defense compound levels remains enigmatic. Here, it is discovered that the VQ domain-containing protein JAVL negatively regulates pigment gland size and the biosynthesis of defense compounds, while the MYC2-like transcription factor GoPGF has the opposite effect.

A dirigent protein complex directs lignin polymerization and assembly of the root diffusion barrier.

Functionally similar to the tight junctions present in animal guts, plant roots have evolved a lignified Casparian strip as an extracellular diffusion barrier in the endodermis to seal the root apoplast and maintain nutrient homeostasis. How this diffusion barrier is structured has been partially defined, but its lignin polymerization and assembly steps remain elusive. Here, we characterize a family of dirigent proteins (DPs) essential for both the localized polymerization of lignin required for Casparian strip biogenesis in the cell wall and for attachment of the strip to the plasma membrane to seal the apoplast.

A new family of proteins is required for tethering of Casparian strip membrane domain and nutrient homoeostasis in rice.

Cell-cell junctions are essential for multicellular organisms to maintain nutrient homoeostasis. A plant-type tight junction, the Casparian strip (CS)-Casparian strip membrane domain (CSD) that seals the paracellular space between adjacent endodermal cells, has been known for more than one hundred years. However, the molecular basis of this structure remains unknown.

Cell type-specific mapping of ion distribution in Arabidopsis thaliana roots.

Cell type-specific mapping of element distribution is critical to fully understand how roots partition nutrients and toxic elements with aboveground parts. In this study, we developed a method that combines fluorescence-activated cell sorting (FACS) with inductively coupled plasma mass spectrometry (ICP-MS) to assess the ionome of different cell populations within Arabidopsis thaliana roots. The method reveals that most elements exhibit a radial concentration gradient increasing from the rhizodermis to inner cell layers, and detected previously unknown ionomic changes resulting from perturbed xylem loading processes.

Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots.

The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis.

Localization and circulation: vesicle trafficking in regulating plant nutrient homeostasis.

Nutrient homeostasis is essential for plant growth and reproduction. Plants, therefore, have evolved tightly regulated mechanisms for the uptake, translocation, distribution, and storage of mineral nutrients. Considering that inorganic nutrient transport relies on membrane-based transporters and channels, vesicle trafficking, one of the fundamental cell biological processes, has become a hotspot of plant nutrition studies.

Sec24C mediates a Golgi-independent trafficking pathway that is required for tonoplast localisation of ABCC1 and ABCC2.

Protein sorting is an essential biological process in all organisms. Trafficking membrane proteins generally relies on the sorting machinery of the Golgi apparatus. However, many proteins have been found to be delivered to target locations via Golgi-independent pathways, but the mechanisms underlying this delivery system remain unknown.

Decreasing nitrogen assimilation under drought stress by suppressing DST-mediated activation of Nitrate Reductase 1.2 in rice.

Nitrogen is an essential nutrient for plant growth and development, and plays vital roles in crop yield. Assimilation of nitrogen is thus fine-tuned in response to heterogeneous environments. However, the regulatory mechanism underlying this essential process remains largely unknown.

The effect of coronary slow flow on left atrial structure and function.

The coronary slow flow phenomenon (CSFP) is common in coronary angiography, however its impact on left atrial (LA) function is still controversial. This study aims to evaluate the LA structure and function of patients with CSFP using two-dimensional speckle tracking echocardiography (2D-STE). Consecutive patients scheduled for coronary angiography from January 2016 to September 2017 were enrolled in this study.

Phytochrome B inhibits darkness-induced hypocotyl adventitious root formation by stabilizing IAA14 and suppressing ARF7 and ARF19.

Adventitious roots (ARs) are an important root type for plants and display a high phenotypic plasticity in response to different environmental stimuli. Previous studies found that dark-light transition can trigger AR formation from the hypocotyl of etiolated Arabidopsis thaliana, which was used as a model for the identification of regulators of AR biogenesis. However, the central regulatory machinery for darkness-induced hypocotyl AR (HAR) remains elusive.

Twadn: an efficient alignment algorithm based on time warping for pairwise dynamic networks.

Background: Network alignment is an efficient computational framework in the prediction of protein function and phylogenetic relationships in systems biology. However, most of existing alignment methods focus on aligning PPIs based on static network model, which are actually dynamic in real-world systems. The dynamic characteristic of PPI networks is essential for understanding the evolution and regulation mechanism at the molecular level and there is still much room to improve the alignment quality in dynamic networks.

A novel algorithm for alignment of multiple PPI networks based on simulated annealing.

Proteins play essential roles in almost all life processes. The prediction of protein function is of significance for the understanding of molecular function and evolution. Network alignment provides a fast and effective framework to automatically identify functionally conserved proteins in a systematic way.

A novel algorithm based on bi-random walks to identify disease-related lncRNAs.

Backgrounds: There is evidence to suggest that lncRNAs are associated with distinct and diverse biological processes. The dysfunction or mutation of lncRNAs are implicated in a wide range of diseases. An accurate computational model can benefit the diagnosis of diseases and help us to gain a better understanding of the molecular mechanism.

Deep Learning Enables Accurate Prediction of Interplay Between lncRNA and Disease.

Many studies have suggested that lncRNAs are involved in distinct and diverse biological processes. The mutation of lncRNAs plays a major role in a wide range of diseases. A comprehensive information of lncRNA-disease associations would improve our understanding of the underlying molecular mechanism that can explain the development of disease.

MD-SVM: a novel SVM-based algorithm for the motif discovery of transcription factor binding sites.

Background: Transcription factors (TFs) play important roles in the regulation of gene expression. They can activate or block transcription of downstream genes in a manner of binding to specific genomic sequences. Therefore, motif discovery of these binding preference patterns is of central significance in the understanding of molecular regulation mechanism.

WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks.

Background: The discovery of functionally conserved proteins is a tough and important task in system biology. Global network alignment provides a systematic framework to search for these proteins from multiple protein-protein interaction (PPI) networks. Although there exist many web servers for network alignment, no one allows to perform global multiple network alignment tasks on users' test datasets.

KF-finder: identification of key factors from host-microbial networks in cervical cancer.

Background: The human body is colonized by a vast number of microbes. Microbiota can benefit many normal life processes, but can also cause many diseases by interfering the regular metabolism and immune system. Recent studies have demonstrated that the microbial community is closely associated with various types of cell carcinoma.

Drives Natural Variation in Leaf Zn Concentration of .

Zinc (Zn) is an essential element for plant growth and development, and Zn derived from crop plants in the diet is also important for human health. Here, we report that genetic variation in () controls natural variation in leaf Zn content. Investigation of the natural variation in leaf Zn content in a world-wide collection of 349 wild collected accessions identified two accessions, Van-0 and Fab-2, which accumulate significantly lower Zn when compared with Col-0.