Multitask knowledge-primed neural network for predicting missing metadata and host phenotype based on human microbiome.

Motivation: Microbial signatures in the human microbiome are closely associated with various human diseases, driving the development of machine learning models for microbiome-based disease prediction. Despite progress, challenges remain in enhancing prediction accuracy, generalizability, and interpretability. Confounding factors, such as host's gender, age, and body mass index, significantly influence the human microbiome, complicating microbiome-based predictions.

The lncRNA20718-miR6022-RLPs module regulates tomato resistance to Phytophthora infestans.

Sl-lncRNA20718 acts as an eTM of Sl-miR6022 regulating its expression thereby affecting SlRLP6/10 expression. SlRLP6/10 regulate PRs expression, ROS accumulation, and JA/ET content thereby affecting tomato resistance to P. infestans.

Enhanced Structure-Based Prediction of Chiral Stationary Phases for Chromatographic Enantioseparation from 3D Molecular Conformations.

The accurate prediction of suitable chiral stationary phases (CSPs) for resolving the enantiomers of a given compound poses a significant challenge in chiral chromatography. Previous attempts at developing machine learning models for structure-based CSP prediction have primarily relied on 1D SMILES strings [the simplified molecular-input line-entry system (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings] or 2D graphical representations of molecular structures and have met with only limited success. In this study, we apply the recently developed 3D molecular conformation representation learning algorithm, which uses rapid conformational analysis and point clouds of atom positions in the 3D space, enabling efficient chemical structure-based machine learning.

Gas-responsive two-dimensional metal-organic framework composites for trace visualization of volatile organic compounds.

Highly sensitive and specific identification of complex volatile organic compound mixtures has always been a huge challenge in the field of gas detection. To address this issue, the gas-responsive two-dimensional metal-organic framework (MOF) composites have been designed for fabricating a colorimetric sensor arrays for extremely sensitive detection of volatile organic compounds (VOCs). The physically exfoliated MOF nanosheets Zn(bim) with large surface area and abundant unsaturated active sites were used for loading various dyes to form dye/Zn(bim) composites.

3DMolMS: prediction of tandem mass spectra from 3D molecular conformations.

Motivation: Tandem mass spectrometry is an essential technology for characterizing chemical compounds at high sensitivity and throughput, and is commonly adopted in many fields. However, computational methods for automated compound identification from their MS/MS spectra are still limited, especially for novel compounds that have not been previously characterized. In recent years, in silico methods were proposed to predict the MS/MS spectra of compounds, which can then be used to expand the reference spectral libraries for compound identification.

The lncRNA39896-miR166b-HDZs module affects tomato resistance to Phytophthora infestans.

The yield and quality of tomatoes (Solanum lycopersicum) is seriously affected by Phytophthora infestans. The long non-coding RNA (lncRNA) Sl-lncRNA39896 is induced after P. infestans infection and was previously predicted to act as an endogenous target mimic (eTM) for the microRNA Sl-miR166b, which function in stress responses.

, Subfamily Genes of Transcription Factors From Cassava, Play an Important Role in Disease Resistance.

Cassava ( Crantz) is an important tropical crop for food, fodder, and energy. Cassava bacterial blight (CBB) caused by pv. () occurs in all cassava growing regions and threatens global cassava production.

Genome-wide identification of cassava MeRboh genes and functional analysis in Arabidopsis.

Plant respiratory burst oxidase homolog (Rboh) gene family encodes NADPH oxidases, and plays important roles in the production of reactive oxygen species (ROS), plant signaling, growth and stress responses. Cassava is an important starchy crops in tropical region. Environmental stresses, such as drought, pathogen, have caused great yield loss.

Function identification of miR394 in tomato resistance to Phytophthora infestans.

MiR394 plays a negative role in tomato resistance to late blight. The lncRNA40787 severing as an eTM for miR394 to regulate LCR and exerting functions in tomato resistance. Tomato (Solanum lycopersicum), which was used as model species for studying the mechanism of plant disease defense, is susceptible to multiple pathogens.

Editing miR482b and miR482c Simultaneously by CRISPR/Cas9 Enhanced Tomato Resistance to .

Late blight, caused by , is severely damaging to the global tomato industry. Micro-RNAs (miRNAs) have been widely demonstrated to play vital roles in plant resistance by repressing their target genes. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) method has been continuously improved and extensively applied to edit plant genomes.

Identification of tomato circular RNAs responsive to Phytophthora infestans.

Circular RNAs (circRNAs), a novel branch of noncoding RNAs, are widespread in eukaryotic cells. Particularly, due to their abilities to bind microRNA (miRNA) and serve as "sponges", circRNAs can regulate gene expression and participate in multiple biological processes. To detect the function of the circRNAs in tomato resistance, in our study, high-throughput sequencing were used to detect the circRNAs in tomatoes before and after Phytophthora infestans (P.

Overexpression of MiR482c in Tomato Induces Enhanced Susceptibility to Late Blight.

Tomato is the highest-value fruit/vegetable crop worldwide. However, the quality and yield of tomatoes are severely affected by late blight. MicroRNA482s (miR482s) are involved in the plant's immune system.

Differential expression of the Hsf family in cassava under biotic and abiotic stresses.

Heat shock transcription factors (Hsfs) are important regulators of biotic and abiotic stress responses in plants. Currently, the Hsf gene family is not well understood in cassava, an important tropical crop. In the present study, 32 genes were identified from the cassava genome database, which were divided into three types based on functional domain and motif distribution analyses.

SpWRKY6 acts as a positive regulator during tomato resistance to Phytophthora infestans infection.

WRKY transcription factors have been widely known to play key regulatory roles in plant disease resistance. In our previous study, characteristics of SpWRKY6 and its role in response to biotic and abiotic stress was studied. To further investigate the function of SpWRKY6 in tomato resistance to Phytophthora infestans (P.

MeBIK1, a novel cassava receptor-like cytoplasmic kinase, regulates PTI response of transgenic Arabidopsis.

Cassava bacterial blight is the most destructive disease in cassava, causing a significant reduction in its production. The innate immunity response, which has a broad spectrum and a persistent effect, is the basal defence of plants in response to pathogens. Isolation and identification of innate immune-related genes in cassava will contribute to understanding the disease resistance mechanism.

Overexpressing OsMAPK12-1 inhibits plant growth and enhances resistance to bacterial disease in rice.

Mitogen-activated protein kinases (MAPKs) play important roles in plant growth and development, plant abiotic stresses signalling pathway and plant-pathogen interactions. However, little is known about the roles of MAPKs in modulating plant growth and pathogen resistance. In this study, we found that OsMAPK12-1, an alternatively spliced form of BWMK1 in rice (Oryza sativa L.

Transcriptome Analysis of Ceriops tagal in Saline Environments Using RNA-Sequencing.

Identification of genes involved in mangrove species' adaptation to salt stress can provide valuable information for developing salt-tolerant crops and understanding the molecular evolution of salt tolerance in halophiles. Ceriops tagal is a salt-tolerant mangrove tree growing in mudflats and marshes in tropical and subtropical areas, without any prior genome information. In this study, we assessed the biochemical and transcriptional responses of C.