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Macroautophagy/autophagy plays a dual role in many physiological processes of multicellular eukaryotes. In plants, autophagy can be used by both host and pathogen for a beneficiary infection outcome. Plants employ a two-tier innate immune system to defend against invading pathogens. Cell surface localized pattern recognition receptors recognize conserved pathogen-associated molecular patterns (PAMPs) and launch pattern-triggered immunity (PTI) to provide broad-spectrum resistance. Pathogens inject a battery of effector proteins into their hosts to counter PTI and compromise the primary immune response. Hosts induce a second layer of defense called effector-triggered immunity (ETI) to counter the effects of these effectors. In addition to ETI and PTI, autophagy is emerging as a central cellular process modulated by both host and pathogens toward their respective advantage. Pathogens lacking the ability to inject effectors are compromised in virulence. However, molecular targets and biochemical characterization of most of these effector proteins remain elusive. In a recent paper we presented a systematic analysis of interaction between autophagy proteins of Arabidopsis thaliana with effectors from bacterial, fungal, oomycete and nematode pathogens. Abbreviations: ATG, autophagy related; BiFC, bimolecular fluorescence complementation; ETI, effector-triggered immunity; PAMPs, pathogen-associated molecular patterns; PTI, pattern-triggered immunity.

Decline in insulin sensitivity due to dysfunction of adipose tissue (AT) is one of the earliest pathogenic events in type 2 diabetes. We hypothesize that differential DNA methylation (DNAm) controls insulin sensitivity and obesity by modulating transcript expression in AT. Integrating AT DNAm profiles with transcript profile data measured in a cohort of 230 African Americans (AAs) from the African American Genetics of Metabolism and Expression cohort, we performed cis-expression quantitative trait methylation (cis-eQTM) analysis to identify epigenetic regulatory loci for glucometabolic trait-associated transcripts. We identified significantly associated cytosine-guanine dinucleotide regions for 82 transcripts (false discovery rate [FDR]-P < 0.05). The strongest eQTM locus was observed for the proopiomelanocortin (POMC; ρ = -0.632, P = 4.70 × 10-27) gene. Epigenome-wide association studies (EWAS) further identified 155, 46, and 168 cytosine-guanine dinucleotide regions associated (FDR-P < 0.05) with the Matsuda index, SI, and BMI, respectively. Intersection of EWAS, transcript level to trait association, and eQTM results, followed by causal inference test identified significant eQTM loci for 23 genes that were also associated with Matsuda index, SI, and/or BMI in EWAS. These associated genes include FERMT3, ITGAM, ITGAX, and POMC In summary, applying an integrative multiomics approach, our study provides evidence for DNAm-mediated regulation of gene expression at both previously identified and novel loci for many key AT transcripts influencing insulin resistance and obesity.

Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2, has resulted thus far in greater than 933,000 deaths worldwide; yet disease pathogenesis remains unclear. Clinical and immunological features of patients with COVID-19 have highlighted a potential role for changes in immune activity in regulating disease severity. However, little is known about the responses in human lung tissue, the primary site of infection. Here we show that pathways related to neutrophil activation and pulmonary fibrosis are among the major up-regulated transcriptional signatures in lung tissue obtained from patients who died of COVID-19 in Wuhan, China. Strikingly, the viral burden was low in all samples, which suggests that the patient deaths may be related to the host response rather than an active fulminant infection. Examination of the colonic transcriptome of these patients suggested that SARS-CoV-2 impacted host responses even at a site with no obvious pathogenesis. Further proteomics analysis validated our transcriptome findings and identified several key proteins, such as the SARS-CoV-2 entry-associated protease cathepsins B and L and the inflammatory response modulator S100A8/A9, that are highly expressed in fatal cases, revealing potential drug targets for COVID-19.

Production of reactive oxygen species (ROS) is critical for successful activation of immune responses against pathogen infection. The plant NADPH oxidase RBOHD is a primary player in ROS production during innate immunity. However, how RBOHD is negatively regulated remains elusive. Here we show that RBOHD is regulated by C-terminal phosphorylation and ubiquitination. Genetic and biochemical analyses reveal that the PBL13 receptor-like cytoplasmic kinase phosphorylates RBOHD's C-terminus and two phosphorylated residues (S862 and T912) affect RBOHD activity and stability, respectively. Using protein array technology, we identified an E3 ubiquitin ligase PIRE (PBL13 interacting RING domain E3 ligase) that interacts with both PBL13 and RBOHD. Mimicking phosphorylation of RBOHD (T912D) results in enhanced ubiquitination and decreased protein abundance. PIRE and PBL13 mutants display higher RBOHD protein accumulation, increased ROS production, and are more resistant to bacterial infection. Thus, our study reveals an intricate post-translational network that negatively regulates the abundance of a conserved NADPH oxidase.

Nucleotide-binding leucine-rich repeat (NLR) immune receptors play a critical role in defence against pathogens in plants and animals. However, we know very little about NLR-interacting proteins and the mechanisms that regulate NLR levels. Here, we used proximity labeling (PL) to identify the proteome proximal to N, which is an NLR that confers resistance to Tobacco mosaic virus (TMV). Evaluation of different PL methods indicated that TurboID-based PL provides more efficient levels of biotinylation than BioID and BioID2 in plants. TurboID-based PL of N followed by quantitative proteomic analysis and genetic screening revealed multiple regulators of N-mediated immunity. Interestingly, a putative E3 ubiquitin ligase, UBR7, directly interacts with the TIR domain of N. UBR7 downregulation leads to an increased amount of N protein and enhanced TMV resistance. TMV-p50 effector disrupts the N-UBR7 interaction and relieves negative regulation of N. These findings demonstrate the utility of TurboID-based PL in plants and the N-interacting proteins we identified enhance our understanding of the mechanisms underlying NLR regulation.

The priority of research efforts over the past two decades has been focused on the effective detection of harmful gases and the development of small, efficient, and reliable nanodimensional sensors. The adsorption of carbon monoxide (CO) gas molecules on zigzag gallium phosphide nanoribbons (zGaPNRs) has been studied using first-principle calculations within the context of Density Functional Theory (DFT). Here, we have evaluated the potential of single-atom thick zGaPNRs in different configurations of nanoribbons for the detection of CO. Many possible configurations of studying the CO molecule adsorption on zGaPNRs have been explored. It is established that the interaction of CO molecules has an impact on the electrical and transport properties of zGaPNRs. The H-GaP-H is the most stable structure with the binding energy ( E b ) of −5.70 eV. The stability is compromised with CO adsorption with CO-GaP-CO being the least stable structure. Pristine structure is semiconducting with the energy band gap ( E G ) of −3.95 eV. The computed sensitivity (S) values are found to be highest for Co-GaPNRs with the S value of 1. 7 7 × 1 0 1 8 and the least sensitive structure is H-GaP-CO with the computed S as 3. 8 4 × 1 0 1 7 . Additionally, it is noted that CO molecules always establish a stable chemical bond with the nanoribbon edges through the C-side. The unique behavior is revealed by the transport characteristics, which demonstrates that when CO adsorption occurs near the Ga edge, the current magnitude is noticeably greater. Our research demonstrates the potential of specific CO adsorption and detection for the development of nanosensors. [ABSTRACT FROM AUTHOR]

Polyhalite-based POLY4, a multi-nutrient source containing potassium, calcium, magnesium, and sulphur, is increasingly recognised for its potential to improve crop yields and soil health in agricultural systems. It is also been considered as a feasible approach for addressing the deficiency in potassium, calcium, and sulphur within a single application source. The present study aimed to investigate the impact of polyhalite-based POLY4 application, either as a complete or partial substitute for traditional potassium fertiliser and gypsum supplement, on the improvement of peanut (Arachis hypogaea) growth and soil quality. An extensive field study was conducted from 2021 and 2022, employing ten distinct nutrient management treatments with three replications in a randomised complete block design. The findings of the study indicated that the application of polyhalite (POLY4) in conjunction with only NP fertilisers resulted in a higher yield advantage (approximately 150-200 kg ha-1) than in plots treated with NPK + gypsum (at 500 kg ha-1) and control plots. The application of polyhalite-based fertiliser (POLY4) at a rate that was 100% equivalent to K along with NP fertilisers resulted in a significant increase in pod yield (5.3-12.8%) over NPK + gypsum and control plots. Thus, the increased crop yield led to an increase in gross returns of 4.88% and in net returns of 4.28% with the application of POLY4 (100%) + NP fertilisers over other treatments. Likewise, variable rates of conventional fertilisers along with POLY4 (100% recommended) + NP + gypsumat 310 kg/ha significantly increased the linoleic acid content (38.5%), oleic acid content, and oil content (48.1%) by reducing palmitic acid (11.96%) content in the groundnut seed. Interestingly, POLY4 use at the 50% recommended rate also resulted in yields that were comparable with those obtained with 100% NPK. Therefore, applying POLY4, a polyhalite fertiliser, in either a 100% or 50% equivalent of essential K can be an effective way of increasing the production of peanut crops and promoting agricultural sustainability. [ABSTRACT FROM AUTHOR]