A pervasive phosphorylation cascade modulation of plant transcription factors in response to abiotic stress.

MAIN CONCLUSION: Transcriptional regulation of stress-responsive genes is a crucial step in establishing the mechanisms behind plant abiotic stress tolerance. A sensitive method of regulating transcription factors activity, stability, protein interaction, and subcellular localization is through phosphorylation. This review highlights a widespread regulation mechanism that involves phosphorylation of plant TFs in response to abiotic stress. Abiotic stress is one of the main components limiting crop yield and sustainability on a global scale. It greatly reduces the land area that is planted and lowers crop production globally. In all living organisms, transcription factors (TFs) play a crucial role in regulating gene expression. They participate in cell signaling, cell cycle, development, and plant stress response. Plant resilience to diverse abiotic stressors is largely influenced by TFs. Transcription factors modulate gene expression by binding to their target gene's cis-elements, which are impacted by genomic characteristics, DNA structure, and TF interconnections. In this review, we focus on the six major TFs implicated in abiotic stress tolerance, namely, DREB, bZIP, WRKY, ABF, MYB, and NAC, and the cruciality of phosphorylation of these transcription factors in abiotic stress signaling, as protein phosphorylation has emerged as one of the key post-translational modifications, playing a critical role in cell signaling, DNA amplification, gene expression and differentiation, and modification of other biological configurations. These TFs have been discovered after extensive study as stress-responsive transcription factors which may be major targets for crop development and important contributors to stress tolerance and crop production.

Protective efficacy of Toxoplasma gondii bivalent MAG1 and SAG1 DNA vaccine against acute toxoplasmosis in BALB/c mice.

Toxoplasma gondii can infect a wide range of warm-blooded animals, causing a global toxoplasmosis zoonotic epidemic. Surface antigen 1 (SAG1) protein is expressed at the proliferative tachyzoite stage, whereas matrix antigen 1 (MAG1) is expressed at the bradyzoite and tachyzoite stages. These two proteins were found to perform protective roles in previous studies; however, their synergetic protective efficacy as a DNA vaccine against toxoplasmosis has not been clarified. In this study, we constructed recombinant pcDNA3.1( +)-TgMAG1 (pMAG1), pcDNA3.1( +)-TgSAG1 (pSAG1), and pcDNA3.1( +)-TgMAG1-TgSAG1 (pMAG1-SAG1) plasmids and administered them intramuscularly to immunize mice. The levels of anti-T. gondii IgG in serum and cytokines, such as Interleukin (IL)-4, IL-10, and Interferon (IFN)-γ, in splenocytes were measured using ELISA and the respective culture supernatants. Lethal doses of T. gondii (type I) RH strain tachyzoites were administered to immunized mice, and mortality was assessed. Conversely, mice infected with low doses of tachyzoites were monitored to determine their survival rates, and parasite burden analyses of the brains and livers were conducted. The bivalent TgMAG1 and TgSAG1 DNA vaccines exhibited excellent protective immunity against toxoplasmosis in mice, with higher serum IgG and splenocyte IFN-γ release levels, longer survival days, and reduced parasite burden in the brain and liver tissues (p < 0.05). These findings provide a new perspective for the development of T. gondii vaccines.

Integrating AI/ML Models for Patient Stratification Leveraging Omics Dataset and Clinical Biomarkers from COVID-19 Patients: A Promising Approach to Personalized Medicine.

The COVID-19 pandemic has presented an unprecedented challenge to the healthcare system. Identifying the genomics and clinical biomarkers for effective patient stratification and management is critical to controlling the spread of the disease. Omics datasets provide a wealth of information that can aid in understanding the underlying molecular mechanisms of COVID-19 and identifying potential biomarkers for patient stratification. Artificial intelligence (AI) and machine learning (ML) algorithms have been increasingly used to analyze large-scale omics and clinical datasets for patient stratification. In this manuscript, we demonstrate the recent advances and predictive accuracies in AI- and ML-based patient stratification modeling linking omics and clinical biomarker datasets, focusing on COVID-19 patients. Our ML model not only demonstrates that clinical features are enough of an indicator of COVID-19 severity and survival, but also infers what clinical features are more impactful, which makes our approach a useful guide for clinicians for prioritization best-fit therapeutics for a given cohort of patients. Moreover, with weighted gene network analysis, we are able to provide insights into gene networks that have a significant association with COVID-19 severity and clinical features. Finally, we have demonstrated the importance of clinical biomarkers in identifying high-risk patients and predicting disease progression.

Activation of TLR2 heterodimers-mediated NF-κB, MAPK, AKT signaling pathways is responsible for Vibrio alginolyticus triggered inflammatory response in vitro.

Vibrio alginolyticus is an important zoonotic marine pathogenic bacterium. Previous studies on the mechanism of innate immune against V. alginolyticus infection have been limited to aquatic animals, however, how V. alginolyticus activates mammalian immune cells has not been fully clarified. Here, ELISA combined RT-qPCR assays were used to detect the secretion and transcription level of pro-inflammatory cytokines and TLRs during V. alginolyticus infection of mice peritoneal macrophages (PMϕs). Western blotting was used to explore the phosphorylation levels of p38, JNK, ERK, AKT and NF-κB protein. Immunofluorescence assay was used to determine the location of NF-κB protein. Inhibition assay was used to study the role of up-regulated TLR in activated signaling pathways and the role of these pathways in the release of pro-inflammatory cytokines. Our data showed that V. alginolyticus can up-regulate the expression levels of IL-1ß, IL-6, IL-12 and TNF-α in PMϕs. In addition, V. alginolyticus stimulation activated the phosphorylation of p38, JNK and ERK were TLR2 heterodimers-dependent, whereas inhibitors of SB203580 (p38), SCH772984 (ERK) and SP600125 (JNK) significantly reduced IL-1ß, IL-6, IL-12 and TNF-α production. We further revealed that V. alginolyticus activated the signaling pathways of AKT via TLR2 heterodimers. The inhibitor of MK-2206 2HCl (AKT) negatively regulated the IL-1ß, IL-6 and TNF-α release levels. Moreover, V. alginolyticus infection of PMϕs resulted in TLR2 heterodimers-mediated activation of NF-κB and induced translocation of phosphorylated NF-κB protein from the cytoplasm into the nucleus via IκBα degradation. V. alginolyticus induced IL-1ß, IL-6, IL-12 and TNF-α release were blocked by the specific NF-κB inhibitor, BAY 11-7082. Taken together, our results suggested that activation of the TLR2 heterodimers-mediated downstream signaling pathways NF-κB, MAPK and AKT is responsible for inflammatory response during Vibrio alginolyticus infection in vitro.

Difenoconazole causes spleen tissue damage and immune dysfunction of carp through oxidative stress and apoptosis.

As the use of pesticides increases year after year, so does the level of residual pesticides in the aquatic environment, posing a serious threat to non-target organisms. Difenoconazole (DFZ), a class of long-lasting fungicides and residues in the marine environment, has been shown to cause damaging effects on different organs of aquatic organisms. However, there is no research on the damage of DFZ to carp spleen tissue. This study aimed to investigate the acute toxic effects of DFZ on the spleen tissue of carp (Cyprinus carpio) by exposing juvenile carp to environmentally relevant concentrations of DFZ. We randomly selected 30 carp, divided them into the Control, Low, and High groups, and then exposed the three groups to 0, 0.488 mg/L DFZ, and 1.953 mg/L DFZ for 96 h respectively. We then investigated the toxic effects caused by DFZ on carp and spleen tissues by detecting changes in spleen histopathologic damage, apoptosis, oxidative stress, inflammation, and blood biochemical parameters. We found that DFZ causes severe histopathology in spleen tissue, including ballooning, structural relaxation, and giant mitochondria. In addition, we found that DFZ caused excessive apoptosis in spleen tissue by TUNEL staining and expression levels of apoptosis-related genes (caspase3, caspase8, caspase9, fas, bax, bcl-2, and p53). The activities and transcript levels of the antioxidant enzymes SOD, CAT, and GSH-Px were significantly down-regulated. In addition, DFZ led to a significant increase in activation of the NF-κB signaling pathway and mRNA levels of pro-inflammatory cytokines il-6, il-1ß, and tnf-α, and a substantial decrease in mRNA levels of anti-inflammatory cytokines il-10 and tgf-ß1 in spleen tissue. Blood biochemical parameters showed that DFZ exposure significantly reduced erythrocyte, leukocyte, hemoglobin, C3, and IgM levels. Collectively, DFZ exposure induced apoptosis, immunosuppression, oxidative stress, and inflammatory responses in the spleen tissue of carp, resulting in spleen tissue damage.

Difenoconazole disrupts the blood-brain barrier and results in neurotoxicity in carp by inhibiting the Nrf2 pathway mediated ROS accumulation.

Excessive use of hard-to-degrade pesticides threatens the ecological health of aquatic systems. This study aimed to investigate difenoconazole (DFZ) residues in the environment induced neurotoxicity in carp and the underlying mechanisms. A total of thirty-six carps were divided into three groups and exposed to 0, 0.5, and 2.0 mg/L DFZ for 96 h, respectively. The alterations in behavior and blood-brain barrier (BBB) were examined, and potential mechanisms were explored using immunological assays and biochemical methods. The results showed that DFZ exposure caused behavioral freezing, reduced feeding, and neuronal necrosis in carp. Mechanistically, DFZ triggered ROS accumulation and destroyed the balance between oxidation and antioxidation with increased lipid peroxidation product MDA contents and reduced antioxidant enzymes SOD and CAT activities in the carp brain by inhibiting the NF-E2-related factor 2 (Nrf2) pathway. The activation of oxidative stress further reduced tight junction proteins and MMP levels, thereby destroying BBB and leading to DFZ leakage into the brain. Increased BBB permeability additionally led to DFZ activation of nuclear factor kappa-B signaling-mediated inflammatory cytokine storm, exacerbating neuroinflammation. Meanwhile, DFZ exposure activated mitochondria-associated apoptosis in the carp's brain by up-regulating Bcl-2 associated X protein, cleaved-caspase3, and cytochrome C and decreasing B-cell lymphoma-2 levels. Interestingly, the carp's brain initiated a protective autophagic response via the PI3K/AKT/TOR pathway intending to counteract the neurotoxicity of DFZ. Overall, we concluded that accumulation of DFZ at high concentrations in the aquatic systems disrupted the BBB and resulted in neurotoxicity in carp through inhibition of Nrf2 pathway-mediated ROS accumulation. This study provides a reference for monitoring DFZ residues in the environment and a new target for the treatment of DFZ-induced neurotoxicity in carp.

Protective Effects of Scutellarin on Acute Alcohol Intestinal Injury.

The present study aims to investigate the roles of scutellarin (SCU) on acute alcohol intestinal injury. Mice were divided into six groups: alcohol, three administration, negative control and positive drug bifendate control. The administration group mice were intraperitoneally injected with SCU for 3 consecutive days followed by alcohol gavage at an interval of 1 h. After the mice were sacrificed, colon tissue damage was evaluated by histopathological examination; the activities of inducible nitric oxide synthase (iNOS) and catalase (CAT), as well as the content of malondialdehyde (MDA) were detected using biochemical kits; the levels of inflammatory cytokines mRNA were determined by real-time fluorescence quantitative PCR; the protein expression levels of hemeoxygenase-1 (HO-1) and phosphorylated nuclear factor-ĸB p65 were measured via western blotting. The results showed that alcohol induced severe colon morphological degradation, epithelia atrophy, and more inflammatory cells infiltration in the submucosa. SCU treatment prevented this process, especially in the middle and high dose groups. Alcohol treatment caused excessive lipid peroxidation product accumulation of MDA, restrained the activity of antioxidant enzyme CAT, induced HO-1 expression in the colon, whereas low dose SCU treatment significantly down-regulated the MDA level, enhanced the CAT level, and accelerated HO-1 signals. SCU prevented alcohol stimulation triggered inflammatory response in colon tissues through significantly downregulating the iNOS activity, transcript levels of Tnf-α, Il-1ß and Il-6, and phosphorylation levels of NF-κB p65. These findings suggest that SCU protects the colon via antioxidant and anti-inflammatory mechanisms, making it a promising drug against alcohol-induced colon damage.

Protective Activities of Scutellarin against Alcohol-Induced Acute Kidney Injury.

Acute alcohol consumption has adverse effects in the kidney, resulting in kidney damage and disease, which are typically accompanied by oxidation and inflammation. Scutellarin (SCU) is the major effective ingredient of breviscapine and its anti-inflammation and antioxidant efficacy has been previously reported. The present study revealed the protective effective of SCU as therapeutic medicine against alcohol-induced inflammation and oxidative stress, leading to acute kidney injury (AKI). The AKI model was established by giving 50 % ethanol (12 mL/kg) via lavage. Kidney tissues were collected and used for histopathology analysis, biochemical assays and qRT-PCR analysis. The therapeutic effects of SCU were evaluated by observing pathological changes from HE-stained kidney tissues. Additionally, the anti-inflammation activity of SCU was evaluated by measuring the relative mRNA expression levels of Tnf-α, Il-1ß, Il-6 and the activity of iNOS. The antioxidant capacity was assessed by measuring the lipid peroxidation marker 'MDA' and antioxidant enzymes activity of SOD, CAT and GSH-Px. The results showed that serious swelling and damage occurred in the renal tubular epithelium of alcohol intake group, accompanying with glomerular atrophy, necrosis and increase of inflammatory infiltration. SCU treatment significantly reduced the damage of diseased renal tubular epithelium and glomerular, and less inflammatory cell emerged. The inflammation cytokines expression levels were elevated and oxidative stress index decreased after alcohol intake compared to the control group. In conclusion, inflammation and oxidative stress occur in the kidney after acute and excessive alcohol intake, SCU exhibited protective roles via its anti-inflammation and antioxidant activity in AKI.

Five Rice Seed-Specific NF-YC Genes Redundantly Regulate Grain Quality and Seed Germination via Interfering Gibberellin Pathway.

NF-YCs are important transcription factors with diverse functions in the plant kingdoms including seed development. NF-YC8, 9, 10, 11 and 12 are close homologs with similar seed-specific expression patterns. Despite the fact that some of the NF-YCs are functionally known; their biological roles have not been systematically explored yet, given the potential functional redundancy. In this study, we generated pentuple mutant pnfyc of NF-YC8-12 and revealed their functions in the regulation of grain quality and seed germination. pnfyc grains displayed significantly more chalkiness with abnormal starch granule packaging. pnfyc seed germination and post-germination growth are much slower than the wild-type NIP, largely owing to the GA-deficiency as exogenous GA was able to fully recover the germination phenotype. The RNA-seq experiment identified a total of 469 differentially expressed genes, and several GA-, ABA- and grain quality control-related genes might be transcriptionally regulated by the five NF-YCs, as revealed by qRT-PCR analysis. The results demonstrated the redundant functions of NF-YC8-12 in regulating GA pathways that underpin rice grain quality and seed germination, and shed a novel light on the functions of the seed-specific NF-YCs.

NLRP3 inflammasome signal pathway involves in Vibrio harveyi-induced inflammatory response in murine peritoneal macrophages in vitro.

Vibrio harveyi, an important zoonotic pathogen, can infect wounds and cause inflammatory response. Understanding the inflammatory response pathways could facilitate the exploration of molecular mechanisms for treating V. harveyi infection. NLR family pyrin domain-containing 3 (NLRP3) inflammasome is involved in the interaction between hosts and pathogenic microorganisms and could be sensed by various pathogen-associated molecular patterns (PAMPs) or damage-associated molecular patterns (DAMPs). Nonetheless, the function of NLRP3 inflammasome in V. harveyi infection remains unclear. In the present study, we established a V. harveyi infection model using murine peritoneal macrophages (PMs). Various techniques, including western blot analysis, enzyme-linked immunosorbent assay (ELISA), RT-qPCR, immunofluorescence, and inhibition assays, were used to explore the molecular mechanism of V. harveyi-induced inflammation. The results showed that many inflammatory cytokines participated in V. harveyi infection, with interleukin (IL)-1ß being the most abundant. Pan-caspase inhibitor pretreatment significantly decreased the secretion of IL-1ß in murine PMs. Moreover, the identification of V. harveyi involved a large number of NLR molecules, especially the NLRP3 receptor, and further studies revealed that NLPR3 inflammasome was activated by V. harveyi infection, as evidenced by puncta-like NLRP3 surrounding cell nuclear, ASC specks in the nucleus and cytoplasm, and ASC oligomerization. Inhibition of NLRP3 inflammasome impaired the release of mature IL-1ß in V. harveyi-infected murine PMs. Furthermore, blocking the secretion of mature IL-1ß could markedly decrease the release of other proinflammatory cytokines, including IL-6, IL-12, and tumor necrosis factor-α. Overall, these data indicated that NLRP3 inflammasome was activated in response to V. harveyi infection and enhanced inflammatory response by promoting IL-1ß secretion in murine PMs.

A Novel Allele Encoding 7-Hydroxymethyl Chlorophyll a Reductase Confers Bacterial Blight Resistance in Rice.

Rice spotted leaf mutants are helpful to investigate programmed cell death (PCD) and defense response pathways in plants. Using a map-based cloning strategy, we characterized novel rice spotted leaf mutation splHM143 that encodes a 7-hydroxymethyl chlorophyll a reductase (OsHCAR). The wild-type (WT) allele could rescue the mutant phenotype, as evidenced by complementation analysis. OsHCAR was constitutively expressed at all rice tissues tested and its expression products localized to chloroplasts. The mutant exhibited PCD and leaf senescence with increased H2O2 (hydrogen peroxide) accumulation, increased of ROS (reactive oxygen species) scavenging enzymes activities and TUNEL (terminal deoxyribonucleotidyl transferase-mediated dUTP nick-end labeling) -positive nuclei, upregulation of PCD related genes, decreased chlorophyll (Chl) contents, downregulation of photosynthesis-related genes, and upregulation of senescence-associated genes. Besides, the mutant exhibited enhanced bacterial blight resistance with significant upregulation of defense response genes. Knockout lines of OsHCAR exhibited spotted leaf phenotype, cell death, leaf senescence, and showed increased resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) coupled with upregulation of five pathogenesis-related marker genes. The overexpression of OsHCAR resulted in increased susceptibility to Xoo with decreased expression of pathogenesis-related marker genes. Altogether, our findings revealed that OsHCAR is involved in regulating cell death and defense response against bacterial blight pathogen in rice.

NF-YB1-YC12-bHLH144 complex directly activates Wx to regulate grain quality in rice (Oryza sativa L.).

Identification of seed development regulatory genes is the key for the genetic improvement in rice grain quality. NF-Ys are the important transcription factors, but their roles in rice grain quality control and the underlying molecular mechanism remain largely unknown. Here, we report the functional characterization a rice NF-Y heterotrimer complex NF-YB1-YC12-bHLH144, which is formed by the binding of NF-YB1 to NF-YC12 and then bHLH144 in a sequential order. Knock-out of each of the complex genes resulted in alteration of grain qualities in all the mutants as well as reduced grain size in crnf-yb1 and crnf-yc12. RNA-seq analysis identified 1496 genes that were commonly regulated by NF-YB1 and NF-YC12, including the key granule-bound starch synthase gene Wx. NF-YC12 and bHLH144 maintain NF-YB1 stability from the degradation mediated by ubiquitin/26S proteasome, while NF-YB1 directly binds to the 'G-box' domain of Wx promoter and activates Wx transcription, hence to regulate rice grain quality. Finally, we revealed a novel grain quality regulatory pathway controlled by NF-YB1-YC12-bHLH144 complex, which has great potential for rice genetic improvement.

Notched Belly Grain 4, a Novel Allele of Dwarf 11, Regulates Grain Shape and Seed Germination in Rice (Oryza sativa L.).

Notched belly grain (NBG) is a type of deformed grain shape that has been associated with inferior appearance and tastes in rice. NBG is coordinated by both environments and genetics. In this study, we report on the first map-based cloning of an NBG gene on chromosome 4, denoted NBG4, which is a novel allele of Dwarf 11 encoding a cytochrome P450 (CYP724B1) involved in brassinosteroid (BR) biosynthesis. A 10-bp deletion in the 7th exon knocked down the level of the NBG4 transcript and shifted the reading frame of the resulting protein. In addition to the dwarf and clustered panicle as previously reported in the allelic mutants, nbg4 grains also displayed retarded germination and NBG due to the physical constraint of deformed hulls caused by abnormal hull elongation. NBG4 is constitutively expressed with the highest level of expression in immature inflorescences. In all, 2294 genes were differentially expressed in nbg4 and wild-type (WT), and evidence is presented that NBG4 regulates OsPPS-2, OsPRA2, OsYUCCA1, sped1-D, and Dwarf that play critical roles in determining plant architecture, panicle development, and seed germination. This study demonstrated that NBG4 is a key node in the brassinosteroid-mediated regulation of rice grain shape.

Construction of a Quantitative Acetylomic Tissue Atlas in Rice (Oryza sativa L.).

PKA (protein lysine acetylation) is a key post-translational modification involved in the regulation of various biological processes in rice. So far, rice acetylome data is very limited due to the highly-dynamic pattern of protein expression and PKA modification. In this study, we performed a comprehensive quantitative acetylome profile on four typical rice tissues, i.e., the callus, root, leaf, and panicle, by using a mass spectrometry (MS)-based, label-free approach. The identification of 1536 acetylsites on 1454 acetylpeptides from 890 acetylproteins represented one of the largest acetylome datasets on rice. A total of 1445 peptides on 887 proteins were differentially acetylated, and are extensively involved in protein translation, chloroplast development, and photosynthesis, flowering and pollen fertility, and root meristem activity, indicating the important roles of PKA in rice tissue development and functions. The current study provides an overall view of the acetylation events in rice tissues, as well as clues to reveal the function of PKA proteins in physiologically-relevant tissues.

Characterizing SARS-CoV-2 Spike Sequences Based on Geographical Location.

With the rapid spread of COVID-19 worldwide, viral genomic data are available in the order of millions of sequences on public databases such as GISAID. This Big Data creates a unique opportunity for analysis toward the research of effective vaccine development for current pandemics, and avoiding or mitigating future pandemics. One piece of information that comes with every such viral sequence is the geographical location where it was collected-the patterns found between viral variants and geographical location surely being an important part of this analysis. One major challenge that researchers face is processing such huge, highly dimensional data to obtain useful insights as quickly as possible. Most of the existing methods face scalability issues when dealing with the magnitude of such data. In this article, we propose an approach that first computes a numerical representation of the spike protein sequence of SARS-CoV-2 using k-mers (substrings) and then uses several machine learning models to classify the sequences based on geographical location. We show that our proposed model significantly outperforms the baselines. We also show the importance of different amino acids in the spike sequences by computing the information gain corresponding to the true class labels.

ViralVectors: compact and scalable alignment-free virome feature generation.

The amount of sequencing data for SARS-CoV-2 is several orders of magnitude larger than any virus. This will continue to grow geometrically for SARS-CoV-2, and other viruses, as many countries heavily finance genomic surveillance efforts. Hence, we need methods for processing large amounts of sequence data to allow for effective yet timely decision-making. Such data will come from heterogeneous sources: aligned, unaligned, or even unassembled raw nucleotide or amino acid sequencing reads pertaining to the whole genome or regions (e.g., spike) of interest. In this work, we propose ViralVectors, a compact feature vector generation from virome sequencing data that allows effective downstream analysis. Such generation is based on minimizers, a type of lightweight "signature" of a sequence, used traditionally in assembly and read mapping - to our knowledge, the first use minimizers in this way. We validate our approach on different types of sequencing data: (a) 2.5M SARS-CoV-2 spike sequences (to show scalability); (b) 3K Coronaviridae spike sequences (to show robustness to more genomic variability); and (c) 4K raw WGS reads sets taken from nasal-swab PCR tests (to show the ability to process unassembled reads). Our results show that ViralVectors outperforms current benchmarks in most classification and clustering tasks. Graphical Abstract showing the all steps of proposed approach. We start by collecting the sequence-based data. Then Data cleaning and preprocessing is applied. After that, we generate the feature embeddings using minimizer based approach. Then Classification and clustering algorithms are applied on the resultant data and predictions are made on the test set.

PWM2Vec: An Efficient Embedding Approach for Viral Host Specification from Coronavirus Spike Sequences.

The study of host specificity has important connections to the question about the origin of SARS-CoV-2 in humans which led to the COVID-19 pandemic-an important open question. There are speculations that bats are a possible origin. Likewise, there are many closely related (corona)viruses, such as SARS, which was found to be transmitted through civets. The study of the different hosts which can be potential carriers and transmitters of deadly viruses to humans is crucial to understanding, mitigating, and preventing current and future pandemics. In coronaviruses, the surface (S) protein, or spike protein, is important in determining host specificity, since it is the point of contact between the virus and the host cell membrane. In this paper, we classify the hosts of over five thousand coronaviruses from their spike protein sequences, segregating them into clusters of distinct hosts among birds, bats, camels, swine, humans, and weasels, to name a few. We propose a feature embedding based on the well-known position weight matrix (PWM), which we call PWM2Vec, and we use it to generate feature vectors from the spike protein sequences of these coronaviruses. While our embedding is inspired by the success of PWMs in biological applications, such as determining protein function and identifying transcription factor binding sites, we are the first (to the best of our knowledge) to use PWMs from viral sequences to generate fixed-length feature vector representations, and use them in the context of host classification. The results on real world data show that when using PWM2Vec, machine learning classifiers are able to perform comparably to the baseline models in terms of predictive performance and runtime-in some cases, the performance is better. We also measure the importance of different amino acids using information gain to show the amino acids which are important for predicting the host of a given coronavirus. Finally, we perform some statistical analyses on these results to show that our embedding is more compact than the embeddings of the baseline models.

Vibrio harveyi infections induce production of proinflammatory cytokines in murine peritoneal macrophages via activation of p38 MAPK and NF-κB pathways, but reversed by PI3K/AKT pathways.

Vibrio harveyi is a zoonotic pathogen that can infect humans through wounds and cause severe inflammatory responses. Previous studies have reported that the Toll like receptors (TLR) mediated MAPK, AKT and NF-κB signaling pathways are involved in innate immune system resistance to pathogen invasion. However, the molecular mechanism of these pathways, as well as their involvement in V. harveyi infection remains elusive. This study established a V. harveyi infection model using murine peritoneal macrophages (PMs). Various techniques, including western blotting, ELISA, RT-qPCR, immunofluorescence, inhibition assays, were used to explore the roles of TLRs, MAPK, AKT and NF-κB signaling pathways in V. harveyi-induced inflammatory responses. ELISA assays showed that V. harveyi infection triggered proinflammatory cytokines secretion in PMs. RT-qPCR and inhibition assays showed that TLR2 participated in V. harveyi infection and up-regulated the proinflammatory cytokines secretion in murine PMs. Western blotting data showed that the phosphorylation of p38, JNK, AKT, and NF-κB p65 were significantly increased partly mediated by TLR2. In addition, immunofluorescence assays revealed that the NF-κB p65 translocated into nucleus in response to V. harveyi infection. The secretion of IL-1ß, IL-6, IL-12, and TNF-α were considerably reduced when the p38 MAPK and NF-κB signaling pathways were blocked, whereas blocking of AKT significantly increased the expression of IL-1ß, IL-6, IL-12, and TNF-α. These findings indicate that V. harveyi infection induces inflammatory responses in murine PMs via activation of p38 MAPK and NF-κB pathways, which are partly mediated by TLR2, but are inhibited by PI3K/AKT pathways.

A Novel mechanisms of the signaling cascade associated with the SAPK10-bZIP20-NHX1 synergistic interaction to enhance tolerance of plant to abiotic stress in rice (Oryza sativa L.).

The bzip transcription factors can modulate the transcriptional expressions of target genes by binding specifically to cis-regulatory elements in the promoter region of stress-related genes, hence regulating plant stress resistance. Here, we investigated a stress-responsive transcription factor Osbzip20 under abiotic stresses. The OsbZIP20-GFP fusion protein predominantly aggregated in the nucleus, in accordance with our subcellular localization. OsbZIP20 transcript was observed in all vegetative tissues with highest levels being detected in the seed. Transcription of Osbzip20 was induced by salinity, exsiccation, and abscisic acid. Overexpression of OsbZIP20 in transgenic rice considerably improved tolerance to salt and drought stresses, as well as increased sensitivity to ABA. Furthermore, abiotic stress responsive genes transcript were found to be remarkably elevated in transgenic rice overexpressing OsbZIP20 than in wild-type plants. SAPK10 was discovered to directly interact with and phosphorylate OsbZIP20. Yeast one-hybrid and luciferase assay revealed that OsbZIP20 acted as a transcriptional stimulator. Interestingly, gel shift assay showed that phosphorylated bZIP20 augmented its DNA-binding affinity to the ABRE element of the NHX1 promoter and induced its transcription. In sum, our findings establish a novel signaling pathway associated with the SAPK10-bZIP20-NHX1 synergistic interaction, as well as a new strategy for enhancing rice drought and salt tolerance.

Aeromonas sobria Induces Proinflammatory Cytokines Production in Mouse Macrophages via Activating NLRP3 Inflammasome Signaling Pathways.

Aeromonas sobria, a common conditional pathogenic bacteria, is widely distributed in the environment and causes gastroenteritis in humans or septicemia in fish. Of all Aeromonas species, A. sobria is the most frequently isolated from human infections especially in immunocompromised subjects. Innate immunity is the first protection system of organism to resist non-specific pathogens invasion; however, the immune response process of hosts against A. sobria infection re\mains unexplored. The present study established an A. sobria infection model using primary mouse peritoneal macrophages (PMφs). The adherence and cytotoxicity of A. sobria on PMφs were determined by May-Grünwald Giemsa staining and LDH release measurement. Pro-inflammatory cytokine expression levels were measured using qPCR, western blotting, and ELISA methods. We also investigated the levels of ASC oligomerization and determined the roles of active caspase-1 in IL-1ß secretion through inhibition assays and explored the activated pattern recognition receptors through immunofluorescence. We further elucidated the roles of activated inflammasome in regulating the host's inflammatory response through inhibition combined with ELISA assays. Our results showed that A. sobria induced lytic cell death and LDH release, whereas it had no adhesive properties on PMφs. A. sobria triggered various proinflammatory cytokine transcription level upregulation, and IL-1ß occupied the highest levels. The pro-IL-1ß protein expression levels increased in a dose-dependent manner with MOI ranging from 1 to 100. This process was regulated by ASC-dependent inflammasome, which cleavage pro-IL-1ß into active IL-1ß p17 with activated caspase-1 p20. Meanwhile, the expression levels of NLRP3 receptor significantly increased, location analysis revealed puncta-like surrounding nuclear, and inhibition of NLRP3 inflammasome downregulated caspase-1 activation and IL-1ß secretion. Blocking of NLRP3 inflammasome activation through K+ efflux and cathepsin B or caspase approaches downregulated A. sobria-induced proinflammatory cytokine production. Overall, these data indicated that A. sobria induced proinflammatory cytokine production in PMφs through activating NLRP3 inflammasome signaling pathways.