Multigenerational Adaptation Can Enhance the Pathogen Resistance of Plants via Changes in Rhizosphere Microbial Community Assembly.

Plants withstand pathogen attacks by recruiting beneficial bacteria to the rhizosphere and passing their legacy on to the next generation. However, the underlying mechanisms involved in this process remain unclear. In our study, we combined microbiomic and transcriptomic analyses to reveal how the rhizosphere microbiome assembled through multiple generations and defense-related genes expressed in Arabidopsis thaliana under pathogen attack stress. Our results showed that continuous exposure to the pathogen Pseudomonas syringae pv tomato DC3000 led to improved growth and increased disease resistance in a third generation of rps2 mutant Arabidopsis thaliana. It could be attributed to the enrichment of specific rhizosphere bacteria, such as Bacillus and Bacteroides. Pathways associated with plant immunity and growth in A. thaliana, such as MAPK signaling pathways, phytohormone signal transduction, ABC transporter proteins, and flavonoid biosynthesis, were activated under the influence of rhizosphere bacterial communities. Our findings provide a scientific basis for explaining the relationship between beneficial microbes and defense-related gene expression. Understanding microbial communities and the mechanisms involved in plant responses to disease can contribute to better plant management and reduction of pesticide use.

Enhanced nitrogen removal by an isolated aerobic denitrifying strain in a vertical-flow constructed wetland.

The addition of bacterial agents is an effective method for improving nitrogen removal from wetlands. Herein, an aerobic denitrifier, RC-15, was added to a vertical-flow constructed wetland (CW), and the presence of functional genes and microbial communities was investigated at different CW depths. For the RC-15-treated CW, the removal of NO3- and TN during the process was significantly greater than in the control. Quantitative PCR revealed that nirS is a dominant denitrifying gene for treating WWTP tailwater. Moreover, the presence of the RC-15 strain significantly enhanced the abundance of the napA gene and nirK gene in the CWs. The napA gene was concentrated in the upper layer of the CWs, and the nirK gene was concentrated in the middle and bottom layers. Compared to the control, the addition of the bacterial agent Trial resulted in a more diverse denitrification pathway, a greater abundance of 16Sr RNA, and a greater number of denitrifying strains. According to the microbial community analysis, Proteobacteria and Chloroflexi dominated denitrification in the CWs. Greater abundances of Thauera, Aeromonas and Ardenticatenales were found at the genus level, indicating that these genera have potential applications in future nitrogen removal projects.

Comparative evaluation of soil accumulation of light stabilizers from biodegradable mulching films versus conventional polyethylene ones.

Light stabilizers are commonly used as additives in mulching films and have environmental persistence, bioaccumulation and ecotoxicity. However, their occurrence and distribution in mulching films and accumulation in mulched soils are seldom reported. This study firstly presents a comprehensive screening of 19 light stabilizers in 65 mulching films and 30 farmland soils collected in China, of which five and eight light stabilizers were 100% detected, respectively. The light stabilizer concentration in biodegradable mulching films was significantly higher than that in polyethylene ones, with median concentrations of 1.75 × 106 µg/kg and 4.86 × 103 µg/kg, respectively. Furthermore, a positive correlation was observed between the light stabilizer concentration in mulching films and in soils. This indicates that mulching films play a critical role in the accumulation of light stabilizers in farmland soils, and biodegradable mulching films significantly increase benzotriazole light stabilizers in soils. Although the light stabilizer concentration in farmland soil is relatively low, the sustainable quantities of mulching film input and the long-term accumulation will still pose a threat to the ecological environment and organism health. Consequently, our work reveals the occurrence and environmental risk of light stabilizers in mulching films and farmland soils and brings attention to light stabilizers in the soil environment.

Neurological Sequelae of COVID-19: A Biochemical Perspective.

Exogenous factors can induce protein expression and modify the proteome which sustains for a certain period of time. The proteins of SARS-CoV-2 are high in valine plus glycine, which possess potent affinity to divalent cations such as calcium. Calcium buildup changes the protein expression profile by enabling the efficient synthesis of proteins rich in amino acids with calcium affinity. Subsequent formation of insoluble and stiff calcium oxalate and aggregates confers cellular stress and causes cell senescence. This scenario accounts for sequelae seen in some patients following recovery from COVID-19.

Biofilm-developed biomass residues as novel bulking agents and microbial carriers for synergistically enhanced bioevaporation: Degradation potential and contribution to metabolic heat.

Economical and easily prepared bulking agents and microbial carriers are essential in the practical application of bioevaporation process. Biofilm-developed biomass residues not only provide structural support and microbial sources but also may contribute metabolic heat to the bioevaporation process, achieving the enhanced water evaporation and synergistic treatment of biomass residues. In this study, biofilm was cultivated on the rice straw, wheat straw, sawdust, corncob, luffa cylindrica and palm first, then those biofilm-developed biomass residues were successfully used as the bulking agents and microbial carriers in food waste bioevaporation. The degradation potential (volatile solid degradation ratio) of those biomass residues was in the order of corncob (23.96%), wheat straw (21.12%), rice straw (14.57%), luffa cylindrica (11.02%), sawdust (-2.87%) and palm (-9.24%). It's primarily the degradation of the major components, cellulose and hemicellulose, in corncob and wheat straw governed the metabolic heat contribution (91.73 and 79.61%) to the bioevaporation process. While the high lignin content in sawdust (14.57%) and palm (28.62%) caused negligible degradation of cellulose and hemicellulose, hence made them only function as structural supporter and did not contribute any metabolic heat. Moreover, though the metabolic heat contribution of rice straw and luffa cylindrica reached 58.19 and 37.84%, their lowest lignocellulose content (62.99 and 65.95%) and their lower density, as well as the dominated Xanthomonas (bacteria) and Mycothermus (fungi) led to their rapid collapse during the repeated cycles of bioevaporation. The greatest abundance of thermophilic bacteria (22.3-88.0%) and thermophilic fungi (82.0-99.3%) was observed in the corncob pile. Furthermore, considering the Staphylococcus (pathogenic bacteria) and Candida (animal pathogen) was effectively inhibited, the biofilm-developed corncob was the most favorable bulking agents and microbial carrier for the synergistic bioevaporation of highly concentrated organic wastewater and biomass residues.

Why Omicron Variant of SARS-CoV-2 is Less Fatal?

The article published by Nie et al. addressed one of the two key questions regarding the Omicron variant of SARS-CoV-2, while the underpinning for the less deadly nature of the variant remains unexplained. The proteins of the Omicron variant have numerous mutations, notably several substitutions of other amino acids by lysine residues. Glycine and valine attract calcium and enhance the formation of stressful, insoluble, and stiff calcium oxalate. Lysine residues in proteins build up chloride via ionic bonds which solubilizes insoluble and rigid divalent salts. The aforementioned mutations have weakened the lethalness of the Omicron variant perhaps via a biochemical mechanism. Despite net gain in favorable mutations versus deleterious mutations, the overall valine plus glycine content is still high in the proteins of Omicron variant of SARS-CoV-2, which remains a public health concern.

Epigenetic Modifications and Neurodegenerative Disorders: A Biochemical Perspective.

Methylations in living cells are methyl groups attached to amino acids, DNA, RNA, and so on. However, their biochemical roles have not been fully defined. A theory has been postulated that methylation leads to hyperconjugation, and the electron-donating feature weakens a nearby chemical bond, which increases the bond length of C4-N4 of 5-methylcytosine, therefore weakening the C4-N4 bond and resulting in stronger protonation or hydrogen bonding of the N4 nitrogen atom. Protonation can give rise to the generation of mutagenic and carcinogenic strong acids such as HCl, which are also capable of solubilizing stressful, insoluble, and stiff salts. Insoluble and rigid salts such as calcium oxalate and/or calcium phosphate were recently proposed as a primary cause of some neurodegenerative disorders. Protonation of nitrogen atoms in 5-methylcytosine enhances the interaction with negatively charged phosphate groups and contributes to the formation of compact heterochromatin. The electronegativity of the oxygen atoms in the modifications of 5-hydroxymethylcytosine or 5-formylcytosine can shorten the lengths of adjacent bonds with no increase of cation affinity in N4. The carboxyl group in 5-carboxylcytosine is a weak acid capable of antagonizing mutagenic HCl and modestly helping solubilize insoluble salts. Electron delocalization of the methyl group in N4-methylcytosine results in a lower affinity of N4 to cations. The positive charge at N3 in the resonance structure of 3-methylcytosine is lessened by the electron-donating attribute of the methyl group attached to the N3 atom, consequently reducing acid formation. The electron delocalization of three methyl groups decreases the positive charge in the amino nitrogen in the side group of lysine 4 in histone H3, weakening interactions with phosphate groups and consequently activating gene expression. The carbonyl oxygen in 8-oxo-7,8-dihydroguanine draws protons and accumulates HCl, accounting for its moderate mutation propensity and potential capacity to solubilize stiff salts. The biochemical insight will further our understanding on the crosstalk of genetics and epigenetics in the etiology of neurodegenerative diseases.

Single-stranded DNA generated by high temperature accepts protons and builds up mutagenic and carcinogenic strong acids.

Malignancies are caused by genetic or environmental factors. Esophageal carcinoma can be triggered by consumption of hot food and beverages. Here we propose that high temperature is one of the culprits and it leads to DNA denaturation. Subsequently the exposed hydrogen bonding acceptors in single stranded DNA attract protons which enhance the formation of mutagenic and carcinogenic strong acids such as HCl. Faster mutation of single-stranded DNA viruses than that of double-stranded DNA viruses lends support to this theory.

Prokaryotic Expression of Phosphoenolpyruvate Carboxylase Fragments from Peanut and Analysis of Osmotic Stress Tolerance of Recombinant Strains.

Phosphoenolpyruvate carboxylase (PEPC) is a ubiquitous cytosolic enzyme that catalyzes the irreversible ß-carboxylation of phosphoenolpyruvate (PEP) in presence of HCO3- to produce oxaloacetate (OAA) during carbon fixation and photosynthesis. It is well accepted that PEPC genes are expressed in plants upon stress. PEPC also supports the biosynthesis of biocompatible osmolytes in many plant species under osmotic stress. There are five isoforms of PEPC found in peanut (Arachis hypogaea L.), namely, AhPEPC1, AhPEPC2, AhPEPC3, AhPEPC4, and AhPEPC5. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that the gene expression patterns of these AhPEPC genes were different in mature seeds, stems, roots, flowers, and leaves. The expression of all the plant type PEPC (PTPCs) (AhPEPC1, AhPEPC2, AhPEPC3, and AhPEPC4) was relatively high in roots, while the bacterial type PEPC (BTPC) (AhPEPC5) showed a remarkable expression level in flowers. Principal component analysis (PCA) result showed that AhPEPC3 and AhPEPC4 are correlated with each other, indicating comparatively associations with roots, and AhPEPC5 have a very close relationship with flowers. In order to investigate the function of these AhPEPCs, the fragments of these five AhPEPC cDNA were cloned and expressed in Escherichia coli (E. coli). The recombinant proteins contained a conserved domain with a histidine site, which is important for enzyme catalysis. Results showed that protein fragments of AhPEPC1, AhPEPC2, and AhPEPC5 had remarkable expression levels in E. coli. These three recombinant strains were more sensitive at pH 9.0, and recombinant strains carrying AhPEPC2 and AhPEPC5 fragments exhibited more growth than the control strain with the presence of PEG6000. Our findings showed that the expression of the AhPEPC fragments may enhance the resistance of transformed E. coli to osmotic stress.

Synthetic antimicrobial agents inhibit aflatoxin production.

Antimicrobial peptides (AMPs) are biologically active molecules that can eradicate bacteria by destroying the bacterial membrane structure, causing the bacteria to rupture. However, little is known about the extent and effect of AMPs on filamentous fungi. In this study, we synthesized small molecular polypeptides by an inexpensive heat conjugation approach and examined their effects on the growth of Aspergillus flavus and its secondary metabolism. The antimicrobial agents significantly inhibited aflatoxin production, conidiation, and sclerotia formation in A. flavus. Furthermore, we found that the expression of aflatoxin structural genes was significantly inhibited, and the intracellular reactive oxygen species (ROS) level was reduced. Additionally, the antimicrobial agents can change membrane permeability. Overall, our results demonstrated that antimicrobial agents, safe to mammalian cells, have an obvious impact on aflatoxin production, which indicated that antimicrobial agents may be adopted as a new generation of potential agents for controlling aflatoxin contamination.

Secondary Chemical Bonding between Insoluble Calcium Oxalate and Carbonyl Oxygen Atoms of GLY and VAL Residues Triggers the Formation of Aß Aggregates and Their Deposition in the Brain.

Despite intense efforts, the cause of Alzheimer's disease is still not fully understood. A chemical and biochemical perspective could shed light on this disorder. Secondary chemical bonding between calcium and carbonyl oxygen atoms of glycine and valine might give rise to aggregates in the brain, which may later result in cell senescence. The decrease of solubility caused by amino acid substitutions in specific risk factors compounds insolubility issue and likely triggers early-onset Alzheimer's disease. Occasionally the enhancement of hydrogen bonding by amino acid replacements can reinforce the aggregates. Therefore, secondary chemical bonding to cations can generate cellular stresses in patients with Alzheimer's disease in addition to other chemical and biochemical interactions such as salt bridge. The distinction between early-onset and late-onset Alzheimer's disease risk factors may lie in the total capacity of a protein or local potency of a protein fragment to bind calcium or/and oxalate as calcium oxalate is highly insoluble and stressful.

Local strong acids: A driving force for metastasis.

Carcinogenesis was postulated as the result of the local buildup of strong acids such as hydrogenchloride which may trigger metastasis. A previous study revealed that bicarbonate raised tumor pH and suppressed metastases. The phosphate groups in DNA on neutrophil extracellular traps possess hydrogen bonding capacity and can accept protons. The proteins commonly found in neutrophil extracellular traps such as CCDC25, myeloperoxidase (MPO), histone H3, peptidylarginine deiminase 4 (PAD4) possess basic amino acid content at about 20.2%, 12.8%, 24.3% and 13.0% respectively, which attracts anions such as chloride. The striking 20.2% basic amino acid content in CCDC25 is similar to that of typical oncoproteins. Local hydrogenchloride may be the dominant impetus for metastasis, accounting for the anticancer effects of virtually all weak organic acids, acetic acid and lactic acid in particular.

Is It Possible to Establish a Tumor-Suppressive Microenvironment With Glycine and Valine Supplement?

A tumorigenic microenvironment can give rise to neoplasm. A shift from this condition to a tumor-suppressive microenvironment is of significant benefit to susceptible individuals. The carbonyl groups of glycine and valine have long bond lengths, consequently generating potent affinities to divalent cations such as calcium. We hypothesize that the formation of insoluble and rigid calcium oxalate augmented by glycine and valine counteracts strong acids such as HCl chemically, thus reducing cancer risks. The anticancer effects of the 2 amino acids can be explained from a chemical and biochemical perspective. A tumor-suppressive microenvironment could be established via the modification of the proteome without genome editing at the DNA level.

Is Weak Acid Beneficial for Addressing Checkpoint Inhibitor-Triggered Cancer Hyper Progression in Anti-PD1/PD-L1 Immunotherapies?

Numerous cases of checkpoint inhibitor-triggered cancer hyperprogression have been documented. A previous hypothesis attributes cancer onset to the local buildup of hydrogen chloride, jointly mediated by hydrogen bond donors and acceptors and basic amino acids. The anti-PD1/PD-L1 immunotherapies may have caused a surge of protons or chloride ions for the effective treatment of neoplasm, thus giving rise to the local formation of hydrogen chloride and subsequently cancer hyperprogression in some susceptible individuals. It was postulated that the local strength of acidity is critical for tumor growth and metastasis, as the intake of weak organic acids reduces cancer risks. The anti-PD1/PD-L1 immunotherapies can be integrated with weak organic acids to reduce adverse reactions and generate better anticancer outcomes.