Reconstructing dynamics correlation network to simultaneously improve activity and stability of 2,3-butanediol dehydrogenase by design of distal interchain disulfide bonds.

The complete enzyme catalytic cycle includes substrate binding, chemical reaction and product release, in which different dynamic conformations are adopted. Due to the complex relationship among enzyme activity, stability and dynamics, the directed evolution of enzymes for improved activity or stability commonly leads to a trade-off in stability or activity. It hence remains a challenge to engineer an enzyme to have both enhanced activity and stability. Here, we have attempted to reconstruct the dynamics correlation network involved with active center to improve both activity and stability of a 2,3-butanediol dehydrogenase (2,3-BDH) by introducing inter-chain disulfide bonds. A computational strategy was first applied to evaluate the effect of introducing inter-chain disulfide bond on activity and stability of three 2,3-BDHs, and the N258C mutation of 2,3-BDH from Corynebacterium glutamicum (CgBDH) was proved to be effective in improving both activity and stability. In the results, CgBDH-N258C showed a different unfolding curve from the wild type, with two melting temperatures (Tm) of 68.3 °C and 50.8 °C, 19.7 °C and 2 °C higher than 48.6 °C of the wild type. Its half-life was also improved by 14.8-fold compared to the wild type. Catalytic efficiency (kcat/Km) of the mutant was increased by 7.9-fold toward native substrate diacetyl and 8.8-fold toward non-native substrate 2,5-hexanedione compared to the wild type. Molecular dynamics simulations revealed that an interaction network formed by Cys258, Arg162, Ala144 and the catalytic residues was reconstructed in the mutant and the dynamics change caused by the disulfide bond could be propagated through the interactions network. This improved the enzyme stability and activity by decreasing the flexibility and locking more "reactive" pose, respectively. Further construction of mutations including A144G showing a 44-fold improvement in catalytic efficiency toward meso-2,3-BD confirmed the role of modifying dynamics correlation network in tunning enzyme activity and selectivity. This study provided important insights into the relationship among dynamics, enzyme catalysis and stability, and will be useful in the designing new enzymes with co-evolution of stability, activity and selectivity.

Identification and characterization of a calcium-binding peptide from salmon bone for the targeted inhibition of α-amylase in digestion.

α-Amylase, essential for carbohydrate digestion, relies on calcium (Ca) for its structural integrity and enzymatic activity. This study explored the inhibitory effect of salmon bone peptides on α-amylase activity through their interaction with the enzyme's Ca-binding sites. Among the various salmon bone hydrolysates, salmon bone trypsin hydrolysate (SBTH) exhibited the highest α-amylase inhibition. The peptide IEELEEELEAER (PIE), with a sequence of Ile-Glu-Glu-Leu-Glu-Glu-Glu-Glu-Leu-Glu-Ala-Glu-Arg from SBTH, was found to specifically target the Ca-binding sites in α-amylase, interacting with key residues such as Asp206, Trp203, His201, etc. Additionally, cellular experiments using 3 T3-L1 preadipocytes indicated PIE's capability to suppress adipocyte differentiation, and decreases in intracellular triglycerides, total cholesterol, and lipid accumulation. In vivo studies also showed a significant reduction in weight gain in the group treated with PIE(6.61%)compared with the control group (33.65%). These findings suggest PIE is an effective α-amylase inhibitor, showing promise for obesity treatment.

Bioavailability and Metabolism of Bioactive Peptide IRW with Angiotensin-Converting Enzyme 2 (ACE2) Upregulatory Activity in Spontaneously Hypertensive Rats.

Peptide IRW is the first food-derived angiotensin-converting enzyme 2 (ACE2) upregulator. This study aimed to investigate the pharmacokinetic characteristics of IRW and identify the metabolites contributing to its antihypertensive activity in spontaneously hypertensive rats (SHRs). Rats were administered 100 mg of IRW/kg of the body weight via an intragastric or intravenous route. The bioavailability (F %) was determined to be 11.7%, and the half-lives were 7.9 ± 0.5 and 28.5 ± 6.8 min for gavage and injection, respectively. Interestingly, significant blood pressure reduction was not observed until 1.5 h post oral administration, or 2 h post injection, indicating that the peptide's metabolites are likely responsible for the blood pressure-lowering activity. Time-course metabolomics revealed a significant increase in the level of kynurenine, a tryptophan metabolite, in blood after IRW administration. Kynurenine increased the level of ACE2 in cells. Oral administration of tryptophan (W), but not dipeptide IR, lowered the blood pressure and upregulated aortic ACE2 in SHRs. Our study supports the key role of tryptophan and its metabolite, kynurenine, in IRW's blood pressure-lowering effects.

Stereodivergent photobiocatalytic radical cyclization through the repurposing and directed evolution of fatty acid photodecarboxylases.

Despite their intriguing photophysical and photochemical activities, naturally occurring photoenzymes have not yet been repurposed for new-to-nature activities. Here we engineered fatty acid photodecarboxylases to catalyse unnatural photoredox radical C-C bond formation by leveraging the strongly oxidizing excited-state flavoquinone cofactor. Through genome mining, rational engineering and directed evolution, we developed a panel of radical photocyclases to facilitate decarboxylative radical cyclization with excellent chemo-, enantio- and diastereoselectivities. Our high-throughput experimental workflow allowed for the directed evolution of fatty acid photodecarboxylases. An orthogonal set of radical photocyclases was engineered to access all four possible stereoisomers of the stereochemical dyad, affording fully diastereo- and enantiodivergent biotransformations in asymmetric radical biocatalysis. Molecular dynamics simulations show that our evolved radical photocyclases allow near-attack conformations to be easily accessed, enabling chemoselective radical cyclization. The development of stereoselective radical photocyclases provides unnatural C-C-bond-forming activities in natural photoenzyme families, which can be used to tame the stereochemistry of free-radical-mediated reactions.

Rationally introducing non-canonical amino acids to enhance catalytic activity of LmrR for Henry reaction.

The use of enzymes to catalyze Henry reaction has advantages of mild reaction conditions and low contamination, but low enzyme activity of promiscuous catalysis limits its application. Here, rational design was first performed to identify the key amino acid residues in Henry reaction catalyzed by Lactococcal multidrug resistance Regulator (LmrR). Further, non-canonical amino acids were introduced into LmrR, successfully obtaining variants that enhanced the catalytic activity of LmrR. The best variant, V15CNF, showed a 184% increase in enzyme activity compared to the wild type, and was 1.92 times more effective than the optimal natural amino acid variant, V15F. Additionally, this variant had a broad substrate spectrum, capable of catalyzing reactions between various aromatic aldehydes and nitromethane, with product yielded ranging from 55 to 99%. This study improved enzymatic catalytic activity by enhancing affinity between the enzyme and substrates, while breaking limited types of natural amino acid residues by introducing non-canonical amino acids into the enzyme, providing strategies for molecular modifications.

Mammalian PIWI-piRNA-target complexes reveal features for broad and efficient target silencing.

The PIWI-interacting RNA (piRNA) pathway is an adaptive defense system wherein piRNAs guide PIWI family Argonaute proteins to recognize and silence ever-evolving selfish genetic elements and ensure genome integrity. Driven by this intensive host-pathogen arms race, the piRNA pathway and its targeted transposons have coevolved rapidly in a species-specific manner, but how the piRNA pathway adapts specifically to target silencing in mammals remains elusive. Here, we show that mouse MILI and human HILI piRNA-induced silencing complexes (piRISCs) bind and cleave targets more efficiently than their invertebrate counterparts from the sponge Ephydatia fluviatilis. The inherent functional differences comport with structural features identified by cryo-EM studies of piRISCs. In the absence of target, MILI and HILI piRISCs adopt a wider nucleic-acid-binding channel and display an extended prearranged piRNA seed as compared with EfPiwi piRISC, consistent with their ability to capture targets more efficiently than EfPiwi piRISC. In the presence of target, the seed gate-which enforces seed-target fidelity in microRNA RISC-adopts a relaxed state in mammalian piRISC, revealing how MILI and HILI tolerate seed-target mismatches to broaden the target spectrum. A vertebrate-specific lysine distorts the piRNA seed, shifting the trajectory of the piRNA-target duplex out of the central cleft and toward the PAZ lobe. Functional analyses reveal that this lysine promotes target binding and cleavage. Our study therefore provides a molecular basis for the piRNA targeting mechanism in mice and humans, and suggests that mammalian piRNA machinery can achieve broad target silencing using a limited supply of piRNA species.

SNHG18 controls vascular smooth muscle cell contractile phenotype and neointimal hyperplasia.

AIMS: Long non-coding RNA (LncRNA) small nucleolar RNA host gene 18 (SNHG18) has been widely implicated in cancers. However, little is known about its functional involvement in vascular diseases. Herein, we attempted to explore a role for SNHG18 in modulating vascular smooth muscle cell (VSMC) contractile phenotype and injury-induced neointima formation. METHODS AND RESULTS: Analysis of single cell RNA sequencing and transcriptomic datasets showed decreased levels of SNHG18 in injured and atherosclerotic murine and human arteries, which is positively associated with VSMC contractile genes. SNHG18 was upregulated in VSMCs by TGFß1 through transcription factors Sp1 and SMAD3. SNHG18 gene gain/loss-of-function studies revealed that VSMC contractile phenotype was positively regulated by SNHG18. Mechanistic studies showed that SNHG18 promotes a contractile VSMC phenotype by up-regulating miR-22-3p. SNHG18 up-regulates miR-22 biogenesis and miR-22-3p production by competitive binding with the A-to-I RNA editing enzyme, adenosine deaminase acting on RNA-2 (ADAR2). Surprisingly, we observed that ADAR2 inhibited miR-22 biogenesis not through increasing A-to-I editing within primary miR-22, but by interfering the binding of microprocessor complex subunit DGCR8 to primary miR-22. Importantly, perivascular SNHG18 overexpression in the injured vessels dramatically up-regulated the expression levels of miR-22-3p and VSMC contractile genes, and prevented injury-induced neointimal hyperplasia. Such modulatory effects were reverted by miR-22-3p inhibition in the injured arteries. Finally, we observed a similar regulator role for SNHG18 in human VSMCs, and a decreased expression level of both SNHG18 and miR-22-3p in diseased human arteries; and we found that the expression level of SNHG18 was positively associated with that of miR-22-3p in both healthy and diseased human arteries. CONCLUSION: We demonstrate that SNHG18 is a novel regulator in governing VSMC contractile phenotype and preventing injury-induced neointimal hyperplasia. Our findings have important implications for therapeutic targeting snhg18/miR-22-3p signalling in vascular diseases.

Ovomucin Hydrolysates Reduce Bacterial Adhesion and Inflammation in Enterotoxigenic Escherichia coli (ETEC) K88-Challenged Intestinal Epithelial Cells.

Enterotoxigenic Escherichia coli (ETEC) K88 is the most common cause of diarrhea in neonatal and postweaning pigs. After adhering to small intestinal epithelial cells via glycoprotein receptor recognition, the pathogen can produce enterotoxins, impair intestinal integrity, trigger watery diarrhea, and induce inflammation via nuclear factor κB (NF-κB) and mitogen-activated protein kinase phosphatase (MAPK) pathways. Inhibiting ETEC K88 adhesion to cell surfaces by interfering with the receptor-fimbriae recognition provides a promising strategy to prevent the initiation and progression of infection. Ovomucin is a highly glycosylated protein in chicken egg white with diverse bioactivities. Ovomucin hydrolysates prepared by the enzymes Protex 26L (OP) and pepsin/pancreatin (OPP) were previously revealed to prevent adhesion of ETEC K88 to IPEC-J2 cells. Herein, we investigated the protective effects of ovomucin hydrolysates on ETEC K88-induced barrier integrity damage and inflammation in IPEC-J2 and Caco-2 cells. Both hydrolysates inhibited ETEC K88 adhesion to cells and protected epithelial cell integrity by restoring transepithelial electronic resistance (TEER) values. Removing sialic acids in the hydrolysates reduced their antiadhesive capacities. Ovomucin hydrolysates suppressed ETEC-induced activation of NF-κB and MAPK signaling pathways in both cell lines. The ability of ETEC K88 in activating calcium/calmodulin-dependent protein kinase 2 (CaMK II), elevating intracellular Ca2+ concentration, and inducing oxidative stress was attenuated by both hydrolysates. In conclusion, this study demonstrated the potential of ovomucin hydrolysates to prevent ETEC K88 adhesion and alleviate inflammation and oxidative stress in intestinal epithelial cells.

Direct and Continuous Monitoring of Multicomponent Antibiotic Gentamicin in Blood at Single-Molecule Resolution.

Point-of-care monitoring of small molecules in biofluids is crucial for clinical diagnosis and treatment. However, the inherent low degree of recognition of small molecules and the complex composition of biofluids present significant obstacles for current detection technologies. Although nanopore sensing excels in the analysis of small molecules, the direct detection of small molecules in complex biofluids remains a challenge. In this study, we present a method for sensing the small molecule drug gentamicin in whole blood based on the mechanosensitive channel of small conductance in Pseudomonas aeruginosa (PaMscS) nanopore. PaMscS can directly detect gentamicin and distinguish its main components with only a monomethyl difference. The 'molecular sieve' structure of PaMscS enables the direct measurement of gentamicin in human whole blood within 10 min. Furthermore, a continuous monitoring device constructed based on PaMscS achieved continuous monitoring of gentamicin in live rats for approximately 2.5 h without blood consumption, while the drug components can be analyzed in situ. This approach enables rapid and convenient drug monitoring with single-molecule level resolution, which can significantly lower the threshold for drug concentration monitoring and promote more efficient drug use. Moreover, this work also lays the foundation for the future development of continuous monitoring technology with single-molecule level resolution in the living body.

Development and validation of a diagnostic nomogram to evaluate tubular atrophy/interstitial fibrosis of IgA nephropathy.

Background: IgA nephropathy (IgAN) is a cause of chronic kidney disease (CKD). Tubular atrophy/interstitial fibrosis is associated with IgAN prognosis. However, simple tools for predicting pathological lesions of IgAN remain limited. Our objective was to develop a tool for evaluating tubular atrophy/interstitial fibrosis in patients with IgAN. Methods: In this cross-sectional study, 410 biopsy-verified IgAN patients were included. The factors associated with the incident interstitial fibrosis or tubular atrophy in IgAN were confirmed by using logistic regression analysis. A nomogram was developed using logistic regression coefficients to evaluate tubular atrophy or interstitial fibrosis. Receiver operating characteristic curves (ROC) and calibration curves were used to determine the discriminative ability and predictive accuracy of the nomogram. Results: In this study, the IgAN patients with tubular atrophy or interstitial fibrosis were older and had a higher percentage of males, hypertension and urinary protein excretion (UPE), with high levels of serum cystatin C, serum creatinine, high-sensitivity C-reactive protein and serum C4. The eGFRcr-cys equation calculated using serum creatinine, cystatin C and UPE were considered independent influencing factors of tubular atrophy or interstitial fibrosis in patients with IgAN. Furthermore, the nomogram demonstrated good discrimination (AUC: 0.87, 95% CI 0.81 to 0.93) and calibration in the validation cohort. Conclusion: The eGFRcr-cys and UPE are associated with tubular atrophy or interstitial fibrosis in patients with IgAN. Diagnostic nomogram can predict tubular atrophy or interstitial fibrosis in IgAN.

Heat-induced pressed gels from canola press cakes: Exploring the impact of starting materials, stirring conditions, and carbohydrase pretreatment.

Alternative plant protein sources offer excellent solutions for tackling the current challenge of food insecurity and sustainability. Inspired by soy tofu, pressed gels represent a robust and versatile way to create protein-enriched plant products. Here, production of heat-induced pressed gels from canola cold-pressed cakes (CPC) and hot-pressed cakes (HPC) was investigated under varied stirring conditions. Pressed gels prepared from CPC resulted in a greater yield and protein recovery than that of HPC. While using carbohydrases as a pretreatment was ineffective in improving yield and protein recovery, applying a stirring condition during heating increased the protein recovery up to 38.3%. Also, stirring condition was proved to be able to modulate the textural properties by controlling the compactness and the size of aggregates. It is revealed that pressed gels are stabilized through a combination of hydrogen bonds, hydrophobic interactions, and disulfide bonds. In comparison to canola press cake, the pressed gels contained less glucosinolates and phenolic compounds, but more phytic acid. A mechanism of formation has been hypothesized based on the nucleation-growth mechanism, and a shift was proposed from diffusion-limited processes in non-stirred pressed gels to reaction-limited process in stirred pressed gels. In conclusion, the potential of canola heat-induced pressed gels was demonstrated both as a stand-alone product and a micro-structured protein extract.

Epidemiology and distribution of cruciate ligament injuries in children and adolescents, with an analysis of risk factors for concomitant meniscal tear.

Introduction: To investigate the epidemiological features and prevalence of cruciate ligament injuries (CLI) in children and adolescents, and to examine the potential risk factors associated with concomitant meniscal tear (MT) among this population. Methods: The demographic data and injury details of children and adolescents with CLI from Southeast China were analyzed to describe their distribution characteristics, alongside an analysis of the prevalence of MTs, the most frequent complication. In addition, binary logistic analysis was employed to ascertain the risk factors linked to MT in individuals suffering from CLI. Results: A total of 203 patients with CLI (n = 206) met the inclusion criteria, with a male-to-female ratio of 2.3:1. Notably, a higher proportion of females were aged ≤16 years old compared to males, who predominated in patients aged >16 years (P = 0.001). Among children and adolescents, anterior cruciate ligament (ACL) injuries were the primary type of CLI, accounting for 88.18% (179/203) of all cases. The majority of cases (132/203, 65.02%) were sustained during sports activities, and sprains were the predominant mechanism of injury (176/203, 86.7%). Additionally, the most common associated injury was an MT (157/203, 77.34%). The posterior horn is the most frequently affected site for both medial MT (62.93% out of 73 cases) and lateral MT (70.19% out of 73 cases). Moreover, vertical tears constituted the majority of medial MTs (59.48% out of 116 cases). Furthermore, patients with a higher BMI faced an increased risk of associated MT in comparison to non-overweight patients (88% vs. 73.86%; P = 0.038). Each increase in BMI unit was linked with a 14% higher probability of associated MT occurrence in children and adolescents with CLI (OR = 1.140; P = 0.036). Discussion: ACL injuries are a common form of knee ligament injury among children and adolescents, especially those over the age of 16, and are often the result of a sprain. Meniscal posterior horn injury is the most commonly associated injury of youth with CLI. Additionally, overweight or obese people with CLI are at a greater risk of developing MT.

A meta-analysis reveals increases in soil organic carbon following the restoration and recovery of croplands in Southwest China.

In China, the Grain for Green Program (GGP) is an ambitious project to convert croplands into natural vegetation, but exactly how changes in vegetation translate into changes in soil organic carbon remains less clear. Here we conducted a meta-analysis using 734 observations to explore the effects of land recovery on soil organic carbon and nutrients in four provinces in Southwest China. Following GGP, the soil organic carbon content (SOCc) and soil organic carbon stock (SOCs) increased by 33.73% and 22.39%, respectively, compared with the surrounding croplands. Similarly, soil nitrogen increased, while phosphorus decreased. Outcomes were heterogeneous, but depended on variations in soil and environmental characteristics. Both the regional land use and cover change indicated by the landscape type transfer matrix and net primary production from 2000 to 2020 further confirmed that the GGP promoted the forest area and regional mean net primary production. Our findings suggest that the GGP could enhance soil and vegetation carbon sequestration in Southwest China and help to develop a carbon-neutral strategy.

N-glycolylneuraminic acid in red meat and processed meat is a health concern: A review on the formation, health risk, and reduction.

One of the most consistent epidemiological associations between diet and human disease risk is the impact of consuming red meat and processed meat products. In recent years, the health concerns surrounding red meat and processed meat have gained worldwide attention. The fact that humans have lost the ability to synthesize N-glycolylneuraminic acid (Neu5Gc) makes red meat and processed meat products the most important source of exogenous Neu5Gc for humans. As our research of Neu5Gc has increased, it has been discovered that Neu5Gc in red meat and processed meat is a key factor in many major diseases. Given the objective evidence of the harmful risk caused by Neu5Gc in red meat and processed meat to human health, there is a need for heightened attention in the field of food. This updated review has several Neu5Gc aspects given including biosynthetic pathway of Neu5Gc and its accumulation in the human body, the distribution of Neu5Gc in food, the methods for detecting Neu5Gc, and most importantly, a systematic review of the existing methods for reducing the content of Neu5Gc in red meat and processed meat. It also provides some insights into the current status and future directions in this area.

Inhibiting acid-sensing ion channel exerts neuroprotective effects in experimental epilepsy via suppressing ferroptosis.

BACKGROUND: Epilepsy is a chronic neurological disease characterized by repeated and unprovoked epileptic seizures. Developing disease-modifying therapies (DMTs) has become important in epilepsy studies. Notably, focusing on iron metabolism and ferroptosis might be a strategy of DMTs for epilepsy. Blocking the acid-sensing ion channel 1a (ASIC1a) has been reported to protect the brain from ischemic injury by reducing the toxicity of [Ca2+ ]i . However, whether inhibiting ASIC1a could exert neuroprotective effects and become a novel target for DMTs, such as rescuing the ferroptosis following epilepsy, remains unknown. METHODS: In our study, we explored the changes in ferroptosis-related indices, including glutathione peroxidase (GPx) enzyme activity and levels of glutathione (GSH), iron accumulation, lipid degradation products-malonaldehyde (MDA) and 4-hydroxynonenal (4-HNE) by collecting peripheral blood samples from adult patients with epilepsy. Meanwhile, we observed alterations in ASIC1a protein expression and mitochondrial microstructure in the epileptogenic foci of patients with drug-resistant epilepsy. Next, we accessed the expression and function changes of ASIC1a and measured the ferroptosis-related indices in the in vitro 0-Mg2+ model of epilepsy with primary cultured neurons. Subsequently, we examined whether blocking ASIC1a could play a neuroprotective role by inhibiting ferroptosis in epileptic neurons. RESULTS: Our study first reported significant changes in ferroptosis-related indices, including reduced GPx enzyme activity, decreased levels of GSH, iron accumulation, elevated MDA and 4-HNE, and representative mitochondrial crinkling in adult patients with epilepsy, especially in epileptogenic foci. Furthermore, we found that inhibiting ASIC1a could produce an inhibitory effect similar to ferroptosis inhibitor Fer-1, alleviate oxidative stress response, and decrease [Ca2+ ]i overload by inhibiting the overexpressed ASIC1a in the in vitro epilepsy model induced by 0-Mg2+ . CONCLUSION: Inhibiting ASIC1a has potent neuroprotective effects via alleviating [Ca2+ ]i overload and regulating ferroptosis on the models of epilepsy and may act as a promising intervention in DMTs.

Chicken Muscle-Derived ACE2-Upregulating Peptide VVHPKESF Reduces Blood Pressure Associated with the ACE2/Ang (1-7)/MasR Axis in Spontaneously Hypertensive Rats.

SCOPE: This study aims to investigate the antihypertensive effect of four chicken muscle-derived angiotensin (Ang)-converting enzymes (ACE)-regulating peptides: Val-Arg-Pro (VRP, ACE inhibition), Leu-Lys-Tyr and Val-Arg-Tyr (LKY and VRY, ACE inhibition and ACE2 upregulation), and Val-Val-His-Pro-Lys-Glu-Ser-Phe (VVHPKESF [V-F], ACE2 upregulation) in spontaneously hypertensive rats. METHODS AND RESULTS: Rats (12-14 weeks old) are grouped: 1) untreated, 2) VRP, 3) LKY, 4) VRY, and 5) V-F. Blood pressure (BP) is monitored using implantable telemetry technology. Over 18-day oral administration of 15 mg kg-1 body weight (BW) per day, only peptide V-F significantly (p < 0.05) reduces BP, decreases circulating Ang II, and increases ACE2 and Ang (1-7) levels, and enhances aortic expressions of ACE2 and Mas receptor (MasR). Peptide V-F also attenuates vascular inflammation (TNFα, MCP-1, IL-1α, IL-15, and cyclooxygenase 2 [COX2]) and vascular oxidative stress (nitrotyrosine). The gastrointestinal (GI)-degraded fragment of peptide V-F, Val-Val-His-Pro-Lys (VVHPK), is also an ACE2-upregulating peptide. Peptides VRP, LKY, and VRY do not reduce BP, possibly due to low bioavailability or other unknown reasons. CONCLUSIONS: Peptide V-F is the first ACE2-upregulating peptide, purified and fractionated from food proteins based on in vitro ACE2 upregulation, that reduces BP associated with the activation of ACE2/Ang (1-7)/MasR axis; the N-terminal moiety VVHPK may be responsible for the antihypertensive effect of V-F.

Canopy nitrogen addition and understory removal destabilize the microbial community in a subtropical Chinese fir plantation.

Subtropical Chinese fir plantations have been experiencing increased nitrogen deposition and understory management because of human activities. Nevertheless, effect of increased nitrogen deposition and understory removal in the plantations on microbial community stability and the resulting consequences for ecosystem functioning is still unclear. We carried out a 5-year experiment of canopy nitrogen addition (2.5 g N m-2 year-1), understory removal, and their combination to assess their influences on microbial community stability and functional potentials in a subtropical Chinese fir plantation. Nitrogen addition, understory removal, and their combination reduced soil bacterial diversity (OUT richness, Inverse Simpson index, Shannon index, and phylogenetic diversity) by 11-18%, 15-24%, and 19-31%; reduced fungal diversity indexes by 3-5%, 5-6%, and 5-7%, respectively. We found that environmental filtering and interspecific interactions together determined changes in bacterial community stability, while changes in fungal community stability were mainly caused by environmental filtering. Fungi were more stable than bacteria under disturbances, possibly from having a more stable network structure. Furthermore, we found that microbial community stability was linked to changes in microbial community functional potentials. Importantly, we observed synergistic interactions between understory removal and nitrogen addition on bacterial diversity, network structure, and community stability. These findings suggest that understory plants play a significant role in promoting soil microbial community stability in subtropical Chinese fir plantations and help to mitigate the negative impacts of nitrogen addition. Hence, it is crucial to retain understory vegetation as important components of subtropical plantations.

Non-canonical amino acids uncover the significant impact of Tyr671 on Taq DNA polymerase catalytic activity.

Responsible for synthesizing the complementary strand of the DNA template, DNA polymerase is a crucial enzyme in DNA replication, recombination and repair. A highly conserved tyrosine (Tyr), located at the C-terminus of the O-helix in family A DNA polymerases, plays a critical role in enzyme activity and fidelity. Here, we combined the technology of genetic code extension to incorporate non-canonical amino acids and molecular dynamics (MD) simulations to uncover the mechanisms by which Tyr671 impacts substrate binding and conformation transitions in a DNA polymerase from Thermus aquaticus. Five non-canonical amino acids, namely l-3,4-dihydroxyphenylalanine (l-DOPA), p-aminophenylalanine (pAF), p-acetylphenylalanine (pAcF), p-cyanophenylalanine (pCNF) and p-nitrophenylalanine (pNTF), were individually incorporated at position 671. Strikingly, Y671pAF and Y671DOPA were active, but with lower activity compared to Y671F and wild-type. Y671pAF showed a higher fidelity than the Y671F, despite both possessing lower fidelity than the wild-type. Metadynamics and long-timescale MD simulations were carried out to probe the role of mutations in affecting protein structure, including open conformation, open-to-closed conformation transition, closed conformation, and closed-to-open conformation transition. The MD simulations clearly revealed that the size of the 671 amino acid residue and interactions with substrate or nearby residues were critical for Tyr671 to determine enzyme activity and fidelity.

Di-(2-ethylhexyl) phthalate (DEHP) contamination suppressed soil microbial biomass carbon and mitigated CO2 emissions against the background of alfalfa from different soils.

Plastic mulching and organic amendments are prevalent agricultural practices worldwide. Plastic mulching has long been suspected as a significant source of DEHP contamination in terrestrial ecosystems. However, effects of DEHP contamination on greenhouse gas emissions and microbial biomass carbon (MBC) remain unclear. Here, a microcosm experiment was set up to assess the impact of DEHP exposure on MBC and carbon dioxide (CO2) emission in two different soils (acidic and alkaline) with the inclusion of alfalfa straw. The treatment includes: (i) control with no amendment (T1); (ii) alfalfa straw addition (20 g kg-1) (T2); (iii) DEHP (10 mg kg-1) + alfalfa straw (T3); and (iv) DEHP (100 mg kg-1) + alfalfa straw (T4). Against the background of alfalfa inclusion, DEHP exposure led to a potential reduction in cumulative CO2 emissions by 16.35 % and 6.91 % in alkaline soil and 12.27 % and 13.65 % in acidic soil for T3 and T4, respectively. The addition of DEHP triggered CO2 emissions and manifested a detrimental negative priming effect in both soil types. In both soils, average CO2 emission fluxes were highest for the T2 treatment. The MBC fluctuated at around 80 mg kg-1 for the control group, alfalfa straw alone (T2) treatment considerably enhanced MBC contents, whereas DEHP contamination in T3 and T4 treatments suppressed the stimulatory effect of alfalfa on MBC in both alkaline and acidic soils. Furthermore, a positive relationship was observed between soil CO2 emissions and MBC in both soils. Overall, these findings highlight the toxic impact of DEHP on MBC and its role in mitigating CO2 emissions in diverse soils. DEHP exposure counters the CO2 emissions induced by alfalfa straw. In addition, the inhibitory effect of DEHP on CO2 fluxes in alkaline soil is less pronounced than in acidic soil. Therefore, further cutting-edge research is crucial since DEHP contamination poses serious ecological threats to agroecosystems.

The complete mitochondrial genome of the Baishanzu horned toad Boulenophrys baishanzuensis (Anura: Megophryidae).

The mitochondrial genome (mitogenome) of Boulenophrys baishanzuensis (Anura: Megophryidae) was sequenced by the Illumina platform. The assembled circular mitogenome of B. baishanzuensis had a total length of 17,040 bp, with a GC content of 41.25%. It consisted of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and a D-loop region. The majority of the PCGs were encoded by the H-strand, while one PCG (nad6) and eight tRNA genes (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser2, tRNA-Glu, and tRNA-Pro) were encoded in the L-strand. Phylogenetic analysis revealed that the newly sequenced species formed a clade with other Boulenophrys species, while the genus Boulenophrys itself formed a sister group with the genus Atympanophrys.