Signal Recognition Particle Research Articles

In silico analysis of the wild-type and mutant-type of BRCA2 gene

BackgroundThe aim of this study was to conduct an in silico analysis of a novel compound heterozygous variant in breast cancer susceptibility gene 2 (BRCA2) to clarify its structure–function relationship and elucidate the molecular mechanisms underlying triple-negative breast cancer (TNBC).MethodsA tumor biopsy sample was obtained from a 42-year-old Chinese woman during surgery, and a maxBRCA™ test was conducted using the patient’s whole blood. We obtained an experimentally determined 3D structure (1mje.pdb) of the BRCA2 protein from the Protein Data Bank (PDB) as a relatively reliable reference. Subsequently, the wild-type and mutant structures were predicted using SWISS-MODEL and AlphaFold, and the accuracy of these predictions was assessed through the SAVES online server. Furthermore, we utilized a high ambiguity-driven protein–protein docking (HADDOCK) algorithm and protein–ligand interaction profiler (PLIP) to predict the pathogenicity of the mutations and elucidate pathogenic mechanisms that potentially underlies TNBC.ResultsHistological examination revealed that the tumor biopsy sample exhibited classical pathological characteristics of TNBC. Furthermore, the maxBRCA™ test revealed two compound heterozygous BRCA2 gene mutations (c.7670 C > T.pA2557V and c.8356G > A.pA2786T). Through performing in silico structural analyses and constructing of 3D models of the mutants, we established that the mutant amino acids valine and threonine were located in the helical domain and oligonucleotide binding 1 (OB1), regions that interact with DSS1.ConclusionOur analysis revealed that substituting valine and threonine in the helical domain region alters the structure and function of BRCA2 proteins. This mutation potentially affects the binding of proteins and DNA fragments and disrupts interactions between the helical domain region and OB1 with DSS1, potentially leading to the development of TNBC. Our findings suggest that the identified compound heterozygous mutation contributes to the clinical presentation of TNBC, providing new insights into the pathogenesis of TNBC and the influence of compound heterozygous mutations in BRCA2.

Mild endoplasmic reticulum stress alleviates FB1-triggered intestinal pyroptosis via the Sec62-PERK pathway

Fumonisin B1 (FB1), a water-soluble mycotoxin released by Fusarium moniliforme Sheld, is widely present in corn and its derivative products, and seriously endangers human life and health. Recent studies have reported that FB1 can lead to pyroptosis, however, the mechanisms by which FB1-induced pyroptosis remain indistinct. In the present study, we aim to investigate the mechanisms of pyroptosis in intestinal porcine epithelial cells (IPEC-J2) and the relationship between FB1-induced endoplasmic reticulum stress (ERS) and pyroptosis. Our experimental results showed that the pyroptosis protein indicators in IPEC-J2 were significantly increased after exposure to FB1. The ERS markers, including glucose-regulated Protein 78 (GRP78), PKR-like ER kinase protein (PERK), and preprotein translocation factor (Sec62) were also significantly increased. Using small interfering RNA silencing of PERK or Sec62, the results demonstrated that upregulation of Sec62 activates the PERK pathway, and activation of the PERK signaling pathway is upstream of FB1-induced pyroptosis. After using the ERS inhibitor 4-PBA reduced the FB1-triggered intestinal injury by the Sec62-PERK pathway. In conclusion, we found that FB1 induced pyroptosis by upregulating Sec62 to activate the PERK pathway, and mild ERS alleviates FB1-triggered damage. It all boils down to one fact, the study provides a new perspective for further, and improving the toxicological mechanism of FB1.Graphical

Uptake of polycyclic aromatic hydrocarbons (PAHs) from PAH–contaminated soils to carrots and Chinese cabbages under the greenhouse and field conditions

Polycyclic aromatic hydrocarbons (PAHs) with the properties of structural stability, semi–volatility, and hydrophobicity are toxic and persistent in environments; thus, their transport and fate in agroecosystems is essential for reducing PAH accumulation in the edible parts of crops. Here, we cultivated cabbages (Brassica pekinensis L.) and carrots (Daucus carota L.) in PAH–contaminated soils under the greenhouse and field conditions. After harvesting, we observed a 9.5–46% reduction in soil ∑PAH concentrations. There were 37% of bioconcentration factors (BCFbs) > 1 and 93% of translocation factors (TFab) > 1, while low–molecular–weight (LMW) PAHs had higher BCFbs than high–molecular–weight (HMW) PAHs. The PAH concentrations showed significant and positive correlations among soils, the belowground parts, and the aboveground parts. The toxicity equivalent concentration (TEQBaP) followed the order of cabbage (greenhouse) > cabbage (field) > carrot (greenhouse) > carrot (field), suggesting potentially higher health risks in cabbage relative to carrot and vegetables under the greenhouse relative to field condition. Our study suggested growing carrots under field conditions as a management strategy for reducing the risks of vegetables grown in PAH–contaminated soils.

Enterocin DD14 can inhibit the infection of eukaryotic cells with enveloped viruses.

Bacteriocins are ribosomally synthesized bacterial peptides endowed with antibacterial, antiprotozoal, anticancer and antiviral activities. In the present study, we evaluated the antiviral activities of two bacteriocins, enterocin DD14 (EntDD14) and lacticaseicin 30, against herpes simplex virus type 1 (HSV-1), human coronavirus 229E (HCoV-229E) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Vero, Huh7 and Vero E6 cells, respectively. In addition, the interactions of these bacteriocins with the envelope glycoprotein D of HSV-1 and the receptor binding domains of HCoV-229E and SARS-CoV-2 have been computationally evaluated using protein-protein docking and molecular dynamics simulations. HSV-1 replication in Vero cells was inhibited by EntDD14 and, to a lesser extent, by lacticaseicin 30 added to cells after virus inoculation. EntDD14 and lacticaseicin 30 had no apparent antiviral activity against HCoV-229E; however, EntDD14 was able to inhibit SARS-CoV-2 in Vero E6 cells. Further studies are needed to elucidate the antiviral mechanism of these bacteriocins.

Docking Proteins Upregulate IL-1β Expression in Lower Esophageal Sphincter Muscle in Esophageal Achalasia.

Background/Objectives: Esophageal achalasia is an archetypal esophageal motility disorder characterized by abnormal peristalsis of the esophageal body and impaired lower esophageal sphincter (LES) relaxation. Methods: In this study, the mRNA expression of docking proteins 1 and 2 (DOK1 and DOK2, respectively) were analyzed and the mechanisms underlying achalasia onset were investigated. Results:DOK1 and DOK2 mRNA levels significantly increased in the LES of patients with achalasia. Moreover, significant correlations were observed between IL-1β and DOK1, IL-1β and DOK2, ATG16L1 and DOK1, and HSV1-miR-H1-3p and DOK2 expression levels. However, a correlation between ATG16L1 and DOK2 or between HSV-miR-H1-3p and DOK1 expression was not observed. In addition, a positive correlation was observed between patient age and DOK1 expression. Microarray analysis revealed a significant decrease in the expression of hsa-miR-377-3p and miR-376a-3p in the LES muscle of patients with achalasia. Conclusions: These miRNAs possessed sequences targeting DOK. The upregulation of DOK1 and DOK2 expression induces IL-1β expression in the LES of achalasia patients, which may contribute to the development of esophageal motility disorder.

Neonicotinoid insecticides in paddy fields: Dissipation dynamics, migration, and dietary risk

Neonicotinoid insecticides (NNIs) have caused widespread contamination of multiple environmental media and posed a serious threat to ecosystem health by accidently injuring non-target species. This study collected samples of water, soil, and rice plant tissues in a water-soil-plant system of paddy fields after spaying imidacloprid (IMI), thiamethoxam (THM), and clothianidin (CLO) to analyze their distribution characteristics and migration procedures and to assess related dietary risks of rice consumption. In the paddy water, the concentrations of NNIs showed a dynamic change of increasing and then decreasing during about a month period, and the initial deposition of NNIs showed a trend of CLO (3.08 μg/L) > THM (2.74 μg/L) > IMI (0.97 μg/L). In paddy soil, the concentrations of the three NNIs ranged from 0.57 to 68.3 ng/g, with the highest residual concentration at 2 h after application, and the concentration trend was opposite to that in paddy water. The initial deposition amounts of IMI, THM, and CLO in the root system were 5.19, 3.02, and 5.24 μg/g, respectively, showing a gradual decrease over time. In the plant, the initial deposition amounts were 19.3, 9.36, and 52.6 μg/g for IMI, THM, and CLO, respectively, exhibiting concentration trends similar to those in the roots. Except for IMI in soil, the dissipation of the NNIs conformed to the first-order kinetic equation in paddy water, soil, and plant. The results of bioconcentration factors (BCFs) and translocation factor (TF) indicated that NNIs can be bi-directionally transported in plants through leaf absorption and root uptake. The risk of NNIs intake through rice consumption was low for all age groups, with a slightly higher risk of exposure in males than in females.

Artificial Floating Islands for the Removal of Nutrients and Improvement of the Quality of Urban Wastewater

A high amount of nutrients can be found in urban wastewater (UW), which makes it difficult to treat. The purpose of this research was to evaluate the potential of the aquatic macrophytes Eichhornia crassipes, Pistia stratiotes, and Salvinia molesta in the treatment of UW. To evaluate the potential of each macrophyte, phytoremediation bioassays were established; the hydraulic retention time for each bioassay was 15 days. The physicochemical analysis of the water samples considered pH, turbidity, electrical conductivity (EC), total dissolved solids (TDS), dissolved oxygen (DO), chemical oxygen demand (COD), total carbon (TC), phosphates (PO43-P), nitrate (NO3-N), and total nitrogen (TN). To evaluate the phytoremediation potential of each plant, the bioconcentration factors (BCFs) and translocation factors (TFs) for NO3-N and PO43-P were evaluated. Likewise, the relative growth rates (RGRs) and total chlorophyll production of the macrophytes were measured. The results showed that the highest efficiency was achieved with the bioassays with E. crassipes, with removal values of 69.7%, 68.8%, 58.7%, 69.4%, 56.3%, and 40.9% for turbidity, COD, TOC, PO43-P, NO3-N, and TN, respectively. The phytoremediation potential results showed that, for BCF, the highest value was 4.88 mg/g of PO43-P with E. crassipes, and for TF, it was 6.17 mg/g of PO43-P with S. molesta. The measurement of RGR and total chlorophyll for E. crassipes showed an increase of 0.00024 gg−1d−1 and an increase of 4.5%, respectively. On the other hand, the other macrophytes suffered decreases in chlorophyll content and RGR. Thus, E. crassipes is defined as the macrophyte with the greatest potential for the UW phytoremediation process.

Genomic analysis of severe COVID-19 considering or not asthma comorbidity: GWAS insights from the BQC19 cohort

BackgroundThe severity of COVID-19 is influenced by various factors including the presence of respiratory diseases. Studies have indicated a potential relationship between asthma and COVID-19 severity.ObjectiveThis study aimed to conduct a genome-wide association study (GWAS) to identify genetic and clinical variants associated with the severity of COVID-19, both among patients with and without asthma.MethodsWe analyzed data from 2131 samples sourced from the Biobanque québécoise de la COVID-19 (BQC19), with 1499 samples from patients who tested positive for COVID-19. Among these, 1110 exhibited mild-to-moderate symptoms, 389 had severe symptoms, and 58 had asthma. We conducted a comparative analysis of clinical data from individuals in these three groups and GWAS using a logistic regression model. Phenotypic data analysis resulted in the refined covariates integrated into logistic models for genetic studies.ResultsConsidering a significance threshold of 1 × 10−6, seven genetic variants were associated with severe COVID-19. These variants were located proximal to five genes: sodium voltage-gated channel alpha subunit 1 (SCN10A), desmoplakin (DSP), RP1 axonemal microtubule associated (RP1), IGF like family member 1 (IGFL1), and docking protein 5 (DOK5). The GWAS comparing individuals with severe COVID-19 with asthma to those without asthma revealed four genetic variants in transmembrane protein with EGF like and two follistatin like domains 2 (TMEFF2) and huntingtin interacting protein-1 (HIP1) genes.ConclusionThis study provides significant insights into the genetic profiles of patients with severe forms of the disease, whether accompanied by asthma or not. These findings enhance our comprehension of the genetic factors that affect COVID-19 severity.Key messagesSeven genetic variants were associated with the severe form of COVID-19;Four genetic variants were associated with the severe form of COVID-19 in individuals with comorbid asthma;These findings help define the genetic component of the severe form of COVID-19 in relation to asthma as a comorbidity.

Protein-Protein Docking and Structural Prediction of KMT2C Variant from Cervical Cancer Whole Exome Sequencing Data

Protein-Protein Docking and Structural Prediction of KMT2C Variant from Cervical Cancer Whole Exome Sequencing Data

Synergistic integration of deep learning with protein docking in cardiovascular disease treatment strategies.

This research delves into the exploration of the potential of tocopherol-based nanoemulsion as a therapeutic agent for cardiovascular diseases (CVD) through an in-depth molecular docking analysis. The study focuses on elucidating the molecular interactions between tocopherol and seven key proteins (1O8a, 4YAY, 4DLI, 1HW9, 2YCW, 1BO9 and 1CX2) that play pivotal roles in CVD development. Through rigorous in silico docking investigations, assessment was conducted on the binding affinities, inhibitory potentials and interaction patterns of tocopherol with these target proteins. The findings revealed significant interactions, particularly with 4YAY, displaying a robust binding energy of -6.39 kcal/mol and a promising Ki value of 20.84 μM. Notable interactions were also observed with 1HW9, 4DLI, 2YCW and 1CX2, further indicating tocopherol's potential therapeutic relevance. In contrast, no interaction was observed with 1BO9. Furthermore, an examination of the common residues of 4YAY bound to tocopherol was carried out, highlighting key intermolecular hydrophobic bonds that contribute to the interaction's stability. Tocopherol complies with pharmacokinetics (Lipinski's and Veber's) rules for oral bioavailability and proves safety non-toxic and non-carcinogenic. Thus, deep learning-based protein language models ESM1-b and ProtT5 were leveraged for input encodings to predict interaction sites between the 4YAY protein and tocopherol. Hence, highly accurate predictions of these critical protein-ligand interactions were achieved. This study not only advances theunderstanding of these interactions but also highlights deep learning's immense potential in molecular biology and drug discovery. It underscores tocopherol's promise as a cardiovascular disease management candidate, shedding light on its molecular interactions and compatibility with biomolecule-like characteristics.

Bioselective and Radiopaque Zinc-Biopolymeric Complex-Based Porous Biomaterials Promote Mammalian Tissue Ingrowth In Vivo While Inhibiting Microbial Biofilm Gene Expression and Biofilm Formation.

Metal-organic complexes have shown astounding bioactive properties; however, they are rarely explored as biomaterials. Recent studies showed that carboxymethyl-chitosan (CMC) genipin-conjugated zinc biomimetic scaffolds have unique bioselective properties. The biomaterial was reported to be mammalian cell-friendly; at the same time, it was found to discourage microbial biofilm formation on its surface, which seemed to be a promising solution to addressing the problem of trauma-associated biofilm formation and development of antimicrobial resistance. However, the mechanically frail characteristics and zinc overload raise concerns and limit the potential of the said biomaterials. Hence, the present work is focused on improving the strength of the earlier scaffold formulations, testing its in vivo efficacy and reaffirming its action against biofilm-forming microbe Staphylococcus aureus. Scaling up of CMC proportion increased rigidity, and 8% CMC was found to be the ideal concentration for robust scaffold fabrication. Freeze-dried CMC scaffolds with or without genipin (GP) cross-linking were conjugated with zinc using 2 M zinc acetate solution. Characterization results indicated that the CMC-Zn scaffolds, without genipin, showed mechanical properties close to bone fillers, resist in vitro enzymatic degradation until 4 weeks, are porous in nature, and have radiopacity close to mandibular bones. Upon implantation in a subcutaneous pocket of Wistar rats, the scaffolds showed tissue in-growth with simultaneous degradation without any signs of toxicity past 28 days. Neither were there any signs of toxicity in any of the vital organs. Considering many superior properties among the other formulations, the CMC-Zn scaffolds were furthered for biofilm studies. CMC-Zn showed negligible S. aureus biofilm formation on its surface as revealed by an alamar blue-based study. RT-PCR analysis revealed that CMC-Zn downregulated the expression of pro-biofilm effector genes such as icaC and clfB. A protein docking study predicted the inhibitory mechanism of CMC-Zn. Although it binds strongly when alone, at high density, it may cause inactivation of the transmembrane upstream activators of the said genes, thereby preventing their dimerization and subsequent inactivation of the effector genes. In conclusion, zinc-conjugated carboxymethyl-chitosan scaffolds are mechanically robust, porous, yet biodegradable, harmless to the host in the long term, they are radiopaque and prevent biofilm gene expression in notorious microbes; hence, they could be a suitable candidate for bone filler applications.

The construction of yeast β-glucan coated-edible dock protein nanomicelles for the encapsulation and sustained release of apigenin

In this study, yeast β-glucan (YG) and edible dock protein (EDP) were used to develop the nanomicelles for delivering apigenin (Api) via self-assembly. Results showed that a stable and uniform Api-EDP-YG composite nanomicelles could be formed when the additive amount of YG was 0.5 wt%, giving the particle size of 351.2 nm and the zeta-potential of −22.59 mV. The composite nanomicelles exhibited a core-shell structure, wherein Api-EDP was a core and YG was a shell. Moreover, hydrogen bonding and van der Waals forces drove the formation of Api-EDP-YG nanomicelles. Meanwhile, the composite nanomicelles can delay the degradation of apigenin in SSF and make it slowly release in SIF, which is benefit for improving its stability and bioavailability. Importantly, the apigenin within the composite nanomicelles displayed a good storage stability and cellular compatibility. These results indicated that the Api-EDP-YG nanomicelles might have a potential application in precision nutritional and healthy foods.

Contribution of early succession regeneration plants to heavy metal remediation in abandoned Artisanal small-scale mining sites in Ghana

Artisanal Small-Scale mining (ASM) is a major land use activity in Ghana. Despite its tremendous contribution to livelihoods, ASM is largely unregulated in the country, illegally operated, leaving most mined out sites unrehabilitated. In this study, we explored the extent to which early succession naturally regenerating plants on two abandoned illegal artisanal small scale mined-out sites (Chamfi and Alluvial types) remediate heavy metals. The study was undertaken in three districts of the Western Region of Ghana. Plots were randomly established in the alluvial, chamfi and reference (control) sites. Within each plot, samples of soil and naturally regenerating plants were collected for determination of bioaccumulation potential, translocation and contamination factor of cadmium (Cd), arsenic (As), lead (Pb), and mercury (Hg) using the Atomic Absorption Spectrophotometer. The results revealed that the concentration of As, Cd, Hg, Pb from soil samples, as well as roots and shoots of the plants collected from the two mined sites were significantly higher than the concentrations in the samples from the control plots. Our results show that heavy metal removal is more significant in plants at the alluvial mined soils than those at the chamfi sites. C. pubescens, C. odorata, and M. pudica were observed to be better cadmium translocators than the other vegetations sampled. Furthermore, plants at the alluvial sites recorded higher Bioaccumulation Factor (BF) in the roots than those at the chamfi sites for lead and arsenic. The study implies that natural regeneration of early successional species can promote contaminant removal on abandoned artisanal mine sites. They however vary in their capacity to accumulate different metals on abandoned soils. Within the context of illegal ASM prevalence, our results suggest that efforts should be made to encourage and minimize disturbances to the growth of early succession plant species as short-term alternative measures in abandoned artisanal mined sites, where reclamation is often neglected.

Investigation of heavy metals uptake in root-shoot of native plant species adjoining wastewater channels.

Metal pollution in water, soil, and vegetation is an emerging environmental issue. Therefore, this study investigated the abundance of heavy metals (HMs) within roots and shoots of native plant species i.e., Bromus pectinatus, Cynodon dactylon, Poa annua, Euphorbia heliscopa, Anagallis arvensis, and Stellaria media grown in the adjoining area of municipal wastewater channels of a Pakistani city of Abbottabad. HMs concentrations (mg L-1) in municipal wastewater were: chromium (Cr) (0.55) > nickel (Ni) (0.09) > lead (Pb) (0.07) > cadmium (Cd) (0.03). Accumulation of HMs in both roots and shoots of plant species varied as B. pectinatus > C. dactylon > P. annua > E. heliscopa > A. arvensis > S. media. Irrespective of the plant species, roots exhibited higher concentrations of HMs than shoots. Higher amount of Cr (131.70 mg kg-1) was detected in the roots of B. pectinatus and the lowest amount (81 mg kg-1) in A. arvensis, Highest Cd concentration was found in the shoot of B. pectinatus and the lowest in the E. heliscopa. The highest concentration of Ni was found in the roots of S. media (37.40 mg kg-1) and the shoot of C. dactylon (15.70 mg kg-1) whereas the lowest Ni concentration was achieved in the roots of A. arvensis (12.10 mg kg-1) and the shoot of E. heliscopa (5.90 mg kg-1). The concentration of HMs in individual plant species was less than 1000 mg kg-1. Considering the higher values (> 1) of biological concentration factor (BCF), biological accumulation co-efficient (BAC), and translocation factor (TF), B. pectinatus and S. media species showed greater potential for HMs accumulation than other species. Therefore, these plants might be helpful for the remediation of HM-contaminated soil.

Combined Effect of Biological and Organic Fertilizers on Agrobiochemical Traits of Corn (Zea mays L.) under Wastewater Irrigation.

Corn (Zea mays L.) is an important annual grain that is cultivated as a food staple around the world. The current study examined the effect of wastewater and a combination of biological and organic fertilizers on the morphological and phytochemical traits of corn, using a factorial experiment based on a randomized complete block design with three replications. The first factor was biological and organic fertilizers at seven levels, including the control (no fertilization), bacterial biological fertilizers (NPK) along with iron and zinc Barvar biofertilizers, fungal biofertilizers made from Mycorrhiza and Trichoderma, biochar, a combination of bacterial and fungal biofertilizers, and a combination of bacterial and fungal biofertilizers with biochar. The second factor was irrigation at two levels (conventional irrigation and irrigation with wastewater). The traits studied included the morphological yield, phenols, flavonoids, polyphenols, glomalin, cadmium content in plant parts, and translocation factor (TF). The results disclosed that the best treatment in regard to the morphological traits was related to conventional water + biochar + mycorrhiza + Trichoderma + NPK. The highest phenol and flavonoid content were observed when biochar + mycorrhiza + Trichoderma + NPK treatments were used in both water treatments. Also, the wastewater + biochar + mycorrhiza + Trichoderma + NPK treatment demonstrated the highest total glomalin and phenylalanine ammonia-lyase (PAL) activity. The obtained results demonstrate that combined biological and organic fertilizer use on corn plants can effectively alleviate the deleterious effects of cadmium present in wastewater.

Pistia Stratiotes based heavy metals phytoremediation of a Himalayan river impacted by hydroelectric plant in an Indo Burma hotspot region

ABSTRACT Present study attempts to study the impact of Serlui-B hydroelectric dam on water quality (‘water-energy nexus’) of a Himalayan river and to devise possible phytotechnology for heavy metals remediation. Physico-chemical characteristics of water were analyzed using ‘American Public Health Association (APHA)’ methods while Atomic Absorption Spectrophotometer (AAS) was used for estimation of heavy metals. To this end, concentrations of Fe and Ni were recorded above permissible limit which can impose public health risks. Therefore, phytoremediation experiments were performed by using Pistia stratiotes L. (water lettuce) and effects of Fe and Ni concentrations (1.0, 2.0, and 5.0 mg/L) on photosynthetic pigments were observed. Phytoremediation investigations using 24 aquaria (of 40.5 L) revealed that P. stratiotes was an effective hyperaccumulator of Fe and Ni with maximum removal efficiency of 96.2% and 92%, respectively. In relation to bioaccumulation indices, the bioconcentration factor (BCF) values decreased with increase in Fe and Ni concentrations, whereas the translocation factor (TF) was noted higher at low concentrations and vice versa. Furthermore, the total chlorophyll content and carotenoid levels in P. stratiotes demonstrated negative significant correlation with the rise in Fe/Ni concentrations that may be considered as an adaptive biochemical strategy to mitigate metals induced oxidative stress. The present study can further be extrapolated to field phytoremediation for ameliorating both physico-chemical and metallic contaminants. Last, the role of microbial biodiversity associated with P. stratiotes should be elucidated in future to help achieve SDG 6 and environmental sustainability.

The mitochondrial carrier homolog 2 is involved in down-regulation of influenza A virus replication.

The mitochondrial carrier homolog 2 (MTCH2) is a mitochondrial outer membrane protein regulating mitochondrial metabolism and functions in lipid homeostasis and apoptosis. Experimental data on the interaction of MTCH2 with viral proteins in virus-infected cells are very limited. Here, the interaction of MTCH2 with PA subunit of influenza A virus RdRp and its effects on viral replication was investigated. The human MTCH2 protein was identified as the influenza A virus PA-related cellular factor with the Y2H assay. The interaction between GST.MTCH2 and PA protein co-expressed in transfected HEK293 cells was evaluated by GST-pull down. The effect of MTCH2 on virus replication was determined by quantification of viral transcript and/or viral proteins in the cells transfected with MTCH2-encoding plasmid or MTCH2-siRNA. An interaction model of MTCH2 and PA was predicted with protein modeling/docking algorithms. It was observed that PA and GST.MTCH2 proteins expressed in HEK293 cells were co-precipitated by glutathione-agarose beads. The influenza A virus replication was stimulated in HeLa cells whose MTCH2 expression was suppressed with specific siRNA, whereas the increase of MTCH2 in transiently transfected HEK293 cells inhibited viral RdRp activity. The results of a Y2H assay and protein-protein docking analysis suggested that the amino terminal part of the viral PA (nPA) can bind to the cytoplasmic domain comprising amino acid residues 253 to 282 of the MTCH2. It is suggested that the host mitochondrial MTCH2 protein is probably involved in the interaction with the viral polymerase protein PA to cause negative regulatory effect on influenza A virus replication in infected cells.

A computational enzymatic optimization for fixing carbon dioxide to starch

Carbon dioxide is fixed and processed into starch by the plants photosynthesis through complicated molecular pathways. While planting and cultivating crops are the major ways to harvest starch, an artificial anabolic pathway has recently been realized in China. Traditional crop production demands extended harvest periods, extensive land, and substantial water use. In contrast, the artificial pathway enhances starch synthesis efficiently, using fewer resources for a more sustainable approach. In 2021, Chinese researchers reported the anabolic starch artificial pathway (ASAP) to synthesize starch in vitro. Although the previous research established a milestone, steps need to be optimized. In this work, enzymatic starch synthesis is chosen to be further engineered, building mutants with similar catalytic functions. Computational tools are used to build an iterative docking-mutating simulation (IDMS). It can automatically finish the cycle of protein mutations and docking. Autodock and Rosetta are used in the coding. 445 different protein mutants are generated and analyzed in silico, among which the best five were chosen for experimental investigation. In the experimental analysis, mutant E shows nearly the same catalytic efficiency as the wild-type in the first hour, with a 2.5-fold expression rate.

Heavy metals immobilization and bioavailability in multi-metal contaminated soil under ryegrass cultivation as affected by ZnO and MnO2 nanoparticle-modified biochar

Pollution by heavy metals (HMs) has become a global problem for agriculture and the environment. In this study, the effects of pristine biochar and biochar modified with manganese dioxide (BC@MnO2) and zinc oxide (BC@ZnO) nanoparticles on the immobilization and bioavailability of Pb, Cd, Zn, and Ni in soil under ryegrass (Lolium perenne L.) cultivation were investigated. The results of SEM–EDX, FTIR, and XRD showed that ZnO and MnO2 nanoparticles were successfully loaded onto biochar. The results showed that BC, BC@MnO2 and BC@ZnO treatments significantly increased shoots and roots dry weight of ryegrass compared to the control. The maximum dry weight of root and shoot (1.365 g pot−1 and 4.163 g pot−1, respectively) was reached at 1% BC@MnO2. The HMs uptake by ryegrass roots and shoots decreased significantly after addition of amendments. The lowest Pb, Cd, Zn and Ni uptake in the plant shoot (13.176, 24.92, 32.407, and 53.88 µg pot−1, respectively) was obtained in the 1% BC@MnO2 treatment. Modified biochar was more successful in reducing HMs uptake by ryegrass and improving plant growth than pristine biochar and can therefore be used as an efficient and cost effective amendment for the remediation of HMs contaminated soils. The lowest HMs translocation (TF) and bioconcentration factors were related to the 1% BC@MnO2 treatment. Therefore, BC@MnO2 was the most successful treatment for HMs immobilization in soil. Also, a comparison of the TF values of plant showed that ryegrass had a good ability to accumulate all studied HMs in its roots, and it is a suitable plant for HMs phytostabilization.

A Targetable Self-association Surface of the Huntingtin exon1 Helical Tetramer Required for Assembly of Amyloid Pre-nucleation Oligomers

Polyglutamine (polyQ) sequences undergo repeat-length dependent formation of disease-associated, amyloid-like cross-β core structures with kinetics and aggregate morphologies often influenced by the flanking sequences. In Huntington’s disease (HD), the httNT segment on the polyQ’s N-terminal flank enhances aggregation rates by changing amyloid nucleation from a classical homogeneous mechanism to a two-step process requiring an ɑ-helix-rich oligomeric intermediate. A folded, helix-rich httNT tetrameric structure suggested to be this critical intermediate was recently reported. Here we employ single alanine replacements along the httNT sequence to assess this proposed structure and refine the mechanistic model. We find that Ala replacement of hydrophobic residues within simple httNT peptides greatly suppresses helicity, supporting the tetramer model. These same helix-disruptive replacements in the httNT segment of an exon-1 analog greatly reduce aggregation kinetics, suggesting that an ɑ-helix rich multimer – either the tetramer or a larger multimer – plays an on-pathway role in nucleation. Surprisingly, several other Ala replacements actually enhance helicity and/or amyloid aggregation. The spatial localization of these residues on the tetramer surface suggests a self-association interface responsible for formation of the octomers and higher-order multimers most likely required for polyQ amyloid nucleation. Multimer docking of the tetramer, using the protein–protein docking algorithm ClusPro, predicts this symmetric surface to be a viable tetramer dimerization interface. Intriguingly, octomer formation brings the emerging polyQ chains into closer proximity at this tetramer-tetramer interface. Further supporting the potential importance of tetramer super-assembly, computational docking with a known exon-1 aggregation inhibitor predicts ligand contacts with residues at this interface.