Machine Learning-Assisted Pattern Recognition of Amyloid Beta Aggregates with Fluorescent Conjugated Polymers and Graphite Oxide Electrostatic Complexes

Five fluorescent positively charged poly­(para-aryleneethynylene) (P1–P5) were designed to construct electrostatic complexes C1–C5 with negatively charged graphene oxide (GO). The fluorescence of conjugated polymers was quenched by the quencher GO. Three electrostatic complexes were enough to distinguish between 12 proteins with 100% accuracy. Furthermore, using these sensor arrays, we could identify the levels of Aβ40 and Aβ42 aggregates (monomers, oligomers, and fibrils) via employing machine learning algorithms, making it an attractive strategy for early diagnosis of Alzheimer’s disease

Additional file 1 of Stability is essential for insecticidal activity of Vip3Aa toxin against Spodoptera exigua

Additional file 1: Table S1. Primer sequences used for the generation of Vip3Aa mutants. Table S2. DNA sequences of Vip3Aa and Vip3Ad. Figure S1. The insecticidal activities of Vip3Aa and Vip3Ad against first-instar larvae of S. exigua. Figure S2. N-terminal sequencing identified cleavage-sites of Vip3Ad processed by Spodoptera exigua midgut juice. (A) Spectrum of 19 PTH-amino acids standards; (B)-(F) N-terminal amino acid identification of Vip3Aa activated-toxin. Figure S3. Amino acid sequence alignment of Vip3Aa and Vip3Ad. The sequences in blue box represented the 65 kDa activated-toxins of Vip3Aa and Vip3Ad. The positions of three extra prolines (P591, P605 and P779) was indicated as (●)

Proteolytic Activation of Bacillus thuringiensis Cry2Ab through a Belt-and-Braces Approach

Proteolytic processing of Bacillus thuringiensis (Bt) crystal toxins by insect midgut proteases plays an essential role in their insecticidal toxicities against target insects. In the present study, proteolysis of Bt crystal toxin Cry2Ab by Plutella xylostella L. midgut proteases (PxMJ) was evaluated. Both trypsin and chymotrypsin were identified involving the proteolytic activation of Cry2Ab and cleaving Cry2Ab at Arg¹³⁹ and Leu¹⁴⁴, respectively. Three Cry2Ab mutants (R139A, L144A, and R139A-L144A) were constructed by replacing residues Arg¹³⁹, Leu¹⁴⁴, and Arg¹³⁹-Leu¹⁴⁴ with alanine. Proteolysis assays revealed that mutants R139A and L144A but not R139A-L144A could be cleaved into 50 kDa activated toxins by PxMJ. Bioassays showed that mutants R139A and L144A were highly toxic against P. xylostella larvae, while mutant R139A-L144A was almost non-insecticidal. Those results demonstrated that proteolysis by PxMJ was associated with the toxicity of Cry2Ab against P. xylostella. It also revealed that either trypsin or chymotrypsin was enough to activate Cry2Ab protoxin. This characteristic was regarded as a belt-and-braces approach and might contribute to the control of resistance development in target insects. Our studies characterized the proteolytic processing of Cry2Ab and provided new insight into the activation of this Bt toxin

Construction of an Efficient Non-natural Enzyme System for Preparation of Testosterone in High Space-Time Yield

Testosterone (TS), an important hormone pharmaceutical and precursor for the synthesis of other steroids, is traditionally produced by a polluting and costly multistep chemical synthesis. Producing TS by a biological method is eco-friendly, while its application is still limited by its low substrate-loading, low conversion, long duration, and low time-space yield. Focusing on these problems, a new enzyme system was constructed in which the carbonyl reductase PmCR was employed to reduce 4-androstene-3,17-dione (4-AD) into TS for the first time coupled with the formate dehydrogenase BstFDH_m. Based on molecular dynamics (MD) simulation, the enzyme system was upgraded by rationally designing PmCR, and the variant L136S was screened with a 14-fold enhanced catalytic efficiency kcat/Km and the highest performance in 4-AD reduction. The testosterone production of the L136S-BstFDH_m system was further enhanced by condition optimization and competence to synthesize TS with the highest reported 4-AD loading (28.8 g/L), conversion (100%), and testosterone time-space yield (2.90 g/L/h) using a microbial method, highlighting its promising application in TS synthesis. The successful attempt in this study not only provides a promising biocatalyst and efficient approach for TS green synthesis but also opens the door to the application of carbonyl reductase in the green synthesis of diverse pharmaceutical sterols

Table_1_Trichostatin A, a Histone Deacetylase Inhibitor, Alleviates Eosinophilic Meningitis Induced by Angiostrongylus cantonensis Infection in Mice.DOCX

Histone deacetylase inhibitor (HDACi) has been used in the treatment of neurodegenerative or autoimmune diseases. Angiostrongyliasis cantonensis caused by Angiostrongylus cantonensis infection is an emerging zoonosis of human eosinophilic meningitis or meningoencephalitis. Progressive neuronal apoptosis is the pathological basis of behavioral dysfunctions in angiostrongyliasis cantonensis. Neurological defects after anthelmintic treatment for angiostrongyliasis cantonensis are still common. In this study, we examined the effects of trichostatin A (TSA), a HDACi, on eosinophilic meningitis induced by A. cantonensis in mice. Intragastric administration of TSA significantly ameliorated brain injury and decreased cognitive impairments in mice at 15 days post-infection. TSA administration effectively reduced the inflammatory factor levels of iNOS, TNF-α, IL-5, IL-6, and IL-13 in infected mice. TSA treatment counteracted apoptosis with reduced expression levels of cleaved caspase-3, -4, -6, and RIP3 in A. cantonensis infected mice. In addition, TSA administration reduced total HDAC activity and increased the acetylation of histone H3 and H4 in the brain tissue of infected mice. The underlying mechanism of TSA on eosinophilic meningitis might be associated with decreased NF-κB p65 nuclear accumulation by inhibiting IκB phosphorylation. Furthermore, a co-expressive network of NF-κB p65 with 22 other genes was constructed according to our previous transcriptomic data in infected mice. We identified the correlations in the gene expression of NF-κB p65 with Lrp10, Il12rb1, Nfkbia, Ube2n, and Ube2d1 in infected mice after TSA administration. Thus, TSA has a protective effect on the progression of eosinophilic meningitis induced by A. cantonensis in mice.</p

Data_Sheet_1_Trichostatin A, a Histone Deacetylase Inhibitor, Alleviates Eosinophilic Meningitis Induced by Angiostrongylus cantonensis Infection in Mice.PDF

Histone deacetylase inhibitor (HDACi) has been used in the treatment of neurodegenerative or autoimmune diseases. Angiostrongyliasis cantonensis caused by Angiostrongylus cantonensis infection is an emerging zoonosis of human eosinophilic meningitis or meningoencephalitis. Progressive neuronal apoptosis is the pathological basis of behavioral dysfunctions in angiostrongyliasis cantonensis. Neurological defects after anthelmintic treatment for angiostrongyliasis cantonensis are still common. In this study, we examined the effects of trichostatin A (TSA), a HDACi, on eosinophilic meningitis induced by A. cantonensis in mice. Intragastric administration of TSA significantly ameliorated brain injury and decreased cognitive impairments in mice at 15 days post-infection. TSA administration effectively reduced the inflammatory factor levels of iNOS, TNF-α, IL-5, IL-6, and IL-13 in infected mice. TSA treatment counteracted apoptosis with reduced expression levels of cleaved caspase-3, -4, -6, and RIP3 in A. cantonensis infected mice. In addition, TSA administration reduced total HDAC activity and increased the acetylation of histone H3 and H4 in the brain tissue of infected mice. The underlying mechanism of TSA on eosinophilic meningitis might be associated with decreased NF-κB p65 nuclear accumulation by inhibiting IκB phosphorylation. Furthermore, a co-expressive network of NF-κB p65 with 22 other genes was constructed according to our previous transcriptomic data in infected mice. We identified the correlations in the gene expression of NF-κB p65 with Lrp10, Il12rb1, Nfkbia, Ube2n, and Ube2d1 in infected mice after TSA administration. Thus, TSA has a protective effect on the progression of eosinophilic meningitis induced by A. cantonensis in mice.</p

Additional file 6 of Genus-level evolutionary relationships of FAR proteins reflect the diversity of lifestyles of free-living and parasitic nematodes

Additional file 6: Table S6. Ligand binding ability of nematode FARs

Table_2_Functional Genetic Diversity and Culturability of Petroleum-Degrading Bacteria Isolated From Oil-Contaminated Soils.DOCX

In this study, we compared the culturability of aerobic bacteria isolated from long-term oil-contaminated soils via enrichment and direct-plating methods; bacteria were cultured at 30°C or ambient temperatures. Two soil samples were collected from two sites in the Shengli oilfield located in Dongying, China. One sample (S0) was close to the outlet of an oil-production water treatment plant, and the other sample (S1) was located 500 m downstream of the outlet. In total, 595 bacterial isolates belonging to 56 genera were isolated, distributed in Actinobacteria, Firmicutes, Bacterioidetes, and Proteobacteria. It was interesting that Actinobacteria and Firmicutes were not detected from the 16S rRNA gene clone library. The results suggested the activation of rare species during culture. Using the enrichment method, 239 isolates (31 genera) and 96 (22 genera) isolates were obtained at ambient temperatures and 30°C, respectively, from S0 soil. Using the direct-plating method, 97 isolates (15 genera) and 163 isolates (20 genera) were obtained at ambient temperatures and 30°C, respectively, from two soils. Of the 595 isolates, 244 isolates (41.7% of total isolates) could degrade n-hexadecane. A greater number of alkane-degraders was isolated at ambient temperatures using the enrichment method, suggesting that this method could significantly improve bacterial culturability. Interestingly, the proportion of alkane degrading isolates was lower in the isolates obtained using enrichment method than that obtained using direct-plating methods. Considering the greater species diversity of isolates obtained via the enrichment method, this technique could be used to increase the diversity of the microbial consortia. Furthermore, phenol hydroxylase genes (pheN), medium-chain alkane monooxygenases genes (alkB and CYP153A), and long-chain alkane monooxygenase gene (almA) were detected in 60 isolates (11 genotypes), 91 isolates (27 genotypes) and 93 isolates (24 genotypes), and 34 isolates (14 genotypes), respectively. This study could provide new insights into microbial resources from oil fields or other environments, and this information will be beneficial for bioremediation of petroleum contamination and for other industrial applications.</p

Expression of <i>GhCAX3</i> and <i>sGhCAX3</i> could impair ABA sensitivity in tobacco plants.

<p>(<b>A</b>) Expression analysis of <i>GhCAX3</i> and <i>sGhCAX3</i> in tobacco by RT-PCR. The <i>EF-1α</i> gene was used as an internal control. (<b>B–C</b>) Comparison of seed germination in WT and transgenic lines under NaCl and ABA treatments. (<b>B</b>) Phenotypic analysis of WT and transgenic seeds germinated on 1/2 MS medium for two weeks under normal condition and in presence of 150 mM NaCl as well as 5 µM ABA. (<b>C</b>) Calculation of germinating seeds with green cotyledons. Percentage of germinating seeds with green cotyledons between WT and transgenic lines grown on 1/2 MS medium containing 5 µM ABA was recorded up to 22 days. (<b>D–E</b>) Statistical (<b>D</b>) and phenotypic (<b>E</b>) analysis of WT and transgenic lines after two weeks treatment by ABA. S-10, L-4 and WT seeds were germinated on 1/2 MS medium for 7 days before transferred onto 1/2 MS medium with different concentrations of ABA as indicated. Photograph was taken after 2 weeks growth. (<b>F</b>) Expression analysis of stress-related genes by RT-PCR. Total RNA was extracted from leaf samples at the indicated time points after ABA treatment. Each column in C and D represents an average of four repeats. ** indicates significant differences relative to the control at P<0.01.</p

Table_1_Functional Genetic Diversity and Culturability of Petroleum-Degrading Bacteria Isolated From Oil-Contaminated Soils.DOCX

<p>In this study, we compared the culturability of aerobic bacteria isolated from long-term oil-contaminated soils via enrichment and direct-plating methods; bacteria were cultured at 30°C or ambient temperatures. Two soil samples were collected from two sites in the Shengli oilfield located in Dongying, China. One sample (S0) was close to the outlet of an oil-production water treatment plant, and the other sample (S1) was located 500 m downstream of the outlet. In total, 595 bacterial isolates belonging to 56 genera were isolated, distributed in Actinobacteria, Firmicutes, Bacterioidetes, and Proteobacteria. It was interesting that Actinobacteria and Firmicutes were not detected from the 16S rRNA gene clone library. The results suggested the activation of rare species during culture. Using the enrichment method, 239 isolates (31 genera) and 96 (22 genera) isolates were obtained at ambient temperatures and 30°C, respectively, from S0 soil. Using the direct-plating method, 97 isolates (15 genera) and 163 isolates (20 genera) were obtained at ambient temperatures and 30°C, respectively, from two soils. Of the 595 isolates, 244 isolates (41.7% of total isolates) could degrade n-hexadecane. A greater number of alkane-degraders was isolated at ambient temperatures using the enrichment method, suggesting that this method could significantly improve bacterial culturability. Interestingly, the proportion of alkane degrading isolates was lower in the isolates obtained using enrichment method than that obtained using direct-plating methods. Considering the greater species diversity of isolates obtained via the enrichment method, this technique could be used to increase the diversity of the microbial consortia. Furthermore, phenol hydroxylase genes (pheN), medium-chain alkane monooxygenases genes (alkB and CYP153A), and long-chain alkane monooxygenase gene (almA) were detected in 60 isolates (11 genotypes), 91 isolates (27 genotypes) and 93 isolates (24 genotypes), and 34 isolates (14 genotypes), respectively. This study could provide new insights into microbial resources from oil fields or other environments, and this information will be beneficial for bioremediation of petroleum contamination and for other industrial applications.</p