Genome-scale cis-acting catabolite-responsive element editing confers Bacillus pumilus LG3145 plant-beneficial functions

Rhizosphere dwelling microorganism such as Bacillus spp. are helpful for crop growth. However, these functions are adversely affected by long-term synthetic fertilizer application. We developed a modified CRISPR/Cas9 system using non-specific single-guide RNAs to disrupt the genome-wide cis-acting catabolite-responsive elements (cres) in a wild-type Bacillus pumilus strain, which conferred dual plant-benefit properties. Most of the mutations occurred around imperfectly matched cis-acting elements (cre-like sites) in genes that are mainly involved in carbon and secondary metabolism pathways. The comparative metabolomics and transcriptome results revealed that carbon is likely transferred to some pigments, such as riboflavin, carotenoid, and lycopene, or non-ribosomal peptides, such as siderophore, surfactin, myxochelin, and bacilysin, through the pentose phosphate and amino acid metabolism pathways. Collectively, these findings suggested that the mutation of global cre-like sequences in the genome might alter carbon flow, thereby allowing beneficial biological interactions between the rhizobacteria and plants.

Comparative metabolomic profiling reveals molecular mechanisms underlying growth promotion and disease resistance in wheat conferred by Piriformospora indica in the field

Piriformospora indica, a plant root-colonizing basidiomycete fungus, exhibits strong growth-promoting activity in symbiosis with a broad range of plants. Here, we report the potential of P. indica to improve growth, yield, and disease resistance in wheat in the field. In the present study, P. indica successfully colonized wheat through chlamydospores and formed dense mycelial networks that covered roots. Plants subjected to the seed soaking (SS) treatment with P. indica chlamydospore suspensions enhanced tillering 2.28-fold compared to the non-inoculated wheat in the tillering stage. In addition, P. indica colonization promoted vegetative growth significantly during the three-leaf, tillering, and jointing stages. Moreover, the P. indica-SS-treatment enhanced wheat yield by 16.37 ± 1.63%, by increasing grains per ear and panicle weight and decreased damage to wheat shoot and root architecture markedly, with high field control effects against Fusarium pseudograminearum (81.59 ± 1.32%), Bipolaris sorokiniana (82.19 ± 1.59%), and Rhizoctonia cerealis (75.98 ± 1.36%). Most of the primary metabolites, such as amino acids, nucleotides, and lipids, involved in vegetative reproduction were increased in P. indica-SS-treatment plants, whereas secondary metabolites, such as terpenoids, polyketides, and alkaloids, decreased following P. indica inoculation. The up-regulated processes of protein, carbohydrate, and lipid metabolism indicated that P. indica colonization increased growth, yield, and disease resistance via the acceleration of plant primary metabolism. In conclusion, P. indica improved morphological, physiological, and metabolic substance levels, and further promoted its growth, yield, and disease resistance in wheat.

Invasive fungal infection is associated with antibiotic exposure in preterm infants: a multi-centre prospective case-control study

BACKGROUND

Previous antibiotic exposure is an important risk factor for invasive fungal infection (IFI). Antibiotic overexposure is common in lower-income countries; however, multi-centre studies concerning IFI in relation to antibiotic exposure are scarce.

AIM

This prospective, multi-centre matched case-control study explored the correlation of IFI and antibiotic exposure in very preterm infants or very-low-birthweight infants admitted to 23 tertiary hospitals in China between 2018 and 2021.

METHODS

Using a 1:2 matched design for gestational age, birth weight and early-onset sepsis (yes/no), the risk factors between infants diagnosed with IFI and infection-free controls were compared. The antibiotic use rate (AUR) was calculated using calendar days of antibiotic therapy in the 4 weeks preceding IFI onset divided by onset day of IFI.

FINDINGS

In total, 6368 infants were included in the study, of which 90 (1.4%) were diagnosed with IFI. Median AUR, length of antibiotic therapy (LOT) and days of antibiotic therapy (DOT) within the 4 weeks preceding IFI onset were 0.90, 18 days and 30 days, respectively. Multi-variate analysis showed that a 10% increase in AUR, each additional day of DOT and LOT, and each additional day of third-generation cephalosporins and carbapenems were notably associated with IFI.

CONCLUSION

Prolonged antibiotic therapy is common before the onset of IFI, and is an important risk factor, especially the use of third-generation cephalosporins and carbapenems. Antibiotic stewardship should be urgently developed and promoted for preterm infants in order to reduce IFI in lower-income countries such as China.

Wobble Editing of Cre-box by Unspecific CRISPR/Cas9 Causes CCR Release and Phenotypic Changes in Bacillus pumilus

CRISPR-associated Cas9 endonuclease (CRISPR/Cas9) systems are widely used to introduce precise mutations, such as knocking in/out at targeted genomic sites. Herein, we successfully disrupted the transcription of multiple genes in Bacillus pumilus LG3145 using a series of unspecific guide RNAs (gRNAs) and UgRNA:Cas9 system-assisted cre-box editing. The bases used as gRNAs shared 30–70% similarity with a consensus sequence, a cis-acting element (cre-box) mediating carbon catabolite repression (CCR) of many genes in Bacillus. This triggers trans-crRNA:Cas9 complex wobble cleavage up/downstream of cre sites in the promoters of multiple genes (up to 7), as confirmed by Sanger sequencing and next-generation sequencing (NGS). LG3145 displayed an obvious CCR release phenotype, including numerous secondary metabolites released into the culture broth, ∼ 1.67 g/L white flocculent protein, pigment overflow causing orange-coloured broth (absorbance = 309 nm), polysaccharide capsules appearing outside cells, improved sugar tolerance, and a two-fold increase in cell density. We assessed the relationship between carbon catabolite pathways and phenotype changes caused by unspecific UgRNA-directed cre site wobble editing. We propose a novel strategy for editing consensus targets at operator sequences that mediates transcriptional regulation in bacteria.

Silencing of ATPase family AAA domain-containing protein 2 inhibits migration and invasion of colorectal cancer cells

Colorectal cancer is one of the most common malignant tumors with a high rate of distant metastasis, postoperative recurrence and mortality. ATPase family AAA domain-containing protein 2 (ATAD2), a member of ATPase family, is highly expressed in various cancers, including colorectal cancer. However, whether ATAD2 plays a role in the migration and invasion of colorectal cancer cells remains unknown. In this study, we established ATAD2 knockdown in colorectal cancer cell lines by RNA interference and found that silencing of ATAD2 inhibited the migration and invasion ability of Caco-2 and SW-480 cells. Moreover, ATAD2 silencing suppressed epithelial-mesenchymal transition (EMT), and reduced the expression and enzymatic activity of matrix metalloproteinases (MMPs) in Caco-2 and SW-480 cells. In summary, our results suggest that silencing of ATAD2 inhibits migration and invasion of colorectal cancer cells by suppressing EMT and decreasing the activity of MMPs. Hence, ATAD2 could be considered as a novel molecular marker of metastatic colorectal cancer, and it may provide new insights for clinical diagnosis and treatment of colorectal cancer.

Correlations of MC4R and MSH2 expression with obesity in colon cancer patients

OBJECTIVE

To investigate the correlations of MC4R and MSH2 with adult obesity, a total of 46 patients with early-stage colon cancer were treated in our hospital between February 2008 and February 2009 and were enrolled.

PATIENTS AND METHODS

Venous blood was regularly drawn from subjects of the observation group and 48 healthy subjects for 6 years. Expression levels of MC4R and MSH2 genes were tested using quantitative polymerase chain reaction analyses, and the ensuing proteins were determined using enzyme-linked immunosorbent assays and Western blotting and immunohistochemical analyses. Finally, correlations with body mass index (BMI) and the presence of colon cancer were identified using multivariate analyses.

RESULTS

Compared with the control group, MSH2 mRNA and protein expression increased significantly over time (p < 0.05) in patients with colon cancer. Moreover, MSH2 expression was correlated with colon cancer progression, and MC4R mRNA and protein expression increase concurrently in comparison with the control group (p < 0.05). Also, the mean BMI among patients with colon cancer was 30.8, whereas that among control subjects was only 21.4. These data indicate a relationship between BMI and colon cancer.

CONCLUSIONS

Expression of MSH2 in patients with colon cancer may promote the expression of the obesity gene MC4R, potentially contributing to body weight gains.

Defective expression of regulatory B cells in iodine-induced autoimmune thyroiditis in non-obese diabetic H-2(h4) mice

INTRODUCTION

The ability of B cells to negatively regulate cellular immune responses and inflammation has been described. The regulatory B (Breg) cells with the unique CD1d(hi)CD5(+)CD19(+) phenotype and the capacity to produce IL-10 are potent negative regulators of inflammation and autoimmunity in several in vivo mouse models of autoimmune disease.

AIM

To investigate whether Breg cell deficiency participates in autoimmune thyroiditis (AIT) in an animal model.

MATERIALS AND METHODS

Non-obese diabetic (NOD).H-2(h4) mice at 4 weeks of age were randomly divided into control and iodine-treated groups; the iodine-treated group received sterile water containing 0.005 % NaI for 10 or 20 weeks. The percentage of CD1d(hi)CD5(+)CD19(+) Bregs, CD4(+)CD25(+)FoxP3(+) regulatory T cells (Treg) and CD4(+)IL17(+) T helper 17 cells (Th17) in splenic mononuclear cells was detected by multicolor flow cytometry. The expression of IL-10 mRNA and TGF-β mRNA in splenocytes was measured by real-time RT-PCR.

RESULTS

NOD.H-2(h4) mice spontaneously develop anti-thyroglobulin autoantibodies and intrathyroidal lymphocyte infiltration when supplied with iodine in drinking water. Mice with AIT had a decreased CD1d(hi)CD5(+)CD19(+) Breg subset and reduced IL-10 mRNA expression in splenocytes compared with controls (p < 0.05) and maintained relatively low levels during the development of thyroiditis. The proportion of Breg cells was negatively correlated with the proportion of Th17 cells, but positively correlated with CD4(+)CD25(+)FoxP3(+) Treg cells in splenocytes (All p < 0.05).

CONCLUSIONS

The defective expression of Breg cells combined with impaired Treg cells and enhanced Th17 cells might play an important role in the development of iodine-induced AIT in NOD.H-2(h4) mice.

Heterogeneous processing and zona pellucida binding activity of pig zonadhesin

Zonadhesin is a mosaic protein in sperm membrane fractions that binds directly and in a species-specific manner to the extracellular matrix (zona pellucida) of the oocyte. The active form of pig zonadhesin from capacitated, epididymal spermatozoa comprises two covalently associated polypeptide chains of M(r) 105,000 (p105) and M(r) 45,000 (p45). Here we report detection and characterization of multiple zonadhesin isoforms in freshly ejaculated cells. Antibodies to the predicted von Willebrand D0-D1, D1, and D3 domains of pig zonadhesin recognized p105, p45, and additional M(r) 60,000-90,000 polypeptides in particulate fractions of uncapacitated cells. Although the p105/45 form constituted a minority of all zonadhesin forms in sperm membrane fractions, it was the predominant form capable of binding to the pig zona pellucida. Zonadhesin-binding sites were distributed over the entire zona pellucida. Anion exchange chromatography resolved active, p105/45 zonadhesin from the p60-90 inactive forms. Without disulfide bond reduction some zonadhesin was M(r) > or = 300,000, including M(r) 300,000 and 900,000 proteins comprising in part multimers of p105/45. The multimeric forms did not bind the zona pellucida as avidly as did the p105/45 monomer. Expressed D1 and D3 domain fragments containing the CG(L/V)CG sequence motif spontaneously formed multimers at -246 mV E(h) in vitro. Double Cys --> Ser mutants of the D1 fragment formed multimers with the same apparent kinetics as the wild type protein. Zonadhesin localized to the apical head of pig spermatozoa. We conclude that a heterogeneous combination of specific proteolysis and intermolecular disulfide bond formation in the sperm head generates multiple forms of zonadhesin with differing avidities for the zona pellucida.

Stability of luteinizing hormone releasing hormone: effects of pH, temperature, pig skin, and enzyme inhibitors

The purpose of this investigation was to determine the stability of luteinizing hormone releasing hormone (LHRH) as a function of solution pH, temperature, and pig skin with and without enzyme inhibitors. LHRH, incubated with a 0.1 M phosphate buffer (pH 2.5-8.1), pig skin, and pig skin with enzyme inhibitors, was analyzed using reversed-phase high performance liquid chromatography. The solution's pH affected the rate constants of LHRH, following apparent first-order kinetics. Maximum stability was achieved at pH 6.05. Therefore, the effect of various temperatures (i.e., 65, 75, 80, and 90 degrees C) was studied on the stability of LHRH at pH 6.05. The activation energy for the overall reaction was 23.4 kcal/mol at pH 6.05. The shelf-life of LHRH at 25 degrees C and pH 6.05, calculated using the Arrhenius equation, was approximately 4 years. The rate constant of LHRH in the skin (area: 9 cm2; thickness: 0.5 mm) was 0.167 hr-1. Out of three inhibitors (i.e., aprotinin, bestatin, and leupeptin), bestatin had the best stabilizing effect on the degradation of LHRH by the skin. The rate constant of LHRH in the presence of bestatin was 0.082 hr-1. Sixty percent of LHRH was found to be degraded in the skin within 5 hr in the absence of enzyme inhibitors, whereas only 33% of LHRH was degraded in the presence of bestatin (an aminopeptidase inhibitor).

Application of solid-phase microextraction to the recovery of explosives and ignitable liquid residues from forensic specimens

A current review of the application of solid-phase microextraction (SPME) to the analysis of ignitable liquids and explosive residues is presented along with experimental results demonstrating the relative effects of controllable variables. Variables discussed include fiber chemistry, adsorption and desorption temperatures, extraction and desorption times, fiber sampling placement (direct, headspace, and partial headspace) and matrix effects, including water content. SPME is shown to be an inexpensive, rapid and sensitive method for the analysis of ignitable liquids and high explosives residues from solid debris samples and from aqueous samples. Explosives are readily detected at parts per trillion concentrations and ignitable liquids are reproducibly detected at levels below those using conventional methods.

Effect of buffer pH, buffer concentration and skin with or without enzyme inhibitors on the stability of [Arg(8)]-vasopressin

The stability of [Arg(8)]-vasopressin (AVP) as a function of buffer pH, buffer concentration, salt concentration, temperature, and skin with and without enzyme inhibitors was investigated. AVP was analyzed by reverse-phase high-performance liquid chromatography. The results indicated that the buffer's pH affected the degradation rate of AVP. Buffer ions (H(2)PO(4)(-) and HPO(4)(2-)) and salt concentrations had no effect on the degradation of AVP. Maximum stability was achieved at pH 3.35 among pH values tested. The activation energy for the overall reaction was 21.5 kcal mol(-1) at pH 3.35. From the Arrhenius equation, the shelf-life of AVP at 25 degrees C and pH 3.35 was calculated to be 1.38 years. The degradation rate of AVP in the skin (area: 9 cm(2), thickness: 0.5 mm) was 0.22 h(-1). Bestatin (an aminopeptidase inhibitor) had the best stabilizing effect on the degradation of AVP by skin among the three enzyme inhibitors (i.e. aprotinin, bestatin, and leupeptin) studied. The degradation rate of AVP in the skin was reduced to 0. 059 h(-1) in the presence of bestatin in comparison with no inhibitor (0.22 h(-1)).

[Determination of trace arsenic using GFAAS with metal-coated graphite tube]

The sensitivity, precision and disturbance-resisting property were studied by using metal-coated graphite tube for electrically heated atomic absorption spectrometry. The surface characteristic of the metal-coated graphite tube was studied by using X-ray diffraction meter and scanning electron microscope. The mechanism of satisfactory performance was discussed.