Month: August 2022

Technology

Comparison of SPR detection of SARS-CoV-2 spike protein with using gold nanorods (AuNRs) and gold nanoparticles (AuNPs)

A group from Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, U.K., etc. has reported about comparison of SPR detection of SARS-CoV-2 spike protein with using gold nanorods (AuNRs) and gold nanoparticles (AuNPs).
https://pubs.acs.org/doi/10.1021/acsmacrolett.1c00716

2,3-sialyllactose was immobilized onto AuNPs and AuNRs to detect SARS-CoV-2 with using a SPR detection method.

To highlight the importance of anisotropic particles (e.g., nanorods), spherical AuNRs were compared with AuNPs.
(1)AuNPs (40nm) showed the maximum aborbance at ∼520 nm, and AuNRs (10 × 38 nm) showed the maximum absorbance at ~780 nm.
(2)Although AuNPs (which generates a signal due to aggregation) did not show significant spectral changes with this spike protein, AuNRs showed spectral change with increasing concentration of spike protein.
(3)The signal output from AuNRs using the primary clinical samples was correlated with the Ct (cycle threshold) values from RT-PCR.

Thus, it has clearly shown that AuNRs are better than AuNPs.

Nature

Human surfactant protein D facilitates SARS-CoV-2 binding and entry in DC-SIGN expressing cells

A group from College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK, etc. has reported that human surfactant protein D (human SP-D) facilitates SARS-CoV-2 binding and entry in DC-SIGN expressing cells
https://www.frontiersin.org/articles/10.3389/fimmu.2022.960733/full

The ability of a recombinant fragment of human SP-D (rfhSP-D) to mediate the binding of SARS-CoV-2 to DC-SIGN expressing cells was evaluated. HEK 293T cells were transfected with a construct containing a DNA sequence of full-length human DC-SIGN to induce DC-SIGN cell surface expression (DC-HEK cells). To assess the effect of rfhSP-D on pseudotypes binding to DC HEK cells, the DC-HEK cells were challenged with rfhSP-D (20µg/ml) treated SARS-CoV-2 Spike protein-expressing pseudotype. Increased binding (~50%) in the treated samples (DC-HEK + SARS-CoV-2 spike Pseudotypes + rfhSP-D) compared to their untreated counterparts (DC-HEK + SARS-CoV-2 spike Pseudotypes) was observed. Similar experiments were done using THP-1 cells treated with PMA and IL-4 to induce the expression of native DC-SIGN. rfhSP-D treatment was found to increase the binding efficiency of the pseudotypes to the THP-1 cells expressing DC-SIGN by ~25%, compared to the untreated controls.

A blind docking approach was attempted to generate SARS-CoV-2 and DC-SIGN complexes. Analysis of the top ranked docked poses revealed that NTD (N-terminal domain) of spike protein interacted with the CRD domain of DC-SIGN. Tripartite complexes were generated by docking C-SIGN and SP-D with Spike protein. The top two docked poses (C1 and C2) were analysed for intermolecular interactions. In both C1 and C2 complexes, DC-SIGN (CRD) interacted with NTD domain of Spike protein. In C1, there were no molecular interactions between Spike protein and rfhSP-D. In C2, Spike protein interacted with rfhSP-D through RBD.

As a conclusion, it was shown that SP-D interacts with RBD and DC-SIGN interacts with NTD of SARS-CoV-2 spike protein, and also SP-D stabilises DC-SIGN and SARS-CoV-2 spike protein interaction.

Technology

Ceruloplasmin with bisecting GlcNAc could be a good biomarker for pancreatic cancer

A group from College of Basic Medical Sciences, Dalian Medical University, Dalian, China, etc. has reported that ceruloplasmin with bisecting GlcNAc could be a good biomarker for pancreatic cancer.
https://www.mdpi.com/2073-4409/11/15/2453/htm

Compared with the normal controls (NC) group, the relative abundances of bisecting glycans, mannosylation, and fucosylation were significantly increased in the pancreatic cancer (PC) group. Compared with the acute pancreatitis (AP) group, the relative abundances of bisecting glycans and fucosylation were significantly enhanced in the PC group; however, the relative abundances of fucosylation seemed similar between the NC and AP groups.

Since glycans are difficult to be developed as biomarkers alone, the serum glycoproteins containing bisecting glycans were pulled down with biotinylated PHA-E lectin and streptavidin agarose beads, and analyzed by nano LC-MS/MS. As a result, three proteins, Ceruloplasmin (Cp), apolipoprotein E (Apo-E), and transferrin (Tf) were listed as biomarker glycoproteins.

Among these candidates, Cp showed the highest performance: the AUC for Cp between NC and AP, NC and PC, and PC and AP, were 0.917, 0.972, and 0.757, respectively.

Nature

Bacilli’s biofilm formation capability is critical to fulfill biocontrol activity against phytopathogens

A group from College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China has reported that the biofilm formation enhanced Bacillus root colonization and its biocontrol activity against phytopathogens.
https://www.frontiersin.org/articles/10.3389/fmicb.2022.972393/full

Bacilli are used as biocontrol agents (BCAs) against phytopathogens and most of them can produce poly-γ-glutamic acid (γ-PGA) as one of the major extracellular polymeric substances (EPSs).

In this study, Bacillus atrophaeus NX-12 (γ-PGA yield: 16.8 g/l) was compared with its γ-PGA synthesis gene knocked out strain NX-12Δpgs from a view point of antifungal ability. The antifungal ability of γ-PGA synthetase-deficient strain NX-12Δpgs (γ-PGA yield: 1.65 g/l) was improved in vitro, while the biocontrol ability of NX-12Δpgs was greatly diminished in situ.

It was proved that γ-PGA produced by NX-12 contributes to the biofilm formation and rhizosphere colonization, which effectively improved biocontrol capability suggesting that the effective colonization of Bacilli as biocontrol agents in the rhizosphere is very important for its function.


NX-12Δpgs (pMA5-pgs) means that the mutant NX-12Δpgs was complemented with a primer pMA5-pgsBCA, where pgsBCA is a γ-PGA synthase gene of NX-12.

Nature, Technology

The crystal structure of Cry78Aa from Bacillus thuringiensis: consists of a lectin domain and a pore-forming domain

A group from Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China, etc. has reported about the crystal structure of Cry78Aa from Bacillus thuringiensis.
https://www.nature.com/articles/s42003-022-03754-6

Biological control methods using Bacillus thuringensis (Bt) as well as genetically modified plants expressing insecticidal proteins from Bt have been proven effective and economic against some insect pests. Cry78Aa is a novel protein identified from the Bt C9F1 strain that effectively kills rice planthoppers, with median lethal concentration (LC50) values against Laodelphax striatellus and Nilaparvata lugens of 6.89 and 15.78 μg ml−1, respectively. The activity of Cry78Aa does not require in vitro activation or any additional components, making it convenient for application in field trials.

In this paper, the crystal structure of Cry78Aa was analyzed in detail. This structure consists of two independent domains: a trefoil domain at the N-terminus, which shares the highest identity with S-type lectin, and a pore-forming domain belonging to the aerolysin family. Bioassays showed that the NTD or CTD of Cry78Aa alone has no toxicity against planthopper nymphs, indicating that its insecticidal activity is dependent on the cooperation of both domains. The NTD of Cry78Aa plays a vital role for its insecticidal activity, probably by recognize galactose derivatives linked to proteins or lipids on the surface of the cell membrane.

Technology

Streptococcal Pharyngitis detection using H-1 antigen (glycan probe) conjugated Gold Nanoparticles

A group from Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran, etc. has reported about a Nanobiosensor based on H-1 antigen-Gold NanoParticles (AuNPs) aggregation detecting M1 Streptococcal Pharyngitis.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9354983/

Streptococcus pyogenes (GAS) is a Gram positive bacterium that causes a wide variety of clinical conditions, ranging from acute pharyngitis to severe invasive diseases. A common method for the diagnosis of streptococcal pharyngitis is a physical examination by a physician and then a bacterial culture of throat swab. Until now, various types of biosensors were developed to diagnose GAS for clinical use. Those are based on antibody-antigen interactions, or on an isothermal nucleic acid amplification technology. Nevertheless, they are not widely used by clinicians worldwide, which may be related to the high cost.

The nanobiosensors based on the aggregation of AuNPs are well-known, and have been studied as an easy-to-use diagnosis of pathogens, where the presence of a specific antigen in a colloidal medium containing bioreceptor–AuNPs conjugates results in the aggregation of nanoparticles. Since it is known that M1 GAS binds to H-1 antigen, in this study, a sugar code present on oral epithelial cells, Lacto-N-fucopentaose I-biotin (H-1-biotin) was conjugated on avidin-AuNPs as an antigen to detect M1 GAS.

Based on the value of red-shift in SPR position, a calibration curve for detection of M1 GAS was plotted at a concentration range from 1 × 102 up to 1 × 107 CFU/ml. It was found that M1 GAS was detected in a wide concentration range (1 × 103 – 1×106 CFU/ml) with a linear response and a short detection time of 20 min.

Technology

Lectins specific to bisecting GlcNAc

A group from Department of Chemistry, Georgia State University, Atlanta GA USA, etc. has reported about lectins specific to bisecting GlcNAc.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9241959/

Many plant lectins could tolerate the bisecting GlcNAc, among which the bindings of PHA-E and Calsepa were enhanced. It was observed that even at a low concentration (1 μg mL−1), PHA-E and Calsepa showed bindings to non-bisected N-glycans, which would pose a significant problem in their wide applications of bisected glycan identification and cancer biomarker discovery. Surprisingly, PHA-L exhibited specific recognition of bisected biantennary N-glycans, which could find promising implementation in probing such structures, e.g., in antibodies, where β1-6-branched glycans are absent.
However, it should be noted that PHA-L has a strong specificity for tri/tetra antennary N-glycans.

Nature, Technology

O-Glycosylation changes in serum IgG3 could be a marker for inflammation development in advanced endometriosis

A group from Division of Laboratory Diagnostics, Faculty of Pharmacy, Wroclaw Medical University, Poland, etc. has reported that O-Glycosylation changes in serum IgG3 could be a marker for inflammation development in advanced endometriosis.
https://www.mdpi.com/1422-0067/23/15/8087/htm

Structurally, human IgG N-linked glycans are typically biantennary complexes. The second N-glycosylation site is found in the VH and VL (heavy and light chain of variable regions, respectively) and has been observed in 15–25% of all serum IgG. The presence of glycans in the IgG Fab region may contribute to higher antibody stability and modulate antigen binding. For IgG3, apart from N-glycans present in the Fab and Fc regions, the presence of O-linked glycans in the hinge region is also observed.

In blood serum, about 10% of IgG3 polyclonal antibodies and about 13% of IgG3 monoclonal antibodies are considered to contain O-glycans. Each IgG3 molecule can contain up to three O-glycans linked to threonine residues in the triple repeat regions within the hinge region. Although the function of IgG O-glycosylation is still not fully understood, the structure of the hinge region is hypothesized to be able to protect the immunoglobulin from proteolytic cleavage, and may also help maintain the extended conformation and flexibility of IgG3.

In this study, it was examined whether O-glycans are expressed in serum IgG in advanced endometriosis, and also whether, additionally to the presence of biantennary N-glycans, there are also highly branched N-glycans in IgG, and if so, whether the degree of their expression is characteristic of advanced endometriosis.

For the analysis of serum IgG O-glycosylation and the expression of multi-antennary N-glycans, lectin-ELISA with lectins specific to O-glycans (MPL, VVL, and Jacalin) and highly branched N-glycans (PHA-L) was used. And also, isolated serum IgG, i-IgG, and native serum IgG, s-IgG, were examined as samples.

The results were striking. In the case of s-IgG, the clinical value was limited. In the case of i-IgG, however, a maximum high clinical value (AUC = 1) was obtained with all four lectins used, both when comparing women with advanced endometriosis to healthy women and healthy women to a non-endometriosis group.
While this research has shown that both the expression of O-glycans and highly branched N-glycans in IgG may have a potential application in the diagnostics of advanced endometriosis, at the present stage of research, these conclusions mainly concern IgG isolated from serum. This makes it difficult to apply this type of determination in routine diagnostics due to the laborious and time-consuming procedure of protein isolation and purification. Nevertheless, this direction of research seems to be promising, and the development of a simple and fast protein isolation procedure is required.

Technology

Fumigation treatment was better than bioagent treatment in continuous cropping fields: Why is that happened?

A group from School of Minerals Processing and Bioengineering, Central South University, Changsha, China, etc. has reported that fumigation treatment was better than bioagent treatment in continuous cropping fields.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9354655/

Continuous cropping alters soil physiochemical properties and microbial community, causes soil salinization and acidification, accumulates harmful microbes, reduces fertilizer efficiency, and leads to severe soil-borne diseases, resulting in yield reduction and huge economic losses in agriculture production.

In this study, fumigation and biological agent treatments were evaluated to alleviate continuous cropping barriers. Three fumigation treatments, namely, chloropicrin (FM1), dazomet (FM2), and untreated control (CK_FM), and three biological treatments, namely, two biological agents (AG1 and AG2) offered by Prof. Jian Ye from the Institute of Microbiology, CAS, and untreated control (CK_AG) were compared.

Compared with the biological agent treatment, fumigation treatment had stronger disease inhibition effects. Furthermore, not only did the fumigation treatment increase pH, but it also increased nutrient availability in soil and stimulated crop growth.

The bacterial diversity was significantly reduced by the application of fumigants, compared with the biological agents, which caused a significant increase in bacterial diversity. This could be explained by the fact that fumigation chemicals are often toxicants to organisms. Fumigants are well-known poisonous substances used in killing insects, nematodes, and other animals or plants that cause damage to foods, seeds, or human dwelling. Although it is widely accepted that the diverse soil microbial community would benefit above-ground crops against disease infection and promote plant growth, this was in contrast to the results obtained in this study for fumigation treatment.

This can be explained as follows: fumigation treatment disrupted the entire soil microbial ecosystem and also leaded to changes in soil characteristics and plant performance, and thereby the crop benefitted from the reassembled rhizosphere microbiome resulting in the effective alleviation of continuous cropping barriers.

Nature, Technology

Stratifin (SFN) and Presepsin (P-SEP) could be used as prognostic biomarkers for severe COVID-19 progression

A group from Division of Medical Safety Science, National Institute of Health Sciences, Japan, etc. has reported that stratifin (SFN) and presepsin (P-SEP) could be used as prognostic biomarkers for severe COVID-19 progression.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9188980/

COVID-19 is a respiratory disease with a wide range of manifestations, from asymptomatic to severe cases with ARDS.18 Although about 80% of patients with COVID-19 experience only mild or moderate symptoms and have a favorable prognosis, the remaining patients worsen to severe or critical stage, and their prognosis, largely driven by severe ARDS, is poor. Therefore, early detection of the severe COVID-19 cases is important.

In the present study, five biomarkers for lung injury, SP-D, KL-6, P-SEP, KAL and SFN were analyzed, all of which have been suggested to be related with ARDS or its typical histological pattern diffuse alveolar damage (DAD), in serum samples collected serially from patients with COVID-19. It was found for the first time that serum SFN was significantly elevated in patients with severe COVID-19 compared to patients with mild or moderate symptoms. SFN, as well as P-SEP which has been suggested as a biomarker for severe COVID-19.

Both serum SFN and P-SEP were obviously elevated at the pre-severe stage. The AUC values [95% CI] of these proteins in diagnosing the pre-severe stage were 0.83 [0.76–0.90] for SFN and 0.79 [0.69–0.89] for P-SEP. When the cutoff values of SFN and P-SEP for discriminating the pre-severe condition from the mild/moderate condition on COVID-19 patients were set at 0.81 ng/mL and 374 pg/mL, the diagnostic sensitivity and specificity were 81.5% and 70.1% for SFN, and 76.9% and 71.9% for P-SEP, respectively.