Month: October 2021

A group from Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan has reported that dual inhibition of TMPRSS2 and Cathepsin B is effective in preventing SARS-CoV-2 infection.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8527102/pdf/main.pdf

iPS cells that stably express ACE2 were used for this experiment, and TMPRSS2 and CTSB (Cathepsin B gene) were suppressed to about 1% or less, by using a CRISPER interference system.

It was found that CTSB and TMPRSS2 are required for SARS-CoV-2 to infect ACE2-iPS cells. It is known that TMPRSS2 is present in the cell membrane and CTSB in endosomes, suggesting TMPRSS2 and CTSB play important roles in endocytosis independent and endocytosis-dependent infection, respectively.

From this experiment, it was shown that Double-knockdown of TMPRSS2 and CTSB reduced the viral load to 0.036±0.021%.

A group from Institute of Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany, etc. has reported that WGA lectin could inhibit infection with SARS-CoV-2 with an IC₅₀ of <10 ng/mL. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8508056/

Vero B4 cells were infected with the SARS-CoV-2PR-1 (Wuhan type) for 1 h and then treated with different concentrations of WGA. Cell culture supernatants were harvested after 3 days and virus production was analyzed via qRT-PCR and Western blot. Treatment with WGA led to a strong reduction of SARS-CoV-2 replication. A concentration of 10 µg/mL WGA completely abolished the presence of viral RNA copies in cell culture supernatants. The inhibitory effect was observed in a dose-dependent manner and was confirmed by Western blot analysis, which revealed an even stronger and dose-responsive reduction of virion production upon treatment with WGA. Collectively, these data provide the first evidence that WGA exhibits antiviral activity against SARS-CoV-2 in Vero B4 cells, with an estimated IC_{50ub> of <10 ng/mL.}

To analyze cytotoxicity of WGA, toxicity assays were performed in VERO B4 and Calu-3 cells. In Vero B4 cells, the TD₅₀ was ≈ 50 µg/mL, resulting in a broad therapeutic window of at least three log stages. These data suggest that WGA could be used to inhibit infection with SARS-CoV-2 in vivo. Let’s expect future clinical studies on this matter.

A group from College of Agronomy, Guangxi University, Nanning, China, etc. has reported effects of intercropping on plant growth promotion and rhizobacteria comparing with monoculture.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8515045/

Two new sugarcane cultivars, ZZ1 and ZZ9, and a local soybean cultivar, GUIZAO2, were used for this experiments. Two intercropping patterns of sugarcanes and soybean (ZZ1J and ZZ9J) were compared with each monoculture (ZZ1M and ZZ9M).

As a result, it was found that the promoting effect of ZZ9–soybean intercropping was more significant than that of intercropping with ZZ1 as shown below.

And, it was also found that the relative abundance of Alphaproteobacteria in ZZ9–soybean intercropping (ZZ9J) was higher than that of ZZ1 intercropping mode (ZZ1J) as shown below. As a note, alphaproteobacteria includes a large number of symbiotic nitrogen-fixing bacteria in soil.

It is quite reasonable to consider that the change observed here would be closely related to the production of crop root exudates, which act as signals mediating root–microbial interactions.

A group from Università del Piemonte Orientale, Department of Health Sciences, Novara, Italy, etc. has reported that SARS-CoV-2 infection could be prevented by targeting autophagy processes with natural products such as Berberine, Baicalin, Resveratrol, Catechin, etc.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8516241/

The mechanisms through which SARS-CoV-2 enter the cells, replicate within, and exit from them are are thought to be as follows.
(1) In brief, the main path for virus entry is via clathrin-mediated or clathrin/caveolae-independent endocytosis. The endocytosed virus can be delivered to the autophagy-lysosomal organelles for degradation. However, the virus RNA can escape from endocytic vesicles (upon cathepsin L-mediated processing of S and virus envelope-membrane fusion), and relocate in the cytoplasm.
(2) Additionally, the virus may enter the cell by lipid blending of the virus envelope and the host cell membrane. Cells expressing ACE2 are specifically targeted by SARS-CoV-2 through the interaction with S protein RBD.
(3) Whichever the path used for entering the cell, the cleavage of the S protein into the subunits S1 and S2 by host proteases such as endosomal cathepsin L, furin, trypsin, transmembrane protease serine protease 2 (TMPRSS-2), or human airway trypsin-like protease is an obligated step for allowing the fusion between the viral envelope and host cell membranes (either endosomal or plasma membrane) and the release of the genome into the cytoplasm.
Accordingly, inhibition of this proteolytic step greatly reduces the cellular viral load. The followings are typical natural products used for this purpose.

Berberine
Berberine significantly interacts with SARS-CoV-2 3CL^PRO, S protein, and ACE2 receptor, suggesting that Berberine could prevent viral entry and fusion and interfere with the autophagy processes and the biogenesis of double-membrane vesicle by affecting the 3CL^PRO-mediated generation of nsps 4–16.

Baicalin and Baicalein
Baicalin interacts with the SARS-CoV-2 S and PL^PRO, nsp4, and 3CL^PRO proteins, suggesting another way to prevent the induction of autophagy

Resveratrol
Resveratrol and its derivatives to strongly and stably block SARS-CoV-2 proteins PL^PRO, RdRp, and S protein. Resveratrol could act as an ACE2 receptor inhibitor, preventing the formation of the S1/ACE2 complex and viral endocytosis, and double-membrane vesicles biogenesis. Furthermore, Resveratrol could impact the autophagic process through inhibition of PL^PRO-mediated generation of nsps.

Catechin
Catechin interferes with SARS-CoV-2 infection and replication by neutralizing 3CL^PRO, S protein RBD, ACE2, S/ACE2 complex, cathepsin L, nsp6, and N protein. Tea polyphenols, including epigallocatechin-3-O-gallate (EGCG) and theaflavin 3,3’di-gallate, can strongly dock to 3CL^PRO, S protein, S/ACE2 complex, PL^PRO, and RdRp.

Procyanidins
procyanidins significantly interacts with SARS-CoV-2 3CL^PRO, nsp1, nsp2, PL^PRO, nsp4, nsp6, nsp7, nsp8, nsp9, nsp10, RdRp, helicase, exon N, NendoU, 2′-O-MT, ORF3a, E protein, M protein, ORF6, ORF7a, ORF8, N protein, ORF10, ACE2, and S protein.

A group from Department of Chemistry, University of Alberta, Edmonton, AB, Canada, etc. has reported that α2-6Sia and its underlying enzyme ST6GAL1 as a potentially important glycan epitope in human Pancreatic ductal adenocarcinoma (PDAC).
https://www.mcponline.org/article/S1535-9476(21)00132-8/fulltext

Lectin Microarray:
In PDAC, significant increases were observed in sialic acids, with changes in both α2-6 (lectins: SNA, TJA-I, PSL, average increase: ~ 2.7 fold) and α2-3sialosides (diCBM40, SLBR-H, SLBR-B, SLBR-N, MAL-I, MAA, ~ 3.4 fold).
Core fucosylation (PSA, LcH, ~ 2.7 fold) and bisecting GlcNAc (PHA-E, ~ 2.2 fold) and poly-LacNAc (WGA, DSA, LEA, ∼ 2.1 fold) also increased relative to normal.

Glycosyltransferases:
Strong ST6GAL1 expression was observed in endothelial, immune cell and the cancerous ductal clusters. In addition, ST6GAL1 levels were associated with reduced survival. The α2-3 sialyltransferase ST3GAL1 was also observed in many cell types, however it was not enriched in cancer-specific ductal cells.

A group from Nanjing Agricultural University, Weigang, Nanjing, China, has reported that the beneficial effects of microbial inoculation can be driven indirectly through effects on the diversity and composition of the resident plant rhizosphere microbiome.
https://pubmed.ncbi.nlm.nih.gov/34641724/

One way to increase microbiome-associated multifunctionality is the introduction of additional rhizobacteria into the soil. For a long time, microorganisms have been selected on the basis of their ability to directly express functions of interest, such as nutrient mineralization, nitrogen fixation or pathogen suppression. However, such direct effects are notoriously unstable as the introduced species fail to establish at the density needed to function in a natural microbiome context. Further, inherent trade-offs in microbial physiology will limit the expression of functions one microbial species or strain can provide to the plant.

It is so important to understand if the potential benefits were driven directly by inoculated rhizobacteria via introduction of essential functions to the microbiome, or indirectly via changes in the resident bacterial community.

In this study, 8 different Pseudomonas strains were used as inoculants at the maximum, and the plant growth enhancement was measured by using tomato.

It was found that increasing probiotic consortium richness increased inoculant colonization success, and was associated with improved plant growth, nutrient assimilation and protection from pathogen infection. Crucially, inoculants caused shifts in the resident microbiome and these effects were magnified with increasing inoculated numbers of Pseudomonas strains, leading to an increase in the abundance of rare taxa and overall microbiome biodiversity. While plant-beneficial functions of Pseudomonas strains in vitro predicted poorly the individual plant growth characteristics. The only notable exception was a positive relationship between the Pseudomonas phosphate solubilization capacity and the plant shoot phosphorus content. Instead, positive effects on the plant growth were best explained by inoculated Pseudomonas-mediated shifts in the resident microbiome, which were associated with phytohormone production and resource competition by the probiotic consortia.

A group from Department of Medicine, Columbia University, New York, etc. has reported that in COVID-19 patnents, urinary Neutrophil Gelatinase-Associated Lipocalin (uNGAL) quantitatively associated with histopathological injury (ATI), the loss of kidney function (AKI), and the severity of patient outcomes.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8497954/

Notably, COVID-19 patients were 2.6-times more likely to present with acute tubular injury (ATI) (35.2% vs. 13.6%, P < 0.0001), 3.9-times more likely to have sustained functional kidney failure (AKI) (17.5% vs. 4.5%, P < 0.0001) and 1.8-times more likely to have more severe disease (Acute Kidney Injury Network (AKIN) stages 2-3, 12.5% vs. 6.8%, P < 0.01). Thus, although loss of kidney function is a common feature of COVID-19 infection, serum creatinine (SCr) is not a sensitive or specific marker of kidney injury.

For example, SCr can only detect kidney dysfunction in retrospect, after enough time has elapsed for the accumulation of SCr to a diagnostic threshold. In addition, clinically significant changes in SCr may not occur in subtotal or focal kidney damage as a result of compensatory changes in uninjured nephrons which can attenuate the rise in SCr. Even when elevations in SCr are apparent, evidence of tubular injury may be lacking, for example in the presence of volume depletion, a common presentation in patients with COVID-19 associated diarrhea. A rise in SCr may also be confounded by the incidence of rhabdomyolysis in COVID-19, which enhances creatinine production.

So, authors has studied the performance of urinary NGAL (uNGAL) and urinary KIM-1 (uKIM-1) in a large cohort of acute COVID-19 patients (444 patients) presenting to the Columbia University Emergency Department at the peak of the New York City pandemic (March-April 2020).

As a result, uNGAL, but not uKIM-1, was associated with the severity of AKI (AKIN stage) as shown below. uNGAL levels increased in a stepwise manner with increasing AKIN stage (P < 0.0001). Similarly, the ROC curve for uNGAL progressively increased with higher AKIN stages (0.70-0.93). uNGAL had 80% specificity and 75% sensitivity to diagnose AKIN stage 2 or 3 at a cutoff level of 150ng/mL.

A group from College of Life Science, South-Central University for Nationalities, Wuhan, China, etc. has reported that Acinetobacter pittii gp-1 promoted soybean growth with its P-stabilization and secretion of indole acetic acid.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8498572/

Acinetobacter pittii gp-1 isolated from agricultural soils is known as a P-solubilizing rhizobacterium, and actually the inoculation of Acinetobacter pittii gp-1 promoted soybean growth significantly as shown below.

200 g of sieved soil + 100 ml of sterile water (CK treatment)
195 g of sieved soil + 5 g of tricalcium phosphate (TCP) + 100 ml of sterile water (Tri treatment)
200 g of sieved soil + 10 ml of bacterial suspension (107 cfu/ml) + 90 ml of sterile water (Sup treatment)
195 g of sieved soil + 5 g of tricalcium phosphate (TCP) + 10 ml of Acinetobacter suspension (107 cfu/ml) + 90 ml of sterile water (Bac treatment)

The indole acetic acid, which is known as phytohormone, content was significantly higher in Bac treatment than in other treatments, which also might promote soybean growth.