Differences in carrot’s rhizosphere bacteria, fungi, and soil enzymes between organic and conventional soils

A group from University of Life Sciences in Lublin, Lublin, Poland, etc. has reported on differences in carrot’s rhizosphere bacteria and fungi etc. between organic and conventional soils.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0256969

Organic farms where natural fertilizers such as compost and manure were used (E1〜E5 in a figure below, average pH=7.08, average soil water content=20.12%) and conventional farms where mainly mineral fertilizers were used (K1〜K5 in a figure below, average pH=6.13, K4 and K5 are the most acidic, average soil water content=14.46%、K5 has the lowest soil water content) are compared in terms of carrot’s rhizospheric bacteria, fungi, and soil enzymes.

about rhizosphere bacteria and fungi,
Organic farms contained more bacterial than fungal cells,
Conventional farms were more abundant in fungi than bacteria, especially the amount of fungi was greatly higher than that of bacteria in K4 and K5, which are the most acidic.
A neutral soil pH favours the growth of bacteria,
Fungi prefer a more acidic growth environment than bacteria.

 Graybars indicate the amount of bacteria and yellow bars indicate the amount of fungi.

about soil enzymes,
L-glutaminase and β-glucosidase were higher in organic farms,
Acid phosphatase was higher in conventional farms.

TIM-3 is overexpressed on CD4+ T cells in both COVID-19 severe patients than in healthy individual

A group from University of Medical Sciences, Babol, Iran, etc. has reported curious phenomena observed in subsets of CD4+ T cells in COVID-19 severe patients comparing in healthy individuals.
https://onlinelibrary.wiley.com/doi/10.1002/iid3.526

Overexpression of TIM-3 on CD4+ T cells was observed in both critical and moderate/severe patients than in healthy individuals, and also CD4+ TIM-3+ CD39+ lymphocytes were significantly higher in the critical patients than in healthy individuals.

Total lymphocytes were remarkably decreased in moderate/severe and critical COVID-19 patients compared with healthy individuals. That is because T cells migrate out of blood vessels into interstitial lung tissue resulting in peripheral T cell lymphopenia. However, regarding the frequency of CD4+ lymphocytes, no significant difference was observed in all groups. In contrast, besides the total lymphocytes, CD8+ lymphocytes were significantly decreased in both ICU and non-ICU COVID-19 patients compared with healthy individuals.

TIM-3 is one of markers of exhausted T cells. Galectin-9 (Gal-9) is one of the TIM-3 ligands, and it has demonstrated that interaction between TIM-3/Gal-9 induces apoptosis of Th1 cells. CD39 is known as an ectoenzyme producing extracellular adenosine by hydrolase of extracellular adenosine triphosphate (ATP). Injured cells secrete extracellular ATP, resulting in pro-inflammatory responses.

Why these subpopulations of CD4+ T-cells increase in COVID-19 is curious and it must be important to maintain those residual lymphocytes vigorously.

R-type lectin, Perinereis nuntia lectin (PnL), from Marine Annelids

A group from University of Chittagong, Bangladesh (containing this blog admin), etc. has reported about R-type lectin, Perinereis nuntia lectin (PnL), isolated from Marine Annelids.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8399747/

Previously, authors isolated PnL, a d-galactose-binding lectin of the R-type lectin family from Perinereis sp.

R-type lectins are derived from the ricin B-chain, a protein toxin consisting of AB subunits, in castor bean seeds. They usually have the three-leaf clover-like β-trefoil fold with Gln-X-Trp (Q-X-W) sequences in each subdomain. Why annelids have R-type lectins, and what physiological functions R-type lectins in annelids have are still uinclear. It would be the first step to identify locations where RnL is expressed.

Overall, PnL was found in extracellular locations after secretion from specific cells at the epidermis, setae, oblique muscle, acicula, nerve cord, and nephridium.
Interestingly, the localization pattern of the Gal/GalNAc-containing glycans was found to be almost identical to the distribution of PnL.

This co-localization is so interesting for blog admin, because the phytotoxin ricin is galactose-specific and clearly targets animal cells. What PnL is really doing?

A novel SARS-CoV-2 virus-like nanoparticle vaccine induced high-titer neutralizing antibodies

A group from Center for Coronavirus Research, University of Minnesota, Saint Paul, USA, etc. has developed a novel SARS-CoV-2 virus-like nanoparticle vaccine.
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009897

A lumazine synthase nanoparticle protein containing a N-terminal protein A tag was used as a structural scaffold of virus-like nanoparticle (VLP) vaccine. The size of nanoparticle was about 15nm in diameter. Then, a complex of the VLP nanoparticle and SARS-CoV-2 RBD (containing a C-terminal Fc tag) was formed as the VLP vaccine. This design of the VLP vaccine allowed 60 copies of Fc-tagged dimeric SARS-CoV-2 RBD, corresponding to 120 copies of SARS-CoV-2 RBD.

Authors has reported that this VLP vaccine induced high-titer neutralizing antibody responses in mice that lasted >2 months and potently inhibited SARS-CoV-2, SARS-CoV-1, and their variants(α, β, and γ variants).

GRFT/Carrageenan combination could provide higher antiviral activity against SARS-CoV-2 than using GRFT or Carrageenan independently

A group from The City University of New York, USA, etc. has reported that GRFT/Carrageenan combination could provide higher antiviral activity against SARS-CoV-2 than using GRFT or Carrageenan independently.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8400000/

GRFT is a homodimeric lectin of 121 aminoacids and six carbohydrate-binding sites with high affinity for high mannose arrays. These mannose arrays are frequently found in viral spikes of important pathogens like HIV, HSV, hepatitis C virus (HCV), ebola virus, and members of the Coronaviridae family. The ability to block HIV in vitro, at picomolar concentrations, makes GRFT one of the most potent molecules inhibiting HIV replication.

Carrageenan is a kind of salfated polysaccharide (repeated structures of galactopyranose disaccharides) and three type of carrageenans are known (κ-Carrageenan (κ-CG), ι-Carrageenan (ι-CG), and λ-Carrageenan (λ-CG)). CG shows antiviral activity, and is generally recognized as safe (GRAS) by the Food and Drug Administration.

The half-maximal effective concentration (EC50) values for GRFT, CG, those mixtures measured against SARS-CoV-2 are summarized below.
——————————–
GRFT, 20.6µg/mL
ι-CG, 7.5µg/mL
λ-CG, 6.1µg/mL
ι-CG + GRFT (1:5), 0.2µg/mL
λ-CG + GRFT (1:5), 0.4µg/mL
——————————–

Let’s expect in vivo studies to be done to confirm this in vitro experimental results obtained with a cell-based pseudoviral infection assay.

Mixtures of Bacillus (1.SG.7, 5.SG.3) and Pseudomonas (2.SG.20, 2.C.19) strains in wheat rhizosphere enhanced growth of roots and mitigated salinity stress

A group from Agricultural University of Athens, Athens, Greece, etc. has reported that the mixtures of Bacillus (1.SG.7, 5.SG.3) and Pseudomonas (2.SG.20, 2.C.19) strains in wheat rhizosphere enhanced the lateral roots abundance and shoots biomass of wheat, and mitigated salinity stress, comparing with the cases used independently.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8400701/

Sixty-eight arylsulfatase (ARS)-producing bacterias were isolated from the rhizosphere of durum wheat on calcareous soil. Phylogenetic analysis showed that most of the isolates belonged to the Pseudomonas and Bacillus genus. From view points of the following items, IAA production, antifungal activity, biofilm formation, and salinity tolerance, Bacterial Strains were selected from the isolated ARS-producing bacterias. Those were Bacillus (1.SG.7, 5.SG.3), Pseudomonas (2.SG.20, 2.C.19, 3.SG.19, 2.C.23, 4.SG.6, 2.SG.8)

All 8 bacterial strains enhanced the number of lateral roots and shoot biomass. The growth-promoting ability was enhanced by using strain mixtures, above all, mixtures of Bacillus (1.SG.7, 5.SG.3) and Pseudomonas (2.SG.20, 2.C.19) strains, enhanced the lateral roots abundance and shoots biomass, mitigated salinity stress.

Since the rhizosphere is a quite complex system including a number of bacterias and fungi, it must be a good way to focus on representative strains as shown here to understand how more effective rhizospheric consortium is formed as plant growth promoting rhizobacteria (PGPR).

SARS-CoV-2 Lambda variant (L452Q, F490S) has higher infectivity than Delta variant (L452R, T478K)

A group from University of Colorado, Aurora, USA, etc. has reported that SARS-CoV-2 Lambda variant has higher infectivity than Delta variant.
https://pubmed.ncbi.nlm.nih.gov/34462744/

The binding affinity of overall antibodies from Pfizer-BioNTech vaccinated individuals droped dramatically (about 3.5 times fold drop for the Delta variant, and about 4.0times fold for the Lambda variant) after six months. These data suggest that the Lambda variant has a better chance than the Delta variant to escape the immunity built by the vaccination.

Although the mutations of L452Q and F490S in RBD of Lambda varient do not bring any enhance of the binding between RBD and ACE2 comparing with Delta variant, both mutations lead to the disruptions of a hydrophobic patch, which is a critical area for the binding of broadly neutralizing antibodies. This could be a reason why Lambda variant has higher infectivity than Delta variant.

C-type lectins (DC-SIGN and L-SIGN) and SIGLEC1 do not act as primary entry receptors of SARS-CoV-2, but act as attachment receptors

A group from Vir Biotechnology, San Francisco, CA, 94158, USA, etc. has reported that C-type lectins (DC-SIGN and L-SIGN) and SIGLEC1 do not act as primary entry receptors of SARS-CoV-2, but act as attachment receptors.
https://www.nature.com/articles/s41586-021-03925-1

HEK293T were transfected with vectors encoding ACE2 or 13 selected lectins (DC-SIGN, L-SIGN, LGALS3, SIGLEC1, SIGLEC3, SIGLEC9, SIGLEC10, MGL, MINCLE, CD147, ASGR1, ASGR2, NRP1). Untransfected HEK293T cells were only weakly permissive to infection, and ACE2 overexpression led to a dramatic increase in pseudovirus entry. Increased infectivity was also observed in HEK293T cells following transfection with C-type lectins DC-SIGN and L-SIGN as well as with SIGLEC1. NRP-1 and CD147 did not enhance SARS-CoV-2 infection in these conditions. A SIGLEC1 blocking antibody inhibited infection of SIGLEC1 expressing HEK293T, supporting the role of this molecule as a new SARS-CoV-2 co-factor. The expression levels of these receptors change from cell to cell, and SIGLEC1 is highly expressed on moocytes, macrophages, and dendritic cells. Therefore, it was suggested that the trans-infection from SARS-CoV-2 attached these cells to target cells would be the most likely in an actual condition. The ectopic expression of DC-SIGN, L-SIGN and SIGLEC1 on HeLa and MRC5 cells did not support infection of ACE2 negative cells, indicating that these lectins do not act as primary entry receptors. Collectively, these data reveal a lectin-facilitated pathway of infection that is evident on cells expressing low levels of ACE2, supporting the notion that SARS-CoV-2 may use these lectins as attachment receptors to thether viral particles facilitating interaction with ACE2.

However, blog admin feels that this paper is lacking a view point of direct infection of SARS-CoV-2 to monocytes and macrophages through phagocytosis. In this case, Fcg receptors recognizing antibody-opsonized viral particles and also C-type lectins and Toll-like receptors recognizing aberrant glycans on SARS-CoV-2 would be key receptors responsible for the direct infection.