Nature, Technology

Multi-omics evaluation was performed using a model in which Arabidopsis was inoculated with Trichoderma spp.

A group from Department for Sustainable Food Process, CRAST Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy, etc. has reported about investigation of Trichoderma-mediated impact of heat, drought, and their combined stress on Arabidopsis thaliana, considering physiological responses, molecular implications at metabolome level, as well as the root and rhizosphere bacterial microbiota.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10484583/#B19

Plants treated with Trichodelma spp. were characterized by an increment of the fresh biomass even during drought and heat stress, suggesting that the increase in fresh weight observed was mainly due to an accumulation of water inside plant tissues.

The inoculation with Trichoderma spp. leaded to increased production of N-containing metabolites (including alkaloids and polyamines), phenylpropanoids, phytoalexins, tarpens, glucosinolates. It was also found that phytoholmons such as auxin-related substances (i.e., indole-3-acetaldehyde, indole-3-carboxaldehyde, and indole-3-ethanol), small peptides, and volatile organic compounds are upregulated by the inoculation with Trichoderma. And also, the soil microbiomes shifted in abundance and composition in response to environmental factors and Trichoderma treatments. Proteobacteria were the most predominant in roots and soil, on average, 89.6% of roots and 59.4 % of soil. Besides Proteobacteria in soil samples, one of the most abundant phyla were Bacteroides and Actinobacteroides.

They concluded that a holobiont approach, in other words, an multi-omics approach, is needed to understand the coordinated and complex dynamic interactions between the plant and its rhizosphere bacteria.

Technology

Concanavalin A (ConA) coated chitosan (CS) nanocarrier-DDS for antibiotic-resistant H. pylori

A group from Tissue Engineering and Regenerative Medicine Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran etc. has reported about a concanavalin A (ConA) coated chitosan (CS) nanocarrier-based drug delivery for the targeted release of peptides to the site of antibiotic-resistant H. pylori infection.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10471652/

Helicobacter pylori is the cause of most cases of stomach ulcers and also causes some digestive cancers. The emergence and spread of antibiotic-resistant strains of H. pylori is one of the most important challenges in the treatment of its infections.

Chitosan was used as an encapsulating agent for CM11 peptide delivery by applying ionotropic gelation method. ConA was used for coating CS nanoparticles to target H. pylori. The size frequency for CS NPs and ConA-CS NPs was about 200 and 350 nm.

The Minimum Inhibitory Concentration (MIC) of the free CM11 peptide against drug-resistant H. pylori SS1 strain was 16 μg/ml while drug-resistant H. pylori SS1 showed MICs and MBCs 64 and >128 μg/ml against clarithromycin and amoxicillin, respectively. To encapsulate the peptide in nanoparticles, twice the MIC concentration of the peptide (32 µg/ml) was used.

CM11-loaded ConA-CS NPs has a higher antibacterial potential compared to the CM11-loaded CS NPs and free CM11 peptide, respectively. While there was no significant difference between the treatment with CM11-loaded ConA-CS NPs and triple antibiotics mixture, which indicates that it has the same effect similar to triple antibiotic therapy. CM11-loaded ConA-CS NPs and CM11-loaded CS NPs significantly reduced drug-resistant H. pylori SS1 after 12 h while amoxicillin and clarithromycin had no killing effect and their growth trend was same as the control group. The CM11-loaded ConA-CS NPs and triple antibiotics mixture were also able to kill drug-resistant H. pylori SS1 within 24 h while for free peptide and CM11-loaded CS NPs was after 48 h.

Nature, Technology

Changes in glycosylation of mitochondrial proteins due to Ischemia‐Reperfusion Injury using lectin microarrays

A group from Department of Cardiac and Pan-Vascular Diseases, Xi’an People’s Hospital (Xi’an Fourth Hospital), Xi’an, China, etc. has reported about changes in glycosylation of mitochondrial proteins due to Ischemia‐Reperfusion Injury using lectin microarrays.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10439394/

Myocardial I/R injury seriously affects the recovery of the cardiac structure and function after cardiac surgery. I/R injury is a major obstacle in current clinical treatment, and its harm cannot be ignored. During severe myocardial ischaemia, the metabolism of myocardial cells is dominated by anaerobic glycolysis, which will cause the accumulation of acidic products and the depletion of ATP. After reperfusion, reactive oxygen species accumulation and Ca2+ overload are induced, leading to the opening of mitochondrial permeability transition pore (mPTP) which further leads to the disruption of the electron transport chain and the reduction of ATP production. As mPTP opens, matrix proteins and mitochondrial DNA are released into the cytoplasm. This process disrupts mitochondrial membrane potential and uncouples oxidative phosphorylation, leading to increased ATP consumption. Ca2+ overload and increased production of oxygen radicals will further activate inflammation and thrombosis, causing disruption of mitochondrial respiration, matrix swelling and mitochondrial membrane rupture, which leads to mitochondrial damage and cell death.

In this study, changes in glycosylation of mitochondrial proteins due to Ischemia‐Reperfusion Injury:I/RI were investigated by using lectin microarrays, and it was found that the expression of glycan structures recognized by LTL and SNA were significantly increased and the expression of glycan structures recognized by ECA were decreased with ischaemia for 45 min. Further analysis showed that the Siaα2-6Gal/GalNAc structure recognized by SNA were significantly increased.

Technology

About recent situations on Lectin microarrays and Glycan microarrays presented in Glyco26

Glyco26 was held at Academia Sinica in Taipei from August 27 to September 1, 2023.

First of all, I would like to summarize the trends in lectin arrays (also called lectin microarrays).
As you may know, lectin arrays appeared in 2005, and two groups, Lara Mahal from the United States and Jun Hirabayashi from Japan, published papers on glycan profiling analysis technology using lectin arrays. The following is one scene of Lara Mahal’s presentation (D010) from the University of Alberta at Glyco26.

Reference：A group of Lara Mahal et al.
Reference：A group of Jun Hirabayashi and Atsushi Kuno et al.
The latter paper adopted an evanescent-field fluorescence excitation method as the excitation technology to get a precise glycan profiling using a lectin array. This method enables detection of very weak biomolecular interactions between lectins immobilized on slide glasses and fluorescently labeled glycoproteins as analytes, non-destructively and directly from the liquid phase. And further, the admin. of this blog was also a co-author of this paper, and this technology was placed on the market as a glycan profiler (named GlycoStation® Reader 1200) in 2007 by myself.

Regarding the progress of researches using lectin arrays or on the lectin arrays themselves in Glyco26, regarding the former, there were presentations from a group of Academia Sinica and a group of AIST.
Wu-Show Su et al., Academia Sinica used lectin arrays for glycan profiling of IL6 secreted from cancer cells (A107), and Atsushi Kuno et al., AIST were verifying the differences in glycosylation at each local tissue site of cardic fibrosis using paraffin-embedded samples. In this study, an advanced glycan profiler, GSR2300 made by emukk LLC, was used, and it was shown that it is possible to get glycan profiling from only 3 cells (C050).
Regarding lectin arrays themselves, two groups gave presentations on arraying human lectins.
Kurt Drickamer et al., ICL develped an array immobilized with a total of 31 types of human lectins, including C-type lectins, Galectins, Siglec, and so forth to screen the binding specificity of these human lectins to pathogenic and commensal micro-organisms. This microarray provides unique information on how various lectins, which are at the forefront of human innate immunity, react with various microorganisms, and this demonstrates the usefulness of human lectin arrays (D026 ). In this study, human lectins were biotinylated and those were immobilized on a streptavidin-covered substrate. In addition, GlycoGenetics announced a microarray product that immobilizes 11 types of human lectins, mainly galectin (C072). Many of the existing lectin arrays are using plant lectins, such as LecChip, and lectin arrays adopting human lectins are a new trend in lectin arrays. However, the glycan binding specificity of human lectins is mainly related to the innate immune system, and therefore the coverage of glycans is not good enough. From the viewpoint of glycan profiling, existing lectin arrays centered on plant lectins are sufficiently powerful, and further they are highly comprehensive (for example, you can refer to arrays using plant lectins (C053) by Jaroslav Katrilik et al. of Slovak Academy of Sciences). So, existing lectin arrays and human lectin arrays will habitat segregation according to the applications, I think.

Next, regarding glycan arrays, as you know, the US CFG glycan arrays have become the de-facto position due to their high comprehensiveness. There were several presentations using this glycan array to evaluate the glycan binding specificity of glycan-binding proteins. One of the most interesting presentation at Glyco26 using glycan arrays would be “Blood Group A enhances SARS-CoV-2 infection” presented by Shang Chuen Wu, Richard Cummings and Sean Stowell et al., Harvard Medical School (A071). Ryuhei Hayashi and Yashuhiro Ozeki et al., Yokohama City Univ. used a unique glycan array (manufactured by GlycoTechnica) to evaluate the glycan binding specificity of marine sponge’s lectins . A newly discovered lectin named Chal18 was shown to have very strong specificity for T-antigen and to exhibited strong cytotoxicity against colorectal cancer cells (A031).
A new trend regarding glycan arrays is the movement to create arrays of glycans using pathogenic bacteria. Laurriel Macali and Todd Lowary et al., Academia Sinica was discussing the glycan binding specificity of mycobacteriophages using glycan arrays that immobilize 66 glycans exstracted from microorganisms. In this glycan array, glycans were immobilized on a slide glass using the neoglycoprotein method (i.e., a method in which a conjugate of an extracted glycan and BSA is made and the BSA is immobilized on the slide glass) (A040).
Microorganisms have a wide variety of glycans, and also their purification is difficult. Furthermore, since the state of glycans actually expressed on the surface of microorganisms and the state of extracted glycans and immobilized on glass slides are not the same, Hau-Ming Jan and Sean Stowell et al., Harvard Medical School proposed a method named MMA (microbe microarray)  in which the microorganisms are directly arrayed on a slide glass, and through studies on interaction of Gal-8 with glycan arrays and MMAs as an example, they concluded that MMA could predict binding properties more accurately than conventional glycan arrays (A048).

At Glyco26, there were a total of 343 presentations, so the admin. might not be able to cover them all and might have overlooked some. I appreciate your understanding about it and I hope this information is of some help to you.

Nature, Technology

Aberrant glycosylation in serum glycoproteins observed in patients with Hashimoto’s thyroiditis

A group from Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China, etc. has reported about aberrant glycosylation observed in Hashimoto’s thyroiditis.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10348014/

Hashimoto’s thyroiditis (HT) is the most common autoimmune thyroid disorder and is characterized by lymphocyte infiltration of the parenchyma and the presence of antibodies specific to thyroid antigens.
In this study, a total of 53 serum samples collected from 27 patients with HT and 26 healthy controls (HCs) were used for lectin microarray analysis, and it was found that the majority of the lectin binding signals in HT group were weakened compared with the HC group, while the Vicia villosa agglutinin (VVA) binding signal was increased.


Mx thinks that the quality of lectin microarrays used was not GOOD enough.

Nature, Technology

KLF12/Gal-1 axis may serve as a novel cancer therapeutic target for patients with immunotherapy resistance

A group from Department of Thoracic Surgery, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China, etc. has reported that KLF12/Gal-1 axis may serve as a novel cancer therapeutic target for patients with immunotherapy resistance.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10432659/

In this study, it was demonstrated that the decline in KLF12 in tumor cells is an important mechanism for immune escape, leading to resistance to anti-PD-1 therapy. Mechanistically, KLF12 could directly bind to the promoter region of Gal-1 and inhibit its expression, and thereby promotes CD8+ T cell infiltration into the tumor microenvironment and kills tumore cells.

Continued research into the mechanisms of action of KLF12 and a new combination immunotherapy for circumventing drug resistance may provide more effective treatment options for patients with cancer.

Technology

A lectibody comprised of a dimeric fragment of the Shiga toxin B-subunit (StxB) and the human CD3 antibody fragment

A group from Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany, etc. has reported about a bispecific lectibody boosting T cell cytotoxicity towards Gb3-positive cancer cells.
https://www.mdpi.com/2073-4409/12/14/1896

A lectibody, comprised of a dimeric fragment of the Shiga toxin B-subunit (StxB) and the human CD3 antibody（clone No. UCHT1）fragment, was produced in E. coli and purified via Ni-NTA affinity chromatography. The StxB-scFv UCHT1 lectibody has bispecificity to T-cells and Gb3-positive cancer cells. The Shiga toxin B-subunit (StxB) can selectively target Gb3-positive cancer cells, and cytotoxic T cells are activated via UCFT1.

In this paper, it was shown that the lectibody could induce the killing of up to 80% of Gb3-overexpressing cancer cells in haemorrhagic and solid tumours.

Technology

Effects of mixed oligosaccharides on cucumber growth and its rhizosphere

A group from Institute of Analysis and Testing, Beijing Academy of Science and Technology, Beijing, China, etc. has reported about mixed oligosaccharides-induced changes in bacterial assembly during cucumber growth.
https://pubmed.ncbi.nlm.nih.gov/37492253/

it was shown that mixed oligisaccharides (in detail, chitin origosaccharides) effectively delayed cucumber leaf senescence and significantly increased cucumber production, and increased the abundance of Methylorubrum spp. and Lechevalieria spp., although bacterial communities in the rhizosphere and bulk soil remained relatively stable across different treatments and sampling periods.
It is known that Methylobacterium produce growth-promoting metabolites by consuming methanol secreted by plants.

Technology

Comparison of Lectin microarrays from a view point of Quality: LecChip has the world highest Quality

Lectin microarrays are extremely powerful in comparative glycan profiling analysis. Furthermore, by using the evanescent-field fluorescence excitation method for lectin microarray analysis, it is possible to monitor weak interactions between lectins and glycans non-destructively, making it possible to perform comparative glycan profiling at the world’s highest quality level.
For details of this technology, please refer to the following.

Products & Services

As of today, there are some lectin microarrays in the world whose manufacturers are unknown, but there are also several products that are manufactured and sold on a commercial basis (PSS, RayBiotech, etc.).
Therefore, I would like to compare their quality from published images refering to papers that have used lectin microarrays in the past few years.
In conclusion, it can be said that there is no lectin microarray with quality superior to LecChip.

LecChip made by GlycoTechnica（Currently LecChips are manufactured by PSS）

Lectin microarray made by RayBiotech (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10348014/)
Spot sizes are irregular,
Some spots are very small,
There are also irregular spots that are hollow and have ring shapes

Lectin microarray, unknown manufacturer (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6636412/)
Probably this was manufactured with a pin-type spotter,
Spot inside is heavily ununiform

Lectin microarray, unknown manufacturer (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8798758/)
Intense voids in the spots

Lectin microarray, unknown manufacturer (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9772556/)
Spot sizes are irregular,
Intense void in the spots,
Spot inside is strongly ununiform,
Some spots are probaly missing

Lectin microarray, unknown manufacturer (https://www.frontiersin.org/articles/10.3389/fchem.2021.637730/full)
Relatively acceptable except for voids in the spots,

Lectin microarray, unknown manufacturer (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7840895/)
Spot sizes are irregular,
Spot inside is heavily ununiform

Nature, Technology

Methanotrophic bacteria can reducing greenhouse gas emissions and promote plant growth at the same time

A group from Institute for Water Research and Department of Microbiology, University of Granada, 18071 Granada, Spain, etc. has reported that methanotrophic bacteria can reducing greenhouse gas emissions and promote plant growth at the same time.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10347144/

Although carbon dioxide (CO2) receives the most attention as a global warming factor, there are other gases to consider, for instance methane (CH4). It is thought that methane is the cause of at least one-fourth of the current gross warming. Atmospheric concentrations of methane are rising rapidly, principally due to anthropogenic contributions, with wastewater treatment facilities, landfills, and livestock considered to be the key producers. The removal of atmospheric methane is needed to offset the steady release of methane, thereby limiting the contribution of this potent greenhouse gas to climate change.

This paper explores the potential of methanotrophic bacteria as plant-growth-promoting rhizobacteria (PGPR) to save plants from droughts and also to reduce greenhouse gas, methain, at the same time. Since methane oxidation leads to water production as a byproduct (i.e., CH4 + O2 = [CH2O] + H2O), it was thought that methane-consuming microbes produce water intracellularly and are capable of surviving with a limited external water supply, releasing excess water into its environment.
Actually, the highest values of relative humidity in vermiculite used as a soil were detected in some methanotrophic innoculated samples, with values of 72.29 ~ 62.26%. It is noteworthy that in the absence of methane, its relative humidity was drastically reduced by almost half. These results suggest that the methanotrophic bacteria could efficiently preserve water using methane-derived metabolic water. And interestingly, the PGPR effect was maximized with the same methanotrophic bacteria, which can help water preservation, at the same time.