Month: June 2023

Technology

prediction of glycan structures from lectin binding yusing a Boltzmann model prediction

A group from Department of Physics, University of California, San Diego, etc. has reported about prediction of glycan structures from lectin binding yusing a Boltzmann model prediction.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10274649/

In this study, it was tested if glycan structures can be predicted from lectin binding patterns. Each lectin has a small set of motifs to which it binds. Since lectins are not expected to have logically complex binding rules, it was thought that shallow neural network topologies to be adequate. A reasonable minimal model for this interaction would be hought to be a fully visible Boltzmann machine, which can be conceptualized as a two layer network.

To be honest, I think that it’s not so accurate than expected. This will be partly because the glycans are a very heterogeneous group, and partly because the binding specificity of lectins is ambiguous. There are many people who are against glycan structure estimation using this kind of lectin panels, and there are a large number of MS/MS adherents.

However, in the context of this paper’s discussion, their thought is the same as mine.
“Information got from lectins is accurate enough in a biological context!”

Nature

O-glycosylation of PD-1 expressed on T-cells

A group from Translational Research Unit, Chulabhorn Research Institute, Bangkok, Thailand, etc. has reported about O-glycosylation of PD-1.
https://www.nature.com/articles/s41598-023-36203-3#Abs1

It was found that the stalk region of PD-1 at T153, S157, S159, and T168 are modified by sialylated O-glycan with core 1–and core 2–based structures.
The most likely function of these modifications would forming a rod-like structure and stretching the receptor on the cell surface with the steric interaction between O-glycans and the peptide backbone in the stalk region.

Nature

Aberrant glycosylation associated with osteoarthritis (OA)

A group from Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an, China, etc. has reported about aberrant glycosylation associated with osteoarthritis (OA).
https://arthritis-research.biomedcentral.com/articles/10.1186/s13075-023-03084-w

The abnormal glycopatterns and heterogeneities of site-specific glycosylation associated with Osteoarthritis (OA) were investigated by using Lectin microarrays and LC-MS/MS.
It was found that abnormal glycosylation, including a high level of α-1,3/6 fucosylation and low level of high-mannose type N-glycan, was obsedeved in OA cartilages.

Heterogeneities of glycoforms on Fibronectin(FN1) and Aggrecan core protein (ACAN) were new features of OA cartilage. These proteins were mainly localized in the extracellular region and extracellular space.
In detail, as for Fibronectin(FN1)-N528, N4H5S2 almost disappered and N4H4F1S1 greatly increased,
as for Aggrecan core protein (ACAN)-N333, N5H8F1 almost disappered and N6H4S1, N4H3F1, N5H3F1, N2H5, N6H4 significantly increased,
and as for Aggrecan core protein (ACAN)-N658, N5H4F1S2, N6H6F1, N6H7, N7H6 almost disappered and N2H11 significantly increased.

Nature, Technology

Human milk is very effective in protecting preterm infants from necrotizing enterocolitis

A group from USDA Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA, etc. has reported that pre- and probiotics are not sufficient for protection from Necrotizing enterocolitis (NEC) in an exclusively formula-based diet.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10255242/

NEC is the leading cause of death resulting from gastrointestinal disease in premature infants, with a mortality rate of 15–40%. It was found about intestinal bacteria that (1)Escherichia-Shigella is Significantly more abundant in healthy piglets and negatively correlates with disease severity, (2) Clostridium sensu stricto 1 and Enterococcus are significantly more abundant in the colon of diseased piglets and correlates with disease severity (see below).

Although dietary probiotic Bifidobacterium longum subsp. infantis (BL. infantis) and sialylactose (3′SL) supplementation had no effect, donor human milk (DHM) significantly reduced the incidence of NEC.

Nature, Technology

Changes in complement component C3 glycosylation in type 1 diabetes complications

A group from Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia, etc. has reported about a new biomarker (c3.Asn939-N2H10) for type 1 diabetes (T1D) complications.
https://www.frontiersin.org/articles/10.3389/fendo.2023.1101154/full

N-glycan profiles of complement component C3 have been profiled in 189 T1D subjects with different status of complication severity. The analysis was conducted by high-mannose glycoprotein enrichment from human blood serum using Con A lectin matrix, Glu-C digestion, glycopeptide purification and subsequent nano-LC-ESI-MS technique.

It was found that only one glycoform, C3.Asn939-N2H10, significantly changed in albuminuria and retinopathy, and also there was the biggest correlation between C3.Asn939-N2H10 and HbA1c.

Technology

A serum biomarker for non-small cell lung cancer (NSCLC): chondroitin sulfate proteoglycan

A group from Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China,etc. has reported about a serum biomarker for non-small cell lung cancer (NSCLC) .
https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-023-02423-4

Plasma versican and plasma exosomal versican expression in NSCLC patients was significantly upregulated and was significantly higher in T3 + T4 patients compared with T1 + T2 patients (P < 0.05) as shown below (ROC curve). Versican is a large chondroitin sulfate proteoglycan. The plasma versican and plasma exosomal versican were detected using an ELISA kit (made in China).

Nature

Alterations in the Glycan modification of Serum Glycoproteins in Attention-Deficit Hyperactivity Disorder (ADHD)

A group from Institute of Chemistry, Slovak Academy of Sciences, SK-84538 Bratislava, Slovakia, etc. has reported about alterations in the Glycan modification of Serum Glycoproteins in Attention-Deficit Hyperactivity Disorder (ADHD).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10218324/

This study is focusing on determining whether serum glycan analysis holds the potential to identify novel ADHD biomarkers based on changes in glycosylation. They applied combined glycan analysis using two different techniques, lectin microarray and MALDI-TOF MS methods.

As a result, it was found that antennary fucosylation increases, di-/triantennary N-glycans with bisecting GlcNAc and α2-3 sialylation decrease in ADHD.

Nature, Technology

n-hexadecanoic acid secreted by tomato roots most strongly promotes biofilm formation of Pseudomonas stutzeri

A group from School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China, etc. has reported that n-hexadecanoic acid secreted by tomato roots most strongly promotes biofilm formation of Pseudomonas stutzeri.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10220591/

Plant growth-promoting rhizobacteria (PGPR) have been widely used in agricultural applications because of their safety, biological control of diseases and insect pests, and ability to induce c abiotic tolerance. It is know that the colonization, chemotaxis, and biofilm formation by PGPR are induced by the root exudates and certain metabolites.

In this study, it was shown that inoculation with a certain concentration of Pseudomonas stutzeri NRCB010 significantly promoted tomato growth and induced significant changes in tomato root exudates. Among those root exudates, n-hexadecanoic acid induced the most remarkable growth, chemotactic response, biofilm formation, and rhizosphere colonization of Pseudomonas stutzeri.