Nitrogen deposition caused higher increases in plant-derived organic carbon than microbial-derived organic carbon in forest soils

Plant- and microbial-derived organic carbon, two components of the soil organic carbon (SOC) pool in terrestrial ecosystems, are regulated by increased atmospheric nitrogen (N) deposition. However, the spatial patterns and driving factors of the responses of plant- and microbial-derived SOC to N deposition in forests are not clear, which hinders our understanding of SOC sequestration. In this study, we explored the spatial patterns of plant- and microbial-derived SOC, and their responses to N addition and elucidated their underlying mechanisms in forest soils receiving N addition at four sites with various soil and climate conditions. Plant- and microbial-derived SOC were quantified using lignin phenols and amino sugars, respectively. N addition increased the total microbial residues by 20.5% on average ranging from 9.4% to 34.0% in temperate forests but not in tropical forests, and the increase was mainly derived from fungal residues. Lignin phenols increased more in temperate forests (average of 63.8%) than in tropical forests (average of 15.7%) following N addition. The ratio of total amino sugars to lignin phenols was higher in temperate forests than in tropical forests and decreased with N addition in temperate forests. N addition mainly regulated soil microbial residues by affecting pH, SOC, exchangeable Ca2+, gram-negative bacteria biomass, and the C:N ratio, while it mainly had indirect effects on lignin phenols by altering SOC, soil C:N ratio, and gram-negative bacteria biomass. Overall, our findings suggested that N deposition caused a greater increase in plant-derived SOC than in microbial-derived SOC and that plant-derived SOC would have a more important role in sequestering SOC under increasing N deposition in forest ecosystems, particularly in temperate forests.

Targeting the glycan epitope type I N-acetyllactosamine enables immunodepletion of human pluripotent stem cells from early differentiated cells

Cell surface biomarkers are fundamental for specific characterization of human pluripotent stem cells (hPSCs). Importantly, they can be applied for hPSC enrichment and/or purification but also to remove potentially teratoma-forming hPSCs from differentiated populations before clinical application. Several specific markers for hPSCs are glycoconjugates comprising the glycosphingolipid (GSL)-based glycans SSEA-3 and SSEA-4. We applied an analytical approach based on multiplexed capillary gel electrophoresis coupled to laser-induced fluorescence detection to quantitatively assess the GSL glycome of human embryonic stem cells and human induced pluripotent stem cells as well as during early stages of differentiation into mesoderm, endoderm, and ectoderm. Thereby, we identified the GSL lacto-N-tetraosylceramide (Lc4-Cer, Galβ1-3GlcNAcβ1-3Galβ1-4Glc-Cer), which comprises a terminal type 1 LacNAc (T1LN) structure (Galβ1-3GlcNAc), to be rapidly decreased upon onset of differentiation. Using a specific antibody, we could confirm a decline of T1LN-terminating glycans during the first four days of differentiation by live-cell staining and subsequent flow cytometry. We could further separate T1LN-positive and T1LN-negative cells out of a mixed population of pluripotent and differentiated cells by magnetic activated cell sorting. Notably, not only the T1LN-positive but also the T1LN-negative population was positive for SSEA-3, SSEA-4, and SSEA-5 while expression of nuclear pluripotency markers OCT4 and NANOG was highly reduced in the T1LN-negative population, exclusively. Our findings suggest T1LN as a pluripotent stem cell-specific glycan epitope that is more rapidly down-regulated upon differentiation than SSEA-3, SSEA-4, and SSEA-5.

Amino Sugar-Enriched Fraction of Korean Red Ginseng Extract Induces the Priming Step of NLRP3 Inflammasome

Intracellular protein complexes, known as inflammasomes, activate caspase-1 and induce the secretion of pro-inflammatory cytokines, namely interleukin (IL)-1β and -18. Korean Red Ginseng extract (RGE) is a known immunomodulator and a potential candidate for the regulation of inflammasomes. The saponins, such as ginsenosides, of RGE inhibit inflammasome signaling, while non-saponin substances containing amino sugars promote the priming step, up-regulating inflammasome components (pro-IL-1β, NLRP3, caspase-1, and Asc). In this study, the amino sugar-enriched fraction (ASEF), which increases only non-saponin components, including amino sugars, without changing the concentration of saponin substances, was used to investigate whether saponin or non-saponin components of RGE would have a greater impact on the priming step. When murine macrophages were treated with ASEF, the gene expression of inflammatory cytokines (IL-1α, TNFα, IL-6, and IL-10) increased. Additionally, ASEF induced the priming step but did not affect the inflammasome activation step, such as the secretion of IL-1β, cleavage of caspase-1, and formation of Asc pyroptosome. Furthermore, the upregulation of gene expression of inflammasome components by ASEF was blocked by inhibitors of Toll-like receptor 4 signaling. Maltol, the main constituent of ASEF, promoted the priming step but inhibited the activation step of the inflammasome, while arginine, sugars, arginine-fructose-glucose, and fructose-arginine, the other main constituents of ASEF, had no effect on either step. Thus, certain amino sugars in RGE, excluding maltol, are believed to be the components that induce the priming step. The priming step that prepares the NLRP3 inflammasome for activation appears to be induced by amino sugars in RGE, thereby contributing to the immune-boosting effects of RGE.

Effects of common artificial sweeteners at environmentally relevant concentrations on soil springtails and their gut microbiota

Artificial sweeteners (AS) are extensively utilized as sugar substitutes and have been recognized as emerging environmental contaminants. While the effect of AS on aquatic organisms has garnered recent attention, their effects on soil invertebrates and gut microbial communities remain unclear. To address this knowledge gap, we exposed springtails (Folsomia candida) to both single and combined treatments of four typical AS (sucralose [SUC], saccharin [SAC], cyclamate [CYC], and acesulfame [ACE]) at environmentally relevant concentrations of 0.01, 0.1 and 1 mg kg-1 in soil. Following the first-generational exposure, the reproduction of juveniles showed a significant increase under all the AS treatments of 0.1 mg kg-1. The transcriptomic analysis revealed significant enrichment of several Kyoto Encyclopedia of Gene and Genome pathways (e.g., glycolysis/gluconeogenesis, pentose and glucuronate interconversions, amino sugar, and nucleotide sugar metabolism, ribosome, and lysosome) in springtails under all AS treatments. Analysis of gut bacterial microbiota indicated that three AS (SUC, CYC, and ACE) significantly decreased alpha diversity, and all AS treatments increased the abundance of the genus Achromobacter. After the sixth-generational exposure to CYC, weight increased, but reproduction was inhibited. The pathways that changed significantly (e.g., extracellular matrix-receptor interaction, amino sugar and nucleotide sugar metabolism, lysosome) were generally similar to those altered in first-generational exposure, but with opposite regulation directions. Furthermore, the effect on the alpha diversity of gut microbiota was contrary to that after first-generational exposure, and more noticeable disturbances in microbiota composition were observed. These findings underscore the ecological risk of AS in soils and improve our understanding of the toxicity effects of AS on living organisms.

GlcNAc6ST2/CHST4 Is Essential for the Synthesis of R-10G-Reactive Keratan Sulfate/Sulfated N-Acetyllactosamine Oligosaccharides in Mouse Pleural Mesothelium

We recently showed that 6-sulfo sialyl N-acetyllactosamine (LacNAc) in O-linked glycans recognized by the CL40 antibody is abundant in the pleural mesothelium under physiological conditions and that these glycans undergo complementary synthesis by GlcNAc6ST2 (encoded by Chst4) and GlcNAc6ST3 (encoded by Chst5) in mice. GlcNAc6ST3 is essential for the synthesis of R-10G-positive keratan sulfate (KS) in the brain. The predicted minimum epitope of the R-10G antibody is a dimeric asialo 6-sulfo LacNAc. Whether R-10G-reactive KS/sulfated LacNAc oligosaccharides are also present in the pleural mesothelium was unknown. The question of which GlcNAc6STs are responsible for R-10G-reactive glycans was an additional issue to be clarified. Here, we show that R-10G-reactive glycans are as abundant in the pulmonary pleura as CL40-reactive glycans and that GlcNAc6ST3 is only partially involved in the synthesis of these pleural R-10G glycans, unlike in the adult brain. Unexpectedly, GlcNAc6ST2 is essential for the synthesis of R-10G-positive KS/sulfated LacNAc oligosaccharides in the lung pleura. The type of GlcNAc6ST and the magnitude of its contribution to KS glycan synthesis varied among tissues in vivo. We show that GlcNAc6ST2 is required and sufficient for R-10G-reactive KS synthesis in the lung pleura. Interestingly, R-10G immunoreactivity in KSGal6ST (encoded by Chst1) and C6ST1 (encoded by Chst3) double-deficient mouse lungs was markedly increased. MUC16, a mucin molecule, was shown to be a candidate carrier protein for pleural R-10G-reactive glycans. These results suggest that R-10G-reactive KS/sulfated LacNAc oligosaccharides may play a role in mesothelial cell proliferation and differentiation. Further elucidation of the functions of sulfated glycans synthesized by GlcNAc6ST2 and GlcNAc6ST3, such as R-10G and CL40 glycans, in pathological conditions may lead to a better understanding of the underlying mechanisms of the physiopathology of the lung mesothelium.

Unveiling the Occurrence and Non-Negligible Role of Amino Sugars in Waste Activated Sludge Fermentation by an Enriched Chitin-Degradation Consortium

Polysaccharides in extracellular polymeric substances (EPS) can form a hybrid matrix network with proteins, impeding waste-activated sludge (WAS) fermentation. Amino sugars, such as N-acetyl-d-glucosamine (GlcNAc) polymers and sialic acid, are the non-negligible components in the EPS of aerobic granules or biofilm. However, the occurrence of amino sugars in WAS and their degradation remains unclear. Thus, amino sugars (∼6.0%) in WAS were revealed, and the genera of Lactococcus and Zoogloea were identified for the first time. Chitin was used as the substrate to enrich a chitin-degrading consortium (CDC). The COD balances for methane production ranged from 83.3 and 95.1%. Chitin was gradually converted to oligosaccharides and GlcNAc after dosing with the extracellular enzyme. After doing enriched CDC in WAS, the final methane production markedly increased to 60.4 ± 0.6 mL, reflecting an increase of ∼62%. Four model substrates of amino sugars (GlcNAc and sialic acid) and polysaccharides (cellulose and dextran) could be used by CDC. Treponema (34.3%) was identified as the core bacterium via excreting chitinases (EC 3.2.1.14) and N-acetyl-glucosaminidases (EC 3.2.1.52), especially the genetic abundance of chitinases in CDC was 2.5 times higher than that of WAS. Thus, this study provides an elegant method for the utilization of amino sugar-enriched organics.

Amino sugars influence Aspergillus fumigatus cell wall polysaccharide biosynthesis, and biofilm formation through interfering galactosaminogalactan deacetylation

Aspergillus fumigatus is a ubiquitous fungal pathogen responsible for a significant number of deaths annually due to invasive aspergillosis infection. While the utilization of diverse carbon sources, including amino sugars, has been explored in other fungi, its impact on A. fumigatus remains uncharted territory. In this study, we investigated A. fumigatus responses to glucose (Glc), glucosamine (GlcN) and N-acetylglucosamine (GlcNAc) as carbon sources. GlcN inhibited growth, reduced sporulation and delayed germination, while GlcNAc had no such effects. Both amino sugars induced alterations in cell wall composition, leading to a reduction in glucan and galactomannan levels while increasing chitin and mannan content, rendering A. fumigatus susceptible to cell wall stress and osmotic stress. GlcN repressed biofilm formation via downregulation of galactosaminogalactan (GAG) cluster genes, notably agd3, which encodes a GAG-specific deacetylase. Moreover, GlcN increased biofilm susceptibility to echinocandins, suggesting its potential for enhancing the effectiveness of antifungal treatments. This study sheds light on the multifaceted effects of amino sugars on A. fumigatus, encompassing growth, cell wall biosynthesis, and biofilm formation, offering promising avenues for innovative aspergillosis treatment strategies.

De Novo Synthetic Approach to 2,4-Diamino-2,4,6-trideoxyhexoses (DATDH): Bacterial and Rare Deoxy-Amino Sugars

A synthetic route to 2,4-diamino-2,4,6-trideoxysugar stereoisomers in 6-7 steps and 22-33% overall yield is described. A key step in this pathway is the carbonyl coupling of d- and l-threoninol or d- and l-allo-threoninol to a phthalimido-allene mediated by chiral iridium-H8-BINAP, which allows for installation of two new chiral centers in one, highly diastereoselective (>20:1 dr) step. This approach provides a more concise, diastereoselective, and versatile method to access these deoxy-amino sugars than is currently available.

[Effects of nitrogen addition on acidolyzable organic nitrogen components and nitrogen mineralization in aggregates of Pinus massoniana plantations in the Three Gorges Reservoir area, China]

We sieved soils from a Pinus massoniana plantation in the Three Gorges Reservoir area into four aggregate sizes, including aggregates of 2000-8000 μm (large macroaggregates), 1000-2000 μm (coarse aggregates), 250-1000 μm (small macroaggregates), and <250 μm (microaggregates). We analyzed the differences in the acidolyzable organic N components and net N mineralization of the aggregates under different N addition levels (30, 60, and 90 kg N·hm-2·a-1, representing by N30, N60 and N90, respectively). The results showed that net nitrification rate of the aggregates ranged from 0.30-3.42 mg N·kg-1 and accounted for more than 80% of net nitrogen mineralization. Compared with the control, addition of 30, 60, and 90 kg N·hm-2·a-1 increased total N by 24.1%-45.5%, 6.4%-34.3%, and 7.9%-42.4% in the large aggregates, coarse aggregate, small macroaggregates, and microaggregates, increased net N mineralization rate by 1.3-7.2, 1.4-6.6, and 1.8-12.9 times, but decreased the contents of available phosphorus by 9.3%-36.9%, 12.2%-56.7%, and 19.2%-61.9%, respectively. The contents of total acidolyzable N, soil organic matter, and rates of net ammonification, net nitrification, and net N mineralization increased as the aggregate size decreased, while available phosphorus contents showed an opposite trend. The levels of acid-hydrolyzable N components were ranked as acidolyzable amino acid N > acidolyzable ammonia N > acidolyzable unknown N> acidolyzable amino sugar N. Total N was the dominant contributor to the increases in acid-hydrolyzable N components. Results of stepwise multiple regression analyses showed that acidoly-zable amino acid N and acidolyzable amino sugar N were predictors of net ammonification rate. Acidolyzable amino sugar N, acidolyzable amino acid N, and acidolyzable ammonia N were predictors of net nitrification, net nitrogen mineralization rate, and net nitrogen mineralization accumulation. The physical structure of aggregates was associa-ted with soil net N mineralization. Addition of N increased the contents and bioavailability of acidolyzable organic N, a large amount of which contributed to soil organic matter levels and the decrease in available phosphorus.

Total Synthesis of a Structurally Complex Tetrasaccharide Repeating Unit of Vibrio cholerae O43

Herein we report the first total synthesis of a densely functionalized tetrasaccharide repeating unit of Vibrio cholerae O43, which contains rare deoxy amino sugars d-quinovosamine and d-viosamine attached with the rare amino acid N-acetyl-l-allothreonine. Synthesis of orthogonally protected rare sugars and unnatural amino acid building blocks, stereoselective construction of three consecutive 1,2-cis glycosidic linkages, amide coupling, and the presence of five nitrogen atoms dispersed over four sugar units as well as the carboxylic acid functionality make the total synthesis a formidable task.

Bidirectional potential effects of DON transformation in vadose zones on groundwater nitrate contamination: Different contributions to nitrification and denitrification

The main cause of groundwater nitrate contamination is the continual downward migration of dissolved nitrogen (N) in vadose zone with leachate. In recent years it has been found that dissolved organic N (DON) rise to forefront due to its great migration capacity and environmental effects. However, it remains unknown how the transformation behaviors of DONs with different properties in vadose zone profile may impact N forms distribution and groundwater nitrate contamination. To address the issue, we conducted a series of 60-day microcosm incubation experiments to investigate the effects of various DONs transformation behaviors on the distribution of N forms, microbial communities, and functional genes. The results revealed that urea and amino acids mineralized immediately after substrates addition. By contrast, amino sugars and proteins caused less dissolved N throughout entire incubation period. The transformation behaviors could substantially alter the microbial communities. Moreover, we discovered that amino sugars remarkably increased the absolute abundances of denitrification function genes. These results delineated that DONs with unique characteristics (such as amino sugar) promoted different N geochemical processes in distinct ways: different contributions to nitrification and denitrification. This can provide new insights for nitrate non-point source pollution control in groundwater.

Size-independent quantification of nanoplastics in various aqueous media using surfaced-enhanced Raman scattering

In this work, we successfully developed an intriguing preparation strategy to reduce the size-dependent effect of nanoplastics (NPLs), which is the limitation of NPLs quantification by surface-enhanced Raman scattering (SERS). This simple and low-cost technique enabled us to quantify different sizes (i.e., 100, 300, 600, and 800 nm) of polystyrene nanospheres (PS NSs) in various aqueous media. The SERS substrate was simply prepared by sputtering gold particles to cover on a glass cover slide. By dissolving PS NSs in toluene and preconcentrating by coffee-ring effect, SERS measurement can quantify NPLs at a very low concentration with a limit of detection (LOD) of approximately 0.10-0.26 μg/mL. The experiment was also conducted in the presence of interferences, including salts, sugars, amino acids, and detergents. The method was validated for quantitative analysis using a mixture of 100-, 300-, 600-, and 800-nm PS NSs in a ratio of 1:1:1:1 in real-world media (i.e., tap water, mineral water, and river water), which successfully approaches the evaluation of PS NSs in the range of 10-40 µg/mL with an LOD of approximately 0.32-0.52 µg/mL.

Faster accumulation and greater contribution of glomalin to the soil organic carbon pool than amino sugars do under tropical coastal forest restoration

Microbial metabolic products play a vital role in maintaining ecosystem multifunctionality, such as soil physical structure and soil organic carbon (SOC) preservation. Afforestation is an effective strategy to restore degraded land. Glomalin-related soil proteins (GRSP) and amino sugars are regarded as stable microbial-derived C, and their distribution within soil aggregates affects soil structure stability and SOC sequestration. However, the information about how afforestation affects the microbial contribution to SOC pools within aggregates is poorly understood. We assessed the accumulation and contribution of GRSP and amino sugars within soil aggregates along a restoration chronosequence (Bare land, Eucalyptus exserta plantation, native species mixed forest, and native forest) in tropical coastal terraces. Amino sugars and GRSP concentrations increased, whereas their contributions to the SOC pool decreased along the restoration chronosequence. Although microaggregates harbored greater microbial abundances, amino sugars and GRSP concentrations were not significantly affected by aggregate sizes. Interestingly, the contributions of amino sugars and GRSP to SOC pools decreased with decreasing aggregate size which might be associated with increased accumulation of plant-derived C. However, the relative change rate of GRSP was consistently greater in all restoration chronosequences than that of amino sugars. The accumulation of GRSP and amino sugars in SOC pools was closely associated with the dynamics of soil fertility and the microbial community. Our findings suggest that GRSP accumulates faster and contributes more to SOC pools during restoration than amino sugars did which was greatly affected by aggregate sizes. Afforestation substantially enhanced soil quality with native forest comprising species sequestering more SOC than the monoculture plantation did. Such information is invaluable for improving our mechanistic understanding of microbial control over SOC preservation during degraded ecosystem restoration. Our findings also show that plantations using arbuscular mycorrhizal plants can be an effective practice to sequester more soil carbon during restoration.

Differential responses of fungal and bacterial necromass accumulation in soil to nitrogen deposition in relation to deposition rate

Influenced by nitrogen (N) deposition, changes in soil organic carbon (SOC) sequestration in terrestrial ecosystems could provide strong feedback to climate change. Mounting evidence showed that microbial necromass contributes substantially to SOC sequestration; however, how N deposition influences microbial necromass accumulation in soils remains elusive. We investigated the impacts of N deposition on soil microbial necromass, assessed by amino sugars, at seven forest sites along a north-south transect in eastern China. We found that the responses of fungal and bacterial necromass accumulation to N deposition depended on the deposition rate, with high N deposition (>50 kg N ha^-1 yr^-1) stimulating fungal necromass accumulation from 29.1 % to 35.2 %, while low N deposition damaging the accumulation of bacterial necromass in soil by 12.1 %. On the whole, N deposition benefitted the dominance of fungal over bacterial necromass, with their ratio being significantly greater at high-N level. The accumulation of microbial necromass was primarily governed by soil properties, including nutrients stoichiometry, clay content and pH, while the composition of microbial necromass was conjointly affected by soil properties and microbial community structure. The latitudinal distribution of microbial necromass contributions to SOC pool was not altered by N deposition, and was firmly controlled by the climatic and edaphic factors. Collectively, our results reveal the impacts of N deposition on microbial necromass accumulation in soil and the geographical pattern across forest ecosystems in eastern China, providing implications for our accurate predictions of global change impacts on SOC sequestration.

Nutrient-Mediated Perception and Signalling in Human Metabolism: A Perspective of Nutrigenomics

The interaction between selective nutrients and linked genes involving a specific organ reveals the genetic make-up of an individual in response to a particular nutrient. The interaction of genes with food opens opportunities for the addition of bioactive compounds for specific populations comprising identical genotypes. The slight difference in the genetic blueprints of humans is advantageous in determining the effect of nutrients and their metabolism in the body. The basic knowledge of emerging nutrigenomics and nutrigenetics can be applied to optimize health, prevention, and treatment of diseases. In addition, nutrient-mediated pathways detecting the cellular concentration of nutrients such as sugars, amino acids, lipids, and metabolites are integrated and coordinated at the organismal level via hormone signals. This review deals with the interaction of nutrients with various aspects of nutrigenetics and nutrigenomics along with pathways involved in nutrient sensing and regulation, which can provide a detailed understanding of this new leading edge in nutrition research and its potential application to dietetic practice.

Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods

BACKGROUND

Camellia oleifera Abel. (C. oleifera) is an important traditional woody species in China that produces edible oil. However, the current literature lacks a proper understanding of C. oleifera's ability to adapt to different photoperiods.

RESULTS

Our results indicate that the photoperiod can significantly impact flowering time in C. oleifera. We grew a total of nine samples under the short day condition (SD), middle day condition (MD) and long day condition (LD). Transcriptome analysis yielded 66.94 Gb of high-quality clean reads, with an average of over 6.73 Gb of reads for per sample. Following assembly, a total of 120,080 transcripts were obtained and 94,979 unigenes annotated. A total of 3475 differentially expressed genes (DEGs) were identified between the SD_MD, SD_LD, and MD_LD gene sets. Moreover, WGCNA identified ten gene modules. Genes in pink module (92 genes) were positively correlated with SD, and negatively correlated with both MD and LD. Genes in the magenta module (42 genes) were positively correlated with MD and negatively correlated with both LD and SD. Finally, genes in the yellow module (1758 genes) were positively correlated with both SD and MD, but negatively correlated with LD. KEGG enrichment analysis revealed that genes in the pink, magenta, and yellow modules were involved in flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism and circadian rhythm pathways. Additionally, eight hub genes (GI, AP2, WRKY65, SCR, SHR, PHR1, ERF106, and SCL3) were obtained through network analysis. The hub genes had high connectivity with other photoperiod-sensitive DEGs. The expression levels of hub genes were verified by qRT-PCR analysis.

CONCLUSION

An increase in light duration promotes earlier flowering of C. oleifera. Flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism, and circadian rhythm pathways may function in the photoperiodic flowering pathway of C. oleifera. We also identified eight hub genes that may play a role in this pathway. Ultimately, this work contributes to our understanding of the photoperiodic flowering pathway of C. oleifera and further informs molecular breeding programs on the plant's photoperiodic sensitivity.

Salt and Metal Tolerance Involves Formation of Guttation Droplets in Species of the Aspergillus versicolor Complex

Three strains of the Aspergillus versicolor complex were isolated from a salty marsh at a former uranium mining site in Thuringia, Germany. The strains from a metal-rich environment were not only highly salt tolerant (up to 20% NaCl), but at the same time could sustain elevated Cs and Sr (both up to 100 mM) concentrations as well as other (heavy) metals present in the environment. During growth experiments when screening for differential cell morphology, the occurrence of guttation droplets was observed, specifically when elevated Sr concentrations of 25 mM were present in the media. To analyze the potential of metal tolerance being promoted by these excretions, proteomics and metabolomics of guttation droplets were performed. Indeed, proteins involved in up-regulated metabolic activities as well as in stress responses were identified. The metabolome verified the presence of amino sugars, glucose homeostasis-regulating substances, abscisic acid and bioactive alkaloids, flavones and quinones.

Detection of innate immune response modulating impurities (IIRMI) in therapeutic peptides and proteins: Impact of excipients

Unintended immunogenicity can affect the safety and efficacy of therapeutic proteins and peptides, so accurate assessments of immunogenicity risk can aid in the selection, development, and regulation of biologics. Product- and process- related impurities can act as adjuvants that activate the local or systemic innate immune response increasing the likelihood of product immunogenicity. Thus, assessing whether products have innate immune response modulating impurities (IIRMI) is a key component of immunogenicity risk assessments. Identifying trace levels of individual IIRMI can be difficult and testing individually for all potential impurities is not feasible. Therefore, to mitigate the risk, cell-based assays that use human blood cells or monocyte-macrophage reporter cell lines are being developed to detect minute quantities of impurities capable of eliciting innate immune activation. As these are cell-based assays, there is concern that excipients could blunt the cell responses, masking the presence of immunogenic IIRMI. Here, we explore the impact of frequently used excipients (non-ionic detergents, sugars, amino acids, bulking agents) on the sensitivity of reporter cell lines (THP-1- and RAW-Blue cells) and fresh human blood cells to detect purified TLR agonists as model IIRMI. We show that while excipients do not modulate the innate immune response elicited by TLR agonists in vivo, they can impact on the sensitivity of cell-based IIRMI assays. Reduced sensitivity to detect LPS, FSL-1, and other model IIRMI was also evident when testing 3 different recombinant drug products, product A (a representative mAb), B (a representative growth factor), C (a representative peptide), and their corresponding formulations. These results indicate that product formulations need to be considered when developing and validating cell-based assays for assessing clinically relevant levels of IIRMI in therapeutic proteins. Optimization of reporter cells, culture conditions and drug product concentration appear to be critical to minimize the impact of excipients and attain sensitive and reproducible assays.

Design, Synthesis, and Antifungal Activities of Hymexazol Glycosides Based on a Biomimetic Strategy

Hymexazol (HYM) is irreplaceable for treating soil-borne diseases due to its high efficiency and low cost, as a broad-spectrum fungicide. However, when HYM is absorbed by plants, it is rapidly converted into two glycoside metabolites, and the antifungal activities of these glycosides are inferior to that of HYM. Therefore, in this study, to maintain strong antifungal activity in vitro and in vivo, HYM was glycosylated with amino sugars that have diverse biological activities to simulate plant glycosylation. The antifungal experiment proved that glycoside 15 has the highest antifungal activity, and N-acetyl glucosamine and HYM had obvious synergistic effects. According to the structure-activity relationship studies, glycoside 15 had greater numbers of active electron-rich regions and front-line orbital electrons due to the introduction of N-acetyl glucosamine. Moreover, glycoside 15 can significantly promote plant growth and induce an increase in plant defense enzyme activity. Additionally, compared to HYM, the results of electron microscopy and proteomics revealed that glycoside 15 has a unique antifungal mechanism. The promising antifungal activity and interactions with plants mean that glycoside 15 is a potential green fungicide candidate. Furthermore, this research conducted an interesting exploration of the agricultural applications of amino sugars.

Glenthmycins A-M: Macrocyclic Spirotetronate Polyketide Antibacterials from the Australian Pasture Plant-Derived Streptomyces sp. CMB-PB041

Chemical investigation of Australian pasture plant-derived Streptomyces sp. CMB-PB041, supported by miniaturized cultivation profiling and molecular network analysis, led to the isolation and characterization of 13 new macrocyclic spirotetronates, glenthmycins A-M (1-13), with structures assigned by detailed spectroscopic analysis, chemical degradation and derivatization, and mechanistic and biosynthetic considerations. Hydrolysis of glenthmycin B (2) yielded the aglycone 14, whose structure and absolute configuration were secured by X-ray analysis, along with the unexpected amino sugar residues glenthose lactams A (15) and B (16), with Mosher analysis of 15 facilitating assignment of absolute configurations of the amino sugar. While the glenthmycins proved to be acid stable, treatment of isomeric glenthmycins (i.e., 3, 6, and 8) with base catalyzed rapid intramolecular trans-esterification to regio-isomeric mixtures (i.e., 3 + 6 + 8). Exposure of 5 to base achieved the same intramolecular trans-esterification and was instrumental in detecting and tentatively identifying two additional minor co-metabolites, glenthmycins N (19) and O (20). A structure-activity relationship analysis carried out on 1-13 and the semisynthetic analogues 14 and 21-26 revealed a promising Gram +ve antibacterial pharmacophore, effective against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE), but with no detectable cytotoxicity to eukaryotic cells (i.e., fungal and human carcinoma). Of particular note, the semisynthetic analogue glenthmycin K 9-valerate (26) was unique among glenthmycins in potently inhibiting growth of the full panel of Gram +ve pathogens (IC₅₀ 0.2-1.6 μM). We conclude with an observation that any future evaluation of the antibacterial potential of glenthmycins and related macrocyclic spirotetronates may do well to include important soil-derived Gram +ve pathogens, such as Bacillus anthrax, Clostridium botulinum, and Rhodococcus equi, the causative agents of anthrax, botulism, and livestock pneumonia.

[Effects of wetland reclamation on amino sugar accumulation in soils of the Sanjiang Plain]

Microbial residues play important roles in the formation and stabilization of soil organic matter. The responses of soil microbial residues to wetland reclamation, however, remain unclear. In this study, we collected soil samples from a native wetland dominated by Calamagrostis angustifolia as well as three agricultural lands cultivated for 5, 15, and 25 years to examine the effects of wetland reclamation on the content of microbial residues (amino sugar analysis). Results showed that soil amino sugar contents were significantly reduced after wetland reclamation, with a positive relationship between the reduction and the duration of reclamation. After 25 years of reclamation, the content of glucosamine, galactosamine, and muramic acid in agricultural soils decreased by 38.0%, 38.1%, and 35.9%, respectively, compared to the natural wetland. The reduction of muramic acid (25.8%) was stronger than glucosamine (14.9%) after 5 years of reclamation, indicating that bacterial-derived microbial residues were more sensitive to wetland reclamation than fungal-derived counterparts in the short term. Total amino sugars were decreased by 21.1%, 34.0%, and 38.0% after 5, 15, and 25 years of wetland reclamation, respectively. The proportion of total amino sugars in soil organic matter was significantly decreased from 4.8% in natural wetland to 4.4% after 25 years of reclamation, indicating that long-term wetland reclamation accelerated the depletion of microbial-derived organic components, and thus changed the composition of soil organic matter. Such changes may affect long-term stabilization of soil organic matter and ecosystem functioning.

Synthesis of N-Acetyllactosamine and N-Acetyllactosamine-Based Bioactives

N-Acetyllactosamine (LacNAc) or more specifically β-d-galactopyranosyl-1,4-N-acetyl-d-glucosamine is a unique acyl-amino sugar and a key structural unit in human milk oligosaccharides, an antigen component of many glycoproteins, and an antiviral active component for the development of effective drugs against viruses. LacNAc is useful itself and as a basic building block for producing various bioactive oligosaccharides, notably because this synthesis may be used to add value to dairy lactose. Despite a significant amount of information in the literature on the benefits, structures, and types of different LacNAc-derived oligosaccharides, knowledge about their effective synthesis for large-scale production is still in its infancy. This work provides a comprehensive analysis of existing production strategies for LacNAc and important LacNAc-based structures, including sialylated LacNAc as well as poly- and oligo-LacNAc. We conclude that direct extraction from milk is too complex, while chemical synthesis is also impractical at an industrial scale. Microbial routes have application when multiple step reactions are needed, but the major route to large-scale biochemical production will likely lie with enzymatic routes, particularly those using β-galactosidases (for LacNAc synthesis), sialidases (for sialylated LacNAc synthesis), and β-N-acetylhexosaminidases (for oligo-LacNAc synthesis). Glycosyltransferases, especially for the biosynthesis of extended complex LacNAc structures, could also play a major role in the future. In these cases, immobilization of the enzyme can increase stability and reduce cost. Processing parameters, such as substrate concentration and purity, acceptor/donor ratio, water activity, and temperature, can affect product selectivity and yield. More work is needed to optimize these reaction parameters and in the development of robust, thermally stable enzymes to facilitate commercial production of these important bioactive substances.

Metabolites of Trichoderma longibrachiatum EF5 inhibits soil borne pathogen, Macrophomina phaseolina by triggering amino sugar metabolism

An endophytic fungal antagonist Trichoderma longibrachiatum EF5 exhibited biocontrol activity against a soil-borne fungal pathogen Macrophomina phaseolina. Under dual co-culture, T. longibrachiatum EF5 showed 58% inhibition against M. phaseolina. Crude soluble metabolites (SMs) extracted from EF5 exhibited biocontrol activity (61%), which is more significant than the cell-free extract. Dual culture of both T. longibrachiatum EF5 and M. phaseolina displayed entangled mycelial structures and retarded hyphal growth. The metabolites responsible for antibiosis and pathogenic activity profiled through GC-MS revealed a total of 131 SMs from axenic culture and upon the interaction of T. longibrachiatum EF5 and M. phaseolina. Interestingly, potential plant-growth-promoting and antimicrobial compounds such as 1- pentanol, 1-hexanol, myristonyl pantothenate, bisabolol, d-Alanine, and diethyl trisulphide were unique with T. longibrachiatum EF5. Few compounds that were not observed or produced minimally under axenic culture were increased during their interaction (e.g., 1,6-anhydro-á-d-Glucopyranose and 5-heptyl dihydro-2(3H)-Furanone), suggesting antimicrobial action against the pathogen. This study also unraveled the induction of amino sugar metabolism when T. longibrachiatum EF5 interacts with M. phaseolina, which is responsible for colonization and counterfeiting the pathogen. Hence T. longibrachiatum EF5 could be a potential biocontrol agent employed for defense priming and plant growth promotion.

Tracing bacterial and fungal necromass dynamics of municipal sludge in landfill bioreactors using biomarker amino sugars

The dynamics of microbial necromass of municipal solid waste over long-term landfill remain unknown. This study presents the first investigation on the dynamics of bacterial and fungal necromass of municipal sludge in non-aeration versus alternating aeration landfill bioreactors by using amino sugar biomarkers. Results showed that under non-aeration treatment, the decomposition rate of muramic acid derived from bacteria is higher than that of fungal-derived glucosamine. The relative change in glucosamine and muramic acid in the early period of landfills under the alternating aeration treatment is consistent with that under non-aeration treatment. However, with the increase in alternating aeration cycles, bacterial necromass muramic acid exerts a lower decomposition rate than fungal necromass glucosamine. Throughout the entire landfill period, galactosamine is the amino sugar with the slowest decomposition rate under non-aeration mode but the amino sugar with the fastest decomposition rate under alternating aeration mode. The present work fills the knowledge gap of microbial necromass dynamics of municipal solid waste in landfills.

[Effects of nitrogen and phosphorus addition on soil microbial community and amino sugar in a temperate forest on Changbai Mountain, Northeast China]

We carried out an experiment including nitrogen addition (N, 50 kg N·hm^-2·a^-1), phosphorus addition (P, 25 kg P·hm^-2·a^-1) and both nitrogen and phosphorus addition (NP, 50 kg N·hm^-2·a^-1+25 kg P·hm^-2·a^-1) in a natural Korean pine broad-leaved mixed forest on Changbai Mountain to examine the effects of single and combined N and P additions on soil microbial community composition and amino sugar. The results showed that N and P addition significantly reduced total microbial biomass by 19.5% and 24.6% in the organic layer of soil, while P addition significantly reduced the biomass of bacteria and fungi by 23.8% and 19.3%, respectively. In the mineral layer, N, P and NP addition significantly increased total microbial biomass by 94.8%, 230.9%, and 115.0% respectively, while the biomass of bacteria and fungi were significantly increased under all the treatments. The fungi to bacteria ratio (F/B) was significantly increased in the organic layer by N addition, while was decreased in the mineral layer soil by NP addition. The Gram-positive bacteria to Gram-negative bacteria ratio showed positive response to N, P and NP addition. Soil amino sugars responded differently to different treatments. N, P and NP addition significantly decreased glucosamine content by 41.3%, 48.8% and 36.4% in the organic layer, while N and NP addition increased muramic acid content by 43.0% and 71.1%, respectively. The contents of glucosamine and muramic acid in the mineral layer did not change significantly in response to N addition but increased significantly in response to both P addition and NP addition. The glucosamine to muramic acid ratio in the organic layer significantly decreased under fertilization treatments, indicating that N and P addition increased the relative contribution of bacteria to soil organic carbon accumulation. The changes in soil amino sugar contents were closely related to the change in microbial community composition after N and P addition, both of which were affected by changes in soil chemical properties.

Galectin 3: an extraordinary multifunctional protein in dermatology. Current knowledge and perspectives

Galectin 3 is a unique ~31 kDa protein that recognizes the N-acetyl-lactosamine structure of several glycoconjugates. It mainly occurs in epithelial and myeloid cells, but is also found in a variety of human cell types. In view of the crucial role played by galectin 3 in the regulation of cellular processes of essential importance and in the pathogenetic mechanisms of diverse disorders, it is not surprising that, particularly in the last three decades, the attention of the scientific community has been increasingly drawn to this extraordinary and multifunctional galectin. In this paper the authors summarize current knowledge on the expression of galectin 3 in normal and diseased human skin, its implications in the pathogenesis, diagnosis and prognosis of cutaneous disorders, and the perspectives of a novel approach to the treatment of the latter using galectin 3 or its inhibitors/antagonists.

Magnetic nanoparticles: essential factors for sustainable environmental applications

In recent years, there has been an increasing use of engineered magnetic nanoparticles for remediation and water treatments, leading to elevated public concerns. To this end, it is necessary to enhance the understanding of how these magnetic nanoparticles react with contaminants and interact with the surrounding environment during applications. This review aims to provide a holistic overview of current knowledge of magnetic nanoparticles in environmental applications, emphasizing studies of zero-valent iron (nZVI), magnetite (Fe3O4) and maghemite (γ-Fe2O3) nanoparticles. Contaminant removal mechanisms by magnetic nanoparticles are presented, along with factors affecting the ability of contaminant desorption. Factors influencing the recovery of magnetic nanoparticles are outlined, describing the challenges of magnetic particle collection. The aggregation of magnetic nanoparticles is described, and methods for enhancing stability are summarized. Moreover, the toxicological effects owing to magnetic nanoparticles are discussed. It is possible that magnetic nanoparticles can be applied sustainably after detailed consideration of these discussed factors.

G-CSF mobilizes slanDCs (6-sulfo LacNAc+ dendritic cells) with a high proinflammatory capacity

Donor dendritic cells (DCs) play a pivotal role in the induction of immunity and tolerance after peripheral blood stem cell transplantation (PBSCT). Treatment of healthy donors with granulocyte-colony stimulating factor (G-CSF) increases the numbers of tolerogenic DCs and T cells among mobilized blood leukocytes in the graft. SlanDCs (6-sulfo LacNAc+ DCs), a major source of IL-12 and TNF-alpha in blood, have not been studied in this respect. Here, we demonstrate that slanDCs (14.9 x 10(6)/L to 64.0 x 10(6)/L) are efficiently mobilized by G-CSF and retain their capacity to produce IL-12 and TNF-alpha at high levels. Furthermore, G-CSF-mobilized slanDCs programmed the differentiation of Th1 cells and displayed a particularly strong capacity to stimulate the proliferation of naive allogeneic T cells. Thus, slanDCs transfused into recipients of allogeneic peripheral blood stem cell (PBSC) transplants are functionally fully capable and may be critical in supporting graft-versus-host disease as well as graft-versus-leukemia effects.

Effect of surfactants on fluoranthene degradation by Pseudomonas alcaligenes PA-10

Two surfactants, Tween 80 and JBR, were investigated for their effect on fluoranthene degradation by a Pseudomonad. Both surfactants enhanced fluoranthene degradation by Pseudomonas alcaligenes PA-10 in shake flask culture. This bacterium was capable of utilising the synthetic surfactant and the biosurfactant as growth substrates and the critical micelle concentration of neither compound inhibited bacterial growth. The biosurfactant JBR significantly increased polycyclic aromatic hydrocarbon (PAH) desorption from soil. Inoculation of fluoranthene-contaminated soil microcosms with P. alcaligenes PA-10 resulted in the removal of significant amounts (45 +/- 5%) of the PAH after 28 days compared to an uninoculated control. Addition of the biosurfactant increased the initial rate of fluoranthene degradation in the inoculated microcosm. The presence of a lower molecular weight PAH, phenanthrene, had a similar effect on the rate of fluoranthene removal.

Human 6-sulfo LacNAc-expressing dendritic cells are principal producers of early interleukin-12 and are controlled by erythrocytes

Early and high-level production of IL-12 is crucial for effective immune responses against pathogens. Up until now, the cells providing this initial IL-12 have remained elusive. Here we show that a subset of human blood dendritic cells (DC) is the principal and primary source of IL-12p70 when blood leukocytes are stimulated with the TLR4-ligand LPS or with CD40-ligand. These so-called slanDC are characterized by the 6-sulfo LacNAc modification of PSGL-1, which is identified by the mAb M-DC8. The IL-12 response of slanDC requires a few hours of in vitro maturation, which is completely blocked in the presence of erythrocytes. This inhibition of maturation depends on the expression of CD47 on erythrocytes and of its ligand SIRPalpha on DC. While strictly controlled in the blood by erythrocytes, the high IL-12- and TNF-alpha-producing capacity of slanDC in tissues may be critical in fighting off pathogens; if uncontrolled, it may lead to adverse inflammatory reactions.

[Dehydrative glycosidation and partially benzylated sugar derivatives]

Dehydrative glycosidation reactions reported by the authors' group are reviewed. The authors' efforts were concentrated on developing reagent systems usable for one-stage-one-pot glycosidation. Such systems could simplify the glycosidation step using 1-OH sugar derivatives, since any preactivation stage for the hemiacetal OH group could be omitted. The systems, utilizing the dehydration potential of sulfonyl chloride, such as the p-nitrobenzenesulfonyl chloride-silver trifluoromethanesulfonate-triethylamine system as well as the p-nitrobenzenesulfonyl chloride-silver trifluoromethanesulfonate-N,N-dimethylacetamide-triethylamine system, were useful for the syntheses of many kinds of oligosaccharides. As a system free from any metals, the authors developed the trimethylsilyl trifluoromethanesulfonate-pyridine (TP) system. During the study of the system containing cobalt (II) bromide, the authors found that the bromide converts 1-OH sugar into the corresponding 1-Br derivative, which is then activated with the cobalt salt to undergo glycosidation with alcohol. To prepare partially benzylated sugar derivatives used as acceptors in the authors' studies, controlled benzylation and forced tritylation were carried out. Short syntheses of a variety of useful sugar derivatives using such convenient procedures are described. As a novel protecting group for the hemiacetal OH group, the authors used the 2-methoxyethyl group. Many kinds of trehalose-type disaccarides we prepared.

The C7N aminocyclitol family of natural products

This review covers microbial secondary metabolites classified in the family of C7N aminocyclitols, a relatively new class of natural products that is increasingly gaining recognition due to their significant biomedical and agricultural uses. Their discovery and structure determinations, their biosynthetic origin, biological properties, chemical synthesis, as well as their further development for pharmaceutical uses are described. The literature from 1970 to July 2002 is reviewed, with 269 references cited.

Preparation and characterisation of chitosans with oligosaccharide branches

The trimer 2-acetamido-2-deoxy-D-glucopyranosyl-beta-(1-->4)-2-acetamido-2-deoxy-D-glucopyranosyl-beta-(1-->4)-2,5-anhydro-D-mannofuranose (A-A-M) was reductively N-alkylated onto a fully de-N-acetylated chitosan (F(A)<0.001, DP(n)=25) to obtain branched chitosans with degree of substitution (DS) of 0.070, 0.23 and 0.40, as determined by 1H NMR spectroscopy. The apparent pK(a) values of the primary and secondary amines of the chitosans substituted with the trimer A-A-M were determined by monitoring the chemical shift of the H-2 of GlcN, and were determined as 6.5-6.9 for the primary (unsubstituted) amines and as 5.0-5.2 for the secondary (substituted) amines. The intrinsic pK(a) values (pK(int)) were found to be 7.3-7.4 for the substituted and 8.7 for the unsubstituted amines. The chitosan branched with A-A-M (DS 0.40) was found to be soluble in aqueous solution over the entire pH range. SEC-MALLS (size-exclusion chromatography with a multi-angle laser light scattering detector) further showed that addition of branches did not affect the molar hydrodynamic volume of the chitosan.

TNF- increases the carbohydrate sulfation of CD44: induction of 6-sulfo N-acetyl lactosamine on N- and O-linked glycans

CD44 and sulfation have both been implicated in leukocyte adhesion. In monocytes, the inflammatory cytokine tumor necrosis factor alpha (TNF-alpha) stimulates CD44 sulfation, and this correlates with the induction of CD44-mediated adhesion events. However, little is known about the sulfation of CD44 or its induction by inflammatory cytokines. We determined that TNF-alpha induces the carbohydrate sulfation of CD44. CD44 was established as a major sulfated cell surface protein on myeloid cells. In the SR91 myeloid cell line, the majority of CD44 sulfation was attributed to the glycosaminoglycan chondroitin sulfate. However, TNF-alpha stimulation increased CD44 sulfation two- to threefold, largely attributed to the increased sulfation of N- and O-linked glycans on CD44. Therefore, TNF-alpha induced a decrease in the percentage of CD44 sulfation due to chondroitin sulfate and an increase due to N- and O-linked sulfation. Furthermore, TNF-alpha induced the expression of 6-sulfo N-acetyl lactosamine (LacNAc)/Lewis x on these cells, which was detected by a monoclonal antibody after neuraminidase treatment. This 6-sulfo LacNAc/Lewis x epitope was induced on N-linked and (to a lesser extent) on O-linked glycans present on CD44. This demonstrates that CD44 is modified by sulfated carbohydrates in myeloid cells and that TNF-alpha modifies both the type and amount of carbohydrate sulfation occurring on CD44. In addition, it demonstrates that TNF-alpha can induce the expression of 6-sulfo N-acetyl glucosamine on both N- and O-linked glycans of CD44 in myeloid cells.

6-Sulfo LacNAc, a novel carbohydrate modification of PSGL-1, defines an inflammatory type of human dendritic cells

The monoclonal antibody M-DC8 defines a major subset of human blood dendritic cells (DCs). Here we identify the M-DC8 structure as 6-sulfo LacNAc, a novel carbohydrate modification of the P selectin glycoprotein ligand 1 (PSGL-1). In contrast to previously described blood DCs, M-DC8+ DCs lack the cutaneous lymphocyte antigen (CLA) on PSGL-1 and fail to bind P and E selectin. Yet they express anaphylatoxin receptors (C5aR and C3aR) and the Fcgamma receptor III (CD16), which recruit cells to inflammatory sites. While sharing with DC1 the expression of myeloid markers and a potent capacity to prime T cells in vitro, M-DC8+ DCs produce far more TNF-alpha in response to the bacterial endotoxin lipopolysaccharide (LPS). Thus, 6-sulfo LacNAc-expressing DCs appear as a novel proinflammatory DC subset.

Characterization and analysis of the PikD regulatory factor in the pikromycin biosynthetic pathway of Streptomyces venezuelae

The Streptomyces venezuelae pikD gene from the pikromycin biosynthetic cluster was analyzed, and its deduced product (PikD) was found to have amino acid sequence homology with a small family of bacterial regulatory proteins. Database comparisons revealed two hypothetical domains, including an N-terminal triphosphate-binding domain and a C-terminal helix-turn-helix DNA-binding motif. Analysis of PikD was initiated by deletion of the corresponding gene (pikD) from the chromosome of S. venezuelae, resulting in complete loss of antibiotic production. Complementation by a plasmid carrying pikD restored macrolide biosynthesis, demonstrating that PikD is a positive regulator. Mutations were made in the predicted nucleotide triphosphate-binding domain, confirming the active-site amino acid residues of the Walker A and B motifs. Feeding of macrolide intermediates was carried out to gauge the points of operon control by PikD. Although the pikD mutant strain was unable to convert macrolactones (10-deoxymethynolide and narbonolide) to glycosylated products, macrolide intermediates (YC-17 and narbomycin) were hydroxylated with high efficiency. To study further the control of biosynthesis, presumed promoter regions from pik cluster loci were linked to the xylE reporter and placed in S. venezuelae wild-type and pikD mutant strains. This analysis demonstrated that PikD-mediated transcriptional regulation occurs at promoters controlling expression of pikRII, pikAI, and desI but not those controlling pikRI or pikC.