Chloroacetamide-Modified Nucleotide and RNA for Bioconjugations and Cross-Linking with RNA-Binding Proteins

Reactive RNA probes are useful for studying and identifying RNA-binding proteins. To that end, we designed and synthesized chloroacetamide-linked 7-deaza-ATP which was a good substrate for T7 RNA polymerase in in vitro transcription assay to synthesize reactive RNA probes bearing one or several reactive modifications. Modified RNA probes reacted with thiol-containing molecules as well as with cysteine- or histidine-containing peptides to form stable covalent products. They also reacted selectively with RNA-binding proteins to form cross-linked conjugates in high conversions thanks to proximity effect. Our modified nucleotide and RNA probes are promising tools for applications in RNA (bio)conjugations or RNA proteomics.

Deformation Behavior of Cross-Linked Supercrystalline Nanocomposites: An in Situ SAXS/WAXS Study during Uniaxial Compression

With the ever-expanding functional applications of supercrystalline nanocomposites (a relatively new category of materials consisting of organically functionalized nanoparticles arranged into periodic structures), it becomes necessary to ensure their structural stability and understand their deformation and failure mechanisms. Inducing the cross-linking of the functionalizing organic ligands, for instance, leads to a remarkable enhancement of the nanocomposites' mechanical properties. It is however still unknown how the cross-linked organic phase redistributes applied loads, how the supercrystalline lattice accommodates the imposed deformations, and thus in general what phenomena govern the overall material's mechanical response. This work elucidates these aspects for cross-linked supercrystalline nanocomposites through an in situ small- and wide-angle X-ray scattering study combined with uniaxial pressing. Because of this loading condition, it emerges that the cross-linked ligands effectively carry and distribute loads homogeneously throughout the nanocomposites, while the superlattice deforms via rotation, slip, and local defects generation.

Entropy based analysis of vertebrate sperm protamines sequences: evidence of potential dityrosine and cysteine-tyrosine cross-linking in sperm protamines

BACKGROUND

Spermatogenesis is the process by which germ cells develop into spermatozoa in the testis. Sperm protamines are small, arginine-rich nuclear proteins which replace somatic histones during spermatogenesis, allowing a hypercondensed DNA state that leads to a smaller nucleus and facilitating sperm head formation. In eutherian mammals, the protamine-DNA complex is achieved through a combination of intra- and intermolecular cysteine cross-linking and possibly histidine-cysteine zinc ion binding. Most metatherian sperm protamines lack cysteine but perform the same function. This lack of dicysteine cross-linking has made the mechanism behind metatherian protamines folding unclear.

RESULTS

Protamine sequences from UniProt's databases were pulled down and sorted into homologous groups. Multiple sequence alignments were then generated and a gap weighted relative entropy score calculated for each position. For the eutherian alignments, the cysteine containing positions were the most highly conserved. For the metatherian alignment, the tyrosine containing positions were the most highly conserved and corresponded to the cysteine positions in the eutherian alignment.

CONCLUSIONS

High conservation indicates likely functionally/structurally important residues at these positions in the metatherian protamines and the correspondence with cysteine positions within the eutherian alignment implies a similarity in function. One possible explanation is that the metatherian protamine structure relies upon dityrosine cross-linking between these highly conserved tyrosines. Also, the human protamine P1 sequence has a tyrosine substitution in a position expecting eutherian dicysteine cross-linking. Similarly, some members of the metatherian Planigales genus contain cysteine substitutions in positions expecting plausible metatherian dityrosine cross-linking. Rare cysteine-tyrosine cross-linking could explain both observations.

Encapsulation of Escherichia coli strain Nissle 1917 in a chitosan-alginate matrix by combining layer-by-layer assembly with CaCl2 cross-linking for an effective treatment of inflammatory bowel diseases

Escherichia coli strain Nissle 1917 (EcN) has been widely shown to effectively treat inflammatory bowel diseases (IBDs). Unfortunately, after oral administration, EcN viability dramatically decreases due to severe environmental factors, including low gastric pH, temperature and osmotic pressure. To address these challenges and improve oral bio-availability, this study utilized layer-by-layer assembly (LbL) and ionic cross-linking with CaCl₂ as a method of EcN encapsulation (GEcN). Upon examination, GEcN cells were shown to maintain their ability to grow and proliferate, but had a slightly longer stationary phase (10 h) relative to free EcN (4 h). When exposed to simulated gastric fluid (SGF), a higher number of GEcN cells survived up to 12 h when compared to the other groups. To assess the therapeutic effect of EcN encapsulation in vivo, a TNBS-induced colitis rat model was established. When compared with the oral administration of free EcN, GEcN exhibited a significantly enhanced anti-inflammatory effect. Furthermore, GEcN treatment showed a lower disease activity index (DAI), decreased pro-inflammatory cytokine expression (MPO, TNF-α, IL-6) and increased anti-inflammatory cytokine expression (IL-10). Additionally, rats that received GEcN had much higher ZO-1 expression levels. These results suggest that EcN encapsulation in a chitosan-alginate matrix when utilizing the LbL assembly with CaCl₂ cross-linking can improve probiotic viability in a gastric environmental and thereby offer a more effective treatment for IBDs.

Mapping hypersensitivity/allergic diseases in the International Classification of Diseases (ICD)-11: cross-linking terms and unmet needs

BACKGROUND

With the aim of actively contributing to the ongoing 11(th) International Classification of Diseases (ICD) revision, an international collaboration led by the European Academy of Allergy and Clinical Immunology (EAACI) has decided to revise the classification of hypersensitivity/allergic diseases and to validate it for ICD-11 by crowdsourcing the allergist community. However, understanding that the construction of a classification was necessary but not sufficient, we developed a mapping strategy in the attempt to better fit it to the ICD-11 linearization structure.

METHODS

The cross-linking terms process has been constructed based on an algorithm in which we prioritized the pre-coordination, followed by the post-coordination when the first step was not possible. If the above strategies failed to identify the entries, the conditions were ruled as "non specific terms", "no code fit properly" or "missing terms".

RESULTS

Amongst the 652 terms distributed in 5 main groups of the Hypersensitivity/Allergic Diseases classification, 169 terms fit directly the codes listed in the ICD-11 beta draft (October 2014 version), 26 were considered as "nonspecific term", 21 were linked to the Foundation by Index, 7 were recorded as inclusions and 2 were cited just in the definition of the condition. The post-coordination was possible for 97 terms, mainly for drug hypersensitivity conditions. We noticed a considerable number of allergen references missing.

CONCLUSION

The proposed strategy of cross-linking terms and the results of this process can actively contribute to updating the hypersensitivity and allergic conditions classification in the ICD-11 beta revision and underlines the need for either a new chapter in ICD-11 possibly entitled Hypersensitivity / Allergic Disorders or at the very least the aggregation of all such diseases under the "Diseases of Immune System" chapter in order for the overlaps to be double parented to the appropriate 'system' chapters.