protein composition
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2022 ◽  
Vol 23 (2) ◽  
pp. 955
Author(s):  
Hana Ujcikova ◽  
Dagoberto Robles ◽  
Xu Yue ◽  
Petr Svoboda ◽  
Yeon Sun Lee ◽  
...  

Chronic pain is associated with time-dependent structural and functional reorganization of the prefrontal cortex that may reflect adaptive pain compensatory and/or maladaptive pain-promoting mechanisms. However, the molecular underpinnings of these changes and whether there are time-dependent relationships to pain progression are not well characterized. In this study, we analyzed protein composition in the medial prefrontal cortex (mPFC) of rats at two timepoints after spinal nerve ligation (SNL) using two-dimensional gel electrophoresis (2D-ELFO) and liquid chromatography with tandem mass spectrometry (LC–MS/MS). SNL, but not sham-operated, rats developed persistent tactile allodynia and thermal hyperalgesia, confirming the presence of experimental neuropathic pain. Two weeks after SNL (early timepoint), we identified 11 proteins involved in signal transduction, protein transport, cell homeostasis, metabolism, and apoptosis, as well as heat-shock proteins and chaperones that were upregulated by more than 1.5-fold compared to the sham-operated rats. Interestingly, there were only four significantly altered proteins identified at 8 weeks after SNL (late timepoint). These findings demonstrate extensive time-dependent modifications of protein expression in the rat mPFC under a chronic neuropathic pain state that might underlie the evolution of chronic pain characterized by early pain-compensatory and later aberrant mechanisms.


Polymers ◽  
2022 ◽  
Vol 14 (2) ◽  
pp. 309
Author(s):  
Siyu Cai ◽  
Baoshuai Han ◽  
Yanjin Xu ◽  
Enyu Guo ◽  
Bin Sun ◽  
...  

Flight feather shafts are outstanding bioinspiration templates due to their unique light weight and their stiff and strong characteristics. As a thin wall of a natural composite beam, the keratinous cortex has evolved anisotropic features to support flight. Here, the anisotropic keratin composition, tensile response, dynamic properties of the cortex, and fracture behaviors of the shafts are clarified. The analysis of Fourier transform infrared (FTIR) spectra indicates that the protein composition of calamus cortex is almost homogeneous. In the middle and distal shafts (rachis), the content of the hydrogen bonds (HBs) and side-chain is the highest within the dorsal cortex and is consistently lower within the lateral wall. The tensile responses, including the properties and dominant damage pattern, are correlated with keratin composition and fiber orientation in the cortex. As for dynamic properties, the storage modulus and damping of the cortex are also anisotropic, corresponding to variation in protein composition and fibrous structure. The fracture behaviors of bent shafts include matrix breakage, fiber dissociation and fiber rupture on compressive dorsal cortex. To clarify, ‘real-time’ damage behaviors, and an integrated analysis between AE signals and fracture morphologies, are performed, indicating that calamus failure results from a straight buckling crack and final fiber rupture. Moreover, in the dorsal and lateral walls of rachis, the matrix breakage initially occurs, and then the propagation of the crack is restrained by ‘ligament-like’ fiber bundles and cross fiber, respectively. Subsequently, the further matrix breakage, interface dissociation and induced fiber rupture in the dorsal cortex result in the final failure.


PROTEOMICS ◽  
2022 ◽  
pp. 2100227
Author(s):  
Shannon P. Smyth ◽  
Brett Nixon ◽  
Amanda L. Anderson ◽  
Heather C. Murray ◽  
Jacinta H. Martin ◽  
...  

2022 ◽  
Vol 23 (1) ◽  
pp. 550
Author(s):  
Tiffany Malleck ◽  
Fatima Fekraoui ◽  
Isabelle Bornard ◽  
Céline Henry ◽  
Eloi Haudebourg ◽  
...  

The bacterium Moorella thermoacetica produces the most heat-resistant spores of any spoilage-causing microorganism known in the food industry. Previous work by our group revealed that the resistance of these spores to wet heat and biocides was lower when spores were produced at a lower temperature than the optimal temperature. Here, we used electron microcopy to characterize the ultrastructure of the coat of the spores formed at different sporulation temperatures; we found that spores produced at 55 °C mainly exhibited a lamellar inner coat tightly associated with a diffuse outer coat, while spores produced at 45 °C showed an inner and an outer coat separated by a less electron-dense zone. Moreover, misarranged coat structures were more frequently observed when spores were produced at the lower temperature. We then analyzed the proteome of the spores obtained at either 45 °C or 55 °C with respect to proteins putatively involved in the spore coat, exosporium, or in spore resistance. Some putative spore coat proteins, such as CotSA, were only identified in spores produced at 55 °C; other putative exosporium and coat proteins were significantly less abundant in spores produced at 45 °C. Altogether, our results suggest that sporulation temperature affects the structure and protein composition of M. thermoacetica spores.


Author(s):  
Abira Chaudhuri ◽  
Koushik Halder ◽  
Asis Datta

AbstractRemarkable diversity in the domain of genome loci architecture, structure of effector complex, array of protein composition, mechanisms of adaptation along with difference in pre-crRNA processing and interference have led to a vast scope of detailed classification in bacterial and archaeal CRISPR/Cas systems, their intrinsic weapon of adaptive immunity. Two classes: Class 1 and Class 2, several types and subtypes have been identified so far. While the evolution of the effector complexes of Class 2 is assigned solely to mobile genetic elements, the origin of Class 1 effector molecules is still in a haze. Majority of the types target DNA except type VI, which have been found to target RNA exclusively. Cas9, the single effector protein, has been the primary focus of CRISPR-mediated genome editing revolution and is an integral part of Class 2 (type II) system. The present review focuses on the different CRISPR types in depth and the application of CRISPR/Cas9 for epigenome modification, targeted base editing and improving traits such as abiotic and biotic stress tolerance, yield and nutritional aspects of tomato breeding.


2022 ◽  
Author(s):  
Katarina Bartalska ◽  
Verena Hübschmann ◽  
Medina Korkut-Demirbaş ◽  
Ryan John Abat Cubero ◽  
Alessandro Venturino ◽  
...  

Brain organoids differentiated from human induced pluripotent stem cells provide a unique opportunity to investigate the development, organization and connectivity of neurons in a complex cellular environment. However, organoids usually lack microglia, brain-resident immune cells which are both present in the early human embryonic brain and participate in neuronal circuit development. Here, we find that microglia innately develop in unguided retinal organoid differentiation between week 3 and 4 in 2.5D culture and appear later in floating, non-pigmented, 3D-cystic compartments. We enriched for cystic structures using a low-dosed BMP4 application and performed mass spectrometry, thus defining the protein composition of microglia-containing compartments. We found that cystic compartments expressed both mesenchymal and epithelial markers with microglia enriched in the mesenchymal region. Interestingly, microglia-like cells started to express the border-associated macrophage marker CD163. The preferential localization of human microglia to a mesenchymal compartment provides insight into the behavior and migration of microglia. The model will ultimately allow detailed study of these enigmatic cells and how they enter and distribute within the human brain.


Nutrients ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 47
Author(s):  
Francesco Maria Calabrese ◽  
Annalisa Porrelli ◽  
Mirco Vacca ◽  
Blandine Comte ◽  
Katharina Nimptsch ◽  
...  

Low-grade inflammatory diseases revealed metabolic perturbations that have been linked to various phenotypes, including gut microbiota dysbiosis. In the last decade, metaproteomics has been used to investigate protein composition profiles at specific steps and in specific healthy/pathologic conditions. We applied a rigorous protocol that relied on PRISMA guidelines and filtering criteria to obtain an exhaustive study selection that finally resulted in a group of 10 studies, based on metaproteomics and that aim at investigating obesity and diabetes. This batch of studies was used to discuss specific microbial and human metaproteome alterations and metabolic patterns in subjects affected by diabetes (T1D and T2D) and obesity. We provided the main up- and down-regulated protein patterns in the inspected pathologies. Despite the available results, the evident paucity of metaproteomic data is to be considered as a limiting factor in drawing objective considerations. To date, ad hoc prepared metaproteomic databases collecting pathologic data and related metadata, together with standardized analysis protocols, are required to increase our knowledge on these widespread pathologies.


2021 ◽  
Author(s):  
Daria A. Egorova ◽  
Andrey A. Solovyev ◽  
Nikita B. Polyakov ◽  
Ksenya A. Danilova ◽  
Anastasya A. Scherbakova ◽  
...  

Extracellular matrix plays a pivotal role in biofilm biology. Despite importance of matrix proteins as potential targets for development of antibacterial therapeutics little is known about matrix proteomes. While P. aeruginosa is one of the most important pathogens with emerging antibiotic resistance only few studies are devoted to matrix proteomes and there are no studies describing matrix proteome for any clinical isolates. As matrix responsible for some extracellular functions, it is expected that protein composition should be different in comparison with embedded in biofilm cells and this difference reflects possible active processes in matrix. Here we report the first matrix proteome for clinical isolate of P. aeruginosa in comparison with embedded cells. We have identified the largest number of proteins in matrix among all published studies. Ten proteins were unique for matrix and not present inside cells, but most of these proteins do not have well described function with respect to extracellular component of biofilm. Functional classification of enriched in matrix proteins resulted in several bioprocess groups of proteins. Top three groups were: oxidation-reduction processes, nucleoside metabolism and fatty acid synthesis. Finally, we discuss obtained data in prism of possible directions for antibiofilm therapeutic development.


Plants ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 1
Author(s):  
Dalma Nagy-Réder ◽  
Zsófia Birinyi ◽  
Marianna Rakszegi ◽  
Ferenc Békés ◽  
Gyöngyvér Gell

Global climate change in recent years has resulted in extreme heat and drought events that significantly influence crop production and endanger food security. Such abiotic stress during the growing season has a negative effect on yield as well as on the functional properties of wheat grain protein content and composition. This reduces the value of grain, as these factors significantly reduce end-use quality. In this study, four Hungarian bread wheat cultivars (Triticum aestivum ssp. aestivum) with different drought and heat tolerance were examined. Changes in the size- and hydrophobicity-based distribution of the total proteins of the samples have been monitored by SE- and RP-HPLC, respectively, together with parallel investigations of changes in the amounts of the R5 and G12 antibodies related to celiac disease immunoreactive peptides. Significant difference in yield, protein content and composition have been observed in each cultivar, altering the amounts of CD-related gliadin, as well as the protein parameters directly related to techno-functional properties (Glu/Gli ratio, UPP%). The extent of changes largely depended on the timing of the abiotic stress. The severity of the negative effect depended on the growth stage in which abiotic stress occurred.


2021 ◽  
Vol 9 (12) ◽  
pp. 2619
Author(s):  
Varvara Y. Sekova ◽  
Leonid I. Kovalyov ◽  
Marina A. Kovalyova ◽  
Natalya N. Gessler ◽  
Maria A. Danilova ◽  
...  

Yeasts cope with a wide range of environmental challenges using different adaptive mechanisms. They can prosper at extreme ambient pH and high temperatures; however, their adaptation mechanisms have not been entirely investigated. Previously, we showed the pivotal role and flexibility of the sugar and lipid composition of Yarrowia lipolytica W 29 upon adaptation to unfavorable conditions. In this study, we showed that extreme pH provoked significant changes in the cell wall proteins expression, with an increase in both the chaperones of heat shock protein HSP60 and some other proteins with chaperone functions. The mitochondria activity changes inducing the VDAC and malate dehydrogenase played an essential role in the adaptation, as did the altered carbohydrate metabolism, promoting its shift towards the pyruvate formation rather than gluconeogenesis. The elevated temperature led to changes in the cell wall proteins and chaperones, the induced expression of the proteins involved in the cell structural organization, ribosomal proteins, and the enzymes of formaldehyde degradation. Moreover, the readjustment of the protein composition and amount under combined stress indicated the promotion of catabolic processes related to scavenging the damaged proteins and lipids. Under all of the stress conditions studied, the process of folding, stress resistance, redox adaptation, and oxidative phosphorylation were the dominant pathways. The combined chronic alkaline and heat stress (pH 9.0, 38 °C) led to cross-adaptation, which caused “switching” over the traditional metabolism to the adaptation to the most damaging stress factor, namely the increased temperature.


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