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Wang K, Richards FM (1975) Reaction of dimethyl-3,3'-dithiobispropionimidate with intact human erythrocytes. Cross-linking of membrane proteins and hemoglobin. J Biol Chem 250:6622–6626 Gast F-U. Mechanistische Untersuchungen zur Fehlerkorrektur bei der ribosomalen Proteinsynthese. Hannover; 1987.

Spahr PF. Amino acid composition of ribosomes from Escherichia Coli. J Mol Biol. 1962;4(5):395–406. Natoli, G. Maintaining cell identity through global control of genomic organization. Immunity 33, 12–24 (2010). For offline cultivated B. subtilis expression cultures, sfGFP as well as split GFP (GFP11-tag combined with the non-fluorescent detector protein) fluorescence was determined after cultivation. In vitro split GFP assay was carried out in B. subtilis cell lysates mixed with a GFP1-10 detector solution. GFP1-10 was produced externally by E. coli BL21(DE3) with pET22b- sfGFP1-10 in inclusion bodies as described previously [ 18] and solved in 100 mM Tris-HCl pH 7.4, 100 mM NaCl, 10% (v/v) glycerol, 173 mM Urea, 10 mM EDTA to obtain the detector solution. For B. subtilis cell lysis, 100 µl of gus or gus11 expressing B. subtilis cultures were mixed with 25 µl PBS buffer (137 mM NaCl, 2.7 mM KCl, 8 mM Na 2HPO 4, 1.76 mM KH 2PO 4, pH 7.4) containing 10 mg/ml lysozyme. After incubation at 37 °C for at least 30 min, 20 µl cell lysates were mixed with 180 µl detector solution and were incubated at room temperature for at least 16 h as described previously [ 17]. Bernstein, B.E. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012). Segal, E. et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 34, 166–176 (2003).Skoczinski P, Volkenborn K, Fulton A, Bhadauriya A, Nutschel C, Gohlke H, Knapp A, Jaeger K-E. Contribution of single amino acid and codon substitutions to the production and secretion of a lipase by Bacillus subtilis. Microb Cell Fact. 2017;16:160. Mullen, A.C. et al. Master transcription factors determine cell-type-specific responses to TGF-β signaling. Cell 147, 565–576 (2011). Krämer CEM, Wiechert W, Kohlheyer D. Time-resolved, single-cell analysis of induced and programmed cell death via non-invasive propidium iodide and counterstain perfusion. Sci Rep. 2016;6:32104. Juxtaposingly, the protein corona also creates new opportunities for diagnostic and personalized nanomedicine; the protein corona can be utilized for disease diagnosis 24, 25, 26, 27, for the optimization of cell internalization 28, 29, 30 or leveraged for improving the in vivo biodistribution 21, 31 of nanomedicines. The enrichment of plasma proteins, particularly rare proteins and glycoproteins, onto NPs can create a protein corona ‘fingerprint’, which can be used for the personalized detection of biomarkers and assist in post-translational modifications in support of risk stratification, prognosis and disease recognition. Selectively coating NPs with purposely designed protein coronas can regulate cell-dependent uptake, promote blood circulation and enhance their therapeutic efficacies. Furthermore, protein corona studies have advanced from the conceptualization on how biosystems ‘see’ and perceive NPs 32 towards the development of new diagnostics and therapies 24, 25, 26, 33, 34, the emergence of the eco-corona 35, 36, 37 and materialization of the biological and ecological impacts induced by protein-corona-coated nanoplastics 38, 39. Artificial intelligence (AI) can be harnessed for data-driven discoveries of NP–biological interactions and complexities. Machine learning algorithms can identify the important variables that affect protein corona formation on specific types of NPs 40 and have predicted diseases in patients using personalized protein corona fingerprints 19, 26. Accordingly, a better understanding of the composition, pattern and decoration of biomolecules at the surface of NPs, supplemented by AI, can facilitate the development of safer and more effective nanomedicine technologies with desired biological fates. Several challenges remain in the field of protein corona research, including NP heterogeneity, interpretation of protein patterns and induced perturbations of immunological and toxicological responses. Through standardization of methodologies and detailed characterization of the protein corona, foundational for data sets that fuel AI, targeted therapeutic and/or diagnostic nanomedicines can be optimized.

Lindner AB, Madden R, Demarez A, Stewart EJ, Taddei F. Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation. Proc Natl Acad Sci USA. 2008;105:3076–81. Implementation of standardized protocols on methodologies and analyses of protein corona can generate extensive multi-omic-based data sets that can be used to teach AI to prognosticate diseases using protein corona fingerprints and to predict protein corona formation on distinct NPs for the fundamental design of nanomedicines. Characterization and prediction of the protein corona are both important to understand the interactions of NPs in biological milieus, yet there is a large discrepancy between the two, as the former comprises substantially more reports than the latter 124, 125. This immense difference is attributed to the disadvantages of existing high-throughput techniques and instruments used to test the biocompatibility and biofouling of nanotechnologies. Protocols for protein corona extraction can vary between laboratories, and thus there is a need for robust and standardized methods 109, 126. Moreover, MS is laborious, expensive and requires a high level of expertise, and such high-throughput analytical experiments are subject to multiple errors and variabilities arising from laboratory-to-laboratory differences in sample preparation and analysis 123. AI and machine learning approaches can overcome these technical barriers and further elucidate the impact of the protein corona by predicting protein adsorption to NPs as well as their biological impacts (Box 1). The sex and age of the biosystems are important in their responses to NPs, yet poorly considered in nanomedicine 145. As such, recent findings on the interactions of the coronavirus with the immune system revealed the critical roles of age 146 and sex 147 on immune responses. For example, it was shown that male-derived immune cells produce higher levels of innate immune cytokines in blood plasma compared with female-derived cells, and more robust T cell activation occurs in female-derived cells compared with male-derived cells during coronavirus infection.

Ramirez-Carrozzi, V.R. et al. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138, 114–128 (2009).

Arnold S, Siemann-Herzberg M, Schmid J, Reuss M. Model-based inference of gene expression dynamics from sequence information. In: Nielsen J, editor. Biotechnology for the future. Advances in biochemical engineering/biotechnology. Berlin: Springer; 2005. p. 89–179.Harwood CR, Wipat A. Sequencing and functional analysis of the genome of Bacillus subtilis strain 168. FEBS Lett. 1996;389:84–7. To investigate which components may increase the elongation rate, we evaluated elasticities and flux control coefficients for different concentrations. The concentration range was chosen on the basis of control scenarios under in vitro and in vivo conditions. Furthermore, we investigated GFP and EFTu as target sequences to identify the impact of codon optimization. O'Neill, L.P., VerMilyea, M.D. & Turner, B.M. Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nat. Genet. 38, 835–841 (2006).

Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007). Petrotchenko EV, Borchers CH (2010) Crosslinking combined with mass spectrometry for structural proteomics. Mass Spectrom Rev 29:862–876 Time-dependent profiling of protein coronas, extracted from human plasma, revealed that the formation of protein corona fingerprints occurs rapidly (~30 s), and the amount of protein in the corona, but not the composition of the protein profile, can change over time 71. Moreover, the rapid formation of the protein corona impacts the kinetic pathophysiology of the NPs. For example, both an increased NP uptake by microvascular endothelial cells and the inhibition of erythrocyte haemolysis were observed upon protein corona formation 71. The study of in situ protein corona formation in complex biological matrices, such as whole blood and plasma, showed that PEGylated gold NPs do not aggregate in these fluidic environments 72. Shankaranarayanan, P., Mendoza-Parra, M.A., van Gool, W., Trindade, L.M. & Gronemeyer, H. Single-tube linear DNA amplification for genome-wide studies using a few thousand cells. Nat. Protoc. 7, 328–338 (2012). More in-depth information and analysis of the biological nanoscale recognition mechanisms and responses are offered in another perspective 32. If the role of sex and age is considered in the design and development of new nanotherapeutics (based on the effects of their potential payloads), NPs with engineered biological identities can target and/or activate sex-associated and/or ageing-associated pathways, which could improve the safety and therapeutic efficacy of nanomedicine products for both sexes and all ages. ProteomicsSpizizen J. Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Proc Natl Acad Sci USA. 1958;44:1072–8. Abdel-Wahab, O. et al. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell 22, 180–193 (2012). Adli, M., Zhu, J. & Bernstein, B.E. Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat. Methods 7, 615–618 (2010).