complex mixtures
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2022 ◽  
Author(s):  
Brandon Alexander Holt ◽  
Hong Seo Lim ◽  
Melanie Su ◽  
McKenzie Tuttle ◽  
Haley Liakakos ◽  
...  

Genome-scale activity-based profiling of proteases requires identifying substrates that are specific to each individual protease. However, this process becomes increasingly difficult as the number of target proteases increases because most substrates are promiscuously cleaved by multiple proteases. We introduce a method - Substrate Libraries for Compressed sensing of Enzymes (SLICE) - for selecting complementary sets of promiscuous substrates to compile libraries that classify complex protease samples (1) without requiring deconvolution of the compressed signals and (2) without the use of highly specific substrates. SLICE ranks substrate libraries according to two features: substrate orthogonality and protease coverage. To quantify these features, we design a compression score that was predictive of classification accuracy across 140 in silico libraries (Pearson r = 0.71) and 55 in vitro libraries (Pearson r = 0.55) of protease substrates. We demonstrate that a library comprising only two protease substrates selected with SLICE can accurately classify twenty complex mixtures of 11 enzymes with perfect accuracy. We envision that SLICE will enable the selection of peptide libraries that capture information from hundreds of enzymes while using fewer substrates for applications such as the design of activity-based sensors for imaging and diagnostics.


2022 ◽  
pp. 131355
Author(s):  
Xingwei Hou ◽  
Kundan Sivashanmugan ◽  
Yong Zhao ◽  
Boxin Zhang ◽  
Alan X. Wang

Processes ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 2129
Author(s):  
Christoph Jensch ◽  
Larissa Knierim ◽  
Martin Tegtmeier ◽  
Jochen Strube

For the first time, a universally applicable and methodical approach from characterization to a PAT concept for complex mixtures is conducted—exemplified on natural products extraction processes. Bearberry leaf (Arctostaphylos uva-ursi) extract is chosen as an example of a typical complex mixture of natural plant origin and generalizable in its composition. Within the quality by design (QbD) based process development the development and implementation of a concept for process analytical technology (PAT), a key enabling technology, is the next necessary step in risk and quality-based process development and operation. To obtain and provide an overview of the broad field of PAT, the development process is shown on the example of a complex multi-component plant extract. This study researches the potential of different process analytical technologies for online monitoring of different component groups and classifies their possible applications within the framework of a QbD-based process. Offline and online analytics are established on the basis of two extraction runs. Based on this data set, PLS models are created for the spectral data, and correlations are conducted for univariate data. In a third run, the prediction potential is researched. Conclusively, the results of this study are arranged in the concept of a holistic quality and risk-based process design and operation concept.


2021 ◽  
Author(s):  
◽  
Matthew Fisk

<p>The design and development of new chemical reactions is crucial for progress in organic synthesis research. Cascade reactions, involving two or more steps carried out in situ in a single pot, provide a step-efficient and atom-economic route to synthesise polycyclic ring systems. The synthesis of new heterocyclic ring systems provides valuable routes towards complex natural products. Previous work in the Harvey group led to the development of a regioselective palladium-catalysed allylic alkylation (Pd-AA) cascade. This research aims to expand the scope and utility of this existing Pd-AA cascade, by optimising the current reaction conditions and exploring a range of non-symmetric pyran-based bis-electrophiles and nitrogen and sulfur-based β-carbonyl bis-nucleophiles.  Isomeric 2,3-unsaturated silyl glycosides based on D-glucose and D-galactose were successfully synthesised. These substrates were assessed as bis-electrophiles in the Pd-AA cascade. The yield of the cascade was successfully optimised with the glucose-derived substrate 4-hydroxy-6-methylpyran-2-one, using Pd₂(dba)₃ and Xantphos, to 87% from the previously reported 77% yield. However, the galactose-derived silyl glycoside formed an undesired pyranone as the major product. Additionally, a series of β-dicarbonyl compounds (4-hydroxy-6-methylpyran-2-one analogues) were assessed as bis-nucleophiles in the Pd-AA cascade, with all of the analogues forming complex mixtures of side products and a fully unsaturated pyranone as the major isolated product.</p>


2021 ◽  
Author(s):  
Asmae Bouziani ◽  
Mohamed Yahya

Mass spectrometers can provide information about molecular composition and chemical structure. However, with complex mixtures, superpositions and even suppression of signals may occur. On the other hand, Chromatography is an ideal technique for separating complexes but is often insufficient for compound identification. Hence, coupling both techniques in order to eliminate the limitations of each technique makes perfect sense. In this contribution, a brief description of mass spectrometry coupled with chromatography in the gas and liquid phase will be discussed to explain the advantages of coupling the two methods. The ionization techniques are also reported and followed by application areas of these techniques. Finally, the recording and treatment of the results are reviewed.


2021 ◽  
Author(s):  
◽  
Matthew Fisk

<p>The design and development of new chemical reactions is crucial for progress in organic synthesis research. Cascade reactions, involving two or more steps carried out in situ in a single pot, provide a step-efficient and atom-economic route to synthesise polycyclic ring systems. The synthesis of new heterocyclic ring systems provides valuable routes towards complex natural products. Previous work in the Harvey group led to the development of a regioselective palladium-catalysed allylic alkylation (Pd-AA) cascade. This research aims to expand the scope and utility of this existing Pd-AA cascade, by optimising the current reaction conditions and exploring a range of non-symmetric pyran-based bis-electrophiles and nitrogen and sulfur-based β-carbonyl bis-nucleophiles.  Isomeric 2,3-unsaturated silyl glycosides based on D-glucose and D-galactose were successfully synthesised. These substrates were assessed as bis-electrophiles in the Pd-AA cascade. The yield of the cascade was successfully optimised with the glucose-derived substrate 4-hydroxy-6-methylpyran-2-one, using Pd₂(dba)₃ and Xantphos, to 87% from the previously reported 77% yield. However, the galactose-derived silyl glycoside formed an undesired pyranone as the major product. Additionally, a series of β-dicarbonyl compounds (4-hydroxy-6-methylpyran-2-one analogues) were assessed as bis-nucleophiles in the Pd-AA cascade, with all of the analogues forming complex mixtures of side products and a fully unsaturated pyranone as the major isolated product.</p>


2021 ◽  
Vol 08 ◽  
Author(s):  
Muhammad Waqar Ashraf ◽  
M.Amin Mir

: The supported ionic liquid (SIL) membranes have demonstrated huge potential for numerous applications in current separation science and catalysis. Membrane technology allows for separation of complex mixtures of gases, vapours, liquids and /or solids below trivial conditions. Simultaneous chemical transformations can also be achieved in membranes by using catalytically active materials comprising the membrane or embedded catalysts in the custom built membrane reactors. In the present editorial, the remarkable contribution of liquid membranes in catalysis is highlighted. Some recent applications are presented and compared with conventional methods. In addition, SILs and their applications in catalysis, catalytic membranes and recent advances in membrane separation processes are briefly described.


2021 ◽  
Author(s):  
Kaitlin Huffman ◽  
Erin Hanson ◽  
Jack Ballantyne

DNA mixtures are a common source of crime scene evidence and are often one of the more difficult sources of biological evidence to interpret. With the implementation of probabilistic genotyping (PG), mixture analysis has been revolutionized allowing previously unresolvable mixed profiles to be analyzed and probative genotype information from contributors to be recovered. However, due to allele overlap, artifacts, or low-level minor contributors, genotype information loss inevitably occurs. In order to reduce the potential loss of significant DNA information from donors in complex mixtures, an alternative approach is to physically separate individual cells from mixtures prior to performing DNA typing thus obtaining single source profiles from contributors. In the present work, a simplified micro-manipulation technique combined with enhanced single-cell DNA typing was used to collect one or few cells, referred to as direct single-cell subsampling (DSCS). Using this approach, single and 2-cell subsamples were collected from 2-6 person mixtures. Single-cell subsamples resulted in single source DNA profiles while the 2-cell subsamples returned either single source DNA profiles or new mini-mixtures that are less complex than the original mixture due to the presence of fewer contributors. PG (STRmixTM) was implemented, after appropriate validation, to analyze the original bulk mixtures, single source cell subsamples, and the 2-cell mini mixture subsamples from the original 2-6-person mixtures. PG further allowed replicate analysis to be employed which, in many instances, resulted in a significant gain of genotype information such that the returned donor likelihood ratios (LRs) were comparable to that seen in their single source reference profiles (i.e., the reciprocal of their random match probabilities). In every mixture, the DSCS approach gave improved results for each donor compared to standard bulk mixture analysis. With the 5- and 6- person complex mixtures, DSCS recovered highly probative LRs (> 1020) from donors that had returned non-probative LRs (<103) by standard methods.


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