Slow motions in nondeuterated proteins: Concerted chemical shift modulations of backbone nuclei

A simple method designed to measure autorelaxation rates of double- and zero-quantum coherences DQC/ZQC{C′N} involving a carbonyl C′ and the neighboring amide N nucleus in protein backbones provides valuable insight into slow motions in spite of interference both from the attached amide proton HN and from remote protons such as Hα in nondeuterated proteins. The method has been applied to human ubiquiti

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Non-Peer Reviewe

Classification of coffee beans by GC-C-IRMS, GC-MS, and 1H-NMR

In a previous work using 1H-NMR we reported encouraging steps towards the construction of a robust expert system for the discrimination of coffees from Colombia versus nearby countries (Brazil and Peru), to assist the recent protected geographical indication granted to Colombian coffee in 2007.This system relies on fingerprints acquired on a 400MHz magnet and is thus well suited for small scale random screening of samples obtained at resellers or coffee shops. However, this approach cannot easily be implemented at harbour's installations, due to the elevated operational costs of cryogenic magnets. This limitation implies shipping the samples to the NMR laboratory, making the overall approach slower and thereby more expensive and less attractive for large scale screening at harbours. In this work, we report on our attempt to obtain comparable classification results using alternative techniques that have been reported promising as an alternative toNMR: GC-MS andGC-C-IRMS.Although statistically significant information could be obtained by all threemethods, the results showthat the quality of the classifiers dependsmainly on the number of variables included in the analysis; hence NMR provides an advantage since more molecules are detected to obtain a model with better predictions

Enhancement of PHA Production by a Mixed Microbial Culture Using VFA Obtained from the Fermentation of Wastewater from Yeast Industry

Wastewater from the yeast production industry (WWY) is potentially harmful to surface water due to its high nitrogen and organic matter content; it can be used to produce compounds of higher commercial value, such as polyhydroxyalkanoates (PHA). PHA are polyester-type biopolymers synthesized by bacteria as energy reservoirs that can potentially substitute petrochemical-derived plastics. In this exploratory work, effluent from WWY was used to produce PHA, using a three-step setup of mixed microbial cultures involving one anaerobic and two aerobic reactors. First, volatile fatty acids (VFA; 2.5 g/L) were produced on an anaerobic batch reactor (reactor A) fed with WWY, using a heat pretreated sludge inoculum to eliminate methanogenic activity. Concurrently, PHA-producing bacteria were enriched using synthetic VFA in a sequencing batch reactor (SBR, reactor C) operated for 78 days. Finally, a polyhydroxybutyrate (PHB)-producing reactor (reactor B) was assembled using the inoculum enriched with PHA-producing bacteria and the raw and distilled effluent from the anaerobic reactor as a substrate. A maximum accumulation of 17% of PHB based on cell dry weight was achieved with a yield of 1.2 g PHB/L when feeding with the distilled effluent. Roche 454 16S rRNA gene amplicon pyrosequencing of the PHA-producing reactor showed that the microbial community was dominated by the PHA-producing bacterial species Paracoccus alcalophilus (32%) and Azoarcus sp. (44%). Our results show promising PHB accumulation rates that outperform previously reported results obtained with real substrates and mixed cultures, demonstrating a sustainable approach for the production of PHA less prone to contamination than a pure culture

Direct low field J-edited diffusional proton NMR spectroscopic measurement of COVID-19 inflammatory biomarkers in human serum

A JEDI NMR pulse experiment incorporating relaxational, diffusional and J-modulation peak editing has been implemented for a low field (80 MHz proton resonance frequency) spectrometer system to measure quantitatively two recently discovered plasma markers of SARS-CoV-2 infection and general inflammation. JEDI spectra capture a unique signature of two biomarker signals from acetylated glycoproteins (Glyc) and the supramolecular phospholipid composite (SPC) signals that are relatively enhanced by the combination of relaxation, diffusion and J-editing properties of the JEDI experiment that strongly attenuate contributions from the other molecular species in plasma. The SPC/Glyc ratio data were essentially identical in the 600 MHz and 80 MHz spectra obtained (R2 = 0.97) and showed significantly different ratios for control (n = 28) versus SARS-CoV-2 positive patients (n = 29) (p = 5.2 × 10−8 and 3.7 × 10−8 respectively). Simplification of the sample preparation allows for data acquisition in a similar time frame to high field machines (∼4 min) and a high-throughput version with 1 min experiment time could be feasible. These data show that these newly discovered inflammatory biomarkers can be measured effectively on low field NMR instruments that do not not require housing in a complex laboratory environment, thus lowering the barrier to clinical translation of this diagnostic technology

Direct low field J-edited diffusional proton NMR spectroscopic measurement of COVID-19 inflammatory biomarkers in human serum.

A JEDI NMR pulse experiment incorporating relaxational, diffusional and J-modulation peak editing has been implemented for a low field (80 MHz proton resonance frequency) spectrometer system to measure quantitatively two recently discovered plasma markers of SARS-CoV-2 infection and general inflammation. JEDI spectra capture a unique signature of two biomarker signals from acetylated glycoproteins (Glyc) and the supramolecular phospholipid composite (SPC) signals that are relatively enhanced by the combination of relaxation, diffusion and J-editing properties of the JEDI experiment that strongly attenuate contributions from the other molecular species in plasma. The SPC/Glyc ratio data were essentially identical in the 600 MHz and 80 MHz spectra obtained (R2 = 0.97) and showed significantly different ratios for control (n = 28) versus SARS-CoV-2 positive patients (n = 29) (p = 5.2 × 10-8 and 3.7 × 10-8 respectively). Simplification of the sample preparation allows for data acquisition in a similar time frame to high field machines (∼4 min) and a high-throughput version with 1 min experiment time could be feasible. These data show that these newly discovered inflammatory biomarkers can be measured effectively on low field NMR instruments that do not not require housing in a complex laboratory environment, thus lowering the barrier to clinical translation of this diagnostic technology

Effects of aging on biological motion discrimination

Peer reviewedPreprin

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation

Extensive studies of the structure–function relationship of antibodies have established that conventional immunoglobulins contain two copies of the antigen-binding fragment (Fab), each of which serves as an autonomous and complete unit for recognizing an antigen. In this paper, we report a previously unidentified mode of antibody–antigen recognition, dubbed “antigen clasping,” where two antigen-binding sites cooperatively clasp one antigen, and the design of a long-neck antibody format that facilitates antigen clasping. Antigen clasping led to recombinant antibodies for histone posttranslational modifications with extraordinarily high specificity, valuable tools for epigenetic research. This study substantially broadens the long-standing paradigm for antibody–antigen recognition

Overview of the nomenclature and network of contributors to the development of bioreactors for human gut simulation using bibliometric tools: a fragmented landscape

The evolution of complex in vitro models of the human gastrointestinal system to interrogate the biochemical functionality of the gut microbiome has augmented our understanding of its role in human physiology and pathology. With 5718 authors from 52 countries, gut bioreactor research reflects the growing awareness of our need to understand the contribution of the gut microbiome to human health. Although a large body of knowledge has been generated from in vitro models, it is scattered and defined by application-specific terminologies. To better grasp the capacity of bioreactors and further our knowledge of the human gastrointestinal system, we have conducted a cross-field bibliometric search and mapped the evolution of human gastrointestinal in vitro research. We present reference material with the aim of identifying key authors and bioreactor types to enable researchers to make decisions regarding the choice of method for simulating the human gut in the context of microbiome functionality