New article in Biological Control

Pseudomonas protegens ML15 and Trichoderma koningiopsis Tr21 co-culture: A potent strategy for suppressing Fusarium cerealis infections in wheat through augmented antifungal metabolite production

Nur Ajijah, Angelika Fiodor, Krzysztof Kazimierczuk, Monika Urbaniak , Elsie Enow , Robert Stasiuk , Łukasz Stępień , Łukasz Dziewit , Kumar Pranaw

Wheat (Triticum aestivum L.), a staple grain consumed worldwide, is heavily affected by Fusarium species, which cause harmful diseases that threaten its production. The present study was conducted to investigate the biocontrol activity of monocultures of Pseudomonas protegens ML15 and Trichoderma koningiopsis Tr21 as well as their co-culture, as a sustainable strategy to combat Fusarium cerealis. The cell-free supernatant and cell-free extract of co-culture demonstrated increased inhibitory effects against F. cerealis, compared to the monocultures. GC-MS analysis revealed that cell-free extract of P. protegens ML15, T. koningiopsis Tr21, and co-culture contained different bioactive metabolites. Pyrrolo[1,2-a]pyrazine-1,4-dione derivatives were major compounds in the cell-free extract of co-culture. Further analysis using NMR and HPLC, revealed that co-culture produced higher concentrations of pyoluteorin, 2,4-diacetylphloroglucinol, and 2,4-di-tert-butylphenol, compared to their respective monocultures. In vivo plant experiments indicated that co-culture treatment reduced F. cerealis infection and improved wheat development. Our findings highlight the exciting potential of co-culturing P. protegens ML15 and T. koningiopsis Tr21 as a formidable biocontrol duo, particularly effective against notorious fungal plant pathogens like Fusarium. This innovative approach holds promise for revolutionizing agricultural practices, offering sustainable solutions to combat crop diseases, and ensuring global food security.

New article in Chemistry – A European Journal

Hydrosilylation of Olefins Activated on Highly Lewis‐Acidic Calcium Cation

Magdalena Grochowska-Tatarczak, K. Koteras, Krzysztof Kazimierczuk, Przemysław J. Malinowski

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The report introduces simple yet highly reactive calcium salt, Ca[Al(ORF)4]2 (RF=C(CF3)3), 1, which effectively catalyses olefin hydrosilylation through an unusual mechanism involving the activation of the alkene molecule. Upon dissolution in o-difluorobenzene (oDFB), 1 forms a highly Lewis acidic [Ca(oDFB)6]2+ complex. Our DFT calculations reveal that fluoride ion affinity is comparable to SbF5. Reactivity tests show that it effectively catalyses the hydrosilylation of olefins with high regioselectivity, also in reactions involving sterically demanding substrates like (iPr)3SiH or tetrasubstituted olefins. Experimental and computational results point to the mechanism where the olefin molecule forms a complex with Ca2+, which significantly facilitates the attack of H-SiR3 on the C=C double bond.

New article in Nano Letters

Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds

Edyta Raczyłło, Dariusz Gołowicz, Tomasz Skóra,  Krzysztof Kazimierczuk and Svyatoslav Kondrat

Metabolites play crucial roles in cellular processes, yet their diffusion in the densely packed interiors of cells remains poorly understood, compounded by conflicting reports in existing studies. Here, we employ pulsed-gradient stimulated-echo NMR and Brownian/Stokesian dynamics simulations to elucidate the behavior of nano- and subnanometer-sized tracers in crowded environments. Using Ficoll as a crowder, we observe a linear decrease in tracer diffusivity with increasing occupied volume fraction, persisting─somewhat surprisingly─up to volume fractions of 30–40%. While simulations suggest a linear correlation between diffusivity slowdown and particle size, experimental findings hint at a more intricate relationship, possibly influenced by Ficoll’s porosity. Simulations and numerical calculations of tracer diffusivity in the E. coli cytoplasm show a nonlinear yet monotonic diffusion slowdown with particle size. We discuss our results in the context of nanoviscosity and discrepancies with existing studies.

New article in The Analyst

A pH-enhanced resolution in benchtop NMR spectroscopy

Paulina Putko, Javier A. Romero, Krzysztof Kazimierczuk

Graphical abstract: A pH-enhanced resolution in benchtop NMR spectroscopy

NMR spectroscopy is one of the most potent methods in analytical chemistry. NMR titration experiments are particularly useful since they measure molecular binding affinities and other concentration-dependent effects. These experiments, however, require a long series of measurements. An alternative to these serial measurements has recently been presented, exploiting a pH (or generally – a concentration) gradient along the NMR tube. The proposed experiment, although efficient, was based on the sensitivity- and hardware-demanding chemical shift imaging (CSI) method. Thus, it is practically limited to high-resolution NMR spectrometers. This paper proposes modifying and adapting the approach to the popular and cost-efficient benchtop NMR machines. Instead of CSI, we use a device that shifts the NMR tube vertically to measure the spectra of different sample volumes, which have different pH values due to the established gradient along the tube. We demonstrate the potential of the method on the test samples of L-tyrosine and 2,6-lutidine, and two real samples from the food industry – an infant formula and an energy drink. The proposed method boosts spectral resolution and allows for the sampling of a broader range of pH values when compared to the original approach.

New article in Journal of Magnetic Resonance

Optimizing measurements of linear changes of NMR signal parameters

Javier A. Romero, Krzysztof Kazimierczuk, Paweł Kasprzak

Serial NMR experiments are commonly applied in variable-temperature studies, reaction monitoring, and other tasks. The resonance frequencies often shift linearly over the series, and the shift rates help to characterize the studied system. They can be determined using a classical fitting of peak positions or a more advanced method of Radon transform. However, the optimal procedure for data collection remains to be determined. In this paper, we discuss how to invest experimental time, i.e., whether to measure more scans at the expense of the number of spectra or vice versa. The results indicate that classical fitting provides slightly less error than the Radon transform, although the latter can be the method of choice for a low signal-to-noise ratio. We demonstrate this fact through theoretical consideration, simulations, and an experiment. Finally, we extend our considerations to the linear fitting of peak amplitudes. Interestingly, the optimal setup for measuring peak height changes differs from the one for resonance frequency changes — fewer spectra with more scans provide better results.

New article in Magnetic Resonance in Chemistry

Supporting the assignment of NMR spectra with variable-temperature experiments

Ewa K. Nawrocka, Michał Jadwiszczak, Piotr J. Leszczyński, Krzysztof Kazimierczuk

Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful tools in analytical chemistry. An important step in the analysis of NMR data is the assignment of resonance frequencies to the corresponding atoms in the molecule being investigated. The traditional approach considers the spectrum’s characteristic parameters: chemical shift values, internuclear couplings, and peak intensities. In this paper, we show how to support the process of assigning a series of spectra of similar organic compounds by using temperature coefficients, that is, the rates of change in chemical shift values associated with given changes in temperature.

 

New article in The Journal of Physical Chemistry C

The Role of Boron Dopant in the Improvement of Electron Transfer in g-C3N4 Photocatalyst

Ewelina Wierzyńska, Klaudia Korytkowska, Krzysztof Kazimierczuk, Tomasz Łęcki, Kamila Zarębska, Krzysztof P. Korona, Marcin Pisarek, Bartosz Furtak, Magdalena Skompska

In this work, graphitic carbon nitride (g-C3N4) was doped with boron by thermal treatment with NaBH4. We have shown that the morphology of the modified polymer gradually changes from graphitic-like to amorphous, with increasing amounts of NaBH4 used for annealing. On the other hand, the boron doping has a very small influence on the band gap energy, as well as on the positions of the valence and conduction band edges of the polymer, but strongly improves the activity of g-C3N4 in the photocatalytic reduction of oxygen and degradation of methyl orange (8-fold increase of the degradation rate constant with respect to that of pure g-C3N4). The enhancement of the photocatalytic properties was explained by the increased rate of charge transport, both in the polymer plane and across the film, due to formation of N–B–N bonds between the adjacent heptazine units and the interlayer Coulomb interactions. The best photocatalytic activity was obtained for samples prepared from a mixture of g-C3N4 and NaBH4 at a moderate weight ratio (4:1), while increased amounts of NaBH4 led to significant and unfavorable changes in both the morphology and molecular structure of the polymer.

New Article in Journal of Biomolecular NMR

Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes

Alexandra Shchukina, Thomas C. Schwarz, Michał Nowakowski, Robert Konrat, Krzysztof Kazimierczuk

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The accelerated acquisition of multidimensional NMR spectra using sparse non-uniform sampling (NUS) has been widely adopted in recent years. The key concept in NUS is that a major part of the data is omitted during measurement, and then reconstructed using, for example, compressed sensing (CS) methods. CS requires spectra to be compressible, that is, they should contain relatively few “significant” points. The more compressible the spectrum, the fewer experimental NUS points needed in order for it to be accurately reconstructed. In this paper we show that the CS processing of similar spectra can be enhanced by reconstructing only the differences between them. Accurate reconstruction can be obtained at lower sampling levels as the difference is sparser than the spectrum itself. In many situations this method is superior to “conventional” compressed sensing. We exemplify the concept of “difference CS” with one such case—the study of alpha-synuclein binding to liposomes and its dependence on temperature. To obtain information on temperature-dependent transitions between different states, we need to acquire several dozen spectra at various temperatures, with and without the presence of liposomes. Our detailed investigation reveals that changes in the binding modes of the alpha-synuclein ensemble are not only temperature-dependent but also show non-linear behavior in their transitions. Our proposed CS processing approach dramatically reduces the number of NUS points required and thus significantly shortens the experimental time.

New Article in Materials Today Communications

The new Morin – based three-dimensional carbon nanostructures with metal oxides deposits. From synthesis to electro- and photocatalytic applicationsRadon peak-picker based on a neural network

Gisya Abdi, Anna Filip, Krzysztof Kazimierczuk , Tomasz Jaroń, Rafał Jurczakowski, Juan Carlos Colmenares, Andrzej Szczurek

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Morin is a natural polyphenolic compound best known for its bioactive properties. Due to its flavonoid structure, Morin may also be considered as a potential precursor of diverse functional materials. Sadly, its poor solubility in water altered its application in this field till now. In this work, by applying simple but effective sol-gel reactions, organic and carbon nanostructures were synthesized and described for the first time. We succeeded in porous materials (BET: 50–600 m2/g) with an original 3D morphology, e.g., hollow hexagonal nanopipes, nanobars, or nanofoams. All received carbons contained metal oxides traces (Co, Zn, Mg, Al), originated from corresponding Lewis acids used as catalysts, and formed after the pyrolysis. The CM-Co samples, having around 7 wt. % of cobalt deposits, were chosen to investigate their suitability for electrochemical conversion of CO2 and photochemical oxidation of benzyl alcohol (BnOH). The CM-Co successfully converted CO2 to CH4 with faradic efficiency (FE) of 12 %, wherein the yield of the reaction was correlated with the applied potential of electrolysis. Furthermore, the CO2 reduction was carried out in ambient conditions. The photochemical oxidation of benzyl alcohol to benzaldehyde yielded 14 % efficiency, while the BnOH oxidation process was realized with a sunlight (UV+VIS) simulator.

New Book Chapter

Chapter 5: The Non-uniform Sampling of 2D NMR Data

Alexandra Shchukina, Paweł Kasprzak, Mateusz UrbańczykKrzysztof Kazimierczuk

Conventional acquisition of two-dimensional (2D) NMR signals is based on an equidistant sampling in both time dimensions. The expected signal bandwidth determines the minimum sampling rate; the desired spectral resolution determines the maximum sampling time. Together, these two principles contribute to a minimum number of sampling points required for satisfactory spectrum quality. Additionally, it takes a few seconds for nuclei to relax between the acquisition of consecutive FID signals in a 2D interferogram. These three requirements cause 2D NMR experiments to last even tens of hours, in extreme cases. One of the standard methods to avoid lengthy data collection is to omit a significant proportion of sampling points during acquisition and reconstruct them later using dedicated algorithms. Such an approach to data acquisition is known as non-uniform sampling (NUS). The reconstruction algorithms exploit specific features of the measured signal, usually some form of compressibility. In this chapter, we will discuss the fundamentals of NUS methods including (a) motivation to use NUS in 2D NMR; (b) basic math behind the reconstruction algorithms; (c) commonly used distributions of sampling points; and (d) the use of related approaches in diffusometry, relaxometry, serial experiments and pure-shift NMR.