Contribution of Molecular Structure to Self-Assembling and Biological Properties of Bifunctional Lipid-Like 4-(N-Alkylpyridinium)-1,4-Dihydropyridines

The design of nanoparticle delivery materials possessing biological activities is an attractive strategy for the development of various therapies. In this study, 11 cationic amphiphilic 4-(N-alkylpyridinium)-1,4-dihydropyridine (1,4-DHP) derivatives differing in alkyl chain length and propargyl moiety/ties number and position were selected for the study of their self-assembling properties, evaluation of their cytotoxicity in vitro and toxicity on microorganisms, and the characterisation of their interaction with phospholipids. These lipid-like 1,4-DHPs have been earlier proposed as promising nanocarriers for DNA delivery. We have revealed that the mean diameter of freshly prepared nanoparti…

Global effects of ade8 deletion on budding yeast metabolism

AbstractPurine auxotrophy is a typical marker for many laboratory yeast strains. Supplementation of additional purine source (like adenine) is necessary to cultivate these strains. If not supplied in adequate amounts, purine starvation sets in. We tested purine starvation effects in budding yeast Saccharomyces cerevisiae ade8 knockout. We explored effects brought by purine starvation in cellular, central carbon metabolism and in the global transcriptome level.We observed that cells cultivated in purine depleted media became significantly more tolerant to severe thermal, oxidative and desiccation stresses when compared to the cells cultivated in media with all necessary supplements. When sta…

Purine Auxotrophic Starvation Evokes Phenotype Similar to Stationary Phase Cells in Budding Yeast

Purine auxotrophy is an abundant trait among eukaryotic parasites and a typical marker for many budding yeast strains. Supplementation with an additional purine source (such as adenine) is necessary to cultivate these strains. If not supplied in adequate amounts, purine starvation sets in. We explored purine starvation effects in a model organism, a budding yeast Saccharomyces cerevisiae ade8 knockout, at the level of cellular morphology, central carbon metabolism, and global transcriptome. We observed that purine-starved cells stopped their cycle in G1/G0 state and accumulated trehalose, and the intracellular concentration of AXP decreased, but adenylate charge remained stable. Cells becam…

Hydrogen-producingEscherichia colistrains overexpressing lactose permease: FT-IR analysis of the lactose-induced stress

The lactose permease gene (lacY) was overexpressed in the septuple knockout mutant of Escherichia coli, previously engineered for hydrogen production from glucose. It was expected that raising the lactose transporter activity would elevate the intracellular lactose concentration, inactivate the lactose repressor, induce the lactose operon, and as a result stimulate overall lactose consumption and conversion. However, overexpression of the lactose transporter caused a considerable growth delay in the recombinant strain on lactose, resembling to some extent the "lactose killing" phenomenon. Therefore, the recombinant strain was subjected to selection on lactose-containing media. Selection on …

Supplementary_material_2 – Supplemental material for Integrating fire-scar, charcoal and fungal spore data to study fire events in the boreal forest of northern Europe

Supplemental material, Supplementary_material_2 for Integrating fire-scar, charcoal and fungal spore data to study fire events in the boreal forest of northern Europe by Normunds Stivrins, Tuomas Aakala, Liisa Ilvonen, Leena Pasanen, Timo Kuuluvainen, Harri Vasander, Mariusz Gałka, Helena R Disbrey, Janis Liepins, Lasse Holmström and Heikki Seppä in The Holocene

Supplementary_material_1 – Supplemental material for Integrating fire-scar, charcoal and fungal spore data to study fire events in the boreal forest of northern Europe

Supplemental material, Supplementary_material_1 for Integrating fire-scar, charcoal and fungal spore data to study fire events in the boreal forest of northern Europe by Normunds Stivrins, Tuomas Aakala, Liisa Ilvonen, Leena Pasanen, Timo Kuuluvainen, Harri Vasander, Mariusz Gałka, Helena R Disbrey, Janis Liepins, Lasse Holmström and Heikki Seppä in The Holocene

Positioning Europe for the EPITRANSCRIPTOMICS challenge

WOS: 000444092300018 PubMed ID: 29671387 The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research. The outcome of this intense research field is the discovery t…

Optimization of Synthetic Media Composition for Kluyveromyces marxianus Fed-Batch Cultivation

The Kluyveromyces marxianus yeast recently has gained considerable attention due to its applicability in high-value-added product manufacturing. In order to intensify the biosynthesis rate of a target product, reaching high biomass concentrations in the reaction medium is mandatory. Fed-batch processes are an attractive and efficient way how to achieve high cell densities. However, depending on the physiology of the particular microbial strain, an optimal media composition should be used to avoid by-product synthesis and, subsequently, a decrease in overall process effi-ciency. Thus, the aim of the present study was to optimise the synthetic growth medium and feeding solution compositions (…

Supplementary_material_2 – Supplemental material for Integrating fire-scar, charcoal and fungal spore data to study fire events in the boreal forest of northern Europe

Supplemental material, Supplementary_material_2 for Integrating fire-scar, charcoal and fungal spore data to study fire events in the boreal forest of northern Europe by Normunds Stivrins, Tuomas Aakala, Liisa Ilvonen, Leena Pasanen, Timo Kuuluvainen, Harri Vasander, Mariusz Gałka, Helena R Disbrey, Janis Liepins, Lasse Holmström and Heikki Seppä in The Holocene

Laser speckle imaging for early detection of microbial colony forming units

In this study, an optical contactless laser speckle imaging technique for the early identification of bacterial colony-forming units was tested. The aim of this work is to compare the laser speckle imaging method for the early assessment of microbial activity with standard visual inspection under white light illumination. In presented research, the growth of Vibrio natriegens bacterial colonies on the solid medium was observed and analyzed. Both – visual examination under white light illumination and laser speckle correlation analysis were performed. Based on various experiments and comparisons with the theoretical Gompertz model, colony radius growth curves were obtained. It was shown that…

Mildronate, the inhibitor of l-carnitine transport, induces brain mitochondrial uncoupling and protects against anoxia-reoxygenation

Abstract The preservation of mitochondrial function is essential for normal brain function after ischaemia-reperfusion injury. l -carnitine is a cofactor involved in the regulation of cellular energy metabolism. Recently, it has been shown that mildronate, an inhibitor of l -carnitine transport, improves neurological outcome after ischaemic damage of brain tissues. The aim of the present study was to elucidate the mitochondria targeted neuroprotective action of mildronate in the model of anoxia-reoxygenation-induced injury. Wistar rats were treated daily with mildronate ( per os ; 100 mg/kg) for 14 days. The acyl-carnitine profile was determined in the brain tissues. Mitochondrial respirati…

Drying enhances immunoactivity of spent brewer's yeast cell wall β-D-glucans.

Due to immunological activity, microbial cell wall polysaccharides are defined as 'biological response modifiers' (BRM). Cell walls of spent brewer's yeast also have some BRM activity. However, up to date there is no consensus on the use of spent brewer's yeast D-glucan as specific BRM in humans or animals. The aim of this paper is to demonstrate the potential of spent brewer's yeast β-D-glucans as BRM, and drying as an efficient pretreatment to increase β-D-glucan's immunogenic activity. Our results revealed that drying does not change spent brewer's yeast biomass carbohydrate content as well as the chemical structure of purified β-D-glucan. However, drying increased purified β-D-glucan TN…

Adenine auxotrophy--be aware: some effects of adenine auxotrophy in Saccharomyces cerevisiae strain W303-1A.

Adenine auxotrophy is a commonly used genetic marker in haploid yeast strains. Strain W303-1A, which carries the ade2-1 mutation, is widely used in physiological and genetic research. Yeast extract-based rich medium contains a low level of adenine, so that adenine is often depleted before glucose. This could affect the cell physiology of adenine auxotrophs grown in rich medium. The aim of our study was to assess the effects of adenine auxotrophy on cell morphology and stress physiology. Our results show that adenine depletion halts cell division, but that culture optical density continues to increase due to cell swelling. Accumulation of trehalose and a coincident 10-fold increase in desicc…

Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles

Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We …

Purine auxotrophy: Possible applications beyond genetic marker

Exploring new drug candidates or drug targets against many illnesses is necessary as "traditional" treatments lose their effectivity. Cancer and sicknesses caused by protozoan parasites are among these diseases. Cell purine metabolism is an important drug target. Theoretically, inhibiting purine metabolism could stop the proliferation of unwanted cells. Purine metabolism is similar across all eukaryotes. However, some medically important organisms or cell lines rely on their host purine metabolism. Protozoans causing malaria, leishmaniasis, or toxoplasmosis are purine auxotrophs. Some cancer forms have also lost the ability to synthesize purines de novo. Budding yeast can serve as an effect…

The influence of fermentation conditions on biomass composition during ethanol biosynthesis from cheese whey lactose concentrate by Kluyveromyces marxianus

Automated microorganisms activity detection on the early growth stage using artificial neural networks

The paper proposes an approach of a novel non-contact optical technique for early evaluation of microbial activity. Noncontact evaluation will exploit laser speckle contrast imaging technique in combination with artificial neural network (ANN) based image processing. Microbial activity evaluation process will comprise acquisition of time variable laser speckle patterns in given sample, ANN based image processing and visualization of obtained results. The proposed technology will measure microbial activity (like growth speed) and implement these results for counting live microbes. It is expected, that proposed technology will help to evaluate number of colony forming units (CFU) and return r…

Laser speckle time-series correlation analysis for bacteria activity detection

The study aims at development and laboratory approbation of non-contact optical technique for early evaluation of microbial activity. Microorganisms’ activity is estimated by laser speckle contrast imaging technique in combination with image processing of obtained time varying speckle patterns. Laser speckle patterns were captured by CMOS sensor during illumination of growing bacteria colonies by low power (<30 mW, 635 nm) stabilized coherent light source. To validate proposed technique and image processing algorithm the vibrio natriegens bacteria are used. After analysis of several different experiments the following results were obtained: In the central part of the colony activity can be …

Supplementary_material_1 – Supplemental material for Integrating fire-scar, charcoal and fungal spore data to study fire events in the boreal forest of northern Europe

Supplemental material, Supplementary_material_1 for Integrating fire-scar, charcoal and fungal spore data to study fire events in the boreal forest of northern Europe by Normunds Stivrins, Tuomas Aakala, Liisa Ilvonen, Leena Pasanen, Timo Kuuluvainen, Harri Vasander, Mariusz Gałka, Helena R Disbrey, Janis Liepins, Lasse Holmström and Heikki Seppä in The Holocene

Glycolipid Biosurfactant Production from Waste Cooking Oils by Yeast: Review of Substrates, Producers and Products

Biosurfactants are a microbially synthesized alternative to synthetic surfactants, one of the most important bulk chemicals. Some yeast species are proven to be exceptional biosurfactant producers, while others are emerging producers. A set of factors affects the type, amount, and properties of the biosurfactant produced, as well as the environmental impact and costs of biosurfactant’s production. Exploring waste cooking oil as a substrate for biosurfactants’ production serves as an effective cost-cutting strategy, yet it has some limitations. This review explores the existing knowledge on utilizing waste cooking oil as a feedstock to produce glycolipid biosurfactants by yeast. The review f…

Whey lactose bioconversion to valuable products by non-conventional yeasts Kluyveromyces marxianus

Enzymes for the NADPH-dependent reduction of dihydroxyacetone and D-glyceraldehyde and L-glyceraldehyde in the mould Hypocrea jecorina

The mould Hypocrea jecorina (Trichoderma reesei) has two genes coding for enzymes with high similarity to the NADP-dependent glycerol dehydrogenase. These genes, called gld1 and gld2, were cloned and expressed in a heterologous host. The encoded proteins were purified and their kinetic properties characterized. GLD1 catalyses the conversion of d-glyceraldehyde and l-glyceraldehyde to glycerol, whereas GLD2 catalyses the conversion of dihydroxyacetone to glycerol. Both enzymes are specific for NADPH as a cofactor. The properties of GLD2 are similar to those of the previously described NADP-dependent glycerol-2- dehydrogenases (EC 1.1.1.156) purified from different mould species. It is a reve…

Portable low-cost open-source wireless spectrophotometer for fast and reliable measurements

This article is based upon COST Action CA16215 and supported by the ERDF , European-Union Project No.1.1.1.2/16/I/001.

Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism

Abstract The non-conventional yeast Kluyveromyces marxianus is an emerging industrial producer for many biotechnological processes. Here, we show the application of a biomass-linked stoichiometric model of central metabolism that is experimentally validated, and mass and charge balanced for assessing the carbon conversion efficiency of wild type and modified K. marxianus. Pairs of substrates (lactose, glucose, inulin, xylose) and products (ethanol, acetate, lactate, glycerol, ethyl acetate, succinate, glutamate, phenylethanol and phenylalanine) are examined by various modelling and optimisation methods. Our model reveals the organism’s potential for industrial application and metabolic engi…

Zirconia nanocrystals as submicron level biological label

Inorganic nanocrystals are of increasing interest for their usage in biology and pharmacology research. Our interest was to justify ZrO2 nanocrystal usage as submicron level biological label in baker's yeast Saccharomyces cerevisia culture. For the first time (to our knowledge) images with sub micro up-conversion luminescent particles in biologic media were made. A set of undoped as well as Er and Yb doped ZrO2 samples at different concentrations were prepared by sol-gel method. The up-conversion luminescence for free standing and for nanocrystals with baker's yeast cells was studied and the differences in up-conversion luminescence spectra were analyzed. In vivo toxic effects of ZrO2 nanoc…

Embedded neural network system for microorganisms growth analysis

This study presents autonomous system for microorganisms’ growth analysis in laboratory environment. As shown in previous research, laser speckle analysis allows detecting submicron changes of substrate with growing bacteria. By using neural networks for speckle analysis, it is possible to develop autonomous system, that can evaluate microorganisms’ growth by using cheap optics and electronics elements. System includes embedded processing module, CMOS camera, 670nm laser diode and optionally WiFi module for connecting to external image storage system. Due to small size, system could be fully placed in laboratory incubator with constant humidity and temperature. By using laser diode, Petri d…

Suppression of intestinal microbiota-dependent production of pro-atherogenic trimethylamine N-oxide by shifting L-carnitine microbial degradation.

Abstract Aims Trimethylamine-N-oxide (TMAO) is produced in host liver from trimethylamine (TMA). TMAO and TMA share common dietary quaternary amine precursors, carnitine and choline, which are metabolized by the intestinal microbiota. TMAO recently has been linked to the pathogenesis of atherosclerosis and severity of cardiovascular diseases. We examined the effects of anti-atherosclerotic compound meldonium, an aza-analogue of carnitine bioprecursor gamma-butyrobetaine (GBB), on the availability of TMA and TMAO. Main methods Wistar rats received L-carnitine, GBB or choline alone or in combination with meldonium. Plasma, urine and rat small intestine perfusate samples were assayed for L-car…

Utilization of different carbohydrates by various Kluyveromyces marxianus strains

Integrating fire-scar, charcoal and fungal spore data to study fire events in the boreal forest of northern Europe

Fire is a major disturbance agent in the boreal forest, influencing many current and future ecosystem conditions and services. Surprisingly few studies have attempted to improve the accuracy of fire-event reconstructions even though the estimates of the occurrence of past fires may be biased, influencing the reliability of the models employing those data (e.g. C stock, cycle). This study aimed to demonstrate how three types of fire proxies – fire scars from tree rings, sedimentary charcoal and, for the first time in this context, fungal spores of Neurospora – can be integrated to achieve a better understanding of past fire dynamics. By studying charcoal and Neurospora from sediment cores f…