Fermentation of cocoa pod husks with Pleurotus salmoneo-stramineus for food applications.

Cocoa pod husks (CPHs), the major side-stream from cocoa production, were valorized through fermentation with Pleurotus salmoneo-stramineus (PSS). Considering ergosterol as a biomarker for the fungal content, the mycelium accounted for 54% of the total biomass after 8 days in submerged cultures. The crude protein content of fermented CPH (CPHF) increased from 7.3 g/100 g DM in CPH to 18.9 g/100 g DM. CPH fermentation resulted in a high biological value of 86 for the protein. The water and oil binding capacities of CPHF were 3.5 mL/g and 2.1 mL/g, respectively. The particle diameter dv,0,90 of CPHF was 373 µm as compared to 526 µm for CPH. The total dietary fiber was 73.4 g/100 g DM in CPHF and 63.6 g/100 g DM in CPH. The amount of soluble fiber was 2.3 g/100 g DM in CPHF and 10.1 g/100 g DM in CPH; the insoluble fraction accounted for 71.1 g/100 g DM and 53.6 g/100 g DM, respectively. Bread doughs with CPH or CPHF were characterized for texture, color, and farinographic properties. The dough hardness, consistency, and browning index increased with the concentration of CPH, whereas for CPHF, springiness and peak viscosities declined. We demonstrate the upcycling of CPH into nutritious and functional ingredients through PSS fermentation.

From accurate genome sequence to biotechnological application: The thermophile Mycolicibacterium hassiacum as experimental model.

Mycobacteria constitute a large group of microorganisms belonging to the phylum Actinobacteria encompassing some of the most relevant pathogenic bacteria and many saprophytic isolates that share a unique and complex cell envelope. Also unique to this group is the extensive capability to use and synthesize sterols, a class of molecules that include active signalling compounds of pharmaceutical use. However, few mycobacterial species and strains have been established as laboratory models to date, Mycolicibacterium smegmatis mc2 155 being the most common one. In this work, we focus on the use of a thermophilic mycobacterium, Mycolicibacterium hassiacum, which grows optimally above 50°C, as an emerging experimental model valid to extend our general knowledge of mycobacterial biology as well as for application purposes. To that end, accurate genomic sequences are key for gene mining, the study of pathogenicity or lack thereof and the potential for gene transfer. The combination of long- and short-massive sequencing technologies is strictly necessary to remove biases caused by errors specific to long-reads technology. By doing so in M. hassiacum, we obtained from the curated genome clues regarding the genetic manipulation potential of this microorganism from the presence of insertion sequences, CRISPR-Cas, type VII ESX secretion systems, as well as lack of plasmids. Finally, as a proof of concept of the applicability of M. hassiacum as a laboratory and industrial model, we used this high-quality genome of M. hassiacum to successfully knockout a gene involved in the use of phytosterols as source of carbon and energy, using an improved gene cassette for thermostable selection and a transformation protocol at high temperature.

Thermal stabilisation of cocoa fruit pulp - Effects on sensory properties, colour and microbiological stability.

To improve cocoa pulp's shelf-life, preservation processes are necessary while maintaining the quality of the pulp. We applied pasteurisation and UHT-treatment and investigated different quality parameters: dry matter content, water activity, total soluble solids, colour and peroxidase activity. Both technologies inactivated peroxidase successfully. The colour of the pasteurised pulp was similar to the fresh, while UHT-treated pulp was more brownish. The sensory properties were investigated in detail by descriptive analysis and the identification of aroma-active volatile organic compounds. Fresh pulp revealed the highest aroma intensity for attribute unripe banana-like, whereas UHT-treated pulp scored highest in the intensity of attribute tropical fruit-like. Pasteurised pulp showed strong similarities to the fresh pulp. Fresh cocoa pulp exhibited 74 aroma-active regions identified by GC-MS/O. UHT-treated and pasteurised pulp accounted for 66 and 60 aroma-active regions, respectively. Five identified substances were only found in the fresh and pasteurised pulp, namely: δ-carene, 1-pentanol, 3-(methylthio)propanol, phenol and δ-undecalactone. Similarly, fresh and UHT-treated pulp shared ten exclusive odorants, such as decanal, geraniol, and δ-nonalactone. The pasteurised and UHT-treated pulp shared two compounds, δ-decalactone and 5-(hydroxymethyl)furfural. Furthermore, the thermally treated pulps could be stored at 4 °C and 23 °C for 24 weeks without observing a significant growth of microorganisms. The rate of non-enzymatic browning was higher in samples stored at 23 °C compared to those stored at 4 °C, leading to higher browning indices. We demonstrated that pasteurisation and ultra-high temperature treatment are suitable technologies for the stabilisation of cocoa fruit pulp. These resulted in prolonged shelf-lifes and minimal changes in the sensory prorperties of the treated pulps, characterised by a reduction in the aroma diversities. This work provides important insights for the thermal stabilisation of further side-streams.

Aroma-active volatiles and rheological characteristics of the plastic mass during conching of dark chocolate.

Chocolate conching is a highly complex, thermomechanical process that transforms the aroma and flow properties of a dry starting material. Different conched plastic masses of dark chocolate were characterized. Rheological characterization of plastic masses was performed for the first time using a closed cavity rheometer (CCR1). In free cocoa butter derived from the plastic masses, acetic acid, benzaldehyde, (R,S)-(±)-linalool, 2,3,5,6-tetramethylpyrazine, and 2-phenylethanol were quantified by stable isotope dilution analysis (SIDA2) and gas chromatography-mass spectrometry. During the conching process, the amount of free cocoa butter increased possibly due to de-agglomeration. The complex viscosity of the plastic mass decreased as a function of conching time. Regarding aroma refinement, the concentrations of all five aroma-active volatiles decreased with increasing conching duration, albeit to varying degrees. The level of acetic acid showed the most pronounced decrease of about 60%, whereas linalool exhibited the lowest decrease in concentration, up to 26%. Overall, a lower polarity or boiling point of the aroma-active volatiles was linked to a stronger decrease in concentration during conching. These data illustrate the influence of conching on texture and the respective aroma changes, which deepens understanding of the conching effect on the sensory quality of dark chocolate.

Immunogenicity of Mycobacterial Extracellular Vesicles Isolated From Host-Related Conditions Informs About Tuberculosis Disease Status.

Tuberculosis (TB) still represents a major global health problem affecting over 10 million people worldwide. The gold-standard procedures for TB diagnosis are culture and nucleic acid amplification techniques. In this context, both lipoarabinomannan (LAM) urine test and rapid molecular tests have been major game changers. However, the low sensitivity of the former and the cost and the prohibitive infrastructure requirements to scale-up in endemic regions of the latter, make the improvement of the TB diagnostic landscape a priority. Most forms of life produce extracellular vesicles (EVs), including bacteria despite differences in bacterial cell envelope architecture. We demonstrated that Mycobacterium tuberculosis (Mtb), the causative agent of TB, produces EVs in vitro and in vivo as part of a sophisticated mechanism to manipulate host cellular physiology and to evade the host immune system. In a previous serology study, we showed that the recognition of several mycobacterial extracellular vesicles (MEV) associated proteins could have diagnostic properties. In this study, we pursued to expand the capabilities of MEVs in the context of TB diagnostics by analyzing the composition of MEVs isolated from Mtb cultures submitted to iron starvation and, testing their immunogenicity against a new cohort of serum samples derived from TB+ patients, latent TB-infected (LTBI) patients and healthy donors. We found that despite the stringent condition imposed by iron starvation, Mtb reduces the number of MEV associated proteins relative to iron sufficient conditions. In addition, TB serology revealed three new MEV antigens with specific biomarker capacity. These results suggest the feasibility of developing a point-of-care (POC) device based on selected MEV-associated proteins.

Peripheral Amino Acid Appearance Is Lower Following Plant Protein Fibre Products, Compared to Whey Protein and Fibre Ingestion, in Healthy Older Adults despite Optimised Amino Acid Profile.

Plant-based proteins are generally characterised by lower Indispensable Amino Acid (IAA) content, digestibility, and anabolic properties, compared to animal-based proteins. However, they are environmentally friendlier, and wider consumption is advocated. Older adults have higher dietary protein needs to prevent sarcopenia, a disease marked by an accelerated loss of muscle mass and function. Given the lower environmental footprint of plant-based proteins and the importance of optimising dietary protein quality among older adults, this paper aims to assess the net peripheral Amino Acid (AA) appearance after ingestion of three different plant protein and fibre (PPF) products, compared to whey protein with added fibre (WPF), in healthy older adults. In a randomised, single-blind, crossover design, nine healthy men and women aged ≥65 years consumed four test meals balanced in AA according to the FAO reference protein for humans, matched for leucine, to optimally stimulate muscle protein synthesis in older adults. A fasted blood sample was drawn at each visit before consuming the test meal, followed by postprandial arterialise blood sampling every 30 min for 3 h. The test meal was composed of a soup containing either WPF or PPF 1-3. The PPF blends comprised pea proteins with varying additional rice, pumpkin, soy, oat, and/or almond protein. PPF product ingestion resulted in a lower maximal increase of postprandial leucine concentration and the sum of branched-chain AA (BCAA) and IAA concentrations, compared to WPF, with no effect on their incremental area under the curve. Plasma methionine and cysteine, and to a lesser extent threonine, appearance were limited after consuming the PPF products, but not WPF. Despite equal leucine doses, the WPF induced greater postprandial insulin concentrations than the PPF products. In conclusion, the postprandial appearance of AA is highly dependent on the protein source in older adults, despite providing equivalent IAA levels and dietary fibre. Coupled with lower insulin concentrations, this could imply less anabolic potential. Further investigation is required to understand the applicability of plant-based proteins in healthy older adults.

Gene and whole genome analyses reveal that the mycobacterial strain JS623 is not a member of the species Mycobacterium smegmatis.

Unexpected differences were found between the genome of strain JS623, used in bioremediation studies, and the genome of strain mc(2) 155, a model organism for investigating basic biology of mycobacteria. Both strains are currently assigned in the databases to the species Mycobacterium smegmatis and, consequently, the environmental isolate JS623 is increasingly included as a representative of that species in comparative genome-based approaches aiming at identifying distinctive traits of the different members of the genus Mycobacterium. We applied traditional molecular taxonomic procedures--inference of single and concatenated gene trees--to re-evaluate the membership of both strains to the same species, adopting the latest accepted cut-off values for species delimitation. Additionally, modern whole genome-based in silico methods where performed in a comprehensive molecular phylogenetic analysis of JS623 and other members of the genus Mycobacterium. These analyses showed that all relevant genome parameters of JS623 clearly separate this strain from M. smegmatis. The strain JS623 should be corrected as Mycobacterium sp. not only in the literature but, even more importantly, in the database entries, as inclusion of the genome wrongly attributed to the M. smegmatis species in comparative studies will result in misleading conclusions.

The essential role of SepF in mycobacterial division.

Mycobacteria lack several of the components that are essential in model systems as Escherichia coli or Bacillus subtilis for the formation of the divisome, a ring-like structure assembling at the division site to initiate bacterial cytokinesis. Divisome assembly depends on the correct placement of the FtsZ protein into a structure called the Z ring. Notably, early division proteins that assist in the localisation of the Z ring to the cytoplasmic membrane and modulate its structure are missing in the so far known mycobacterial cell division machinery. To find mycobacterium-relevant components of the divisome that might act at the level of FtsZ, a yeast two-hybrid screening was performed with FtsZ from Mycobacterium tuberculosis. We identified the SepF homolog as a new interaction partner of mycobacterial FtsZ. Depending on the presence of FtsZ, SepF-GFP fusions localised in ring-like structures at potential division sites. Alteration of SepF levels in Mycobacterium smegmatis led to filamentous cells, indicating a division defect. Depletion of SepF resulted in a complete block of division. The sepF gene is highly conserved in the M. tuberculosis complex members. We therefore propose that SepF is an essential part of the core division machinery in the genus Mycobacterium.

WhiB5, a transcriptional regulator that contributes to Mycobacterium tuberculosis virulence and reactivation.

The proteins belonging to the WhiB superfamily are small global transcriptional regulators typical of actinomycetes. In this paper, we characterize the role of WhiB5, a Mycobacterium tuberculosis protein belonging to this superfamily. A null mutant was constructed in M. tuberculosis H37Rv and was shown to be attenuated during both progressive and chronic mouse infections. Mice infected with the mutant had smaller bacillary burdens in the lungs but a larger inflammatory response, suggesting a role of WhiB5 in immunomodulation. Most interestingly, the whiB5 mutant was not able to resume growth after reactivation from chronic infection, suggesting that WhiB5 controls the expression of genes involved in this process. The mutant was also more sensitive than the wild-type parental strain to S-nitrosoglutathione (GSNO) and was less metabolically active following prolonged starvation, underscoring the importance of GSNO and starvation in development and maintenance of chronic infection. DNA microarray analysis identified 58 genes whose expression is influenced by WhiB5, including sigM, encoding an alternative sigma factor, and genes encoding the constituents of two type VII secretion systems, namely, ESX-2 and ESX-4.

New modules for PCR-based gene targeting in Candida albicans: rapid and efficient gene targeting using 100 bp of flanking homology region.

The use of PCR-based techniques for directed gene alterations has become a standard tool in Saccharomyces cerevisiae. In our efforts to increase the speed of functional analysis of Candida albicans genes, we constructed a modular system of plasmid vectors and successfully applied PCR-amplified functional analysis (FA)-cassettes in the transformation of C. albicans. These cassettes facilitate: (a) gene disruptions; (b) tagging of 3'-ends of genes with green fluorescent protein (GFP); and (c) replacements of endogenous promoters to achieve regulated expression. The modules consists of a core of three selectable marker genes, CaURA3, CaHIS1 and CaARG4. Modules for C-terminal GFP-tagging were generated by adding GFP-sequences flanked at the 5'-end by a (Gly-Ala)3-linker and at the 3'-end by the S. cerevisiae URA3-terminator to these selection markers. Promoter exchange modules consist of the respective marker genes followed by the regulatable CaMAL2 or CaMET3 promoters at their 3'-ends. In order to ensure a reliably high rate of homologous gene targeting, the flanking homology regions required a size of 100 bp of gene-specific sequences, which were provided with the oligonucleotide primers. The use of shorter flanking homology regions produced unsatisfactory results with C. albicans strain BWP17. With these new modules only a minimal set of primers is required to achieve the functional analysis of C. albicans genes and, therefore, provides a basic tool to increase the number of functionally characterized C. albicans genes of this human pathogen in the near future.

An expression system for the functional analysis of pheromone genes in the tetrapolar basidiomycete Schizophyllum commune.

The investigation of putative pheromone genes of basidiomycetes has been difficult since the small open reading frames are essentially annotated on the basis of a C-terminal farnesylation signal. In order to identify the functional reading frame, expression of small DNA fragments in the fungus is necessary. The expression system developed in the presented paper allows fusion to the promoter of the tef1 gene encoding the constitutively and highly expressed translation elongation factor EF1alpha. This system has been shown to be functional using an easily selectable gene, ura1. The application to identification of functional pheromone genes has been shown with the newly detected bap2(4) gene. The Bap2(4) pheromone is the first Balpha pheromone gene activating only a single receptor specificity.

Evolution of multispecific mating-type alleles for pheromone perception in the homobasidiomycete fungi.

The evolution of multiple, independent and multispecific mating-type loci is a feature unique to homobasidiomycete fungi. To propose a model of evolution, data assembled for the wood-rotting fungus Schizophyllum commune were analyzed. In one mating-type locus, pheromone receptors and several pheromones are encoded which have been investigated in some detail and can be used to understand the ligand-receptor interactions and activation of signal transduction which are essential to sexual propagation. Previous models for the evolution of new alleles were complicated and involved three subsequent steps (without selectable phenotype) prior to the establishment of a new stable pheromone-receptor pair. This paper presents a model for the evolution of new specificities by recombination and selection that incorporates the multi-state receptor activation recently established for S. commune, explaining differential responses to different pheromones in one receptor molecule. The model takes into account the occurrence of multiple pheromone genes in each locus and unilateral nuclear donor/acceptor strains that may in nature act as steps in the evolution of new specificities. A second homobasidiomycete fungus, Coprinus cinereus, was similarly characterized at the molecular level. Data acquired in this system support the conclusion that the presented model can be generalized.

The little difference: in vivo analysis of pheromone discrimination in Schizophyllum commune.

The B mating type of Schizophyllum commune is defined by a multi-specific pheromone/receptor system. The interaction of pheromone receptors and their ligands, encoded by the Balpha locus, triggers sexual development. The receptors belong to the family of G protein-coupled seven-transmembrane-domain receptors, while the ligands are small lipopeptide pheromones. A productive interaction is only possible between molecules derived from different specificities. There is no induction of sexual development by pheromones of self-specificity. Since there are nine versions of different specificity for pheromones and receptors in Balpha, this system can be used to study multi-ligand discrimination. We investigated pheromone discrimination using chimeric receptor molecules and the influence of single point mutations on activation profiles of the receptor.