A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models.

Constraint-based metabolic models have been used for decades to predict the phenotype of microorganisms in different environments. However, quantitative predictions are limited unless labor-intensive measurements of media uptake fluxes are performed. We show how hybrid neural-mechanistic models can serve as an architecture for machine learning providing a way to improve phenotype predictions.

Revision of the genus Pollanisus Walker, 1854(Lepidoptera: Zygaenidae: Procridinae).

The genus Pollanisus is endemic for Australia. Its revision is mainly based on head studies and includes 21 known species and 7 new species, Pollanisus jumbun sp. n.

Inferring biologically relevant molecular tissue substructures by agglomerative clustering of digitized spatial transcriptomes with multilayer.

Spatially resolved transcriptomics (SrT) can investigate organ or tissue architecture from the angle of gene programs that define their molecular complexity. However, computational methods to analyze SrT data underexploit their spatial signature. Inspired by contextual pixel classification strategies applied to image analysis, we developed MULTILAYER to stratify maps into functionally relevant molecular substructures.

A new zygaenid moth species from Kangaroo Island, South Australia (Lepidoptera: Zygaenidae: Procridinae).

A new species of forester moths, Pollanisus hyacinthus sp. nov., is described from Kangaroo Island, South Australia.

Mechanically Robust Electrospun Hydrogel Scaffolds Crosslinked via Supramolecular Interactions.

One of the major challenges in the processing of hydrogels based on poly(ethylene glycol) (PEG) is to create mechanically robust electrospun hydrogel scaffolds without chemical crosslinking postprocessing. In this study, this is achieved by the introduction of physical crosslinks in the form of supramolecular hydrogen bonding ureido-pyrimidinone (UPy) moieties, resulting in chain-extended UPy-PEG polymers (CE-UPy-PEG) that can be electrospun from organic solvent. The resultant fibrous meshes are swollen in contact with water and form mechanically stable, elastic hydrogels, while the fibrous morphology remains intact.

A bioartificial environment for kidney epithelial cells based on a supramolecular polymer basement membrane mimic and an organotypical culture system.

Renal applications in healthcare, such as renal replacement therapies and nephrotoxicity tests, could potentially benefit from bioartificial kidney membranes with fully differentiated and functional human tubular epithelial cells. A replacement of the natural environment of these cells is required to maintain and study cell functionality cell differentiation in vitro. Our approach was based on synthetic supramolecular biomaterials to mimic the natural basement membrane (BM) on which these cells grow and a bioreactor to provide the desired organotypical culture parameters.

Development of Non-Cell Adhesive Vascular Grafts Using Supramolecular Building Blocks.

Cell-free approaches to in situ tissue engineering require materials that are mechanically stable and are able to control cell-adhesive behavior upon implantation. Here, the development of mechanically stable grafts with non-cell adhesive properties via a mix-and-match approach using ureido-pyrimidinone (UPy)-modified supramolecular polymers is reported. Cell adhesion is prevented in vitro through mixing of end-functionalized or chain-extended UPy-polycaprolactone (UPy-PCL or CE-UPy-PCL, respectively) with end-functionalized UPy-poly(ethylene glycol) (UPy-PEG) at a ratio of 90:10.

A modular approach to easily processable supramolecular bilayered scaffolds with tailorable properties.

Engineering of anisotropic tissues demands extracellular matrix (ECM) mimicking scaffolds with an asymmetric distribution of functionalities. We here describe a convenient, modular approach based on supramolecular building blocks to form electrospun bilayered scaffolds with tailorable properties. Polymers and peptides functionalized with hydrogen-bonding ureido-pyrimidinone (UPy) moieties can easily be mixed-and-matched to explore new material combinations with optimal properties.

Novel tomato flavours introduced by plastidial terpenoid pathway engineering.

Until recently breeding efforts centred on high-yield production while sacrificing flavour and taste quality traits of mass produced food products, such as tomatoes. The recent publication of Davidovich-Rikanati et al. demonstrates the technical feasibility of the genetical engineering of pathways in tomato plants to modify their fruit flavour profile in a proof-of-concept approach.

L-alanine auxotrophy of Lactobacillus johnsonii as demonstrated by physiological, genomic, and gene complementation approaches.

Using a chemically defined medium without L-alanine, Lactobacillus johnsonii was demonstrated to be strictly auxotrophic for that amino acid. A comparative genetic analysis showed that all known genes involved in L-alanine biosynthesis are absent from the genome of L. johnsonii.

The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533.

Lactobacillus johnsonii NCC 533 is a member of the acidophilus group of intestinal lactobacilli that has been extensively studied for their "probiotic" activities that include, pathogen inhibition, epithelial cell attachment, and immunomodulation. To gain insight into its physiology and identify genes potentially involved in interactions with the host, we sequenced and analyzed the 1.99-Mb genome of L.

Molecular characterization and expression analysis of the dextransucrase DsrD of Leuconostoc mesenteroides Lcc4 in homologous and heterologous Lactococcus lactis cultures.

The gene encoding the dextransucrase DsrD from the industrial strain Leuconostoc mesenteroides Lcc4 was isolated by PCR using degenerate primers recognizing conserved regions present in other dextransucrase-encoding genes from Leuconostoc spp. and Southern blot analyses on total genomic DNA. N-terminal sequence analysis of the active protein recovered in the culture showed that the secreted protein of 165 kDa is devoid of a 42 aa prepeptide which is removed post-translationally, most likely by signal peptidase cleavage.

Species specific identification of nine human Bifidobacterium spp. in feces.

Based on the 16S rDNA sequences, species specific primers were designed for the rapid identification by DNA amplification of nine human Bifidobacterium spp., namely B. adolescentis, B.

Evolution of the bacterial species Lactobacillus delbrueckii: a partial genomic study with reflections on prokaryotic species concept.

The species Lactobacillus delbrueckii consists at present of three subspecies, delbrueckii, lactis and bulgaricus, showing a high level of DNA-DNA hybridization similarity but presenting markedly different traits related to distinct ecological adaptation. The internal genetic heterogeneity of the bacterial species L. delbrueckii was analyzed.

Genetic and biochemical characterization of exopolysaccharide biosynthesis by Lactobacillus delbrueckii subsp. bulgaricus.

Lactobacillus delbrueckiisubsp. bulgaricus produces exopolysaccharides (EPSs), which play a role in the rheological properties of fermented food products. Lb.

DNA sequence and functional analysis of Lactobacillus delbrueckii subsp. lactis plasmids pN42 and pJBL2.

The plasmids pN42 and pJBL2 were isolated from the Lactobacillus delbrueckii subsp. lactis strains NCC88 and JCL414. DNA sequence determination and bioinformatic analysis revealed a strikingly conserved genetic organization containing five major, highly conserved open reading frames (ORFs).

Regulation and adaptive evolution of lactose operon expression in Lactobacillus delbrueckii.

Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp.

Transformation of Endomyces fibuliger based on its gene for orotidine-5'-phosphate decarboxylase.

Endomyces fibuliger is a yeast used in the production of Chinese rice wine. It secretes enzymes such as glucoamylase, alpha-amylase and acid protease. Very little is known of the genetics of E.

Genomics, molecular genetics and the food industry.

The production of foods for an increasingly informed and selective consumer requires the coordinated activities of the various branches of the food chain in order to provide convenient, wholesome, tasty, safe and affordable foods. Also, the size and complexity of the food sector ensures that no single player can control a single process from seed production, through farming and processing to a final product marketed in a retail outlet. Furthermore, the scientific advances in genome research and their exploitation via biotechnology is leading to a technology driven revolution that will have advantages for the consumer and food industry alike.

The development of functional foods: lessons from the gut.

Functional foods have resulted from the gradual recognition that healthy diets result from eating nutritious foods and from the identification of the mechanisms by which foods modulate metabolism and health. After initial successes with foods that reduce blood cholesterol level, probiotic bacteria and prebiotic carbohydrates have now also demonstrated added health benefits. As ingredients become more complex, the need to stabilize such ingredients in foods become increasingly important to the success of functional foods.

Functionality of probiotics and intestinal lactobacilli: light in the intestinal tract tunnel.

The commercial interest in functional foods that contain live microorganisms, also termed probiotics, is paralleled by increasing scientific attention to their functionality in the digestive tract. Most studies are focused on intestinal Lactobacillus species, which are part of the natural gastro-intestinal microbiota, and include analysis of colonisation factors and other interactions with the host, the design of novel or improved strains with specific health benefits, and the application of sophisticated molecular tools to determine their fate and activity in situ.

D-Lactate dehydrogenase gene (ldhD) inactivation and resulting metabolic effects in the Lactobacillus johnsonii strains La1 and N312.

Lactobacillus johnsonii La1, a probiotic bacterium with demonstrated health effects, grows in milk, where it ferments lactose to D- and L-lactate in a 60:40% ratio. The D-lactate dehydrogenase (D-LDH) gene (ldhD) of this strain was isolated, and an in vitro-truncated copy of that gene was used to inactivate the genomic copy in two strains, La1 and N312, by gene replacement. For that, an 8-bp deletion was generated within the cloned ldhD gene to inactivate its function.

Probiotics in the new millennium.

Beneficial effects on human health by specific probiotic microorganisms such as prevention of gastrointestinal tract infections immune stimulation, and balancing of the intestinal microflora have been established in numerous clinical trials. The successful probiotic strains which are mainly members of Lactobacillus and more recently Bifidobacterium naturally found in the human intestinal tract, have been traditionally incorporated into fermented milk products but have excellent potential for further inclusion in functional foods and health-related products. While the health claims are generally accepted by both scientists and consumers, often the molecular mechanisms underlying the probiotic properties remains controversial.

Transcriptional regulation and evolution of lactose genes in the galactose-lactose operon of Lactococcus lactis NCDO2054.

The genetics of lactose utilization within the slow-lactose-fermenting Lactococcus lactis strain NCDO2054 was studied with respect to the organization, expression, and evolution of the lac genes. Initially the beta-galactosidase gene (lacZ) was cloned by complementation of an Escherichia coli mutant on a 7-kb HpaI fragment. Nucleotide sequence analysis of the complete fragment revealed part of a gal-lac operon, and the genes were characterized by inactivation and complementation analyses and in vitro enzyme activity measurements.