570 Biowissenschaften, Biologie
Refine
Document Type
- Article (4) (remove)
Language
- English (4)
Has Fulltext
- yes (4)
Is part of the Bibliography
- no (4)
Keywords
- BLAST algorithm (1)
- Bacterial genomics (1)
- Bioactive peptides (1)
- Continuous process (1)
- Food protein (1)
- FurB (1)
- Genomic databases (1)
- Immobilization (1)
- Künstliches Seegras (1)
- Metagenomics (1)
Food protein hydrolysates are often produced in unspecific industrial batch processes. The hydrolysates composition underlies process-related fluctuations and therefore the obtained peptide fingerprint and bioactive properties may vary. To overcome this obstacle and enable the production of specific hydrolysates with selected peptides, a ceramic capillary system was developed and characterized for the continuous production of a consistent peptide composition. Therefore, the protease Alcalase was immobilized on the surface of aminosilane modified yttria stabilized zirconia capillaries with a pore size of 1.5 μm. The loading capacity was 0.3 μg enzyme per mg of capillary with a residual enzyme activity of 43%. The enzyme specific peptide fingerprint produced with this proteolytic capillary reactor system correlated with the degree of hydrolysis, which can be controlled over the residence time by adjusting the flow rate. Common food proteins like casein, sunflower and lupin protein isolates were tested for continuous hydrolysis in the developed reactor system. The peptide formation was investigated by high-performance liquid chromatography. Various trends were found for the occurrence of specific peptides. Some are just intermediately occurring, while others cumulate by time. Thus, the developed continuous reactor system enables the production of specific peptides with desired bioactive properties.
Background: Maintenance of metal homeostasis is crucial in bacterial pathogenicity as metal starvation is the most important mechanism in the nutritional immunity strategy of host cells. Thus, pathogenic bacteria have evolved sensitive metal scavenging systems to overcome this particular host defence mechanism. The ruminant pathogen Mycobacterium avium ssp. paratuberculosis (MAP) displays a unique gut tropism and causes a chronic progressive intestinal inflammation. MAP possesses eight conserved lineage specific large sequence polymorphisms (LSP), which distinguish MAP from its ancestral M. avium ssp. hominissuis or other M. avium subspecies. LSP14 and LSP15 harbour many genes proposed to be involved in metal homeostasis and have been suggested to substitute for a MAP specific, impaired mycobactin synthesis.
Results: In the present study, we found that a LSP14 located putative IrtAB-like iron transporter encoded by mptABC was induced by zinc but not by iron starvation. Heterologous reporter gene assays with the lacZ gene under control of the mptABC promoter in M. smegmatis (MSMEG) and in a MSMEGΔfurB deletion mutant revealed a zinc dependent, metalloregulator FurB mediated expression of mptABC via a conserved mycobacterial FurB recognition site. Deep sequencing of RNA from MAP cultures treated with the zinc chelator TPEN revealed that 70 genes responded to zinc limitation. Remarkably, 45 of these genes were located on a large genomic island of approximately 90 kb which harboured LSP14 and LSP15. Thirty-five of these genes were predicted to be controlled by FurB, due to the presence of putative binding sites. This clustering of zinc responsive genes was exclusively found in MAP and not in other mycobacteria.
Conclusions: Our data revealed a particular genomic signature for MAP given by a unique zinc specific locus, thereby suggesting an exceptional relevance of zinc for the metabolism of MAP. MAP seems to be well adapted to maintain zinc homeostasis which might contribute to the peculiarity of MAP pathogenicity.
Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species) and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer.
Worldwide, seagrass meadows are under threat. Consequently, there is a strong need for seagrass restoration to guarantee the provision of related ecosystem services such as nutrient cycling, carbon sequestration and habitat provision. Seagrass often grows in vast meadows in which the presence of seagrass itself leads to a reduction of hydrodynamic energy. By modifying the environment, seagrass thus serves as foundation species and ecosystem engineer improving habitat quality for itself and other species as well as positively affecting its own fitness. On the downside, this positive feedback mechanism can render natural recovery of vanished and destroyed seagrass meadows impossible. An innovative approach to promote positive feedback mechanisms in seagrass restoration is to create an artificial seagrass (ASG) that mimics the facilitation function of natural seagrass. ASG could provide a window of opportunity with respect to suitable hydrodynamic and light conditions as well as sediment stabilization to allow natural seagrass to re-establish. Here, we give an overview of challenges and open questions for the application of ASG to promote seagrass restoration based on experimental studies and restoration trials and we propose a general approach for the design of an ASG produced from biodegradable materials. Considering positive feedback mechanisms is crucial to support restoration attempts. ASG provides promising benefits when habitat conditions are too harsh for seagrass meadows to re-establish themselves.