Aquaponics nomenclature matters: it is about principles and technologies and not as much about coupling

The food production system ‘aquaponics’ has moved a long way from its inceptions in the 1970s and 1980s. This paper suggests that it is the principle of aquaponics that should define what aquaponics is and then the rest follows according to systems and technologies. This paper supports the Palm et al. (Aquac Int. 2018;26(3):813–42) position of having a nutrient supply threshold (>50%) from the feed via the aquatic organisms to the plants. We test the most recent alternative definitions (e.g. Baganz et al. Rev Aquac. 2021;14:252–64) that overcomplicate existing definitions and nomenclature. Any new definition needs to be referential to existing terms and prop- erly tested. This paper does exactly that, concluding that several recent changes by Baganz et al. (Rev Aquac. 2021;14:252–64) are not needed. We also debate that the key principle behind aquaponics is ‘all about coupling’. Whilst coupling is an important aspect, existing technologies and those that will emerge are far more complex. Finally, this paper highlights the idiosyncrasies in the term aquaponics and we sug- gest an alternative term ‘aquaorganoponics’, which in essence better describes the principles of aquaponics (s.s.) which transfers natural organic compounds combined with microbes in water from the aquaculture unit to the plants

PEDIA: prioritization of exome data by image analysis.

PURPOSE: Phenotype information is crucial for the interpretation of genomic variants. So far it has only been accessible for bioinformatics workflows after encoding into clinical terms by expert dysmorphologists. METHODS: Here, we introduce an approach driven by artificial intelligence that uses portrait photographs for the interpretation of clinical exome data. We measured the value added by computer-assisted image analysis to the diagnostic yield on a cohort consisting of 679 individuals with 105 different monogenic disorders. For each case in the cohort we compiled frontal photos, clinical features, and the disease-causing variants, and simulated multiple exomes of different ethnic backgrounds. RESULTS: The additional use of similarity scores from computer-assisted analysis of frontal photos improved the top 1 accuracy rate by more than 20-89% and the top 10 accuracy rate by more than 5-99% for the disease-causing gene. CONCLUSION: Image analysis by deep-learning algorithms can be used to quantify the phenotypic similarity (PP4 criterion of the American College of Medical Genetics and Genomics guidelines) and to advance the performance of bioinformatics pipelines for exome analysis

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses

European contribution to the study of ROS: A summary of the findings and prospects for the future from the COST action BM1203 (EU-ROS).

The European Cooperation in Science and Technology (COST) provides an ideal framework to establish multi-disciplinary research networks. COST Action BM1203 (EU-ROS) represents a consortium of researchers from different disciplines who are dedicated to providing new insights and tools for better understanding redox biology and medicine and, in the long run, to finding new therapeutic strategies to target dysregulated redox processes in various diseases. This report highlights the major achievements of EU-ROS as well as research updates and new perspectives arising from its members. The EU-ROS consortium comprised more than 140 active members who worked together for four years on the topics briefly described below. The formation of reactive oxygen and nitrogen species (RONS) is an established hallmark of our aerobic environment and metabolism but RONS also act as messengers via redox regulation of essential cellular processes. The fact that many diseases have been found to be associated with oxidative stress established the theory of oxidative stress as a trigger of diseases that can be corrected by antioxidant therapy. However, while experimental studies support this thesis, clinical studies still generate controversial results, due to complex pathophysiology of oxidative stress in humans. For future improvement of antioxidant therapy and better understanding of redox-associated disease progression detailed knowledge on the sources and targets of RONS formation and discrimination of their detrimental or beneficial roles is required. In order to advance this important area of biology and medicine, highly synergistic approaches combining a variety of diverse and contrasting disciplines are needed.The EU-ROS consortium (COST Action BM1203) was supported by the European Cooperation in Science and Technology (COST). The present overview represents the final Action dissemination summarizing the major achievements of COST Action BM1203 (EU-ROS) as well as research news and personal views of its members. Some authors were also supported by COST Actions BM1005 (ENOG) and BM1307 (PROTEOSTASIS), as well as funding from the European Commission FP7 and H2020 programmes, and several national funding agencies

Spearmint (<i>Mentha spicata</i>) Cultivation in Decoupled Aquaponics with Three Hydro-Components (Grow Pipes, Raft, Gravel) and African Catfish (<i>Clarias gariepinus</i>) Production in Northern Germany

Mint (Mentha spicata) was cultivated in different hydroponic components: grow pipes, a raft and an ebb-and-flood gravel substrate system irrigated with aquaculture effluents from intensive African catfish (Clarias gariepinus) production under decoupled aquaponic conditions in northern Germany. The spearmint grew well and plant heights above ground were not significantly different between the gravel (57.7 ± 13.1 cm), raft (58.0 ± 17.7 cm) and grow pipe components (63.6 ± 9.9 cm). Root lengths and root fresh weights were two-fold and four-fold higher in raft (64.3 ± 20.5 cm; 42.8 ± 29.9 g) and grow pipes (59.4 ± 15.2 cm; 41.3 ± 25.7 g) compared with gravel substrate (29.7 ± 7.8 cm; 9.4 ± 9.4 g; raft = grow pipes > gravel). Spearmint leaf number was significantly higher in the grow pipes (770.0 ± 224.4) than in the gravel substrate (499.8 ± 228.4) with intermediate values in the raft. Significantly highest mean fresh biomass was found in the raft (1275.6 ± 33.4 g), followed by grow pipes (1042.0 ± 35.8 g) and gravel substrate (686.3 ± 98.2 g; raft > grow pipes > gravel). M. spicata, under aquaponics, grows best in grow pipe and raft components. An increase in pipe diameter for the grow pipes and a reduction in the channel height for the raft components could optimize aquaponic culture conditions for both industrial production and the hobby sector in the future

Spearmint (Mentha spicata) Cultivation in Decoupled Aquaponics with Three Hydro-Components (Grow Pipes, Raft, Gravel) and African Catfish (Clarias gariepinus) Production in Northern Germany

Mint (Mentha spicata) was cultivated in different hydroponic components: grow pipes, a raft and an ebb-and-flood gravel substrate system irrigated with aquaculture effluents from intensive African catfish (Clarias gariepinus) production under decoupled aquaponic conditions in northern Germany. The spearmint grew well and plant heights above ground were not significantly different between the gravel (57.7 &plusmn; 13.1 cm), raft (58.0 &plusmn; 17.7 cm) and grow pipe components (63.6 &plusmn; 9.9 cm). Root lengths and root fresh weights were two-fold and four-fold higher in raft (64.3 &plusmn; 20.5 cm; 42.8 &plusmn; 29.9 g) and grow pipes (59.4 &plusmn; 15.2 cm; 41.3 &plusmn; 25.7 g) compared with gravel substrate (29.7 &plusmn; 7.8 cm; 9.4 &plusmn; 9.4 g; raft = grow pipes &gt; gravel). Spearmint leaf number was significantly higher in the grow pipes (770.0 &plusmn; 224.4) than in the gravel substrate (499.8 &plusmn; 228.4) with intermediate values in the raft. Significantly highest mean fresh biomass was found in the raft (1275.6 &plusmn; 33.4 g), followed by grow pipes (1042.0 &plusmn; 35.8 g) and gravel substrate (686.3 &plusmn; 98.2 g; raft &gt; grow pipes &gt; gravel). M. spicata, under aquaponics, grows best in grow pipe and raft components. An increase in pipe diameter for the grow pipes and a reduction in the channel height for the raft components could optimize aquaponic culture conditions for both industrial production and the hobby sector in the future

Aquaponics (s.l.) Production of Spearmint (Mentha spicata) with African Catfish (Clarias gariepinus) in Northern Germany

Aquaponics production of spearmint (Mentha spicata) was evaluated under commercial grow-out conditions of African catfish (Clarias gariepinus) in Northern Germany (Mecklenburg-Western Pomerania). Fish batch production under different stocking densities in an extensive aquacultural unit (EAU) and an intensive aquacultural unit (IAU) was connected to conventional plant cultivation on ebb-and-flood planting tables and compared to a liquid fertilizer control. The best growth parameters of M. spicata were found under the intensive stocking density of C. gariepinus (IAU), resulting in a plant leaf area of 10.9 &plusmn; 2.5 cm2, leaf length of 8.6 &plusmn; 1.6 cm, and a cut fresh biomass from aboveground of 31.8 &plusmn; 13.8 g/plant, compared to the EAU (5.6 &plusmn; 2.1 cm2; 5.4 &plusmn; 1.4 cm; 17.4 &plusmn; 4.7 g/plant) and the control (5.7 &plusmn; 2.2 cm2; 5.5 &plusmn; 1.4 cm; 11.2 &plusmn; 5.3 g/plant). The fresh biomass of the whole plants was not significantly different between the EAU (165.5 &plusmn; 71.7 g/plant) and the IAU (190.7 &plusmn; 105.6 g/plant), though the latter gained more weight. The initial fish number ratio between the EAU and the IAU of 1/4 increased the M. spicata leaf area by twofold in the IAU. Our results demonstrate that aquaponics (s.l.) production of M. spicata is possible under the direct use of effluent waters from intensive African catfish cultivation without the addition of any liquid fertilizer

Growth of Basil (<i>Ocimum basilicum</i>) in DRF, Raft, and Grow Pipes with Effluents of African Catfish (<i>Clarias gariepinus</i>) in Decoupled Aquaponics

Basil (Ocimum basilicum) was cultivated in Rostock, Northern Germany, in a decoupled aquaponic system with African catfish (Clarias gariepinus) under intensive rearing conditions by using three hydroponic components, the dynamic root floating technique (DRF), the raft technique, and grow pipes. A 25% of the recommended feed input still allowed African catfish growth and provided adequate nitrogen and calcium levels in the process water. After 36 days, the plants were examined with respect to 16 different growth parameters. DRF performed significantly better than raft and/or grow pipes in 11 parameters. Total weight of basil was significantly higher in DRF (107.70 ± 34.03 g) compared with raft (82.02 ± 22.74 g) and grow pipes (77.86 ± 23.93 g). The economically important leaf biomass was significantly higher in wet and dry weight under DRF cultivation (45.36 ± 13.53 g; 4.96 ± 1.57 g) compared with raft (34.94 ± 9.44 g; 3.74 ± 1.04 g) and grow pipes (32.74 ± 9.84 g; 3.75 ± 1.22 g). Two main factors limited plant growth: an unbalanced nutrient concentration ratio and high water temperatures with an average of 28 °C (max 34.4 °C), which resulted in reduced root activity in raft and grow pipes. DRF was able to maintain root activity through the 5 cm air space between the shoots and the nutrient solution and thus produced significantly more biomass. This suggests DRF to be used for basil aquaponics under glass house conditions with high-temperature scenarios. Future studies are needed to optimize nutrient loads and examine systems with the plant roots exposed to air (Aeroponics)