A genome-wide approach for identification and characterisation of metabolite-inducible systems

© 2020, The Author(s). Inducible gene expression systems are vital tools for the advancement of synthetic biology. Their application as genetically encoded biosensors has the potential to contribute to diagnostics and to revolutionise the field of microbial cell factory development. Currently, the number of compounds of biological interest by far exceeds the number of available biosensors. Here, we address this limitation by developing a generic genome-wide approach to identify transcription factor-based inducible gene expression systems. We construct and validate 15 functional biosensors, provide a characterisation workflow to facilitate forward engineering efforts, exemplify their broad-host-range applicability, and demonstrate their utility in enzyme screening. Previously uncharacterised interactions between sensors and compounds of biological relevance are identified by employing the largest reported library of metabolite-responsive biosensors in an automated high-throughput screen. With the rapidly growing genomic data these innovative capabilities offer a platform to vastly increase the number of biologically detectable molecules

Probiotici i lekovito bilje u uzgoju šarana (cyprinus carpio l.) u zemljanim bazenima - uticaj na prirast ribe, zdravlje i proizvodne rezultate

The aim of the paper is to present the results of feeding carp with traditional grain diet (triticale + wheat) supplemented with probiotics and/or herbs. As probiotics, the EmFarma concentrate, provided by ProBiotics Polska, Poland,was used. This preparation contains consortia of the following microbial bacteria and fungi: Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium longum, Lactobacillus acidophilus, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus delbrueckii, Lactobacillus plantarum, Lactococcus diacetylactis, Lactococcus lactis, Streptococcus thermophilus, Bacillus subtilis var natto, Saccharomyces cerevisiae and Rhodopseudomonas palustris. The concentrate of probiotic microorganisms was added to the ground corn in an amount of 2 liters of preparation per 1 ton of feed. Prior to adding to the feedstuff, the probiotics were diluted in water. The amount of added water was approximately 10% of feed weight. After mixing probiotics with corn, the feed was left for two hours for swelling. The composition of herbs consisted of powdered Terminalia chebula, Phyllantus emblica, Andrographis paniculata, Tinospora cordifolia and Boerhaavia difusa. The herbal preparation was obtained from the Farmwet company, Poland. The blend of herbs was added in the amount of 3 kg per ton of ground corn feed. The powdered herbs were mixed with grinded corn, moistened with water amounting to approximately 10% of feed dose and left for two hours for swelling. Six feeding groups were examined: - I - natural food only (control group) - II - ground mix of corn - III - ground mix of corn supplemented with probiotics - IV - ground mix of corn supplemented with herbs - V - ground mix of corn supplemented with probiotics and herb - VI - pelleted feed Aller Aqua (referential group) Experimental diets were used for feeding carp fingerlings (C1), two-year restocking material (C2) and consumable carps (C3). Stocking densities of carp, were as follows: - for C1– 20000 ind./ha - for C2– 5000 ind./ha - for C3–1500 ind./ha The following parameters were measured and analyzed: - final body mass (g/ind.) - yield (kg/ha) - survival rate (S) - FCR (kg) - Fulton’s coefficient (F) - number of parasites (Trichodina–Trich., Chilodonella–Chil., Epistylis–Epist., Costia,) - level of lisozyme (mg/l) - level of gamma globulins (g/l)Cilj ovog rada je da prikaže rezultate ishrane šarana tradicionalnom smešom žitarica (tritikale + pšenica) sa dodatkom probiotika i/ili lekovitog bilja. Kao probiotik korišćen je koncentrat EmFarma, koji je obezbedio "ProBiotics Polska" iz Poljske. Ova smesa sadrži skup sledećih mikroorganizama, bakterija i gljivica: Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium longum, Lactobacillus acidophilus, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus delbrueckii, Lactobacillus plantarum, Lactococcus diacetylactis, Lactococcus lactis, Streptococcus thermophilus, Bacillus subtilis var natto, Saccharomyces cerevisiae and Rhodopseudomonas palustris. Koncentrat probiotskih mikroorganizama dodat je u mleveni kukuruz u količini od 2 litra preparata na 1 tonu hraniva. Pre dodavanja hranivima probiotski preparat je razređen u vodi. Količina dodate vode bila je oko 10% od težine hrane. Posle mešanja probiotika sa kukuruzom, hranivo je ostavljeno dva sata da nabubri. Lekovito bilje sastojalo se od praha Terminalia chebula, Phyllantus emblica, Andrographis paniculata, Tinospora cordifolia i Boerhaavia difusa. Biljni preparat dobijen je od kompanije Farmwet iz Poljske. Mešavina bilja dodata je u količini od 3 kg na tonu kukuruzne prekrupe. Bilje u prahu pomešano je sa prekrupom, zatim navlaženo vodom u količini od oko 10% od doze hrane i ostavljeno dva sata da nabubri. Ispitivanje je vršeno na šest hranidbenih grupa: - I - samo prirodna hrana (kontrolna grupa) - II - smeša sa kukuruznom prekrupom - III - smeša sa kukuruznom prekrupom obogaćena probioticima - IV - smeša sa kukuruznom prekrupom obogaćena lekovitim biljem - V - smeša sa kukuruznom prekrupom obogaćena probioticima i lekovitim biljem - VI - peletirana hrana Aller Aqua (referentna grupa) Eksperimentalne smeše korišćene su za ishranu šaranske mlađi (C1), dvogodišnjaka za dalji uzgoj (C2) i konzumnih šarana (C3). Gustine nasada šarana bile su sledeće: - za C1– 20000 jedinki/ha - za C2– 5000 jedinki/ha - za C3–1500 jedinki/ha Sledeći parametri su mereni i analizirani: - završna telesna masa (g/jedinka) - prinos (kg/ha) - stopa preživljavanja (S) - stopa konverzije hrane, FCR (kg) - Fultonov koeficijent (F) - broj parazita (Trichodina–Trich., Chilodonella–Chil., Epistylis–Epist., Costia,) - nivo lizozima (mg/l) - nivo gama globulina (g/l

Percutaneous Large-Bore Pulmonary Thrombectomy with the FlowTriever Device: Initial Experience in Intermediate-High and High-Risk Patients

Objectives: This retrospective cohort study investigates outcomes of patients with intermediate-high and high-risk pulmonary embolism (PE) who were treated with transfemoral mechanical thrombectomy (MT) using the large-bore Inari FlowTriever aspiration catheter system. Material and Methods: Twenty-seven patients (mean age 56.1 +/- 15.3 years) treated with MT for PE between 04/2021 and 11/2021 were reviewed. Risk stratification was performed according to European Society of Cardiology (ESC) guidelines. Clinical and hemodynamic characteristics before and after the procedure were compared with the paired Student's t test, and duration of hospital stay was analyzed with the Kaplan-Meier estimator. Procedure-related adverse advents were assessed. Results: Of 27 patients treated, 18 were classified as high risk. Mean right-to-left ventricular ratio on baseline CT was 1.7 +/- 0.6. After MT, a statistically significant reduction in mean pulmonary artery pressures from 35.9 +/- 9.6 to 26.1 +/- 9.0 mmHg (p = 0.002) and heart rates from 109.4 +/- 22.5 to 82.8 +/- 13.8 beats per minute (p < 0.001) was achieved. Two patients died of prolonged cardiogenic shock. Three patients died of post-interventional complications of which a paradoxical embolism can be considered related to MT. One patient needed short cardiopulmonary resuscitation during the procedure due to clot displacement. Patients with PE as primary driver of clinical instability had a median intensive care unit (ICU) stay of 2 days (0.5-3.5 days). Patients who developed PE as a complication of an underlying medical condition spent 11 days (9.5-12.5 days) in the ICU. Conclusion: In this small study population of predominantly high-risk PE patients, large-bore MT without adjunctive thrombolysis was feasible with an acceptable procedure-related complication rate

High-resolution monitoring of catchment nutrient response to the end of the 2011-2012 drought in England, captured by the demonstration test catchments.

The Demonstration Test Catchments (DTC) project is a UK Government funded initiative to test the effectiveness of on-farm mitigation measures designed to reduce agricultural pollution without compromising farm productivity. Three distinct catchments in England have been chosen to test the efficacy of mitigation measures on working farms in small tributary sub-catchments equipped with continuous water quality monitoring stations. The Hampshire Avon in the south is a mixed livestock and arable farming catchment, the River Wensum in the east is a lowland catchment with predominantly arable farming and land use in the River Eden catchment in the north-west is predominantly livestock farming. One of the many strengths of the DTC as a national research platform is that it provides the ability to investigate catchment hydrology and biogeochemical response across different landscapes and geoclimatic characteristics, with a range of differing flow behaviours, geochemistries and nutrient chemistries. Although numerous authors present studies of individual catchment responses to storms, no studies exist of multiple catchment responses to the same rainfall event captured with in situ high-resolution nutrient monitoring at a national scale. This paper brings together findings from all three DTC research groups to compare the response of the catchments to a major storm event in April 2012. This was one of the first weather fronts to track across the country following a prolonged drought period affecting much of the UK through 2011–2012, marking an unusual meteorological transition when a rapid shift from drought to flood risk occurred. The effects of the weather front on discharge and water chemistry parameters, including nitrogen species (NO3-N and NH4-N) and phosphorus fractions (total P (TP) and total reactive P (TRP)), measured at a half-hourly time step are examined. When considered in the context of one hydrological year, flow and concentration duration curves reveal that the weather fronts resulted in extreme flow, nitrate and TP concentrations in all three catchments but with distinct differences in both hydrographs and chemographs. Hysteresis loops constructed from high resolution data are used to highlight an array of potential pollutant sources and delivery pathways. In the Hampshire Avon DTC, transport was dominated by sub-surface processes, where phosphorus, largely in the soluble form, was found to be transport-limited. In the Wensum DTC, transport was largely dominated by rapid sub-surface movement due to the presence of under-drainage, which mobilised large quantities of nitrate during the storm. In the Eden DTC, transport was found to be initially dominated by surface runoff, which switched to subsurface delivery on the falling limb of the hydrograph, with the surface delivery transporting large amounts of particulate phosphorus to the river, with a transport-limited response. The lack of exhaustion of nutrient delivery in response to such extreme flow generation indicates the size of the nutrient pools stored in these catchments, and highlights the scale of the challenges faced by environmental managers when designing mitigation measures to reduce the flux of nutrients to UK river systems from diffuse agricultural sources

Strand specificity of ribonucleotide excision repair in Escherichia coli

In Escherichia coli, replication of both strands of genomic DNA is carried out by a single replicase—DNA polymerase III holoenzyme (pol III HE). However, in certain genetic backgrounds, the low-fidelity TLS polymerase, DNA polymerase V (pol V) gains access to undamaged genomic DNA where it promotes elevated levels of spontaneous mutagenesis preferentially on the lagging strand. We employed active site mutants of pol III (pol IIIα_S759N) and pol V (pol V_Y11A) to analyze ribonucleotide incorporation and removal from the E. coli chromosome on a genome-wide scale under conditions of normal replication, as well as SOS induction. Using a variety of methods tuned to the specific properties of these polymerases (analysis of lacI mutational spectra, lacZ reversion assay, HydEn-seq, alkaline gel electrophoresis), we present evidence that repair of ribonucleotides from both DNA strands in E. coli is unequal. While RNase HII plays a primary role in leading-strand Ribonucleotide Excision Repair (RER), the lagging strand is subject to other repair systems (RNase HI and under conditions of SOS activation also Nucleotide Excision Repair). Importantly, we suggest that RNase HI activity can also influence the repair of single ribonucleotides incorporated by the replicase pol III HE into the lagging strand

The oddity effect drives prey choice but not necessarily attack time

The tendency of predators to preferentially attack phenotypically odd prey in groups (the oddity effect) is a clear example of how predator cognition can impact behaviour and morphology in prey. Through targeting phenotypically odd prey, predators are thought to avoid the cognitive constraints that delay and limit the success of attacks on homogenous prey groups (the confusion effect). In addition to influencing which prey a predator will attack, the confusion and oddity effects would also predict that attacks on odd prey can occur more rapidly than attacking the majority prey type, as odd prey are more easily targeted, but this prediction has yet to be tested. Here, we used kerri tetra fish, Inpaichthys kerri, presented with mixed phenotypic groups of Daphnia dyed red or black to investigate whether odd prey in groups are preferentially attacked and whether these attacks were faster than those on the majority prey type. In agreement with previous work, odd prey were targeted and attacked more often than expected from their frequency in the prey groups, regardless of whether the odd prey was red in a group of black prey or vice versa. However, no difference was found in the time taken to attack odd vs. majority prey items, contrary to our predictions. Our results suggest that the time taken to make an attack is determined by a wider range of factors or is subject to greater variance than the choice of which prey is selectively targeted in a group

Increasing crop rotational diversity can enhance cereal yields

Diversifying agriculture by rotating a greater number of crop species in sequence is a promising practice to reduce negative impacts of crop production on the environment and maintain yields. However, it is unclear to what extent cereal yields change with crop rotation diversity and external nitrogen fertilization level over time, and which functional groups of crops provide the most yield benefit. Here, using grain yield data of small grain cereals and maize from 32 long-term (10–63 years) experiments across Europe and North America, we show that crop rotational diversity, measured as crop species diversity and functional richness, enhanced grain yields. This yield benefit increased over time. Only the yields of winter-sown small grain cereals showed a decline at the highest level of species diversity. Diversification was beneficial to all cereals with a low external nitrogen input, particularly maize, enabling a lower dependence on nitrogen fertilisers and ultimately reducing greenhouse gas emissions and nitrogen pollution. The results suggest that increasing crop functional richness rather than species diversity can be a strategy for supporting grain yields across many environments

Increasing crop rotational diversity can enhance cereal yields

9 Pág.Diversifying agriculture by rotating a greater number of crop species in sequence is a promising practice to reduce negative impacts of crop production on the environment and maintain yields. However, it is unclear to what extent cereal yields change with crop rotation diversity and external nitrogen fertilization level over time, and which functional groups of crops provide the most yield benefit. Here, using grain yield data of small grain cereals and maize from 32 long-term (10–63 years) experiments across Europe and North America, we show that crop rotational diversity, measured as crop species diversity and functional richness, enhanced grain yields. This yield benefit increased over time. Only the yields of winter-sown small grain cereals showed a decline at the highest level of species diversity. Diversification was beneficial to all cereals with a low external nitrogen input, particularly maize, enabling a lower dependence on nitrogen fertilisers and ultimately reducing greenhouse gas emissions and nitrogen pollution. The results suggest that increasing crop functional richness rather than species diversity can be a strategy for supporting grain yields across many environments.G.V., R.B. and S.H. acknowledge FORMAS grants 2018-02872 and 2018-02321. TMB acknowledges USDA AFRI grant 2017-67013-26254. LTEs managed by SRUC were supported by the Scottish Government RESAS Strategic Research Programme under project D3-, Healthy Soils for a Green Recovery. Swedish LTEs were funded by the Swedish University of Agricultural Sciences (SLU). We thank the Lawes Agricultural Trust and Rothamsted Research for data from the e-RA database. The Rothamsted Long-term Experiments National Capability (LTE-NC) was supported by the UK BBSRC (Biotechnology and Biological Sciences Research Council, BBS/E/C/000J0300) and the Lawes Agricultural Trust. The Woodslee site was supported by the Agro-Ecosystem Resilience Program (Agriculture & Agri-Food Canada) and field management provided by field crews over 6 decades is appreciated. La Canaleja LTE (Spain) was supported by RTA2017-00006-C03-01 project (Ministry of Science and Innovation. El Encín LTEs were supported by Spanish Ministry of Economy and Competitiveness funds (projects AGL2002-04186-C03-01.03, AGL2007-65698-C03-01.03, AGL2012-39929-C03-01 of which L. Navarrete was the P.I). R.A., A.G.D. and E.H.P. are also grateful to all members of the Weed Science Group from El Encín Experimental Station for their technical assistance in managing the experiments. The Brody/Poznan University of Life Sciences long-term experiments were funded by the Polish Ministry of Education and Science. We acknowledge the E-Obs dataset from the EU-FP6 project UERRA (http://www.uerra.eu) and the Copernicus Climate Change Service, and the data providers in the ECA&D project (https://www.ecad.eu/).Peer reviewe