Flavonoids are natural polyphenol secondary metabolites that are widely produced in planta. Flavonoids are ubiquities in human dietary intake and exhibit a myriad of health benefits. Flavonoids-induced biological activities are strongly influenced by their in situ availability in the human GI tract, as well as the levels of which are modulated by interaction with the gut bacteria. As such, assessing flavonoids–microbiome interactions is considered a key to understand their physiological activities. Here, we review the interaction between the various classes of dietary flavonoids (flavonols, flavones, flavanones, isoflavones, flavan-3-ols and anthocyanins) and gut microbiota. We aim to provide a holistic overview of the nature and identity of flavonoids on diet and highlight how flavonoids chemical structure, metabolism and impact on humans and their microbiomes are interconnected. Emphasis is placed on how flavonoids and their biotransformation products affect gut microbiota population, influence gut homoeostasis and induce measurable physiological changes and biological benefits.

Protoporphyrinogen oxidase (PPO) is an important target for discovering new herbicides that interfere with the synthesis of porphyrin. To discover new PPO inhibitors with improved biological activity, a series of new diphenyl ethers containing tetrahydrophthalimide were designed and synthesized. Among them, J6.1 (IC50 = 4.7 nM) and J6.3 (IC50 = 30.0 nM) show higher maize (Zea mays L.) PPO inhibitory activity than the commercial herbicides oxyfluorfen (IC50 = 117.9 nM) and flumioxazin (IC50 = 157.1 nM). The greenhouse herbicidal activity of J6.3 is comparable to that of oxyfluorfen, and it is greater than that of flumioxazin. Even at a dose of 300 g ai ha−1, cotton (Gossypium hirsutum L.) and peanut (Arachis hypogaea L.) show greater tolerance to J6.3, suggesting that J6.3 could be used for further development of new herbicide candidates in those fields. In addition, molecular docking has been used to further study the mechanism of action of J6.3. The results show that the introduction of a nitro group and tetrahydrophthalimide into the diphenyl ether structure is beneficial to biological activity.

The persistence of biologically active metribuzin [4-amino-6-(1,1-dimethylethyl)-3-(methylthio)-1,2,4-triazin-5(4H)-one] and its ethylthio analog [4-amino-6-(1,1-dimethylethyl)-3-(ethylthio)-1,2,4-triazin-5(4H)-one] were compared using an intact-plant chlorophyll fluorescence bioassay technique with oats (Avena sativa L.) and wheat (Triticum aestivum L.). Degradation of metribuzin phytotoxicity at concentrations of 0 to 1 ppm (w/w) ai in a Pond Creek silt loam soil was linear over time, with a half-life of 8 days at 35 C. Initial degradation of the biologically active ethylthio analog was much more rapid than for metribuzin, with a decrease in rate at later time intervals. A quadratic function best described this degradation pattern. The initial degradation rate of phytotoxicity for the ethylthio analog indicated a half-life of 4 days at 35 C. Soil pH had no significant influence on the activity or persistence of either herbicide within the range 4.9 to 6.9.

The efficacy of Alternaria helianthi on imazaquin-susceptible and -resistant biotypes of common cocklebur was evaluated with and without imazaquin. A. helianthi caused severe damage to both biotypes when applied at 80,000 conidia ml−1 at the five- to six-leaf stage. Symptoms included necrotic lesions, stunting, and mortality. Mortality from imazaquin at 140 g ai ha−1 was 0 and 100% and mortality from A. helianthi at 80,000 conidia ml−1 was 33 to 75% and 67 to 100% for resistant and susceptible biotypes, respectively, and surviving plants showed reduction in height, dry weight, and number of new leaves. The combination of imazaquin at 18 g ai ha−1 and A. helianthi at 40,000 conidia ml−1 was not synergistic or antagonistic in killing common cocklebur.

Fumonisin B1 (FB1) sprayed on intact jimsonweed plants at 10 to 200 μg ml–1 caused chlorosis and necrosis on three- to four-leaf plants and reduced their height and biomass. Excised leaves of jimsonweed were necrotic on both surfaces after treatment with FB1 at 10 to 200 μg ml–1. The degree of damage increased with the concentration of FB1. The minimum amount of FB1 that damaged excised leaves was 0.05 μg. The symptoms of toxicity on sensitive plants varied with concentration of FB1. Symptoms observed included: chlorosis (creeping cucumber), necrosis (jimsonweed and common sunflower), black leaf lesions (sicklepod), curl of tissues (soybean), stunting, defoliation (hemp sesbania and northern jointvetch), and death (prickly sida, spurred anoda, northern jointvetch, and jimsonweed). Monocots (barley, bermudagrass, corn, johnsongrass, rice, sorghum, and wheat) were not visibly affected by FB1. This is the first evidence of the phytotoxic properties of fumonisin B1 against a wide variety of weeds and crop cultivars.

There is growing interest in monitoring soil biological health to complement the traditional evaluation of soil physical and chemical characteristics in agricultural fields. Activity of soil microorganisms mediates many essential soil processes that affect fertility, and, therefore, essential to the successful adoption of precision agriculture. However, there are technical limitations to cost-effective monitoring of spatial and temporal dynamics of soil biological activity across agricultural landscapes. This paper summarizes three consecutive studies on in situ measurement of soil biological activity. The first study reveals spatial heterogeneity of microbial population growth in three agricultural fields using bio-films. In the second study, microbiological activity was analyzed using a substrate-induced respiration technique. This technique was evaluated through a series of soil toxicity experiments that involved a comparison of fresh and autoclaved soil samples. Finally, the aim of the third study was to develop a portable instrumented system to evaluate carbon dioxide concentrations in soil by extracting air stored within the soil pores. This instrument was tested under various conditions to quantify the effects of soil moisture, compaction and presence of glucose (artificially increased microbial respiration). Optimization of the discussed techniques will allow for detailed mapping of these indices of soil biological health and their interactions with the physical and chemical environment at any specific point in time.

Natural products represent a vast repository of materials and compounds with evolved biological activity, including phytotoxicity. Some of these compounds can be used directly or as templates for herbicides. The molecular target sites of these compounds are often unique. Strategies for the discovery of these materials and compounds are outlined. Numerous examples of individual phytotoxins and crude preparations with weed management potential are provided. An example of research to find a natural product solution of a unique pest management problem (blue-green algae in aquaculture) is described. Finally, the problems associated with natural products for pest control are discussed.

Flavonoids, a group of natural substances with variable phenolic structures, are found in fruits, vegetables, grains, bark, roots, stems, flowers, tea and wine. These natural products are well known for their beneficial effects on health and efforts are being made to isolate the ingredients so called flavonoids. Flavonoids are now considered as an indispensable component in a variety of nutraceutical, pharmaceutical, medicinal and cosmetic applications. This is attributed to their anti-oxidative, anti-inflammatory, anti-mutagenic and anti-carcinogenic properties coupled with their capacity to modulate key cellular enzyme function. Research on flavonoids received an added impulse with the discovery of the low cardiovascular mortality rate and also prevention of CHD. Information on the working mechanisms of flavonoids is still not understood properly. However, it has widely been known for centuries that derivatives of plant origin possess a broad spectrum of biological activity. Current trends of research and development activities on flavonoids relate to isolation, identification, characterisation and functions of flavonoids and finally their applications on health benefits. Molecular docking and knowledge of bioinformatics are also being used to predict potential applications and manufacturing by industry. In the present review, attempts have been made to discuss the current trends of research and development on flavonoids, working mechanisms of flavonoids, flavonoid functions and applications, prediction of flavonoids as potential drugs in preventing chronic diseases and future research directions.

Bryophytes (including mosses, liverworts and hornworts) are a heterogeneous group of terrestrial plants, which comprise over 24,000 species worldwide. Given the various biological activities reported from bryophytes, they have a huge commercial potential. Due to their minute size and rather small biomass in various ecosystems, bryophytes are a seldom part of ethnomedicine and rarely subject to medicinal and chemical analyses. Still, hundreds of novel natural products have been isolated from bryophytes. Bryophytes have been shown to contain numerous potentially useful natural products, including polysaccharides, lipids, rare amino acids, terpenoids, phenylpropanoids, quinones and many other specialized metabolites. Additionally, different bryophyte extracts and isolated compounds have shown antimicrobial, antiviral, cytotoxic, nematocidal, insecticidal, effects on smooth and non-striated muscles, weight loss, plant growth regulators and allelopathic activities. Bryophytes also cause allergies and contact dermatitis. All these effects highlight bryophytes as potential source for herbal remedies and production of chemicals to be used in various products.

Conservation agriculture (CA) systems are based upon minimal soil disturbance; crop residue retention and crop rotation and/or intercrop association are increasingly seen to recycle nutrients, increase yield and reduce production costs. This study examines the effects of CA practices on crop productivity, profitability and soil quality under the conditions encountered by smallholder farmers in two farming communities from 2005 to 2011 in Malawi, as part of the contribution to remedy a lack of supporting agronomic research for these relatively new systems. The drier agroenvironment of Lemu of Bazale Extension Planning Area (EPA) is characterized by sandy clay loam soils and lower rainfall. Here, CA showed positive benefits on maize yield after the first season of experimentation, with highest increases of 2.7 Mg ha−1 and 2.3 Mg ha−1 more yield in CA monocrop maize and CA maize–legume intercrop, respectively, than the conventional tillage in the driest season of 2009/10. In the high rainfall environment of Zidyana EPA (characterized by sandy loam soils), substantial maize yield benefits resulted in the fifth season of experimentation. Farmers spent at most 50 days ha−1 (US$140) producing maize under CA systems compared with 62 days ha−1(US$176) spent under conventional tillage practices. In Lemu, both CA systems resulted in gross margins three times higher than that of the conventional control plot, while in Zidyana, CA monocrop maize and CA maize–legume intercrop resulted in 33 and 23% higher gross margins, respectively, than conventional tillage. In Zidyana, the earthworm population was highest (48 earthworms m−2 in the first 30 cm) in CA monocrop maize, followed by a CA maize–legume intercropping (40 earthworms) and lowest (nine earthworms) in conventionally tilled treatment. In both study locations CA monocrop maize and CA maize–legume intercrop gave higher water infiltration than the conventional treatment. Improvements in crop productivity, overall economic gain and soil quality have made CA an attractive system for farmers in Malawi and other areas with similar conditions. However, for extensive adoption of CA by smallholder farmers, cultural beliefs that crop production is possible without the ubiquitous ridge and furrow system and residue burning for mice hunting have to be overcome.

At present, bulk liquid water on the surface and near-subsurface of Mars does not exist due to the scarcity of condensed- and gas-phase water, pressure and temperature constraints. Given that the nuclei of soil and ice, that is, the soil solid and ice lattice, respectively, are coated with adsorbed and/or thin liquid films of water well below 273 K and the availability of water limits biological activity, we quantify lower and upper limits for the thickness of such adsorbed/water films on the surface of the Martian regolith and for subsurface ice. These limits were calculated based on experimental and theoretical data for pure water ice and water ice containing impurities, where water ice containing impurities exhibit thin liquid film enhancements, ranging from 3 to 90. Close to the cold limit of water stability (i.e. 273 K), thin liquid film thicknesses at the surface of the Martian regolith is 0.06 nm (pure water ice) and ranges from 0.2 to 5 nm (water ice with impurities). An adsorbed water layer of 0.06 nm implies a dessicated surface as the thickness of one monolayer of water is 0.3 nm but represents 0.001–0.02% of the Martian atmospheric water vapour inventory. Taking into account the specific surface area (SSA) of surface-soil (i.e. top 1 mm of regolith and 0.06 nm adsorbed water layer), shows Martian surface-soil may contain interfacial water that represents 6–66% of the upper- and lower-limit atmospheric water vapour inventory and almost four times and 33%, the lower- and upper-limit Martian atmospheric water vapour inventory. Similarly, taking the SSA of Martian soil, the top 1 mm or regolith at 5 nm thin liquid water thickness, yields 1.10×1013 and 6.50×1013 litres of waters, respectively, 55–325 times larger than Mars’ atmospheric water vapour inventory. Film thicknesses of 0.2 and 5 nm represent 2.3×104–1.5×106 litres of water, which is 6.0×10−7–4.0×10−4%, respectively, of a 10 pr μm water vapour column, and 3.0×10−6–4.0×10−4% and 6.0×10−6–8.0×10−4%, respectively, of the Martian atmospheric water vapour inventory. Thin liquid film thicknesses on/in subsurface ice were investigated via two scenarios: (i) under the idealistic case where it is assumed that the diurnal thermal wave is equal to the temperature of ice tens of centimetres below the surface, allowing for such ice to experience temperatures close to 273 K and (ii) under the, likely, realistic scenario where the diurnal thermal wave allows for the maximum subsurface ice temperature of 235 K at 1 m depth between 30°N and 30°S. Scenario 1 yields thin liquid film thicknesses ranging from 11 to 90 nm; these amounts represent 4×106–3.0×107 litres of water. For pure water ice, Scenario 2 reveals that the thickness of thin liquid films contained on/within Martian subsurface is less than 1.2 nm, several molecular layers thick. Conversely, via the effect of impurities at 235 K allows for a thin liquid film thickness on/within subsurface ice of 0.5 nm, corresponding to 6.0×104 litres of water. The existence of thin films on Mars is supported by data from the Mars Exploration Rovers (MERs) Spirit and Opportunity's Alpha Proton X-ray Spectrometer instrumentation, which have detected increased levels of bromine beneath the immediate surface, suggestive of the mobilization of soluble salts by thin films of liquid water towards local cold traps. These findings show that biological activity on the Martian surface and subsurface is not limited by nanometre dimensions of available water.

The DagA gene and DagA(▽), which is a DagA gene encoding sequence without signal peptide, were cloned from genome DNA of Pseudoalteromonas atlantica 19262 by polymerase chain reaction (PCR). After ligation with pET21 vector, DagA and DagA(▽) were respectively expressed in Escherichia coli ER2566 using molecular chaperones DsbC and FkpA. A strain of ER2566-pET21a-DagA(▽)-DsbC was screened as a highly effective expressing system in the form of an inclusion body that had the target protein with up to 60% total bacterial protein. DagA protein was renatured and purified by dissolving it in 8 mol/l of urea, using Ni-NTA resin affinity chromatography and refolding using the urea gradient method. DagA with a molecular weight of ~30.8 kDa was identified by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and had the ability to digest agarose. In a pH range of 4.8–6.8, DagA maintained a bioactivity greater than 60%, with 5.8 being the optimum pH, and it exhibited activity at temperatures from 37°C to 60°C, with 55°C being the optimum temperature.

The bovine interferon-tau (bIFN-τ) gene, with signal sequence, was obtained through polymerase chain reaction (PCR) from bovine early embryos and subcloned into a pGEM-T vector. After being verified, the fragments, with or without signal sequence, were inserted into the expression vector pET-30a(+). Two recombinant plasmids were induced to express the recombinant proteins by isopropyl β-d-1-thiogalactopyranoside. The results showed that the bIFN-τ gene could be obtained from five bovine blastocysts by PCR without extraction of genomic DNA. It had 99% homology with nucleotides and 97% with amino acids in the GenBank sequence (accession number: XM_593584). The products of recombinant bIFN-τ, minus signal sequence, expressed in pET-30a(+) were analysed by SDS-PAGE. A new 20 kDa protein was detected and its molecular weight was as expected. The antiviral activity of recombinant bIFN-τ was 1×104 IU/mg using a standard cytopathic reduction assay. Marked morphological changes were induced by recombinant bIFN-τ in bovine endometrial epithelial cells. The cell volume was larger than that of controls and a lot of vesicles appeared in the cytoplasm after 24 h culture in the presence of 2.9 μg/ml recombinant bIFN-τ. In conclusion, a purified recombinant, biologically active bIFN-τ was obtained in this experiment.

Duck interleukin (IL)-18 mature protein gene was amplified by reverse transcription-polymerase chain reaction (RT-PCR) from total RNA extracted from Ma duck (Tadorna ferruginea) splenocytes. The PCR product was cloned into pGEM-T Easy vector for sequencing. The result revealed that the nucleotide sequence of duck IL-18 mature protein gene (mDuIL-18) consisted of a 513 bp band. A prokaryotic plasmid of mDuIL-18, pQE30-mDuIL18, was obtained by subcloning the encoding region of the DuIL-18 mature peptide into pQE30. pQE30-mDuIL18 transformed Escherichia coli M15. The expression of mDuIL-18 gene was identified by SDS-PAGE and Western blotting. Its molecular weight was 19.76 kDa, and could be specifically recognized by rabbit sera to chicken IL-18. The expressed products existed as inclusion bodies. After being degenerated, then renatured, the activities of the inclusion bodies were detected by methyl thiazolyl tetrazolium (MTT) assay. In ducks injected intramuscularly with mDuIL-18 protein (150 ng or 200 ng per duck) and Avian influenza virus (AIV) vaccine 2 weeks after immunization, the average titres of haemagglutination inhibition (HI) antibodies to AIV reached 7.5–7.7 log2, while those of HI antibody ranged between 6.3 and 6.6 log2 in ducks vaccinated with AIV vaccine only or with 100 ng mDuIL-18 and AIV vaccine. The results clearly showed that 150 ng mDuIL-18 per duck strengthened the in vivo immune responses induced by the inactivated oil emulsion AIV vaccine.

Equations were developed to predict soil matric potential as a function of soil water content, texture and bulk density in sandy soils. The equations were based on the additivity hypothesis - that water-retention of a whole soil depends on the proportions of several particle size fractions, each with fixed water-retention characteristics. The new model is an advancement over previously published models in that it embodies three basic properties of water-retention curves: a) matric potential is zero at saturation water content, b) matric potential approaches -∞ as water content approaches zero, and c) volumetric water content in dry soil is proportional to bulk density. Values of model parameters were taken from the literature, or estimated by fitting model predictions to data for sandy soils with low organic matter content. Most of the variation in water-release curves in the calibration data was explained by texture, with negligible effects of bulk density and sand particle size. The model predicted that variation in clay content among soils within the sand and loamy sand textural classes had substantial effects on water-retention curves. An understanding of how variation in texture among sandy soils contributes to matric potential is necessary for interpreting biological activity in arid environments.

To evaluate the bioactivity of bovine milk from different stages of lactation on human intestinal tissue, a human fetal small intestinal cell line was used as a model system. Milk samples representing six stages of lactation: days 1, 2–3, 6–7 and weeks 12 and 24 after parturition, 1 week before drying off, and milk-like secretion from two stages of the dry period: 7 weeks and 3–4 weeks before expected calving, were collected from 64 Holstein Friesian cows. The whey fraction of the milk or milk-like secretion was added to the culture medium in concentrations ranging from 0·078% to 10%. The growth-promoting activity of whey was measured by determining the incorporation of [3H]thymidine into DNA for the last 24 h of the culture period. Whey fractions from all six stages of lactation stimulated growth of intestinal cells. The growth-promoting activity of colostrum or milk significantly decreased within the first week after calving. The growth-promoting activity in mature milk increased gradually during lactation to reach a level significantly higher than that obtained with colostrum. The growth-promoting activity of whey from milk-like secretion collected after drying off was lower than that of colostrum. Whey from different stages of lactation contained significantly different concentrations of TGF-β1 (0·5–27 ng/ml) and TGF-β2 (12–1219 ng/ml). However, neither the differences in TGF-β1 and TGF-β2, nor the differences in IGF-I and IGF-binding proteins could fully explain the differences in growth-promoting activity of colostrums or milk from different stages of lactation, suggesting that other factors were also involved. The present study showed that bovine milk contained a number of biologically active components that affected growth and development of human intestinal tissue. The results showed that the growth-promoting activity of colostrum and milk was dependent on the stage of lactation in accordance with previous results obtained with mammary epithelial cells. The changes in growth-promoting activity with stage of lactation were probably related to changes in concentrations of several growth factors.

Powders from dry leaves of four plant species: Ficus carica (Moraceae), Eucalyptus globulus (Myrtaceae), Olea europaea (Oleacea) and Citrus limon (Rutaceae), were evaluated under controlled conditions (30±1°C and 70±5% RH), for their biological activity against Callosobruchus maculatus (Coleoptera: Bruchidae), and were compared to a powder from cloves of myrtle Syzygium aromaticum (Myrtaceae) and to eugenol (the essential oil from cloves). Once mixed with seeds of chickpea Cicer arietinum at doses of 1 to 5% (w/w), all the five powders significantly reduced adult longevity. Among these tested botanicals, clove powder was the most toxic as adult survival in treated seeds was less than 24h, even at the lowest dosage of 1%. The powders from dry leaves also reduced fecundity while that from cloves completely inhibited oviposition in C. maculatus. Indeed, the mean number of eggs laid in chickpea seeds treated with powders from dry leaves of the four plant species above varied from 273.2±30.3 to 373.8±58.2 against 401.8±37.9 in the control (untreated seeds). At the highest dose of 5%, all powders significantly reduced the number of emerging adults: 149.3±46.7 in treatment with O. europaea, 139.8±25.1 with E. globulus, 82.8±48.1 with C. limon, 31.5±20.5 in treatment with F. carica and 0.0±0.0 with S. aromaticum. Tests with lower doses (0,1–0,5%) of clove powder revealed that from the dose of 0.2% and above, C. maculatus adults died before laying eggs. Treatments with eugenol at 5μl/50g seeds (v/w), significantly reduced adult longevity (1±0.0 day), the number of eggs laid (0.0±0.0 egg) and adult emergence rate (0.0±0.0 adult), compared to the control used in this test where these parameters are respectively 7.00±0.8 days, 1134.4±204.2 eggs and 745.6±144.9 adults of the first generation.

Saponins are steroid or triterpenoid glycosides, common in a large number of plants and plant products that are important in human and animal nutrition. Several biological effects have been ascribed to saponins. Extensive research has been carried out into the membrane-permeabilising, immunostimulant, hypocholesterolaemic and anticarcinogenic properties of saponins and they have also been found to significantly affect growth, feed intake and reproduction in animals. These structurally diverse compounds have also been observed to kill protozoans and molluscs, to be antioxidants, to impair the digestion of protein and the uptake of vitamins and minerals in the gut, to cause hypoglycaemia, and to act as antifungal and antiviral agents. These compounds can thus affect animals in a host of different ways both positive and negative.