Harmonising the bioassessment of large rivers in the absence of near‐natural reference conditions – a case study of the Danube River

1. International river catchments pose challenges for effective water resource management. Catchment‐wide strategies are often complicated by differences in national bioassessment and quality classification. Intercalibration efforts aim to harmonise these differences, but rely on the consistent delineation of near‐natural reference sites that are almost unavailable in today’s landscape, especially for large rivers. 2. We introduce the concept of alternative benchmarking that is based on the notion of aquatic communities at similar (low) levels of impairment associated with least‐disturbed conditions (LDC) as defined by abiotic criteria. Using data acquired during the second Joint Danube Survey, we defined LDC sites based on a multivariate gradient of anthropogenic pressures, mostly related to morphological deterioration, that spans the entire navigable Danube. 3. The river was subdivided into four stretches, each featuring homogeneous biological assemblages. Indirect gradient analysis revealed relationships between the pressure gradient and selected features of the macroinvertebrate and macrophyte community but not for diatoms or phytoplankton. 4. We identified biological metrics suitable for the quality classification of individual stretches or the entire river. Impoundment is the major hydromorphological alteration on the Danube but various metrics still responded significantly to differences in the morphological condition of sites not affected by impoundment. 5. A comparison of macroinvertebrate sampling techniques (airlift versus kick‐and‐sweep) revealed differences in how the acquired data reflect the effects of anthropogenic pressure. Biological metrics based only on kick‐and‐sweep sample data were insensitive to habitat deterioration in the heavily modified Upper Danube. 6. This study exemplifies the empirical approach of alternative benchmarking in intercalibration and offers practical solutions to some of the challenges of large river bioassessment.     

人致肺纤维化相关因子的克隆和生物信息学分析

几丁质酶是自然界广泛存在的一类降解几丁质的水解酶类,但是直至近些年才在哺乳动物体内发现存在有几丁质酶样蛋白.早年曾于矽肺大鼠中纯化出矽诱导的支气管肺泡灌洗蛋白iSBLP58,体外具有促进人胚肺成纤维细胞2BS增殖的作用,N端测序显示与哺乳动物几丁质酶蛋白家族成员具有高度同源性.生物信息学分析表明,来源于人的结肠、肾和胃的几个表达序列标签(EST)克隆和大鼠的这一蛋白质序列匹配.随后成功地从人肾RNA样品中克隆到一组cDNA,其序列及相应的氨基酸序列彼此高度相似,并与GenBank中的几个人几丁质酶蛋白高度相似.和人基因组序列比较,揭示这些分子可能来自于同一基因,为可变剪切的产物.     

Engineering Natural and Synthetic Resistance for Nematode Management

Bioengineering strategies are being developed that will provide specific and durable resistance against plant-parasitic nematodes in crops. The strategies come under three categories: (i) transfer of natural resistance genes from plants that have them to plants that do not, to mobilize the defense mechanisms in susceptible crops; (ii) interference with the biochemical signals that nematodes exchange with plants during parasitic interactions, especially those resulting in the formation of specialized feeding sites for the sedentary endoparasites—many nematode genes and many plant genes are potential targets for manipulation; and (iii) expression in plant cells of proteins toxic to nematodes.     

Implementation of hypocalcaemia prevention programmes in commercial dairy herds: From theory to practice

Hypocalcaemia prevention programmes have been widely studied in experimental settings, but their feasibility has not been assessed under field conditions. The main objective of this study was to evaluate, in the context of small dairy farms in western France, whether and how dairy farmers implement prevention programmes and manage the feeding of dry cows to prevent hypocalcaemia. Seventy-nine commercial Holstein dairy farms in Brittany (France) were enrolled in a qualitative study in 2019. We conducted in-person interviews with the farmers to 1) understand the rationale behind the type and seasonality of prevention programmes they implemented and 2) assess how closely they followed common recommendations when implementing them. Most farmers (80 %) used at least one prevention programme, especially supplying a mineral mix formulated to meet the needs of dry cows in late gestation (53 %), acidifying the diet in late gestation (37 %), and supplying calcium at calving (oral or injectable form, 37 %). The use of programmes depended on whether the diet composition varied throughout the year. Among farmers who provided an acidified diet, 25 % did not supply a specific mineral mix to dry cows to ensure an adequate amount of P, Ca, and Mg, which could decrease the effectiveness of the acidification programme. A lack of reliability in feeding practices, such as not weighing feed or not delivering feed frequently enough, was identified for 61 % of contributing farms. Management practices could result in supplying an unsuitable amount of P, Ca, or Mg immediately before calving; for example, inappropriate batching practices around calving were identified for 22 % (cows) to 32 % (heifers) of farms. In addition, nearly all contributing farmers had no processes in place to monitor the effectiveness of the programmes implemented. Reasons for this overall lack of compliance should be explored.     

High-level expression of a tobacco chitinase gene in Nicotiana sylvestris. Susceptibility of transgenic plants to Cercospora nicotianae infection

Endochitinases (E.C. 3.2.14, chitinase) are believed to be important in the biochemical defense of plants against chitin-containing fungal pathogens. We introduced a gene for class I (basic) tobacco chitinase regulated by Cauliflower Mosaic Virus 35S-RNA expression signals into Nicotiana sylvestris. The gene was expressed to give mature, enzymatically active chitinase targeted to the intracellular compartment of leaves. Most transformants accumulated extremely high levels of chitinase-up to 120-fold that of non-transformed plants in comparable tissues. Unexpectedly, some transformants exhibited chitinase levels lower than in non-transformed plants suggesting that the transgene inhibited expression of the homologous host gene. Progeny tests indicate this effect is not permanent. High levels of chitinase in transformants did not substantially increase resistance to the chitin-containing fungus Cercospora nicotiana, which causes Frog Eye disease. Therefore class I chitinase does not appear to be the limiting factor in the defense reaction to this pathogen.     

Relations between trophic state indicators and plant biomass in Florida lakes

We collected quantitative data on macrophyte abundance and water quality in 319 mostly shallow, polymictic, Florida lakes to look for relationships between trophic state indicators and the biomasses of plankton algae, periphyton, and macrophytes. The lakes ranged from oligotrophic to hypereutrophic with total algal chlorophylls ranging from 1 to 241 mg m^–3. There were strong positive correlations between planktonic chlorophylls and total phosphorus and total nitrogen, but there were weak inverse relationships between the densities of periphyton and the trophic state indicators total phosphorus, total nitrogen and algal chlorophyll and a positive relationship with Secchi depth. There was no predictable relationship between the abundance of emergent, floating-leaved, and submersed aquatic vegetation and the trophic state indicators. It was only at the highest levels of nutrient concentrations that submersed macrophytes were predictably absent and the lakes were algal dominated. Below these levels, macrophyte abundance could be high or low. The phosphorus–chlorophyll and phosphorus–Secchi depth relationships were not influenced by the amounts of aquatic vegetation present indicating that the role of macrophytes in clearing lakes may be primarily to reduce nutrient concentrations for a given level of loading. Rather than nutrient concentrations controlling macrophyte abundance, it seems that macrophytes acted to modify nutrient concentrations.     

Expression and signal regulation of the alternative oxidase genes under abiotic stresses

Plants in their natural environment frequently face various abiotic stresses, such as drought, high salinity, and chilling. Plant mitochondria contain an alternative oxidase （AOX）, which is encoded by a small family of nuclear genes. AOX genes have been shown to be highly responsive to abiotic stresses. Using transgenic plants with varying levels of AOX expression, it has been confirmed that AOX genes are im- portant for abiotic stress tolerance. Although the roles of AOX under abiotic stresses have been extensively studied and there are several excellent reviews on this topic, the differential expression patterns of the AOX gene family members and the signal regulation of AOX gene（s） under abiotic stresses have not been extensively summarized. Here, we review and discuss the current progress of these two important issues.     

Toward insights on antimicrobial selectivity of host defense peptides via machine learning model interpretation

Host defense peptides are promising candidates for the development of novel antibiotics. To realize their therapeutic potential, high levels of target selectivity is essential. This study aims to identify factors governing selectivity via the use of the random forest algorithm for correlating peptide sequence information with their bioactivity data. Satisfactory predictive models were achieved from out-of-bag prediction that yielded accuracies and Matthew's correlation coefficients in excess of 0.80 and 0.57, respectively. Model interpretation through the use of variable importance metrics and partial dependence plots indicated that the selectivity was heavily influenced by the composition and distribution patterns of molecular charge and solubility related parameters. Furthermore, the three investigated bacterial target species (Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus) likely had a significant influence on how selectivity was realized as there appears to be a similar underlying selectivity mechanism on the basis of charge-solubility properties (i.e. but which is tailored according to the target in question).