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A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics
No full textThe understanding of global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110–200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g. habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures
Aphid resistance in Capsicum maps to a locus containing LRR-RLK gene analogues
No full textKey message: A QTL for aphid resistance on pepper chromosome 2 was identified and validated. This QTL affects aphid survival and reproduction, and was fine mapped to a locus containing LRR-RLK analogues. Abstract: Myzus persicae is one of the most threatening insect pests that adversely affects pepper (Capsicum) cultivation. Resistance to aphids was previously identified in Capsicum baccatum. This study aimed at elucidating the genetics of aphid resistance in C. baccatum. A QTL analysis was carried out for M. persicae resistance in an F2 population derived from an intraspecific cross between a highly resistant plant and a susceptible plant. Survival and reproduction were used as resistance parameters. Interval mapping detected two QTLs affecting aphid survival (Rmpas-1) and reproduction (Rmprp-1), respectively, both localized in the same area and sharing the same top marker on chromosome 2. Use of this marker as co-factor in multiple-QTL mapping analysis revealed a second, minor QTL (Rmprp-2) only affecting aphid reproduction, on chromosome 4. Fine mapping confirmed the effects of Rmpas-1 and Rmprp-1 and narrowed the major QTL Rmprp-1 down to a genomic region of 96 kb which is predicted to encode four analogues of resistance genes of the receptor-like kinase family containing a leucine-rich repeat domain (LRR-RLKs). This work provides not only initial information for breeding aphid-resistant pepper varieties, but also forms the basis for future molecular analysis of gene(s) involved in aphid resistance.</p
Cucurbits
No full textSeveral cucurbits species are cultivated in greenhouses worldwide. The most important genera are (1) Cucurbita, which includes squash, pumpkin, zucchini and gourds, (2) Citrullus, which includes watermelon and (3) Cucumis, which includes cucumber and various melons. Pests and diseases affecting cucurbit crops can vary considerably in relation to geographic area and cropping system. Growing in soil or on hydroponics strongly determines the presence of certain soil pathogens or nematodes. Also the way the crop is cultivated, the number of cropping cycles and the transition between cycles strongly affects the performance of pests, diseases and biological control agents. The main pests and diseases detrimental to cucurbits in various parts of the globe are reported here, along with the most effective or sustainable control strategies currently applied to manage them. Many pests can be controlled very successfully with natural enemies, but despite the recent developments on microbiological control agents, integrated pest management (IPM) with a low input of pesticides and, particularly fungicides, remains challenging in cucurbits, mainly because of viruses and diseases that are difficult to manage biologically or with selective control methods. Plant breeding programmes that develop disease tolerant cultivars that can be combined with arthropod natural enemies for pest control are promising to further develop robust IPM systems for cucurbits
Proteomics perspective on auxin biology
No full textThe plant hormone auxin profoundly affects many aspects of plant growth and development. Since its discovery, the pathway leading to alteration in gene expression has been well documented. Strikingly, this nuclear auxin pathway (NAP) is short and consist of only three dedicated components, the SCF TIR1/AFB auxin receptor complex, AUX/IAA co-repressors and the auxin transcription factors (ARFs). Due to the simplicity of this pathway, a major question in the auxin field is how specificity is determined. In Chapter 1, I provide an introduction of the NAP, other physiological effects elicited by auxin, and how proteomic approaches might shed more light on auxin signalling. In Chapter 2, we provide a deeper insight into ARFs by dissecting and highlighting current views on ARF functioning. Since ARFs are the direct output of the NAP, we reason that the specificity within auxin signalling must be controlled by ARFs. Numerous aspects of ARF functioning may contribute to specificity. This can be deducted from specific cellular expression of ARFs, the promotor architecture where ARFs bind to, the combinatorial interactions amongst the NAP components and the functioning of ARF domains. We highlight that, although the DBD and PB1 domains of ARFs have been structurally and to some extent functionally resolved, the specificity in ARF functioning might reside in the middle region. From predictions, it appears that the middle region is intrinsically disordered. This might provide a signalling hub for ARF functioning. Intrinsically disordered regions have no structure but can provide platforms for co-factor interactions. That ARF co-factors are important for auxin output has been reported in a scattered fashion and is not clearly documented. We therefore, in Chapter 3, investigated which co-factors interact with ARFs. We utilized an unbiased quantitative affinity purification mass spectrometry approach to decipher the ARF interactome. Initial strategies utilizing conventional AP-MS/MS proved to be too cumbersome to retrieve ARF co-factors. We reasoned that the co-factors are probably too transient to survive the affinity purification procedure, and utilized crosslinkers to “freeze” and maintain the interactions during purification procedure. Optimisation of this strategy proved to be too cumbersome to be applied in a holistic ARF interactomic approach. Eventually, we integrated and optimized proximity labelling using BioID. This strategy tags neighbouring proteins with a biotin group within the cell allowing to capture “interacting” proteins of ARFs. Through this approach, we identified ARF-ARF and ARF-TPL interactions. Besides the regulation of the NAP by auxin other non-NAP effects have been described. Auxin can for example elicit rapid membrane depolarisation and Ca2+ spiking. Other reports also implicated kinase cascades in auxin dependent processes. To dissect this, we employed (phospho)proteomic techniques. It can be generally noted that the field of plant proteomics is not as advanced as the field of animal proteomics. Therefore in Chapter 4, we first integrated and optimized sample preparation techniques for shotgun and phosphoproteomic techniques in plant. We interrogated single-vessel-based approaches and offline stagetip-based peptide fractionation techniques to gain deeper and reproducible proteomes. Our results show that simple and cost-effective strategies can be employed to generate high-quality proteome coverage for plant research. Further efforts were undertaken to compare phosphopeptide enrichment strategies. This revealed that metal based phosphopeptide methods outperform metal-oxide based methods. In Chapter 5, we employed the optimized phosphopeptide enrichment procedure to dissect whether fast auxin response is mediated by phosphorylation dependent processes. Our results show that auxin can elicit rapid phosphorylation changes within 2 minutes and that these responses are TIR1-independent. Physiological responses to auxin are widespread in the plant kingdom, and can also be detected in algae that lack NAP components. We therefore further asked if the fast phosphorylation response may be part of a more ancient auxin response system. Our analysis revealed a deep evolutionarily conserved auxin response, and identified a PB1 domain-containing MAPKKK to mediate auxin-dependent regulation. Eventually, in Chapter 6 we conclude this thesis and discuss the implications and context of our results. We further provide perspectives for future plant proteomic studies
Identification of QTLs Associated with Nitrogen Use Efficiency and Related Traits in a Diploid Potato Population
No full textDeveloping N use efficient potato varieties requires exploring the genetic basis of nitrogen use efficiency (NUE) and associated agronomic and physiological traits. In order to identify QTLs for NUE and NUE-related traits, and to determine the relationships between the traits and QTLs in potato, a diploid potato mapping population (CxE) was evaluated in the field in Ethiopia under low and high N fertilizer levels. QTL detection was performed using interval mapping and multiple QTL mapping (MQM). A total of 52 putative QTLs were identified for ten traits, of which 28 QTLs were detected under low N availability while the remaining 24 QTLs were detected under high N conditions. Several QTLs were location and N level specific, suggesting the presence of QTL x environment interaction. A region on linkage group V (21-38 cM) accumulated the largest number of QTLs. This region coincides with the earliness locus encoded by the CDF1 gene, suggesting that earliness has a profound influence on NUE. A putative second QTL region on linkage group V located 20 cM from the earliness locus (38-56 cM) and a region on linkage group IV (60-72 cM) might be useful other regions to focus on, for NUE improvement in potato. To verify the stability of the identified QTLs and to use these for the detection of possible candidate genes, further multi-environment trials with larger population size may be required.</p
Functional replacement of isoprenoid pathways in Rhodobacter sphaeroides
No full textAdvances in synthetic biology and metabolic engineering have proven the potential of introducing metabolic by-passes within cell factories. These pathways can provide a more efficient alternative to endogenous counterparts due to their insensitivity to host's regulatory mechanisms. In this work, we replaced the endogenous essential 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis in the industrially relevant bacterium Rhodobacter sphaeroides by an orthogonal metabolic route. The native 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway was successfully replaced by a heterologous mevalonate (MVA) pathway from a related bacterium. The functional replacement was confirmed by analysis of the reporter molecule amorpha-4,11-diene after cultivation with [4-13C]glucose. The engineered R. sphaeroides strain relying exclusively on the MVA pathway was completely functional in conditions for sesquiterpene production and, upon increased expression of the MVA enzymes, it reached even higher sesquiterpene yields than the control strain coexpressing both MEP and MVA modules. This work represents an example where substitution of an essential biochemical pathway by an alternative, heterologous pathway leads to enhanced biosynthetic performance.</p
A vision for hydrological prediction
No full textIMproving PRedictions and management of hydrological EXtremes (IMPREX) was a European Union Horizon 2020 project that ran from September 2015 to September 2019. IMPREX aimed to improve society's ability to anticipate and respond to future extreme hydrological events in Europe across a variety of uses in the water-related sectors (flood forecasting, drought risk assessment, agriculture, navigation, hydropower and water supply utilities). Through the engagement with stakeholders and continuous feedback between model outputs and water applications, progress was achieved in better understanding the way hydrological predictions can be useful to (and operationally incorporated into) problem-solving in the water sector. The work and discussions carried out during the project nurtured further reflections toward a common vision for hydrological prediction. In this article, we summarized the main findings of the IMPREX project within a broader overview of hydrological prediction, providing a vision for improving such predictions. In so doing, we first presented a synopsis of hydrological and weather forecasting, with a focus on medium-range to seasonal scales of prediction for increased preparedness. Second, the lessons learned from IMPREX were discussed. The key findings were the gaps highlighted in the global observing system of the hydrological cycle, the degree of accuracy of hydrological models and the techniques of post-processing to correct biases, the origin of seasonal hydrological skill in Europe and user requirements of hydrometeorological forecasts to ensure their appropriate use in decision-making models and practices. Last, a vision for how to improve these forecast systems/products in the future was expounded, including advancing numerical weather and hydrological models, improved earth monitoring and more frequent interaction between forecasters and users to tailor the forecasts to applications. We conclude that if these improvements can be implemented in the coming years, earth system and hydrological modelling will become more skillful, thus leading to socioeconomic benefits for the citizens of Europe and beyond.</p
Evaluation of the presence of potential hazardous substances from plastic and textile fibre recycling
No full textIndustrial production of poly-β-hydroxybutyrate from CO<sub>2</sub> : Can cyanobacteria meet this challenge?
No full textThe increasing impact of plastic materials on the environment is a growing global concern. In regards to this circumstance, it is a major challenge to find new sources for the production of bioplastics. Poly-β-hydroxybutyrate (PHB) is characterized by interesting features that draw attention for research and commercial ventures. Indeed, PHB is eco-friendly, biodegradable, and biocompatible. Bacterial fermentation processes are a known route to produce PHB. However, the production of PHB through the chemoheterotrophic bacterial system is very expensive due to the high costs of the carbon source for the growth of the organism. On the contrary, the production of PHB through the photoautotrophic cyanobacterium system is considered an attractive alternative for a low-cost PHB production because of the inexpensive feedstock (CO2 and light). This paper regards the evaluation of four independent strategies to improve the PHB production by cyanobacteria: (i) the design of the medium; (ii) the genetic engineering to improve the PHB accumulation; (iii) the development of robust models as a tool to identify the bottleneck(s) of the PHB production to maximize the production; and (iv) the continuous operation mode in a photobioreactor for PHB production. The synergic effect of these strategies could address the design of the optimal PHB production process by cyanobacteria. A further limitation for the commercial production of PHB via the biotechnological route are the high costs related to the recovery of PHB granules. Therefore, a further challenge is to select a low-cost and environmentally friendly process to recover PHB from cyanobacteria.</p