Exploring the Leaf Beetle Fauna (Coleoptera: Chrysomelidae) of an Ecuadorian Mountain Forest Using DNA Barcoding

Background

Tropical mountain forests are hotspots of biodiversity hosting a huge but little known diversity of insects that is endangered by habitat destruction and climate change. Therefore, rapid assessment approaches of insect diversity are urgently needed to complement slower traditional taxonomic approaches. We empirically compare different DNA-based species delimitation approaches for a rapid biodiversity assessment of hyperdiverse leaf beetle assemblages along an elevational gradient in southern Ecuador and explore their effect on species richness estimates.

Methodology/Principal Findings

Based on a COI barcode data set of 674 leaf beetle specimens (Coleoptera: Chrysomelidae) of 266 morphospecies from three sample sites in the Podocarpus National Park, we employed statistical parsimony analysis, distance-based clustering, GMYC- and PTP-modelling to delimit species-like units and compared them to morphology-based (parataxonomic) species identifications. The four different approaches for DNA-based species delimitation revealed highly similar numbers of molecular operational taxonomic units (MOTUs) (n = 284–289). Estimated total species richness was considerably higher than the sampled amount, 414 for morphospecies (Chao2) and 469–481 for the different MOTU types. Assemblages at different elevational levels (1000 vs. 2000 m) had similar species numbers but a very distinct species composition for all delimitation methods. Most species were found only at one elevation while this turnover pattern was even more pronounced for DNA-based delimitation.

Conclusions/Significance

Given the high congruence of DNA-based delimitation results, probably due to the sampling structure, our study suggests that when applied to species communities on a regionally limited level with high amount of rare species (i.e. ~50% singletons), the choice of species delimitation method can be of minor relevance for assessing species numbers and turnover in tropical insect communities. Therefore, DNA-based species delimitation is confirmed as a valuable tool for evaluating biodiversity of hyperdiverse insect communities, especially when exact taxonomic identifications are missing.     

GAP promoter‐based fed‐batch production of highly bioactive core streptavidin by Pichia pastoris

Streptavidin is a homotetrameric protein binding the vitamin biotin and peptide analogues with an extremely high affinity, which leads to a large variety of applications. The biotin‐auxotrophic yeast Pichia pastoris has recently been identified as a suitable host for the expression of the streptavidin gene, allowing both high product concentrations and productivities. However, so far only methanol‐based expression systems have been applied, bringing about increased oxygen demand, strong heat evolution and high requirements for process safety, causing increased cost. Moreover, common methanol‐based processes lead to large proportions of biotin‐blocked binding sites of streptavidin due to biotin‐supplemented media. Targeting these problems, this paper provides strategies for the methanol‐free production of highly bioactive core streptavidin by P. pastoris under control of the constitutive GAP promoter. Complex were superior to synthetic production media regarding the proportion of biotin‐blocked streptavidin. The optimized, easily scalable fed‐batch process led to a tetrameric product concentration of up to 4.16 ± 0.11 µM of biotin‐free streptavidin and a productivity of 57.8 nM h^?1 based on constant glucose feeding and a successive shift of temperature and pH throughout the cultivation, surpassing the concentration in un‐optimized conditions by a factor of 3.4. Parameter estimation indicates that the optimized conditions caused a strongly increased accumulation of product at diminishing specific growth rates (μ ≈ D < 0.01 h^?1), supporting the strategy of feeding. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:855–864, 2016     

High‐Performance Liquid Chromatographic Resolution of Neutral and Cationic Hetero[6]Helicenes

Cationic hetero[6]helicenes 1⁺ , 2⁺ and 3⁺ have been recently disclosed. Herein we report on their enantiomeric separation using high‐performance liquid chromatography. Separation of the antipodes can be achieved in preparative scale on neutral adducts with Chiralcel OD‐I or Chiralpak ID CSP. Selectivity factors of 1.90, 1.67, and 1.96 were obtained for 1-H , 2-H , and 3-H , respectively. Separation can also be performed on the carbenium ions on regular Chiralpak IA CSP using water‐containing eluents, thus allowing for enantiomeric purity determinations in aqueous environments. Resolution of neutral and cationic helicenes is also achieved on more recently developed LARIHC columns. The versatility of the cyclofructan phases allows for baseline separations for both cases and their loading capabilities are demonstrated. Finally, the configurational stability of 1⁺ , 2⁺ , and 3⁺ was measured. For each replacement of an oxygen atom by an amino group, the racemization barrier increases significantly (ΔG^? = 29.8, 36.3 and >37 kcal mol^‐1 for 1⁺ , 2⁺ , and 3⁺ respectively). Chirality 28:282–289, 2016. © 2016 Wiley Periodicals, Inc.     

Inverse Optical Cavity Design for Ultrabroadband Light Absorption Beyond the Conventional Limit in Low‐Bandgap Nonfullerene Acceptor–Based Solar Cells

In the subwavelength regime, several nanophotonic configurations have been proposed to overcome the conventional light trapping or light absorption enhancement limit in solar cells also known as the Yablonovitch limit. It has been recently suggested that establishing such limit should rely on computational inverse electromagnetic design instead of the traditional approach combining intuition and a priori known physical effect. In the present work, by applying an inverse full wave vector electromagnetic computational approach, a 1D nanostructured optical cavity with a new resonance configuration is designed that provides an ultrabroadband (≈450 nm) light absorption enhancement when applied to a 107 nm thick active layer organic solar cell based on a low‐bandgap (1.32 eV) nonfullerene acceptor. It is demonstrated computationally and experimentally that the absorption enhancement provided by such a cavity surpasses the conventional limit resulting from an ergodic optical geometry by a 7% average over a 450 nm band and by more than 20% in the NIR. In such a cavity configuration the solar cells exhibit a maximum power conversion efficiency above 14%, corresponding to the highest ever measured for devices based on the specific nonfullerene acceptor used.     

MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements

In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome‐scale studies to characterize both model and non‐model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome‐wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular the high molecular weight DNA required as starting material, the reduced number of common loci among investigated samples, and the short length of the sequenced site‐associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.) and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms—enabling the exploration of diverse evolutionary and conservation questions.     

Accurate quantification of dimethylamine (DMA) in human urine by gas chromatography-mass spectrometry as pentafluorobenzamide derivative: evaluation of the relationship between DMA and its precursor asymmetric dimethylarginine (ADMA) in health and disease

Dimethylamine [DMA, (CH(3))(2)NH)] is abundantly present in human urine. Main sources of urinary DMA have been reported to include trimethylamine N-oxide, a common food component, and asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide (NO) synthesis. ADMA is excreted in the urine in part unmetabolized and in part after hydrolysis to DMA by dimethylarginine dimethylaminohydrolase (DDAH). Here we describe a GC-MS method for the accurate and rapid quantification of DMA in human urine. The method involves use of (CD(3))(2)NH as internal standard, simultaneous derivatization with pentafluorobenzoyl chloride and extraction in toluene, and selected-ion monitoring of m/z 239 for DMA and m/z 245 for (CD(3))(2)NH in the electron ionization mode. GC-MS analysis of urine samples from 10 healthy volunteers revealed a DMA concentration of 264+/-173 microM equivalent to 10.1+/-1.64 micromol/mmol creatinine. GC-tandem MS analysis of the same urine samples revealed an ADMA concentration of 27.3+/-15.3 microM corresponding to 1.35+/-1.2 micromol/mmol creatinine. In these volunteers, a positive correlation (R=0.83919, P=0.0024) was found between urinary DMA and ADMA, with the DMA/ADMA molar ratio being 10.8+/-6.2. Elevated excretion rates of DMA (52.9+/-18.5 micromol/mmol creatinine) and ADMA (3.85+/-1.65 micromol/mmol creatinine) were found by the method in 49 patients suffering from coronary artery disease, with the DMA/ADMA molar ratio also being elevated (16.8+/-12.8). In 12 patients suffering from end-stage liver disease, excretion rates of DMA (47.8+/-19.7 micromol/mmol creatinine) and ADMA (5.6+/-1.5 micromol/mmol creatinine) were found to be elevated, with the DMA/ADMA molar ratio (9.17+/-4.2) being insignificantly lower (P=0.46). Between urinary DMA and ADMA there was a positive correlation (R=0.6655, P<0.0001) in coronary artery disease, but no correlation (R=0.27339) was found in end-stage liver disease.     

Increased production of bacteriocin ST4SA byEnterococcus mundtii ST4SA in modified corn steep liquor

Enterococcus mundtii ST4SA produces a broad-spectrum bacteriocin (bacST4SA), active against Gram-positive and Gramnegative bacteria. Growth in corn steep liquor (CSL) with a sugar content of 5.0 and 10.0 g/l yielded bacST4SA levels of 12800 AU/ml. A four-fold increase in bacST4SA production (51200 AU/ml) was recorded in CSL with a sugar content of 7.5 g/l supplemented with 6.5 g/l yeast extract (CSL-YE). Poor growth and low levels of bacST4SA production were observed when cells were grown in CSL-YE controlled at pH 5.5. Fermentation at pH 7.5 yielded 25600 AU/ml after 6 h, but the activity levels decreased to approximately 1000 AU/ml during the next 6 h. Adjustment of the culture pH from 6.5 to 5.5 after 6 h of fermentation extended bacST4SA activity (51200 AU/ml) over 8 h. Activity then decreased to 25600 AU/ml and was maintained this level for 10 h. Optimal levels of bacST4SA production (102400 AU/ml) were obtained after 6 h of fermentation in CSL-YE supplemented with 7.5 g/l glucose at the start of the fermentation. This level of production was maintained by changing the culture pH from 6.5 after 6 h of fermentation to pH 5.5. This study proved that bacST4SA could be produced at high levels in an inexpensive industrial medium byE. mundtii ST4SA.     

Adaptive Ecosocial System Sustainability Enhancement in Sub-Saharan Africa

A conceptual framework is developed and used for improving the livelihood of Sub-Saharan communities faced with multiple stresses resulting from adverse environments, vector-transmitted diseases, and limited food. Ecosocial systems are the units for management. The accumulation of ecological, economic, and social capital is the objective of management, the reduction of maintenance costs is the key strategy, and technologies must satisfy ecological, economic, and social criteria. Interacting social system components are communities, facilitators, scientists, and political as well as administrative organizations. An adaptive approach to management allows flexibility in human and financial resource allocation and results in changes in knowledge and efficacy of management operations. The implementation strategy at two sites in Ethiopia relies on a two-stage procedure. In Stage 1, human and cattle health management set the conditions for development. In Stage 2, the ecosocial system is kept on a trajectory to enhanced ecological, economic, and social capital. In each stage, the assignment of responsibilities leads to four implementation phases. In Stage 1, successful precision targeting of tsetse and drug-based Trypanosoma spp. control increased the economic and social capital at the Luke site in southwestern Ethiopia but threatened the ecological capital because of overstocking and land degradation. In Stage 2, a women’s group living in the outskirts of Addis Ababa (Ethiopia) transformed barren land into a horticultural enterprise to enhance ecosystem service provision, including production of horticultural goods, and increase soil fertility expressed by nutrients and water availability. This article reviews concepts on human livelihood improvement in Sub-Saharan Africa and identifies principles that became important during project execution.