Improvement of homologous GH10 xylanase production by deletion of genes with predicted function in the Aspergillus nidulans secretion pathway

Filamentous fungi are important cell factories for large-scale enzyme production. However, production levels are often low, and this limitation has stimulated research focusing on the manipulation of genes with predicted function in the protein secretory pathway. This pathway is the major route for the delivery of proteins to the cell exterior, and a positive relationship between the production of recombinant enzymes and the unfolded protein response (UPR) pathway has been observed. In this study, Aspergillus nidulans was exposed to UPR-inducing chemicals and differentially expressed genes were identified by RNA-seq. Twelve target genes were deleted in A. nidulans recombinant strains producing homologous and heterologous GH10 xylanases. The knockout of pbnA (glycosyltransferase), ydjA (Hsp40 co-chaperone), trxA (thioredoxin) and cypA (cyclophilin) improved the production of the homologous xylanase by 78, 171, 105 and 125% respectively. Interestingly, these deletions decreased the overall protein secretion, suggesting that the production of the homologous xylanase was specifically altered. However, the production of the heterologous xylanase and the secretion of total proteins were not altered by deleting the same genes. Considering the results, this approach demonstrated the possibility of rationally increase the production of a homologous enzyme, indicating that trxA, cypA, ydjA and pbnA are involved in protein production by A. nidulans.     

Multispectral canopy reflectance improves spatial distribution models of Amazonian understory species

Species distribution models are required for the research and management of biodiversity in the hyperdiverse tropical forests, but reliable and ecologically relevant digital environmental data layers are not always available. We here assess the usefulness of multispectral canopy reflectance (Landsat) relative to climate data in modelling understory plant species distributions in tropical rainforests. We used a large dataset of quantitative fern and lycophyte species inventories across lowland Amazonia as the basis for species distribution modelling (SDM). As predictors, we used CHELSA climatic variables and canopy reflectance values from a recent basin-wide composite of Landsat TM/ETM+ images both separately and in combination. We also investigated how species accumulate over sites when environmental distances were expressed in terms of climatic or surface reflectance variables. When species accumulation curves were constructed such that differences in Landsat reflectance among the selected plots were maximised, species accumulated faster than when climatic differences were maximised or plots were selected in a random order. Sixty-nine species were sufficiently frequent for species distribution modelling. For most of them, adequate SDMs were obtained whether the models were based on CHELSA data only, Landsat data only or both combined. Model performance was not influenced by species’ prevalence or abundance. Adding Landsat-based environmental data layers overall improved the discriminatory capacity of SDMs compared to climate-only models, especially for soil specialist species. Our results show that canopy surface reflectance obtained by multispectral sensors can provide studies of tropical ecology, as exemplified by SDMs, much higher thematic (taxonomic) detail than is generally assumed. Furthermore, multispectral datasets complement the traditionally used climatic layers in analyses requiring information on environmental site conditions. We demonstrate the utility of freely available, global remote sensing data for biogeographical studies that can aid conservation planning and biodiversity management.     

Effect of deltamethrin-incorporated nets on mobility and survivorship of Halyomorpha halys (Hemiptera: Pentatomidae) adults and nymphs in the laboratory

The brown marmorated stink bug, Halyomorpha halys Stål (Hemiptera: Pentatomidae), is an invasive pest that attacks specialty and row crops in North America and Europe. There has been a concerted effort to reduce frequent broad-spectrum insecticide applications made on vulnerable crops. One tool that has emerged recently is the use of long-lasting insecticide-treated nets (LLINs) as a killing agent. Here, we conducted bioassays to evaluate the effect of direct contact on deltamethrin-impregnated LLINs on the behaviour and survivorship of H. halys nymphs and adults in the laboratory. Following exposure at three different durations (1.25, 4.25 or 7.25 min), vertical and horizontal mobility of adults and nymphs and the flight capacity of adults were recorded and compared with individuals that were not exposed (control). Exposure to LLINs reduced the horizontal distance and velocity and increased the angular velocity of adults only but reduced vertical mobility of adults and nymphs. Adult flights were not significantly affected by LLIN exposure. Mortality of adults and nymphs at 7-day post-exposure ranged from 73% to 77% regardless of exposure time. We discuss our findings within the context of the potential for and limitations of deploying LLINs in vulnerable crops to manage H. halys populations.     

β‐amyloid model core peptides: Effects of hydrophobes and disulfides

The mechanism by which a disordered peptide nucleates and forms amyloid is incompletely understood. A central domain of β‐amyloid (Aβ21–30) has been proposed to have intrinsic structural propensities that guide the limited formation of structure in the process of fibrillization. In order to test this hypothesis, we examine several internal fragments of Aβ, and variants of these either cyclized or with an N‐terminal Cys. While Aβ21–30 and variants were always monomeric and unstructured (circular dichroism (CD) and nuclear magnetic resonance spectroscopy (NMRS)), we found that the addition of flanking hydrophobic residues in Aβ16–34 led to formation of typical amyloid fibrils. NMR showed no long‐range nuclear overhauser effect (nOes) in Aβ21–30, Aβ16–34, or their variants, however. Serial ¹H‐¹⁵N‐heteronuclear single quantum coherence spectroscopy, ¹H‐¹H nuclear overhauser effect spectroscopy, and ¹H‐¹H total correlational spectroscopy spectra were used to follow aggregation of Aβ16–34 and Cys‐Aβ16–34 at a site‐specific level. The addition of an N‐terminal Cys residue (in Cys‐Aβ16–34) increased the rate of fibrillization which was attributable to disulfide bond formation. We propose a scheme comparing the aggregation pathways for Aβ16–34 and Cys‐Aβ16–34, according to which Cys‐Aβ16–34 dimerizes, which accelerates fibril formation. In this context, cysteine residues form a focal point that guides fibrillization, a role which, in native peptides, can be assumed by heterogeneous nucleators of aggregation.     

What would it take to describe the global diversity of parasites?

How many parasites are there on Earth? Here, we use helminth parasites to highlight how little is known about parasite diversity, and how insufficient our current approach will be to describe the full scope of life on Earth. Using the largest database of host–parasite associations and one of the world’s largest parasite collections, we estimate a global total of roughly 100 000–350 000 species of helminth endoparasites of vertebrates, of which 85–95% are unknown to science. The parasites of amphibians and reptiles remain the most poorly described, but the majority of undescribed species are probably parasites of birds and bony fish. Missing species are disproportionately likely to be smaller parasites of smaller hosts in undersampled countries. At current rates, it would take centuries to comprehensively sample, collect and name vertebrate helminths. While some have suggested that macroecology can work around existing data limitations, we argue that patterns described from a small, biased sample of diversity aren’t necessarily reliable, especially as host–parasite networks are increasingly altered by global change. In the spirit of moonshots like the Human Genome Project and the Global Virome Project, we consider the idea of a Global Parasite Project: a global effort to transform parasitology and inventory parasite diversity at an unprecedented pace.     

A fair fight between molecular marker types in a seascape genetics setting

From its inception, population genetics has been nearly as concerned with the genetic data type—to which analyses are brought to bear—as it is with the analysis methods themselves. The field has traversed allozymes, microsatellites, segregating sites in multilocus alignments and, currently, single nucleotide polymorphisms (SNPs) generated by high‐throughput genomic sequencing methods, primarily whole genome sequencing and reduced representation library (RRL) sequencing. As each emerging data type has gained traction, it has been compared to existing methods, based on its relative ability to discern population structural complexity at increasing levels of resolution. However, this is usually done by comparing the gold standard in one data type to the gold standard in the new data type. These gold standards frequently differ in power and in sampling density, both across a genome and throughout a spatial range. In this issue of Molecular Ecology, D’Aloia et al. apply the high‐throughput approach as fully as possible to microsatellites, nuclear loci and SNPs genotyped through an RRL method; this is coupled with a spatially dense sampling scheme. Completing a battery of population genetics analyses across data types (including a series of down‐sampled data sets), the authors find that SNP data are slightly more sensitive to fine‐scale genetic structure, and the results are more resilient to down‐sampling than microsatellites and nonrepetitive nuclear loci. However, their results are far from an unqualified victory for RRL SNP data over all previous data types: the authors note that modest additions to the microsatellites and nuclear loci data sets may provide the necessary analytical power to delineate the fine‐scale genetic structuring identified by SNPs. As always, as the field begins to fully embrace the newest thing, good science reminds us that traditional data types are far from useless, especially when combined with a well‐designed sampling scheme.     

Long‐term persistence of wildlife populations in a pastoral area

Facilitating coexistence between people and wildlife is a major conservation challenge in East Africa. Some conservation models aim to balance the needs of people and wildlife, but the effectiveness of these models is rarely assessed. Using a case‐study approach, we assessed the ecological performance of a pastoral area in northern Tanzania (Manyara Ranch) and established a long‐term wildlife population monitoring program (carried out intermittently from 2003 to 2008 and regularly from 2011 to 2019) embedded in a distance sampling framework. By comparing density estimates of the road transect‐based long‐term monitoring to estimates derived from systematically distributed transects, we found that the bias associated with nonrandom placement of transects was nonsignificant. Overall, cattle and sheep and goat reached the greatest densities and several wildlife species occurred at densities similar (zebra, wildebeest, waterbuck, Kirk's dik‐dik) or possibly even greater (giraffe, eland, lesser kudu, Grant's gazelle, Thomson's gazelle) than in adjacent national parks in the same ecosystem. Generalized linear mixed models suggested that most wildlife species (8 out of 14) reached greatest densities during the dry season, that wildlife population densities either remained constant or increased over the 17‐year period, and that herbivorous livestock species remained constant, while domestic dog population decreased over time. Cross‐species correlations did not provide evidence for interference competition between grazing or mixed livestock species and wildlife species but indicate possible negative relationships between domestic dog and warthog populations. Overall, wildlife and livestock populations in Manyara Ranch appear to coexist over the 17‐year span. Most likely, this is facilitated by existing connectivity to adjacent protected areas, effective anti‐poaching efforts, spatio‐temporal grazing restrictions, favorable environmental conditions of the ranch, and spatial heterogeneity of surface water and habitats. This long‐term case study illustrates the potential of rangelands to simultaneously support wildlife conservation and human livelihood goals if livestock grazing is restricted in space, time, and numbers.