Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery

The rapid increase of publicly available microbial genome sequences has highlighted the presence of hundreds of thousands of biosynthetic gene clusters (BGCs) encoding valuable secondary metabolites. The experimental characterization of new BGCs is extremely laborious and struggles to keep pace with the in silico identification of potential BGCs. Therefore, the prioritisation of promising candidates among computationally predicted BGCs represents a pressing need. Here, we propose an output ordering and prioritisation system (OOPS) which helps sorting identified BGCs by a wide variety of custom-weighted biological and biochemical criteria in a flexible and user-friendly interface. OOPS facilitates a judicious prioritisation of BGCs using G+C content, coding sequence length, gene number, cluster self-similarity and codon bias parameters, as well as enabling the user to rank BGCs based upon BGC type, novelty, and taxonomic distribution. Effective prioritisation of BGCs will help to reduce experimental attrition rates and improve the breadth of bioactive metabolites characterized.     

High-density linkage maps constructed in sweet cherry (<Emphasis Type="Italic">Prunus avium</Emphasis> L.) using cross- and self-pollination populations reveal chromosomal homozygosity in inbred families and non-syntenic regions with the peach genome

The landrace sweet cherry (Prunus avium L.) cultivar ‘Cristobalina’ is a useful resource for sweet cherry breeding due to several important traits, including low chilling requirement, early maturity date, and self-compatibility. In this work, three families (N?=?325), derived from ‘Cristobalina’, were used to develop high-density genetic maps using the RosBREED 6K Illumina Infinium® cherry SNP array. Two of the families were derived from self-pollination, which allowed construction of the first F₂ genetic maps in the species. The other map developed was from an interspecific cross of cultivars ‘Vic’?×?‘Cristobalina’. The maps developed include 511 to 816 mapped SNPs covering 622.4 to 726.0 cM. Mapped SNP marker order and position were compared to the sweet cherry and peach genome sequences, and a high degree of synteny was observed. However, inverted and small translocated regions between peach and sweet cherry genomes were observed with the most noticeable inversion at the top of LG5. The progeny resulting from self-pollination also revealed a high level of homozygosity, as large presumably homozygous regions as well as entire homozygous LGs were observed. These maps will be used for genetic analysis of relevant traits in sweet cherry breeding by QTL analysis, and self-pollination populations will be useful for investigating inbreeding depression in a naturally outbreeding species.     

Cultural,economic, and ecological factors influencing management of wild plants and mushrooms interchanged in Purépecha markets of Mexico

Background

Traditional markets outstandingly contribute to conservation of biocultural diversity, social relations, and cultural values. These markets reflect life strategies and forms people of a region interact with their biodiversity and territories, as well as traditional ecological knowledge and management practices. To understand the factors motivating plant and mushroom management, we analyzed the resources cultural and economic values, their role in people’s subsistence, and the relation of these values with the resources spatial and temporal availability. Our study based on the supposition that traditional markets are settings of interchange of resources with the highest importance for people’s life in a region. Also, that the cultural, economic, and ecological factors influence values of the resources, and the demand on them determine pressures on the most valuable resources which, when scarce, motivate management innovation, otherwise become extinct.

Methods

We documented cultural, economic, and ecological aspects, as well as management techniques of wild and weedy plants and mushrooms interchanged in three traditional markets of the Pátzcuaro Lake region, in central-western Mexico. For doing that, from February 2015 to March 2018, we conducted 175 visits to markets and 89 semi-structured interviews to producers, gatherers, and sellers of wild and weedy plants and mushrooms. Based on participant observation and interviews, we identified variables related to culture, economic, and ecological aspects, as well as management regimes of resources and management systems, which were documented and used as indicators for quantitative analyses. Through principal components analyses (PCA), we determined the indexes of cultural and economic importance (ICEI), management intensity (IMI), and ecological risk (IR) of the resources studied. For conducting that, we classified plant and mushroom species according to their cultural, economic, ecological, and technological indicators, respectively. The score of the first principal component was considered as the index for each group of variables, respectively. To identify relations between cultural importance and risk, we performed linear regression analyses between ICEI and IR indexes.

Results

We recorded 57 species of wild and weedy plants used as food, medicine, and ornamental, and 17 species of edible mushrooms. The variables with the highest weight in the ICEI are related to the need of a resource according to people, its recognizing, the number of communities and markets offering it in markets, its explicit preference expressed by people, the effort invested in obtaining it, and the form it is interchanged. Gathering is practiced in all mushrooms and wild and weedy plants from forests and agricultural areas; 11 species in addition receive 1 or more forms of management (enhancing, selective let standing, propagation through seeds or vegetative parts, transplantation, and/or protection). The management intensity and complexity are explained by variables related to management practices and systems. Plants receiving selective management have the higher management intensity. Silvicultural management (in situ management in forests) was recorded in all species of mushrooms, as well as in more than 80% of medicinal, ceremonial and ornamental plants, and in more than 50% of the edible plants. In agricultural systems, people manage more than 90% of the edible plants recorded to be under a management regime, 25% of the managed medicinal plants, and 30.7% of the managed ceremonial and ornamental plants. In homegardens, people manage 41.6% of the medicinal plants recorded and 26.6% of the edible plants, to have them available near home. Nearly 63% of the species interchanged in the markets studied are gathered in forests without any other management form. In this group are included all mushroom species, 61.5% of ceremonial/ornamental plants, 50% of medicinal, and 33.3% of edible plants. The linear regression between ICEI an IER is significantly negative for edible species with high management intensity R²?=?0.505 (p?=?0.0316), because of their management. But in medicinal and ornamental plants, the risk is high if the cultural importance increases, even when management practices like transplanting and propagation in homegardens are carried out.

Conclusions

Traditional markets are settings of interchange of products, knowledge, and experiences, where the ongoing factors and processes motivating management innovation can be identified and documented. This approach allows documenting processes occurring at regional level but would be benefited from deeper studies at local level in communities.

     

Adeno-associated virus gene delivery of broadly neutralizing antibodies as prevention and therapy against HIV-1

Vectored gene delivery of HIV-1 broadly neutralizing antibodies (bNAbs) using recombinant adeno-associated virus (rAAV) is a promising alternative to conventional vaccines for preventing new HIV-1 infections and for therapeutically suppressing established HIV-1 infections. Passive infusion of single bNAbs has already shown promise in initial clinical trials to temporarily decrease HIV-1 load in viremic patients, and to delay viral rebound from latent reservoirs in suppressed patients during analytical treatment interruptions of antiretroviral therapy. Long-term, continuous, systemic expression of such bNAbs could be achieved with a single injection of rAAV encoding antibody genes into muscle tissue, which would bypass the challenges of eliciting such bNAbs through traditional vaccination in naïve patients, and of life-long repeated passive transfers of such biologics for therapy. rAAV delivery of single bNAbs has already demonstrated protection from repeated HIV-1 vaginal challenge in humanized mouse models, and phase I clinical trials of this approach are underway. Selection of which individual, or combination of, bNAbs to deliver to counter pre-existing resistance and the rise of escape mutations in the virus remains a challenge, and such choices may differ depending on use of this technology for prevention versus therapy.     

The mitochondrial phosphatase PPTC7 orchestrates mitochondrial metabolism regulating coenzyme Q10 biosynthesis

Coenzyme Q₁₀ (CoQ₁₀) is a redox molecule critical for the proper function of energy metabolism and antioxidant defenses. Despite its essential role in cellular metabolism, the regulation of CoQ₁₀ biosynthesis in humans remains mostly unknown. Herein, we determined that PPTC7 is a regulatory protein of CoQ₁₀ biosynthesis required for human cell survival. We demonstrated by in vitro approaches that PPTC7 is a bona fide protein phosphatase that dephosphorylates the human COQ7. Expression modulation experiments determined that human PPTC7 dictates cellular CoQ₁₀ content. Using two different approaches (PPTC7 over-expression and caloric restriction), we demonstrated that PPTC7 facilitates and improves the human cell adaptation to respiratory conditions. Moreover, we determined that the physiological role of PPTC7 takes place in the adaptation to starvation and pro-oxidant conditions, facilitating the induction of mitochondrial metabolism while preventing the accumulation of ROS. Here we unveil the first post-translational mechanism regulating CoQ₁₀ biosynthesis in humans and propose targeting the induction of PPTC7 activity/expression for the treatment of CoQ₁₀-related mitochondrial diseases.     

Complex selection on a regulator of social cognition: Evidence of balancing selection,regulatory interactions and population differentiation in the prairie vole Avpr1a locus

Adaptive variation in social behaviour depends upon standing genetic variation, but we know little about how evolutionary forces shape genetic diversity relevant to brain and behaviour. In prairie voles (Microtus ochrogaster), variants at the Avpr1a locus predict expression of the vasopressin 1a receptor in the retrosplenial cortex (RSC), a brain region that mediates spatial and contextual memory; cortical V1aR abundance in turn predicts diversity in space use and sexual fidelity in the field. To examine the potential contributions of adaptive and neutral forces to variation at the Avpr1a locus, we explore sequence diversity at the Avpr1a locus and throughout the genome in two populations of wild prairie voles. First, we refine results demonstrating balancing selection at the locus by comparing the frequency spectrum of variants at the locus to a random sample of the genome. Next, we find that the four single nucleotide polymorphisms that predict high V1aR expression in the RSC are in stronger linkage disequilibrium than expected by chance despite high recombination among intervening variants, suggesting that epistatic selection maintains their association. Analysis of population structure and a haplotype network for two populations revealed that this excessive LD was unlikely to be due to admixture alone. Furthermore, the two populations differed considerably in the region shown to be a regulator of V1aR expression despite the extremely low levels of genomewide genetic differentiation. Together, our data suggest that complex selection on Avpr1a locus favours specific combinations of regulatory polymorphisms, maintains the resulting alleles at population‐specific frequencies, and may contribute to unique patterns of spatial cognition and sexual fidelity among populations.