Biology subjects

Voss, R.

Publications and source records attributed to Voss, R..

4 recordsLinked to original sources

bioRxiv2024

Citizen science informs demand-driven breeding of opportunity crops

CONTEXTOpportunity crops, also known as neglected and underutilized species (NUS), offer benefits to diversify food systems with nutritious and climate-resilient foods. A major limitation to incorporate these crops in farming systems is the lack of improved varieties impedes farmers accessing quality planting material of these crops. OBJECTIVESThe study explored how citizen science methods can support demand-driven breeding and seed production of opportunity crops using leafy amaranth - a nutritious and hardy vegetable- as a case study. The study identified farmer preferences and market segments, with particular attention to gender and social differentiation. METHODSWe used the tricot approach to conduct participatory on-farm trials of 14 varieties with 2,063 farmers from Benin, Mali, and Tanzania. We then analyzed farmer trait and varietal preferences in aggregate and among segments of farmers, generated using cluster analysis. RESULTSFarmers overall preferences for amaranth varieties was driven principally by plant survival, yield, leaf size, taste, and marketability. Distinct farmer segments (older women generalists, young women specialists, older men generalists, and young men specialists) preferred different varieties depending on gender, business-orientation. DISCUSSION AND CONCLUSIONThe farmer segments identified here, along with their unique variety preferences provide valuable information for breeders and seed enterprises, and support demand-driven amaranth breeding and seed system development. We specifically noted the need for breeding programs to understand the preferences of young amaranth specialists, both men and women, and to explore organoleptic and market-related properties of amaranth. SIGNIFICANCEOur findings on differentiated producer preferences will support scaling seed supply of amaranth in Africa to diversify farming systems with a climate-resilient and nutritious crop. The methods used and lessons learned from our citizen science exercise can be applied to enhance breeding and seed supply of other opportunity crops that are underutilized in Africa or other continents. HighlightsO_LIFarmer citizen science methods reveal seed market insights for opportunity crops C_LIO_LIAmaranth variety preferences vary widely across gender, age, and countries C_LIO_LIYoung amaranth producers focus on market and sensory traits compared to old producers C_LIO_LILarge-scale farmer feedback guides opportunity crop breeding for diverse segments C_LI

plant biology↗

bioRxiv2023

Model-free Identification of Phenotype-Relevant Variables From Dose Response Data

Complex phenotypic changes occur during development and in response to injury and disease. Identifying key regulators of phenotypic change is a shared aim of many different fields of research, including life history, tissue regeneration, and cancer. These examples of phenotypic change involve coordinated changes in cellular behaviors and associated changes in gene expression which if disrupted, can alter and even block completion of the phenotypic transition. Experimental treatments that effectively block the completion of a phenotypic transition can be quantitatively manipulated to identify key regulatory genes through changes in transcriptional dose response. In this paper, we present a "model free" approach to identify "bifurcation-like" behaviors of key regulatory genes by tracking spikes in their transcriptional sensitivities. Genes that exhibit such behavior are predicted to comprise nodes in subnetworks or modules that regulate the phenotypic transition. We applied our method to an in-silico data set where we also studied the impact of noise in the predictions. We also applied the method to a gene expression data that were collected during tail regeneration in axolotls. Our code for gene identification, which can be extended more generally to other component variables of complex phenotypic change, is freely available via the following GitHub site github.com/alanavc/id-vars-from-resp-data.

developmental biology↗

bioRxiv2022

Building model prototypes from time-course data

A primary challenge in building predictive models from temporal data is selecting the appropriate model topology and the regulatory functions that describe the data. Software packages are available for equation learning of continuous models, but not for discrete models. In this paper we introduce a method for building model prototypes. These model prototypes consist of a wiring diagram and a set of discrete functions that can explain the time course data. The method takes as input a collection of time course data or discretized measurements over time. After network inference, we use our toolbox to simulate the prototype model as a stochastic Boolean model. Our method provides a model that can qualitatively reproduce the patterns of the original data and can further be used for model analysis, making predictions, and designing interventions. We applied our method to a time-course, gene-expression data that were collected during salamander tail regeneration under control and intervention conditions. The inferred model captures important regulations that were previously validated in the research literature and gives novel interactions for future testing. The toolbox for inference and simulations is freely available at github.com/alanavc/prototype-model.

systems biology↗

bioRxiv2021

Evolution of the nitric oxide synthase family in vertebrates and novel insights in gill development

Nitric oxide (NO) is an ancestral key signaling molecule essential for life and has enormous versatility in biological systems, including cardiovascular homeostasis, neurotransmission, and immunity. Although our knowledge of nitric oxide synthases (Nos), the enzymes that synthesize NO in vivo, is substantial, the origin of a large and diversified repertoire of nos gene orthologs in fish with respect to tetrapods remains a puzzle. The recent identification of nos3 in the ray-finned fish spotted gar, which was considered lost in the ray-finned fish lineage, changed this perspective. This prompted us to explore nos gene evolution and expression in depth, surveying vertebrate species representing key evolutionary nodes. This study provides noteworthy findings: first, nos2 experienced several lineage-specific gene duplications and losses. Second, nos3 was found to be lost independently in two different teleost lineages, Elopomorpha and Clupeocephala. Third, the expression of at least one nos paralog in the gills of developing shark, bichir, sturgeon, and gar but not in arctic lamprey, suggest that nos expression in this organ likely arose in the last common ancestor of gnathostomes. These results provide a framework for continuing research on nos genes roles, highlighting subfunctionalization and reciprocal loss of function that occurred in different lineages during vertebrate genome duplications.

evolutionary biology↗