Biology subjects

Kellogg, E.

Publications and source records attributed to Kellogg, E..

3 recordsLinked to original sources

bioRxiv2022

Transforming a head direction signal into a goal-oriented steering command

To navigate, we must continuously estimate the direction we are headed in, and we must use this information to guide our path toward our goal1. Direction estimation is accomplished by ring attractor networks in the head direction system2,3. However, we do not understand how the sense of direction is used to guide action. Drosophila connectome analyses4,5 recently revealed two cell types (PFL2 and PFL3) that connect the head direction system to the locomotor system. Here we show how both cell types combine an allocentric head direction signal with an internal goal signal to produce an egocentric motor drive. We recorded their activity as flies navigated in a virtual reality environment toward a goal stored in memory. Strikingly, PFL2 and PFL3 populations are both modulated by deviation from the goal direction, but with opposite signs. The amplitude of PFL2 activity is highest when the fly is oriented away from its goal; activating these cells destabilizes the current orientation and drives turning. By contrast, total PFL3 activity is highest around the goal; these cells generate directional turning to correct small deviations from the goal. Our data support a model where the goal is stored as a sinusoidal pattern whose phase represents direction, and whose amplitude represents salience. Variations in goal amplitude can explain transitions between goal-oriented navigation and exploration. Together, these results show how the sense of direction is used for feedback control of locomotion.

neuroscience↗

bioRxiv2022

Plant conservation assessment at scale: rapid triage of extinction risks

SummaryO_LIThe IUCN Red List criteria are widely used to determine extinction risks of plant and animal life. Here, we use The Red Lists criterion B, Geographic Range Size, to provide preliminary conservation assessments of the members of a large tribe of grasses, the Andropogoneae, with [~]1100 species, including maize, sorghum, and sugarcane and their wild relatives. C_LIO_LIWe use georeferenced occurrence data from the Botanical Information and Ecology Network (BIEN) and automated individual species assessments using ConR to demonstrate efficacy and accuracy in using time-saving tools for conservation research. We validate our results with those from the IUCN-authorized assessment tool, GeoCAT. C_LIO_LIWe discovered a remarkably large gap in digitized information, with slightly more than 50% of the Andropogoneae lacking sufficient information for assessment. ConR and GeoCAT largely agree on which taxa are of least concern (>90%) or possibly threatened (<10%), highlighting that automating assessments with ConR is a viable strategy for preliminary conservation assessments of large plant groups. Results for crop wild relatives are similar to those for the entire data set. C_LIO_LIIncreasing digitization and collection needs to be a high priority. Available rapid assessment tools can then be used to identify species that warrant more comprehensive investigation. C_LI Societal Impact StatementThe current rate of global biodiversity loss creates a pressing need to increase efficiency and throughput of extinction risk assessments in plants. We must assess as many plant species as possible, working with imperfect knowledge, to address the habitat loss and seemingly countless extinction threats of the Anthropocene. Large-scale, preliminary conservation assessments can play a fundamental role in setting priorities for more in-depth investigation.

plant biology↗

bioRxiv2022

A happy accident: a novel turfgrass reference genome

Poa pratensis, commonly known as Kentucky bluegrass, is a popular cool-season grass species used as turf in lawns and recreation areas globally. Despite its substantial economic value, a reference genome had not previously been assembled due to the genomes relatively large size and biological complexity that includes apomixis, polyploidy, and interspecific hybridization. We report here a fortuitous de novo assembly and annotation of a P. pratensis genome. Instead of sequencing the genome of a C4 grass, we accidentally sampled and sequenced tissue from a weedy P. pratensis whose stolon was intertwined with that of the C4 grass. The draft assembly consists of 6.09 Gbp with an N50 scaffold length of 65.1 Mbp, and a total of 118 scaffolds, generated using PacBio long reads and Bionano optical map technology. We annotated 256K gene models and found 58% of the genome to be composed of transposable elements. To demonstrate the applicability of the reference genome, we evaluated population structure and estimated genetic diversity in P. pratensis collected from three North American prairies, two in Manitoba, Canada and one in Colorado, USA. Our results support previous studies that found high genetic diversity and population structure within the species. The reference genome and annotation will be an important resource for turfgrass breeding and study of bluegrasses.

plant biology↗