Cell Wall Dynamics in the parasitic plant () and rice pathosystem.

In the plant-plant pathosystem of rice () and the parasitic plant , cell walls from either plant are important defensive and offensive structures. Here we reveal cell wall dynamics in both and rice using simultaneous RNA sequencing. We used weighted gene co-expression network analysis (WGCNA) to home in on cell wall modification processes occurring in interactions with a resistant rice cultivar (Nipponbare) compared to a susceptible one (IAC 165).

Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates.

Predicting phenotypes from a combination of genetic and environmental factors is a grand challenge of modern biology. Slight improvements in this area have the potential to save lives, improve food and fuel security, permit better care of the planet, and create other positive outcomes. In 2022 and 2023 the first open-to-the-public Genomes to Fields (G2F) initiative Genotype by Environment (GxE) prediction competition was held using a large dataset including genomic variation, phenotype and weather measurements and field management notes, gathered by the project over nine years.

Predicting gene expression responses to environment in using natural variation in DNA sequence.

The evolution of gene expression responses are a critical component of adaptation to variable environments. Predicting how DNA sequence influences expression is challenging because the genotype to phenotype map is not well resolved for regulatory elements, transcription factor binding, regulatory interactions, and epigenetic features, not to mention how these factors respond to environment. We tested if flexible machine learning models could learn some of the underlying regulatory genotype to phenotype map.

Climate biogeography of linking distribution models and individual variation.

Aim: Patterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. If species distributions are determined by environmental constraints, then populations near range margins may have reduced performance and be adapted to harsher environments. Model organisms are potentially important systems for biogeographical studies, given the available range-wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity.

Resolving intergenotypic Striga resistance in sorghum.

Genetic underpinnings of host-pathogen interactions in the parasitic plant Striga hermonthica, a root parasitic plant that ravages cereals in sub-Saharan Africa, are unclear. We performed a comparative transcriptome study on five genotypes of sorghum exhibiting diverse resistance responses to S. hermonthica using weighted gene co-expression network analysis (WGCNA).

COVID19 Diagnosis Using Chest X-rays and Transfer Learning.

A pandemic of respiratory illnesses from a novel coronavirus known as Sars-CoV-2 has swept across the globe since December of 2019. This is calling upon the research community including medical imaging to provide effective tools for use in combating this virus. Research in biomedical imaging of viral patients is already very active with machine learning models being created for diagnosing Sars-CoV-2 infections in patients using CT scans and chest x-rays.

Detecting Intra-Field Variation in Rice Yield With Unmanned Aerial Vehicle Imagery and Deep Learning.

Unmanned aerial vehicles (UAVs) equipped with multispectral sensors offer high spatial and temporal resolution imagery for monitoring crop stress at early stages of development. Analysis of UAV-derived data with advanced machine learning models could improve real-time management in agricultural systems, but guidance for this integration is currently limited. Here we compare two deep learning-based strategies for early warning detection of crop stress, using multitemporal imagery throughout the growing season to predict field-scale yield in irrigated rice in eastern Arkansas.

Engines of change: Transposable element mutation rates are high and variable within Daphnia magna.

Transposable elements (TEs) represent a major portion of most eukaryotic genomes, yet little is known about their mutation rates or how their activity is shaped by other evolutionary forces. Here, we compare short- and long-term patterns of genome-wide mutation accumulation (MA) of TEs among 9 genotypes from three populations of Daphnia magna from across a latitudinal gradient. While the overall proportion of the genome comprised of TEs is highly similar among genotypes from Finland, Germany, and Israel, populations are distinguishable based on patterns of insertion site polymorphism.

Physiological and ecological warnings that dodders pose an exigent threat to farmlands in Eastern Africa.

Invasive holoparasitic plants of the genus Cuscuta (dodder) threaten African ecosystems due to their rapid spread and attack on various host plant species. Most Cuscuta species cannot photosynthesize and hence rely on host plants for nourishment. After attachment through a peg-like organ called a haustorium, the parasites deprive hosts of water and nutrients, which negatively affects host growth and development.

Transfer learning with chest X-rays for ER patient classification.

One of the challenges with urgent evaluation of patients with acute respiratory distress syndrome (ARDS) in the emergency room (ER) is distinguishing between cardiac vs infectious etiologies for their pulmonary findings. We conducted a retrospective study with the collected data of 171 ER patients. ER patient classification for cardiac and infection causes was evaluated with clinical data and chest X-ray image data.

Seeds attached to refrigerated shipping containers represent a substantial risk of nonnative plant species introduction and establishment.

The initial processes for successful biological invasions are transport, introduction, and establishment. These can be directly influenced or completely avoided through activities that reduce the number and frequency of entering nonnative propagules. Economic and environmental benefits through preventative monitoring programs at early stages of invasion far outweigh the long-term costs associated with mitigating ecological and economic impacts once nonnative species establish and spread.

Genomics of natural history collections for understanding evolution in the wild.

A long-standing question in biology is how organisms change through time and space in response to their environment. This knowledge is of particular relevance to predicting how organisms might respond to future environmental changes caused by human-induced global change. Usually researchers make inferences about past events based on an understanding of current static genetic patterns, but these are limited in their capacity to inform on underlying past processes.

Genomic history and ecology of the geographic spread of rice.

Rice (Oryza sativa) is one of the world's most important food crops, and is comprised largely of japonica and indica subspecies. Here, we reconstruct the history of rice dispersal in Asia using whole-genome sequences of more than 1,400 landraces, coupled with geographic, environmental, archaeobotanical and paleoclimate data. Originating around 9,000 yr ago in the Yangtze Valley, rice diversified into temperate and tropical japonica rice during a global cooling event about 4,200 yr ago.

Genomics of sorghum local adaptation to a parasitic plant.

Host-parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop (L.

Exploring the Unmet Needs of Parents of Adolescent Girls with Heavy Menstrual Bleeding and Dysmenorrhea: A Qualitative Study.

Study Objective: To provide insight into the unmet needs of parents of adolescents with heavy menstrual bleeding or dysmenorrhea, in the context of their daughters' menstrual concerns.

Design: Qualitative interview study using semi-structured interviews.

Setting: Gynecology outpatient clinic at The Royal Children's Hospital, Melbourne, Australia.

Unmet Needs and Experiences of Adolescent Girls with Heavy Menstrual Bleeding and Dysmenorrhea: A Qualitative Study.

Study Objective: To identify and examine the key areas of need and explore the experiences of adolescent girls with heavy menstrual bleeding and/or dysmenorrhea.

Design And Setting: Qualitative interview study using semi-structured interviews. Gynaecology outpatient clinic at The Royal Children's Hospital, Melbourne, Australia.

Molecular signatures of host specificity linked to habitat specialization in sea anemones.

Rising ocean temperatures associated with global climate change induce breakdown of the symbiosis between coelenterates and photosynthetic microalgae of the genus . Association with more thermotolerant partners could contribute to resilience, but the genetic mechanisms controlling specificity of hosts for particular types are poorly known. Here, we characterize wild populations of a sea anemone laboratory model system for anthozoan symbiosis, from contrasting environments in Caribbean Panama.

Natural Variation in Responses to Acute Heat and Cold Stress in a Sea Anemone Model System for Coral Bleaching.

Rising ocean temperatures disrupt the symbiosis between corals and their microalgae, accelerating global decline of coral reef ecosystems. Because of the difficulty of performing laboratory experiments with corals, the sea anemone Aiptasia has emerged as an important model system for molecular studies of coral bleaching and symbiosis. Here, we investigate natural variation in bleaching responses among different genetic lineages of Aiptasia.

Genome-wide polymorphism and signatures of selection in the symbiotic sea anemone Aiptasia.

Background: Coral reef ecosystems are declining in response to global climate change and anthropogenic impacts. Yet patterns of standing genetic variation within cnidarian species, a major determinant of adaptive potential, are virtually unknown at genome-scale resolution. We explore patterns of genome-wide polymorphism and identify candidate loci under selection in the sea anemone Aiptasia, an important laboratory model system for studying the symbiosis between corals and dinoflagellate algae of the genus Symbiodinium.