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1. High-throughput plant phenotyping: a role for metabolomics?

Author:
Robert D. Hall; John C. D’Auria; Antonio C. Silva Ferreira; Yves Gibon; Dariusz Kruszka; Puneet Mishra; Rick van de Zedde
Source:
Trends in plant science 2022 v.27 no.6 pp. 549-563
ISSN:
1360-1385
Subject:
genotype-phenotype correlation; phenotype,   etc   ; metabolites; metabolomics;     Show all 4 Subjects
Abstract:
... High-throughput (HTP) plant phenotyping approaches are developing rapidly and are already helping to bridge the genotype–phenotype gap. However, technologies should be developed beyond current physico-spectral evaluations to extend our analytical capacities to the subcellular level. Metabolites define and determine many key physiological and agronomic features in plants and an ability to integrate ...
DOI:
10.1016/j.tplants.2022.02.001

2. Evaluating biostimulants via high-throughput field phenotyping: Biophysical traits retrieval through PROSAIL inversion

Author:
Giulia Antonucci; Giorgio Impollonia; Michele Croci; Eleonora Potenza; Andrea Marcone; Stefano Amaducci
Source:
Smart agricultural technology 2023 v.3 pp. 100067
ISSN:
2772-3755
Subject:
phenotype,   etc   ; artificial intelligence; canopy; drought; industry; irrigation; model validation; radiative transfer; remote sensing; summer; tomatoes; uncertainty;     Show all 12 Subjects
Abstract:
... Drought management largely depends on the availability of timely, accurate and integrated information about its characteristics. Concurrently, biostimulants could represent a sustainable measure to foster the resilience of cropping systems under water-limited conditions. Nevertheless, scientific recognition of the potential of biostimulants has not grown as fast as the interest from industry: ther ...
DOI:
10.1016/j.atech.2022.100067

3. A deep learning method for oriented and small wheat spike detection (OSWSDet) in UAV images

Author:
Jianqing Zhao; Jiawei Yan; Tianjie Xue; Suwan Wang; Xiaolei Qiu; Xia Yao; Yongchao Tian; Yan Zhu; Weixing Cao; Xiaohu Zhang
Source:
Computers and electronics in agriculture 2022 v.198 pp. 107087
ISSN:
0168-1699
Subject:
phenotype,   etc   ; agriculture; electronics; wheat;     Show all 4 Subjects
Abstract:
... Detecting and characterizing spikes from wheat field images is essential in wheat growth monitoring for precision farming. Along with various technological developments, deep-learning-based methods have remarkably improved wheat spike detection performance. However, detecting small and overlapping wheat spikes in UAV images is still challenging because high spike occlusion and complex background c ...
DOI:
10.1016/j.compag.2022.107087

4. Adaptation to urban environments

Author:
Sarah E. Diamond; Eric G. Prileson; Ryan A. Martin
Source:
Current opinion in insect science 2022 v.51 no. pp. 100893
ISSN:
2214-5745
Subject:
phenotype,   etc   ; asymmetry; insects; urbanization;     Show all 4 Subjects
Abstract:
... Despite widespread evidence of urban evolution, the adaptive nature of these changes is often unclear. We review different phenotypic and molecular lines of evidence used for assessing urban adaptation, discussing the benefits and limitations of each approach, and rare examples of their integration. We then provide a synthesis of local adaptation to urban and rural environments. These data were dr ...
DOI:
10.1016/j.cois.2022.100893

5. Approaches to studying the developmental switch of Strongyloides – Moving beyond the dauer hypothesis

Author:
Mark Viney; Robert Morris
Source:
Molecular and biochemical parasitology 2022 v.249 pp. 111477
ISSN:
0166-6851
Subject:
phenotype,   etc   ; Strongyloides; genotype; parasitology;     Show all 4 Subjects
Abstract:
... Strongyloides’ developmental switch between direct, parasitic and indirect, free-living development has intrigued, confused, and fascinated biologists since it was first discovered more than 100 years ago. Proximately, the switch is controlled by environmental conditions that developing larvae are exposed to, but genotypes differ in their sensitivity to these cues. Ultimately, selection will act o ...
DOI:
10.1016/j.molbiopara.2022.111477

6. Recent trends and advances in hyperspectral imaging techniques to estimate solar induced fluorescence for plant phenotyping

Author:
P. Mangalraj; Byoung-Kwan Cho
Source:
Ecological indicators 2022 v.137 pp. 108721
ISSN:
1470-160X
Subject:
phenotype,   etc   ; ecosystems; fluorescence; vegetation;     Show all 4 Subjects
Abstract:
... Inevitable environmental changes empower the researchers to understand and analyze the plant traits for improving the ecosystem. Solar-induced fluorescence (SIF) is one of the functional traits to analyze the vegetation and assess plant phenotyping. Estimation of SIF through hyperspectral imaging technique gaining its popularity in the recent days than any other estimating techniques due to its co ...
DOI:
10.1016/j.ecolind.2022.108721

7. Segmentation of structural parts of rosebush plants with 3D point-based deep learning methods

Author:
Kaya Turgut; Helin Dutagaci; Gilles Galopin; David Rousseau
Source:
Plant methods 2022 v.18 no.1 pp. 20
ISSN:
1746-4811
Subject:
phenotype,   etc   ; data collection; geometry;     Show all 3 Subjects
Abstract:
... BACKGROUND: Segmentation of structural parts of 3D models of plants is an important step for plant phenotyping, especially for monitoring architectural and morphological traits. Current state-of-the art approaches rely on hand-crafted 3D local features for modeling geometric variations in plant structures. While recent advancements in deep learning on point clouds have the potential of extracting ...
DOI:
10.1186/s13007-022-00857-3

8. Stridulation is unimportant for effective parental care in two species of burying beetle

Author:
Matthew Schrader; Jack Galanek
Source:
Ecological entomology 2022 v.47 no.1 pp. 18-24
ISSN:
0307-6946
Subject:
phenotype,   etc   ; acoustics; entomology; stridulation;     Show all 4 Subjects
Abstract:
... 1. Communication among family members is often essential for navigating the social and trophic interactions that arise during parental care. In insects, this communication is often accomplished via pheromonal signals. However, some insects also produce acoustic signals (stridulations) during parental care. 2. Burying beetles (Nicrophorus spp) audibly stridulate during mating and parental care and ...
DOI:
10.1111/een.13086

9. Expanding Phenotype of Poirier–Bienvenu Syndrome: New Evidence from an Italian Multicentrical Cohort of Patients

Author:
Alessandro Orsini; Andrea Santangelo; Francesca Bravin; Alice Bonuccelli; Diego Peroni; Roberta Battini; Thomas Foiadelli; Veronica Bertini; Angelo Valetto; Michele Iacomino; Vincenzo Nigro; Anna Laura Torella; Marcello Scala; Valeria Capra; Maria Stella Vari; Anna Fetta; Veronica Di Pisa; Francesca Montanari; Roberta Epifanio; Paolo Bonanni; Roberto Giorda; Francesca Operto; Grazia Pastorino; Esra Sarigecili; Esra Sardaroglu; Cetin Okuyaz; Sevgan Bozdogan; Luciana Musante; Flavio Faletra; Caterina Zanus; Alessandro Ferretti; Federico Vigevano; Pasquale Striano; Duccio Maria Cordelli
Source:
Genes 2022 v.13 no.2 pp. -
ISSN:
2073-4425
Subject:
genotype-phenotype correlation; phenotype,   etc   ; epilepsy; genes; genetic analysis; heterozygosity; mutation; neurons; patients; retrospective studies; synaptic transmission;     Show all 11 Subjects
Abstract:
... Background: Poirier–Bienvenu Neurodevelopmental Syndrome (POBINDS) is a rare disease linked to mutations of the CSNK2B gene, which encodes for a subunit of caseinkinase CK2 involved in neuronal growth and synaptic transmission. Its main features include early-onset epilepsy and intellectual disability. Despite the lack of cases described, it appears that POBINDS could manifest with a wide range of ...
DOI:
10.3390/genes13020276

10. An integrative paleolimnological approach for studying evolutionary processes

Author:
Maria Cuenca-Cambronero; Colin J. Courtney-Mustaphi; Ryan Greenway; Oliver Heiri; Cameron M. Hudson; Leighton King; Kimberley D. Lemmen; Marvin Moosmann; Moritz Muschick; Nare Ngoepe; Ole Seehausen; Blake Matthews
Source:
Trends in ecology & evolution 2022 v.37 no.6 pp. 488-496
ISSN:
0169-5347
Subject:
phenotype,   etc   ; evolution; sediments; species diversity;     Show all 4 Subjects
Abstract:
... The field of paleolimnology has made tremendous progress in reconstructing past biotic and abiotic environmental conditions of aquatic ecosystems based on sediment records. This, together with the rapid development of molecular technologies, provides new opportunities for studying evolutionary processes affecting lacustrine communities over multicentennial to millennial timescales. From an evoluti ...
DOI:
10.1016/j.tree.2022.01.007

11. dCas9-mediated dysregulation of gene expression in human induced pluripotent stem cells during primitive streak differentiation

Author:
Viktor Haellman; Martin Pirkl; Arslan Akmammedov; Pratik Saxena; Niko Beerenwinkel; Renato Paro; Ana Palma Teixeira; Martin Fussenegger
Source:
Metabolic engineering 2022 v.73 pp. 70-81
ISSN:
1096-7176
Subject:
phenotype,   etc   ; epigenetics; genes; humans; transcriptomics;     Show all 5 Subjects
Abstract:
... CRISPR-based systems have fundamentally transformed our ability to study and manipulate stem cells. We explored the possibility of using catalytically dead Cas9 (dCas9) from S. pyogenes as a platform for targeted epigenetic editing in stem cells to enhance the expression of the eomesodermin gene (EOMES) during differentiation. We observed, however, that the dCas9 protein itself exerts a potential ...
DOI:
10.1016/j.ymben.2022.06.003

12. Bayesian optimization of multivariate genomic prediction models based on secondary traits for improved accuracy gains and phenotyping costs

Author:
Kosuke Hamazaki; Hiroyoshi Iwata
Source:
Theoretical and applied genetics 2022 v.135 no.1 pp. 35-50
ISSN:
0040-5752
Subject:
phenotype,   etc   ; Bayesian theory; genomics; models; prediction;     Show all 5 Subjects
Abstract:
... KEY MESSAGE: We propose a novel approach to the Bayesian optimization of multivariate genomic prediction models based on secondary traits to improve accuracy gains and phenotyping costs via efficient Pareto frontier estimation. Multivariate genomic prediction based on secondary traits, such as data from various omics technologies including high-throughput phenotyping (e.g., unmanned aerial vehicle ...
DOI:
10.1007/s00122-021-03949-1

13. Heterozygosity of the Complex Corfu δ0β+ Thalassemic Allele (HBD Deletion and HBB:c.92+5G>A) Revisited

Author:
Christos Kattamis; Myrto Skafida; Polyxeni Delaporta; Christina Vrettou; Joanne Traeger-Synodinos; Christalena Sofocleous; Antonis Kattamis
Source:
Biology 2022 v.11 no.3 pp. -
ISSN:
2079-7737
Subject:
phenotype,   etc   ; alleles; hemoglobin; heterozygosity; thalassemia; Greece;     Show all 6 Subjects
Abstract:
... The Corfu δ⁰β⁺ thalassemic allele is a unique thalassemic allele consisting of the simultaneous presence in cis of a deletion of the δ-globin (Hemoglobin Subunit Delta, HBD) and a single nucleotide variant in the β-globin gene (Hemoglobin Subunit Beta, HBB). The allele has, so far, been described in individuals of Greek origin. The objectives of the study are to ascertain the prevalence of the Cor ...
DOI:
10.3390/biology11030432

14. Metabolic interactions shape a community's phenotype

Author:
Chrats Melkonian; Michael F. Seidl; Justin J.J. van der Hooft; Marjon G.J. de Vos
Source:
Trends in microbiology 2022 pp. -
ISSN:
0966-842X
Subject:
phenotype,   etc   ; abiotic stress; auxotrophs; metabolism; microbiology;     Show all 5 Subjects
Abstract:
... Metabolic interactions between auxotrophs and prototrophs in microbial communities are understudied. Yu, Correia-Melo and colleagues showed how intra-cellular as well as inter-cellular metabolism affects community fitness in the absence and presence of abiotic stress, i.e., drugs. ...
DOI:
10.1016/j.tim.2022.05.001

15. A calculation method of phenotypic traits of soybean pods based on image processing technology

Author:
Haotian He; Xiaodan Ma; Haiou Guan
Source:
Ecological informatics 2022 v.69 pp. 101676
ISSN:
1574-9541
Subject:
phenotype,   etc   ; color; equations; leaves; rapid methods; soybeans;     Show all 6 Subjects
Abstract:
... As a homologous organ of the leaf, the pod is an essential factor in determining the yield and quality of the grain. The physiological and ecological characteristics of pods are a critical basis for soybean breeding and yield estimation. In order to avoid time-consuming and laborious problems in the traditional manual measurement process, a fast calculation method of pod's phenotypic traits was pr ...
DOI:
10.1016/j.ecoinf.2022.101676

16. A frameshift deletion in the GDF9 gene in Icelandic Loa prolific sheep

Author:
Lars‐Erik Holm; Christian Bendixen; Emma Eythorsdottir; Jon H. Hallsson
Source:
Animal genetics 2022 v.53 no.2 pp. 220-223
ISSN:
0268-9146
Subject:
phenotype,   etc   ; Loa; animal genetics; genes; mutation; progeny;     Show all 6 Subjects
Abstract:
... Several genetic variants have been shown to affect the mean number of offspring in different sheep breeds. Here, we analyzed samples from Icelandic sheep with the aim of identifying the genetic cause of the Icelandic Loa phenotype using three previously identified prolificacy genes as candidates. We demonstrate that a 4‐bp frameshift deletion positioned in the mature region of the GDF9 protein in ...
DOI:
10.1111/age.13168

17. Evolutionary bet‐hedging reconsidered: What is the mean–variance trade‐off of fitness?

Author:
Yukio Yasui
Source:
Ecological research 2022 v.37 no.3 pp. 406-420
ISSN:
0912-3814
Subject:
phenotype,   etc   ; computers; extinction; genotype; population size; variance;     Show all 6 Subjects
Abstract:
... In traditional theories, bet‐hedging in evolutionary biology is defined as a trade‐off between the within‐generation arithmetic mean fitness (AMF) of a genotype and between‐generation variance (BGV) in AMF across generations. The rationale of this definition is that a bet‐hedger genotype suppresses the BGV to increase between‐generation geometric mean fitness (GMF; an index of long‐term sustainabi ...
DOI:
10.1111/1440-1703.12303

18. Extracellular vesicles as an alternative copper-secretion mechanism in bacteria

Author:
Steeve Lima; Jorge Matinha-Cardoso; Joaquín Giner-Lamia; Narciso Couto; Catarina C. Pacheco; Francisco J. Florencio; Phillip C. Wright; Paula Tamagnini; Paulo Oliveira
Source:
Journal of hazardous materials 2022 v.431 pp. 128594
ISSN:
0304-3894
Subject:
phenotype,   etc   ; copper; evolution; homeostasis; metal tolerance; metallochaperones;     Show all 6 Subjects
Abstract:
... Metal homeostasis is fundamental for optimal performance of cell metabolic pathways. Over the course of evolution, several systems emerged to warrant an intracellular metal equilibrium. When exposed to growth-challenging copper concentrations, Gram-negative bacteria quickly activate copper-detoxification mechanisms, dependent on transmembrane-protein complexes and metallochaperones that mediate me ...
DOI:
10.1016/j.jhazmat.2022.128594

19. Foraging behavior plasticity in antlion larvae Myrmeleon brasiliensis (Neuroptera, Myrmeleontidae)

Author:
Alfredo Raúl Abot; Edihanne Gamarra Arguelho; Tatiane do Nascimento Lima
Source:
International journal of tropical insect science 2022 v.42 no.1 pp. 591-595
ISSN:
1742-7592
Subject:
phenotype,   etc   ; Myrmeleon; ecosystems; insects; phenotypic plasticity; reproduction;     Show all 6 Subjects
Abstract:
... The biotic and abiotic factors of an ecosystem exert an influence on the behavior and survival of organisms, which adapt to changes in these factors to ensure their reproduction and survival. Phenotypic plasticity regards any type of change induced by the environment without the need for genetic modifications. The aim of the present study was to evaluate whether the investment of the antlion, Myrm ...
DOI:
10.1007/s42690-021-00577-6

20. Genomic perspectives on epigenetics

Author:
Jung-Shin Lee; Nam-Soo Kim
Source:
Genes & genomics 2022 v.44 no.3 pp. 247-249
ISSN:
1976-9571
Subject:
phenotype,   etc   ; epigenetics; genomics; intergenic DNA; molecular biology;     Show all 5 Subjects
Abstract:
... For much of the twentieth century, it was accepted that genes dictate phenotypes. Nevertheless, genetics in combination with molecular biology and genomics has facilitated the explanation of some peculiar molecular phenomena. Most eukaryotic genomes are crammed with noncoding DNA, which was previously hypothesized to be selfish DNA, with only a small fraction of sequences encoding proteins. We now ...
DOI:
10.1007/s13258-022-01225-0