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Journal of Animal Science Feb 2021Genetic strategies aimed at improving general immune competence (IC) have the potential to reduce the incidence and severity of disease in beef production systems, with...
Genetic strategies aimed at improving general immune competence (IC) have the potential to reduce the incidence and severity of disease in beef production systems, with resulting benefits of improved animal health and welfare and reduced reliance on antibiotics to prevent and treat disease. Implementation of such strategies first requires that methodologies be developed to phenotype animals for IC and demonstration that these phenotypes are associated with health outcomes. We have developed a methodology to identify IC phenotypes in beef steers during the yard weaning period, which is both practical to apply on-farm and does not restrict the future sale of tested animals. In the current study, a total of 838 Angus steers, previously IC phenotyped at weaning, were categorized as low (n = 98), average (n = 653), or high (n = 88) for the IC phenotype. Detailed health and productivity data were collected on all steers during feedlot finishing, and associations between IC phenotype, health outcomes, and productivity were investigated. A favorable association between IC phenotype and number of mortalities during feedlot finishing was observed with higher mortalities recorded in low IC steers (6.1%) as compared with average (1.2%, P < 0.001) or high (0%, P = 0.018) IC steers. Disease incidence was numerically highest in low IC steers (15.3 cases/100 animals) and similar in average IC steers (10.1 cases/100 animals) and high IC steers (10.2 cases/100 animals); however, differences between groups were not significant. No significant influence of IC phenotype on average daily gain was observed, suggesting that selection for improved IC is unlikely to incur a significant penalty to production. The potential economic benefits of selecting for IC in the feedlot production environment were calculated. Health-associated costs were calculated as the sum of lost production costs, lost capital investment costs, and disease treatment costs. Based on these calculations, health-associated costs were estimated at AUS$103/head in low IC steers, AUS$25/head in average IC steers, and AUS$4/head in high IC steers, respectively. These findings suggest that selection for IC has the potential to reduce mortalities during feedlot finishing and, as a consequence, improve the health and welfare of cattle in the feedlot production environment and reduce health-associated costs incurred by feedlot operators.
Topics: Animal Feed; Animals; Cattle; Diet; Phenotype; Weaning
PubMed: 33476384
DOI: 10.1093/jas/skab016 -
Current Opinion in Biotechnology Dec 2020Raman spectroscopy and chemometric analyses are used to characterize phenotypes of biological samples. The approach is relevant in biotechnology to identify and monitor... (Review)
Review
Raman spectroscopy and chemometric analyses are used to characterize phenotypes of biological samples. The approach is relevant in biotechnology to identify and monitor productive cell cultures. It can also detect the presence of pathogens in food products and screen for disease in clinical applications. Raman-based phenotyping is of interest because it is inexpensive, rapid, label-free, and is not obscured by water molecules. Here, recent applications in microbial species and tissue identification, isogenic cell/tissue phenotype changes, and characterizing biological fluids were surveyed along with the myriad spectral processing and chemometric analysis approaches. Suggestions are also given to help standardize and solidify Raman-based phenotyping as an -omics analysis method. These include offering repositories for raw spectral data and molecular assignment libraries.
Topics: Biotechnology; Cell Culture Techniques; Phenotype; Spectrum Analysis, Raman
PubMed: 33142112
DOI: 10.1016/j.copbio.2020.09.007 -
Current Protocols Dec 2023Individuals of European descent have historically been the focus of genetic studies and possess relatively homogenous genomes. As a result, analytical methods have been...
Individuals of European descent have historically been the focus of genetic studies and possess relatively homogenous genomes. As a result, analytical methods have been developed and optimized with such genomes in mind. African-descent and Latino individuals generally possess genomes of greater architectural complexity due to mosaic genomic ancestry, which can extensively and intricately impact phenotypic expression. As such, genetic analyses of admixed individuals require that genetic admixture be quantified to accurately model the impact of genetic variation on phenotypic expression. In this overview, we explore how fundamental genetic concepts such as linkage disequilibrium and differential allele frequency interact with genetic admixture to uniquely influence phenotypes in admixed individuals. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
Topics: Humans; Gene Frequency; Genetics, Population; Linkage Disequilibrium; Phenotype; Genome, Human
PubMed: 38146906
DOI: 10.1002/cpz1.953 -
Neuropsychopharmacology : Official... Jan 2021The broad adoption and use of smartphones has led to fundamentally new opportunities for capturing social, behavioral, and cognitive phenotypes in free-living settings,... (Review)
Review
The broad adoption and use of smartphones has led to fundamentally new opportunities for capturing social, behavioral, and cognitive phenotypes in free-living settings, outside of research laboratories and clinics. Predicated on the use of existing personal devices rather than the introduction of additional instrumentation, smartphone-based digital phenotyping presents us with several opportunities and challenges in data collection and data analysis. These two aspects are strongly coupled, because decisions about what data to collect and how to collect it constrain what statistical analyses can be carried out, now and years later, and therefore ultimately determine what scientific, clinical, and public health questions may be asked and answered. Digital phenotyping combines the excitement of fast-paced technologies, smartphones, cloud computing and machine learning, with deep mathematical and statistical questions, and it does this in the service of a better understanding our own behavior in ways that are objective, scalable, and reproducible. We will discuss some fundamental aspects of collection and analysis of digital phenotyping data, which takes us on a brief tour of several important scientific and technological concepts, from the open-source paradigm to computational complexity, with some unexpected insights provided by fields as varied as zoology and quantum mechanics.
Topics: Data Collection; Machine Learning; Phenotype; Research Design; Smartphone
PubMed: 32679583
DOI: 10.1038/s41386-020-0771-3 -
Molecular Systems Biology Jun 2020Pooled genetic screening is a powerful method to systematically link genotype to phenotype and gain insights into biological processes, but applying it to visual...
Pooled genetic screening is a powerful method to systematically link genotype to phenotype and gain insights into biological processes, but applying it to visual phenotypes such as cell morphology or protein localization has remained a challenge. In their recent work, Fowler and colleagues (Hasle et al, 2020) describe an elegant approach for high-throughput cell sorting according to visual phenotypes based on selective photoconversion. This allows combining the advantages of high-content phenotyping by fluorescence microscopy with the efficiency of pooled screening to dissect complex phenotypes.
Topics: Genotype; Microscopy, Fluorescence; Phenotype
PubMed: 32543109
DOI: 10.15252/msb.20209640 -
Journal of Forensic and Legal Medicine May 2022Forensic DNA Phenotyping (FDP) has provided better understanding of various phenotypic features (e.g., height, skin colour, eye colour, structure and shape of scalp... (Review)
Review
INTRODUCTION
Forensic DNA Phenotyping (FDP) has provided better understanding of various phenotypic features (e.g., height, skin colour, eye colour, structure and shape of scalp hair, baldness, facial features etc.) and associated genetic variations. The current study was designed to investigate the genetic variants and their potential contribution towards accurate phenotype prediction systems. Short Tandem Repeat (STR) based DNA typing method can be uninformative or with little potential to solve a crime in absence of suspect DNA profile in the database. Forensic DNA Phenotyping (FDP), prediction of externally visible characteristics (EVCs) from the crime scene DNA would certainly provide a new dimension to personal identification. The aim of this review paper is to highlight the significance and future prospects of FDP.
RESULTS
A comprehensive literature review was conducted using PubMed and similar e-databases with keywords from two main components-phenotype and the associated genetic variants. To ensure a thorough literature review, searches were extended using the snowballing technique from reference lists. Key data extracted were type of study, sample characteristics (sample size, age, geographical location and ancestry), details of SNPs studied and prediction accuracies.
CONCLUSION
Phenotyping tools based on genotyping and statistical analysis for the prediction of human pigmentation are propitious in solving cold cases. This indicates the inevitability of future studies for the identification of new genetic markers for accurate prediction of phenotype or EVCs via genome-wide association study (GWAS) in diverse global populations.
Topics: Crime; DNA; Forensic Genetics; Genome-Wide Association Study; Humans; Phenotype; Polymorphism, Single Nucleotide
PubMed: 35427851
DOI: 10.1016/j.jflm.2022.102351 -
Biologie Aujourd'hui 2020Phenotypic plasticity describes the ability of a given genotype to produce different phenotypes in response to distinct environmental conditions. It has major... (Review)
Review
Phenotypic plasticity describes the ability of a given genotype to produce different phenotypes in response to distinct environmental conditions. It has major implications in agronomy, animal husbandry and medicine and is also thought to facilitate evolution. Phenotypic plasticity is widely observed in the wild. It is only relatively recently that the mechanisms involved in phenotypic plasticity have been analysed. Thanks to laboratory experiments we understand better how environmental conditions are involved in phenotypic variations. This article introduces major concepts from the phenotypic plasticity field, presents briefly mechanisms involved in phenotypic plasticity and discusses the links between phenotypic plasticity and evolution.
Topics: Adaptation, Physiological; Animals; Biological Evolution; Gene-Environment Interaction; Genetic Variation; Humans; Phenotype; Temperature
PubMed: 32773027
DOI: 10.1051/jbio/2020004 -
The European Respiratory Journal Jul 2022Chronic lung allograft dysfunction (CLAD) is the principal cause of graft failure in lung transplant recipients and prognosis depends on CLAD phenotype. We used a...
BACKGROUND
Chronic lung allograft dysfunction (CLAD) is the principal cause of graft failure in lung transplant recipients and prognosis depends on CLAD phenotype. We used a machine learning computed tomography (CT) lung texture analysis tool at CLAD diagnosis for phenotyping and prognostication compared with radiologist scoring.
METHODS
This retrospective study included all adult first double lung transplant patients (January 2010-December 2015) with CLAD (censored December 2019) and inspiratory CT near CLAD diagnosis. The machine learning tool quantified ground-glass opacity, reticulation, hyperlucent lung and pulmonary vessel volume (PVV). Two radiologists scored for ground-glass opacity, reticulation, consolidation, pleural effusion, air trapping and bronchiectasis. Receiver operating characteristic curve analysis was used to evaluate the diagnostic performance of machine learning and radiologist for CLAD phenotype. Multivariable Cox proportional hazards regression analysis for allograft survival controlled for age, sex, native lung disease, cytomegalovirus serostatus and CLAD phenotype.
RESULTS
88 patients were included (57 bronchiolitis obliterans syndrome (BOS), 20 restrictive allograft syndrome (RAS)/mixed and 11 unclassified/undefined) with CT a median 9.5 days from CLAD onset. Radiologist and machine learning parameters phenotyped RAS/mixed with PVV as the strongest indicator (area under the curve (AUC) 0.85). Machine learning hyperlucent lung phenotyped BOS using only inspiratory CT (AUC 0.76). Radiologist and machine learning parameters predicted graft failure in the multivariable analysis, best with PVV (hazard ratio 1.23, 95% CI 1.05-1.44; p=0.01).
CONCLUSIONS
Machine learning discriminated between CLAD phenotypes on CT. Both radiologist and machine learning scoring were associated with graft failure, independent of CLAD phenotype. PVV, unique to machine learning, was the strongest in phenotyping and prognostication.
Topics: Allografts; Bronchiolitis Obliterans; Graft vs Host Disease; Humans; Lung; Lung Diseases; Lung Transplantation; Lung, Hyperlucent; Machine Learning; Phenotype; Primary Graft Dysfunction; Prognosis; Retrospective Studies; Risk Factors; Tomography, X-Ray Computed
PubMed: 34949699
DOI: 10.1183/13993003.01652-2021 -
Ecology Letters Apr 2023Heterogeneity among individuals in fitness components is what selection acts upon. Evolutionary theories predict that selection in constant environments acts against...
Heterogeneity among individuals in fitness components is what selection acts upon. Evolutionary theories predict that selection in constant environments acts against such heterogeneity. But observations reveal substantial non-genetic and also non-environmental variability in phenotypes. Here, we examine whether there is a relationship between selection pressure and phenotypic variability by analysing structured population models based on data from a large and diverse set of species. Our findings suggest that non-genetic, non-environmental variation is in general neither truly neutral, selected for, nor selected against. We find much variations among species and populations within species, with mean patterns suggesting nearly neutral evolution of life-course variability. Populations that show greater diversity of life courses do not show, in general, increased or decreased population growth rates. Our analysis suggests we are only at the beginning of understanding the evolution and maintenance of non-genetic non-environmental variation.
Topics: Biological Evolution; Adaptation, Physiological; Phenotype; Selection, Genetic
PubMed: 36756864
DOI: 10.1111/ele.14174 -
Nature Ecology & Evolution Oct 2022Organismal-grade multicellularity has been achieved only in animals, plants and fungi. All three kingdoms manifest phenotypically disparate body plans but their...
Organismal-grade multicellularity has been achieved only in animals, plants and fungi. All three kingdoms manifest phenotypically disparate body plans but their evolution has only been considered in detail for animals. Here we tested the general relevance of hypotheses on the evolutionary assembly of animal body plans by characterizing the evolution of fungal phenotypic variety (disparity). The distribution of living fungal form is defined by four distinct morphotypes: flagellated; zygomycetous; sac-bearing; and club-bearing. The discontinuity between morphotypes is a consequence of extinction, indicating that a complete record of fungal disparity would present a more homogeneous distribution of form. Fungal disparity expands episodically through time, punctuated by a sharp increase associated with the emergence of multicellular body plans. Simulations show these temporal trends to be non-random and at least partially shaped by hierarchical contingency. These trends are decoupled from changes in gene number, genome size and taxonomic diversity. Only differences in organismal complexity, characterized as the number of traits that constitute an organism, exhibit a meaningful relationship with fungal disparity. Both animals and fungi exhibit episodic increases in disparity through time, resulting in distributions of form made discontinuous by extinction. These congruences suggest a common mode of multicellular body plan evolution.
Topics: Animals; Biological Evolution; Fungi; Phenotype; Plants
PubMed: 35970862
DOI: 10.1038/s41559-022-01844-6