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1. An integrative U method for joint analysis of multi-level omic data

Author:
Geng, Pei; Tong, Xiaoran; Lu, Qing
Source:
BMC genetics 2019 v.20 no.1 pp. 40
ISSN:
1471-2156
Subject:
phenotype,   etc   ; cost effectiveness; models; variance;     Show all 4 Subjects
Abstract:
... BACKGROUND: The advance of high-throughput technologies has made it cost-effective to collect diverse types of omic data in large-scale clinical and biological studies. While the collection of the vast amounts of multi-level omic data from these studies provides a great opportunity for genetic research, the high dimensionality of omic data and complex relationships among multi-level omic data brin ...
DOI:
10.1186/s12863-019-0742-z

2. On titles and royalty: a terminological discussion over castes in myrmecology

Author:
Silva, T. S. R.; Feitosa, R. M.
Source:
Insectes sociaux 2019 v.66 no.1 pp. 25-35
ISSN:
0020-1812
Subject:
phenotype,   etc   ; Formicidae; social insects; terminology;     Show all 4 Subjects
Abstract:
... Our knowledge of the processes related to the expression of distinct phenotypes in ants has significantly increased in the past few years. However, myrmecologists still face significant difficulties while addressing distinct patterns related to reproductive biology in ants. In the present work, we provide a theoretical discussion on the current limitations found in the process of caste representat ...
DOI:
10.1007/s00040-018-0672-1

3. The Concept of Ontogenesis Polyvariance and Modern Evolutionary Morphology

Author:
Notov, A. A.; Zhukova, L. A.
Source:
Biology bulletin of the Russian Academy of Sciences 2019 v.46 no.1 pp. 47-55
ISSN:
1062-3590
Subject:
phenotype,   etc   ; mathematics and statistics; ontogeny;     Show all 3 Subjects
Abstract:
... The possibilities of using the concept of ontogeny polyvariance in evolutionary morphology are considered. The concept is aimed at identifying the full range of options associated with various aspects concerning the organization of living organisms. In conjunction with the analysis of the correlation structure of traits and methods of population meronomy, the proposed approach can help to elucidat ...
DOI:
10.1134/S1062359019010072

4. In search of nutritional anti-aging targets: TOR inhibitors, SASP modulators, and BCL-2 family suppressors

Author:
Sharma, Rohit; Padwad, Yogendra
Source:
Nutrition 2019 v.65 pp. 33-38
ISSN:
0899-9007
Subject:
phenotype,   etc   ; apoptosis; functional foods; nutritional intervention; rapamycin;     Show all 5 Subjects
Abstract:
... In pursuit of developing anti-aging or age-delaying strategies, nutritional interventions have long been considered promising candidates. However, emerging advances in the understanding of the causes and effects of senescence per se have enhanced the prospects of a more focused approach in the exploration of therapies aimed at the modulation of aging. The aim of this study was to review recent dev ...
DOI:
10.1016/j.nut.2019.01.020

5. Host, Symbionts, and the Microbiome: The Missing Tripartite Interaction

Author:
Brinker, Pina; Fontaine, Michael C.; Beukeboom, Leo W.; Falcao Salles, Joana
Source:
Trends in microbiology 2019 v.27 no.6 pp. 480-488
ISSN:
0966-842X
Subject:
phenotype,   etc   ; Wolbachia; endosymbionts; microbiome; microorganisms; symbiosis;     Show all 6 Subjects
Abstract:
... Symbiosis between microbial associates and a host is a ubiquitous feature of life on earth, modulating host phenotypes. In addition to endosymbionts, organisms harbour a collection of host-associated microbes, the microbiome that can impact important host traits. In this opinion article we argue that the mutual influences of the microbiome and endosymbionts, as well as their combined influence on ...
DOI:
10.1016/j.tim.2019.02.002

6. Cell Form and Function: Interpreting and Controlling the Shape of Adherent Cells

Author:
Prasad, Ashok; Alizadeh, Elaheh
Source:
Trends in biotechnology 2019 v.37 no.4 pp. 347-357
ISSN:
0167-7799
Subject:
phenotype,   etc   ; cell biology; engineering; human health; surveys;     Show all 5 Subjects
Abstract:
... Beautiful images of animal cells cultured on surfaces are ubiquitous in biological research, but these shapes also carry valuable information about the cells and the organism that they came from. Cell morphology is an emergent property of the cellular phenotype as well as of the physiological and signaling state of the cell. Many functional changes in cells cause stereotypical changes in cellular ...
DOI:
10.1016/j.tibtech.2018.09.007

7. Habitat choice stabilizes metapopulation dynamics by enabling ecological specialization

Author:
Mortier, Frederik; Jacob, Staffan; Vandegehuchte, Martijn L.; Bonte, Dries
Source:
Oikos 2019 v.128 no.4 pp. 529-539
ISSN:
0030-1299
Subject:
phenotype,   etc   ; genes; habitats; models; population dynamics;     Show all 5 Subjects
Abstract:
... Dispersal is a key trait responsible for the spread of individuals and genes among local populations, thereby generating eco‐evolutionary interactions. Especially in heterogeneous metapopulations, a tight coupling between dispersal, population dynamics and the evolution of local adaptation is expected. In this respect, dispersal should counteract ecological specialization by redistributing locally ...
DOI:
10.1111/oik.05885

8. Indirect effects on fitness between individuals that have never met via an extended phenotype

Author:
Fisher, David N.; Haines, Jessica A.; Boutin, Stan; Dantzer, Ben; Lane, Jeffrey E.; Coltman, David W.; McAdam, Andrew G.
Source:
Ecology letters 2019 v.22 no.4 pp. 697-706
ISSN:
1461-023X
Subject:
phenotype,   etc   ; Tamiasciurus hudsonicus; males; population dynamics; squirrels;     Show all 5 Subjects
Abstract:
... Interactions between organisms are ubiquitous and have important consequences for phenotypes and fitness. Individuals can even influence those they never meet, if they have extended phenotypes that alter the environments others experience. North American red squirrels (Tamiasciurus hudsonicus) guard food hoards, an extended phenotype that typically outlives the individual and is usually subsequent ...
DOI:
10.1111/ele.13230

9. Interactions in the ESCRT-III network of the yeast Saccharomyces cerevisiae

Author:
Brune, Thomas; Kunze-Schumacher, Heike; Kölling, Ralf
Source:
Current genetics 2019 v.65 no.2 pp. 607-619
ISSN:
0172-8083
Subject:
phenotype,   etc   ; Saccharomyces cerevisiae; mutation; prediction; proteins; yeasts;     Show all 6 Subjects
Abstract:
... Here, we examine the genetic interactions between ESCRT-III mutations in the yeast Saccharomyces cerevisiae. From the obtained interaction network, we make predictions about alternative ESCRT-III complexes. By the successful generation of an octuple deletion strain using the CRISPR/Cas9 technique, we demonstrate for the first time that ESCRT-III activity as a whole is not essential for the life of ...
DOI:
10.1007/s00294-018-0915-8

10. The measurement of coevolution in the wild

Author:
Week, Bob; Nuismer, Scott L.
Source:
Ecology letters 2019 v.22 no.4 pp. 717-725
ISSN:
1461-023X
Subject:
phenotype,   etc   ; coevolution; models; sexual reproduction; statistical analysis;     Show all 5 Subjects
Abstract:
... Coevolution has long been thought to drive the exaggeration of traits, promote major evolutionary transitions such as the evolution of sexual reproduction and influence epidemiological dynamics. Despite coevolution’s long suspected importance, we have yet to develop a quantitative understanding of its strength and prevalence because we lack generally applicable statistical methods that yield numer ...
DOI:
10.1111/ele.13231

11. The Genetic Basis of Metabolic Disease

Author:
Barroso, Inês; McCarthy, Mark I.
Source:
Cell 2019 v.177 no.1 pp. 146-161
ISSN:
0092-8674
Subject:
phenotype,   etc   ; genome; genomics; loci; metabolic diseases;     Show all 5 Subjects
Abstract:
... Recent developments in genetics and genomics are providing a detailed and systematic characterization of the genetic underpinnings of common metabolic diseases and traits, highlighting the inherent complexity within systems for homeostatic control and the many ways in which that control can fail. The genetic architecture underlying these common metabolic phenotypes is complex, with each trait infl ...
DOI:
10.1016/j.cell.2019.02.024

12. The role of αβ T-cells in spontaneous regression of melanoma tumors in swine

Author:
Cizkova, Jana; Sinkorova, Zuzana; Strnadova, Kristyna; Cervinkova, Monika; Horak, Vratislav; Sinkora, Jiri; Stepanova, Katerina; Sinkora, Marek
Source:
Developmental and comparative immunology 2019 v.92 pp. 60-68
ISSN:
0145-305X
Subject:
phenotype,   etc   ; T-lymphocytes; loci; melanoma; models; swine;     Show all 6 Subjects
Abstract:
... Using a porcine model, we describe Melanoma-Associated CD4+CD8hi T-lymphocytes (MATL) in peripheral blood that increase during melanoma regression. These MATL possess the CD4+CD8hi phenotype and they have their direct counterparts in Tumor Infiltrating Lymphocytes (TIL) isolated from melanoma loci. Both MATL and CD4+CD8hi TIL have a similar expression of selected markers indicating that they repre ...
DOI:
10.1016/j.dci.2018.10.001

13. C4 anatomy can evolve via a single developmental change

Author:
Lundgren, Marjorie R.; Dunning, Luke T.; Olofsson, Jill K.; Moreno‐Villena, Jose J.; Bouvier, Jacques W.; Sage, Tammy L.; Khoshravesh, Roxana; Sultmanis, Stefanie; Stata, Matt; Ripley, Brad S.; Vorontsova, Maria S.; Besnard, Guillaume; Adams, Claire; Cuff, Nicholas; Mapaura, Anthony; Bianconi, Matheus E.; Long, Christine M.; Christin, Pascal‐Antoine; Osborne, Colin P.
Source:
Ecology letters 2019 v.22 no.2 pp. 302-312
ISSN:
1461-023X
Subject:
phenotype,   etc   ; Alloteropsis; C4 photosynthesis; grasses; leaves;     Show all 5 Subjects
Abstract:
... C₄ photosynthesis is a complex trait that boosts productivity in warm environments. Paradoxically, it evolved independently in numerous plant lineages, despite requiring specialised leaf anatomy. The anatomical modifications underlying C₄ evolution have previously been evaluated through interspecific comparisons, which capture numerous changes besides those needed for C₄ functionality. Here, we qu ...
DOI:
10.1111/ele.13191

14. Sharing the Right Data Right: A Symbiosis with Machine Learning

Author:
Tsaftaris, Sotirios A.; Scharr, Hanno
Source:
Trends in plant science 2019 v.24 no.2 pp. 99-102
ISSN:
1360-1385
Subject:
phenotype,   etc   ; artificial intelligence; data collection; symbiosis;     Show all 4 Subjects
Abstract:
... In 2014 plant phenotyping research was not benefiting from the machine learning (ML) revolution because appropriate data were lacking. We report the success of the first open-access dataset suitable for ML in image-based plant phenotyping suitable for machine learning, fuelling a true interdisciplinary symbiosis, increased awareness, and steep performance improvements on key phenotyping tasks. ...
DOI:
10.1016/j.tplants.2018.10.016

15. Characterization of Pleurotus djamor neohaplonts recovered by production of protoplasts and chemical dedikaryotization

Author:
Hernández, Abraham Sánchez; Valenzuela Cobos, Juan Diego; Martínez, Joel Herrera; Arce, Ramón Villanueva; de las Mercedes Gómez y Gomez, Yolanda; Segura, Paola Berenice Zarate; Aguilar, María Eugenia Garín; Lara, Hermilo Leal; del Toro, Gustavo Valencia
Source:
3 Biotech 2019 v.9 no.1 pp. 24
ISSN:
2190-572X
Subject:
phenotype,   etc   ; Pleurotus djamor; hybrids; microsatellite repeats; protoplasts;     Show all 5 Subjects
Abstract:
... Production of hybrid strains is accomplished by mating monosporic isolates or neohaplonts, obtained either by chemical dedikaryotization or by production of protoplast. However, differences in growth rate among recovered neohaplonts have been reported. The presence of phenotypic and genetic changes among the neohaplonts recovered either by chemical dedikaryotization or by production of protoplast, ...
DOI:
10.1007/s13205-018-1532-4

16. Evolutionary and ecological functional genomics, from lab to the wild

Author:
Zaidem, Maricris L.; Groen, Simon C.; Purugganan, Michael D.
Source:
Theplant journal 2019 v.97 no.1 pp. 40-55
ISSN:
0960-7412
Subject:
phenotype,   etc   ; genomics; phenotypic variation; plant response;     Show all 4 Subjects
Abstract:
... Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutiona ...
DOI:
10.1111/tpj.14167

17. Evolution in the light of fitness landscape theory

Author:
Fragata, Inês; Blanckaert, Alexandre; Dias Louro, Marco António; Liberles, David A.; Bank, Claudia
Source:
Trends in ecology & evolution 2019 v.34 no.1 pp. 69-82
ISSN:
0169-5347
Subject:
phenotype,   etc   ; evolution; genotype; models; molecular biology;     Show all 5 Subjects
Abstract:
... By formalizing the relationship between genotype or phenotype and fitness, fitness landscapes harbor information on molecular and evolutionary constraints. The shape of the fitness landscape determines the potential for adaptation and speciation, as well as our ability to predict evolution. Consequently, fitness landscape theory has been invoked across the natural sciences and across multiple leve ...
DOI:
10.1016/j.tree.2018.10.009

18. Exploring the Diversity of Plant Metabolism

Author:
Fang, Chuanying; Fernie, Alisdair R.; Luo, Jie
Source:
Trends in plant science 2019 v.24 no.1 pp. 83-98
ISSN:
1360-1385
Subject:
phenotype,   etc   ; domestication; evolution; genetic variation; metabolism; metabolites;     Show all 6 Subjects
Abstract:
... Plants produce a huge array of metabolites, far more than those produced by most other organisms. Unraveling this diversity and its underlying genetic variation has attracted increasing research attention. Post-genomic profiling platforms have enabled the marriage and mining of the enormous amount of phenotypic and genetic diversity. We review here achievements to date and challenges remaining tha ...
DOI:
10.1016/j.tplants.2018.09.006

19. Analysis of the Phenotypes in the Rett Networked Database

Author:
Frullanti, Elisa; Papa, Filomena T.; Grillo, Elisa; Clarke, Angus; Ben-Zeev, Bruria; Pineda, Mercedes; Bahi-Buisson, Nadia; Bienvenu, Thierry; Armstrong, Judith; Roche Martinez, Ana; Mari, Francesca; Nissenkorn, Andreea; Lo Rizzo, Caterina; Veneselli, Edvige; Russo, Silvia; Vignoli, Aglaia; Pini, Giorgio; Djuric, Milena; Bisgaard, Anne-Marie; Ravn, Kirstine; Bosnjak, Vlatka Mejaski; Hayek, Joussef; Khajuria, Rajni; Montomoli, Barbara; Cogliati, Francesca; Pintaudi, Maria; Hadzsiev, Kinga; Craiu, Dana; Voinova, Victoria; Djukic, Aleksandra; Villard, Laurent; Renieri, Alessandra
Source:
International Journal of Genomics 2019 v.2019
ISSN:
2314-4378
Subject:
genotype-phenotype correlation; phenotype,   etc   ; clinical trials; databases; females; genes; mutation; nervous system diseases; patients;     Show all 9 Subjects
Abstract:
... Rett spectrum disorder is a progressive neurological disease and the most common genetic cause of intellectual disability in females. MECP2 is the major causative gene. In addition, CDKL5 and FOXG1 mutations have been reported in Rett patients, especially with the atypical presentation. Each gene and different mutations within each gene contribute to variability in clinical presentation, and sever ...
DOI:
10.1155/2019/6956934

20. Identification of a novel mutation in FBN1 in a Chinese family with inherited ectopia lentis by targeted NGS

Author:
Cao, Danmin; Xu, Zequan; Gu, Shuyan; Li, Kai; Bao, Xianyi; Zhou, Yanli; Yin, Dan; Chen, Jianjun; Wang, Yong
Source:
Gene 2019 v.689 pp. 51-55
ISSN:
0378-1119
Subject:
genotype-phenotype correlation; phenotype,   etc   ; clinical examination; high-throughput nucleotide sequencing; inheritance (genetics); mutation;     Show all 6 Subjects
Abstract:
... To diagnose a Chinese family with inherited ectopia lentis in a genetic method and analyze the genotype-phenotype correlation.The phenotype of each family member was identified by detailed clinical examination. We used targeted next generation sequencing (NGS) to identify mutations in FBN1 in an efficient and accurate way. The mutation in FBN1 was confirmed in all affected family members by Sanger ...
DOI:
10.1016/j.gene.2018.12.005