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1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens

Author:
Daley, Timothy P.; Lin, Zhixiang; Lin, Xueqiu; Liu, Yanxia; Wong, Wing Hung; Qi, Lei S.
Source:
Genome biology 2018 v.19 no.1 pp. 159
ISSN:
1474-760X
Subject:
phenotype,   etc   ; gene editing; models;     Show all 3 Subjects
Abstract:
... Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortunately, two problems exist, particularly for CRISPRi/a screens: variability in guide efficiency and large rare off-target effects. We present a method, CRISPhieRmix, that resolves these issues ...
DOI:
10.1186/s13059-018-1538-6

13. Using Morphology to Test DNA-Based Phylogenetic Relationships within the Guiana Shield Catfish Tribe Lithoxini (Siluriformes: Loricariidae)

Author:
Armbruster, Jonathan W.; Greene, Lauren; Lujan, Nathan K.
Source:
Copeia 2018 v.106 no.4 pp. 671-680
ISSN:
0045-8511
Subject:
phenotype,   etc   ; Loricariidae; catfish; synapomorphy;     Show all 4 Subjects
Abstract:
... As DNA-based phylogenetic analyses have exploded, historically phenotype-based evolutionary hypotheses throughout the tree of life have been rewritten. However, rarely are DNA-based phylogenetic hypotheses tested via the reanalysis of phenotypic data. Skeletons representing all four recognized genera of the Guiana Shield endemic suckermouth armored catfish clade Lithoxini were examined to test a r ...
DOI:
10.1643/CI-18-121

14. Engineered basement membranes: from in vivo considerations to cell-based assays

Author:
Perry, Guillaume; Xiao, Wenjin; Welsh, Gavin I.; Perriman, Adam W.; Lennon, Rachel
Source:
Integrative biology 2018 v.10 no.11 pp. 680-695
ISSN:
1757-9708
Subject:
phenotype,   etc   ; drugs; screening;     Show all 3 Subjects
Abstract:
... Improvements in the physiological relevance of cell-based assays have been enabled by the development of various interdisciplinary methods. However, due to their complexity, in vivo structures such as basement membranes (BMs), which regulate the phenotype of adherent cells, are still difficult to mimic in vitro. The reconstruction of a physiologically relevant BM is crucially important to develop ...
DOI:
10.1039/c8ib00138c

15. Microbiome: Focus on Causation and Mechanism

Author:
Fischbach, Michael A.
Source:
Cell 2018 v.174 no.4 pp. 785-790
ISSN:
0092-8674
Subject:
phenotype,   etc   ; industry; microbiome; microorganisms;     Show all 4 Subjects
Abstract:
... There is tremendous enthusiasm for the microbiome in academia and industry. This Perspective argues that in order to realize its potential, the field needs to focus on establishing causation and molecular mechanism with an emphasis on phenotypes that are large in magnitude, easy to measure, and unambiguously driven by the microbiota. ...
DOI:
10.1016/j.cell.2018.07.038

16. Are females in good condition better able to cope with costly males?

Author:
Iglesias-Carrasco, Maider; Jennions, Michael D; Zajitschek, Susanne R K; Head, Megan L
Source:
Behavioral ecology 2018 v.29 no.4 pp. 876-884
ISSN:
1465-7279
Subject:
phenotype,   etc   ; copulation; females; males;     Show all 4 Subjects
Abstract:
... The net gains females obtain from mating might depend on both her phenotype and that of her mate. We manipulated male and female conditions to determine their effects on mating behavior and fitness. Females mated with males in better condition started dislodging males sooner and had shorter copulations than females mated to poor condition males. However, there was no detectable fitness cost to fem ...
DOI:
10.1093/beheco/ary059

17. Bidirectionality of hormone-behavior relationships and satellite-caller dynamics in green treefrogs

Author:
Crocker-Buta, Sarah P; Leary, Christopher J
Source:
Behavioral ecology 2018 v.29 no.4 pp. 948-957
ISSN:
1465-7279
Subject:
phenotype,   etc   ; Hylidae; mating behavior;     Show all 3 Subjects
Abstract:
... Interpretation of hormonal disparities among alternative mating phenotypes is confounded by the bidirectionality of hormone–behavior relationships. We show that size, condition, and vocal attractiveness predicted mating tactic switches during vocal playback experiments in green treefrogs, but hormone level did not, even though hormone administration has been shown to cause changes in tactic expres ...
DOI:
10.1093/beheco/ary047

18. Evaluation of the chitin-binding dye Congo red as a selection agent for the isolation, classification, and enumeration of ascomycete yeasts

Author:
Linder, Tomas
Source:
Archives of microbiology 2018 v.200 no.4 pp. 671-675
ISSN:
0302-8933
Subject:
phenotype,   etc   ; Ascomycota; dyes; yeasts;     Show all 4 Subjects
Abstract:
... Thirty-nine strains of ascomycete yeasts representing 35 species and 33 genera were tested for their ability to grow on solid agar medium containing increasing concentrations of the chitin-binding dye Congo red. Six strains were classified as hypersensitive (weak or no growth at 10 mg/l Congo red), five were moderately sensitive (weak or no growth at 50 mg/l), three were moderately tolerant (weak ...
DOI:
10.1007/s00203-018-1498-y

19. The emerging roles for the chromatin structure regulators CTCF and cohesin in neurodevelopment and behavior

Author:
Davis, Liron; Onn, Itay; Elliott, Evan
Source:
Cellular and molecular life sciences 2018 v.75 no.7 pp. 1205-1214
ISSN:
1420-682X
Subject:
phenotype,   etc   ; chromatin; humans; neurodevelopment;     Show all 4 Subjects
Abstract:
... Recent genetic and technological advances have determined a role for chromatin structure in neurodevelopment. In particular, compounding evidence has established roles for CTCF and cohesin, two elements that are central in the establishment of chromatin structure, in proper neurodevelopment and in regulation of behavior. Genetic aberrations in CTCF, and in subunits of the cohesin complex, have bee ...
DOI:
10.1007/s00018-017-2706-7

20. Degradation of endogenous proteins and generation of a null-like phenotype in zebrafish using Trim-Away technology

Author:
Chen, Xiao; Liu, Mi; Lou, Hongyan; Lu, Yiyi; Zhou, Meng-Tao; Ou, Rongying; Xu, Yunsheng; Tang, Kai-Fu
Source:
Genome biology 2019 v.20 no.1 pp. 19
ISSN:
1474-760X
Subject:
phenotype,   etc   ; Danio rerio; antibodies; embryo (animal); embryogenesis; models; proteins;     Show all 7 Subjects
Abstract:
... Trim-Away is a recent technique to rapidly deplete a protein from any cell type. Guided by antibodies, TRIM21 selects proteins for destruction. However, the applicability of this method in model organisms has not been investigated. Here, we show that Trim-Away can degrade proteins in zebrafish embryos. Trim-Away depletes proteins faster than morpholinos, which enables analysis of protein function ...
DOI:
10.1186/s13059-019-1624-4