scholarly journals Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion

2020 ◽  
Vol 12 (9) ◽  
pp. 1616-1622
Author(s):  
Susan A Smith ◽  
Xyrus X Maurer-Alcalá ◽  
Ying Yan ◽  
Laura A Katz ◽  
Luciana F Santoferrara ◽  
...  
Keyword(s):  
Single Cell ◽  
Functional Annotation ◽  
Trophic Ecology ◽  
Genome Architecture ◽  
Ecological Research ◽  
Model Species ◽  
Dna Elimination ◽  
Genomic Biology ◽  
Transcriptome Resource ◽  
And Inversion

Abstract Schmidingerella arcuata is an ecologically important tintinnid ciliate that has long served as a model species in plankton trophic ecology. We present a partial micronuclear genome and macronuclear transcriptome resource for S. arcuata, acquired using single-cell techniques, and we report on pilot analyses including functional annotation and genome architecture. Our analysis shows major fragmentation, elimination, and scrambling in the micronuclear genome of S. arcuata. This work introduces a new nonmodel genome resource for the study of ciliate ecology and genomic biology and provides a detailed functional counterpart to ecological research on S. arcuata.

scholarly journals Automatic Gene Function Prediction in the 2020’s

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1264
Author(s):  
Stavros Makrodimitris ◽  
Roeland C. H. J. van Ham ◽  
Marcel J. T. Reinders
Keyword(s):  
Functional Annotation ◽  
Protein Sequences ◽  
Research Area ◽  
Function Prediction ◽  
Research Field ◽  
Model Species ◽  
Large Step ◽  
Gene Functions ◽  
Performance Gains ◽  
The Way

The current rate at which new DNA and protein sequences are being generated is too fast to experimentally discover the functions of those sequences, emphasizing the need for accurate Automatic Function Prediction (AFP) methods. AFP has been an active and growing research field for decades and has made considerable progress in that time. However, it is certainly not solved. In this paper, we describe challenges that the AFP field still has to overcome in the future to increase its applicability. The challenges we consider are how to: (1) include condition-specific functional annotation, (2) predict functions for non-model species, (3) include new informative data sources, (4) deal with the biases of Gene Ontology (GO) annotations, and (5) maximally exploit the GO to obtain performance gains. We also provide recommendations for addressing those challenges, by adapting (1) the way we represent proteins and genes, (2) the way we represent gene functions, and (3) the algorithms that perform the prediction from gene to function. Together, we show that AFP is still a vibrant research area that can benefit from continuing advances in machine learning with which AFP in the 2020s can again take a large step forward reinforcing the power of computational biology.

scholarly journals Combining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell

2018 ◽  
Vol 13 (5) ◽  
pp. 1034-1061 ◽  
Author(s):  
David Lando ◽  
Srinjan Basu ◽  
Tim J Stevens ◽  
Andy Riddell ◽  
Kai J Wohlfahrt ◽  
...  
Keyword(s):  
Single Cell ◽  
Fluorescence Imaging ◽  
Genome Architecture ◽  
3D Genome

scholarly journals Phenotyping single-cell motility in microfluidic confinement

2021 ◽  
Author(s):  
Samuel A Bentley ◽  
Vasileios Anagnostidis ◽  
Hannah Laeverenz Schlogelhofer ◽  
Fabrice Gielen ◽  
Kirsty Y Wan
Keyword(s):  
Single Cell ◽  
Genetic Basis ◽  
Marine Alga ◽  
Reaction Network ◽  
Droplet Microfluidics ◽  
Model Species ◽  
Active Systems ◽  
Locomotor Behaviour ◽  
Cellular Excitability ◽  
First Time

At all scales, the movement patterns of organisms serve as dynamic read-outs of their behaviour and physiology. We devised a novel droplet microfluidics assay to encapsulate single algal microswimmers inside closed arenas, and comprehensively studied their roaming behaviour subject to a large number of environmental stimuli. We compared two model species, Chlamydomonas reinhardtii (freshwater alga, 2 cilia), and Pyramimonas octopus (marine alga, 8 cilia), and detailed their highly-stereotyped behaviours and the emergence of a trio of macroscopic swimming states (smooth-forward, quiescent, tumbling or excitable backward). Harnessing ultralong timeseries statistics, we reconstructed the species-dependent reaction network that underlies the choice of locomotor behaviour in these aneural organisms, and discovered the presence of macroscopic non-equilibrium probability fluxes in these active systems. We also revealed for the first time how microswimmer motility changes instantaneously when a chemical is added to their microhabitat, by inducing deterministic fusion between paired droplets - one containing a trapped cell, and the other, a pharmacological agent that perturbs cellular excitability. By coupling single-cell entrapment with unprecedented tracking resolution, speed and duration, our approach offers unique and potent opportunities for diagnostics, drug-screening, and for querying the genetic basis of micro-organismal behaviour.

scholarly journals Pars Pro Toto: Every Single Cell Matters

2021 ◽  
Vol 12 ◽  
Author(s):  
Fien Christiaens ◽  
Balkan Canher ◽  
Fien Lanssens ◽  
Anchal Bisht ◽  
Simon Stael ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Single Cell ◽  
Tree Species ◽  
Repair Process ◽  
Model Species ◽  
Modus Operandi ◽  
Different Types ◽  
Agricultural Applications ◽  
Regeneration Response ◽  
Self Repair

Compared to other species, plants stand out by their unparalleled self-repair capacities. Being the loss of a single cell or an entire tissue, most plant species are able to efficiently repair the inflicted damage. Although this self-repair process is commonly referred to as “regeneration,” depending on the type of damage and organ being affected, subtle to dramatic differences in the modus operandi can be observed. Recent publications have focused on these different types of tissue damage and their associated response in initiating the regeneration process. Here, we review the regeneration response following loss of a single cell to a complete organ, emphasizing key molecular players and hormonal cues involved in the model species Arabidopsis thaliana. In addition, we highlight the agricultural applications and techniques that make use of these regenerative responses in different crop and tree species.

scholarly journals Single-Cell Analysis of the 3D Topologies of Genomic Loci Using Genome Architecture Mapping

2020 ◽  
Author(s):  
Lonnie R. Welch ◽  
Catherine Baugher ◽  
Yingnan Zhang ◽  
Trenton Davis ◽  
William F. Marzluff ◽  
...  
Keyword(s):  
Single Cell ◽  
Molecular Mechanisms ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Geometric Model ◽  
Embryonic Stem ◽  
Specific Gene ◽  
Genome Architecture ◽  
Cell Analysis ◽  
Thin Sections

AbstractAlthough each cell within an organism contains a nearly identical genome sequence, the three-dimensional (3D) packing of the genome varies among individual cells, influencing cell-type-specific gene expression. Genome Architecture Mapping (GAM) is the first genome-wide experimental method for capturing 3D proximities between any number of genomic loci without ligation. GAM overcomes several limitations of 3C-based methods by sequencing DNA from a large collection of thin sections sliced from individual nuclei. The GAM technique measures locus co-segregation, extracts radial positions, infers chromatin compaction, requires small numbers of cells, does not depend on ligation, and provides rich single-cell information. However, previous analyses of GAM data focused exclusively on population averages, neglecting the variation in 3D topology among individual cells.We present the first single-cell analysis of GAM data, demonstrating that the slices from individual cells reveal intercellular heterogeneity in chromosome conformation. By simultaneously clustering both slices and genomic loci, we identify topological variation among single cells, including differential compaction of cell cycle genes. We also develop a geometric model of the nucleus, allowing prediction of the 3D positions of each slice. Using GAM data from mouse embryonic stem cells, we make new discoveries about the structure of the major mammalian histone gene locus, which is incorporated into the Histone Locus Body (HLB), including structural fluctuations and putative causal molecular mechanisms. Our methods are packaged as SluiceBox, a toolkit for mining GAM data. Our approach represents a new method of investigating variation in 3D genome topology among individual cells across space and time.

scholarly journals Adult insect personality in the wild -- Calopteryx splendens as a model for field studies

2021 ◽  
Author(s):  
Maria Gołąb ◽  
Szymon Sniegula ◽  
Andrzej Antoł ◽  
Tomas Brodin
Keyword(s):  
Field Studies ◽  
Ecological Research ◽  
Model Species ◽  
Personality Differences ◽  
The Past ◽  
Adult Insect ◽  
In The Wild ◽  
First Time ◽  
Calopteryx Splendens ◽  
Trait Correlation

Animal personality has received increasing interest and acknowledgement within ecological research over the past two decades. However, some areas are still poorly studied and need to be developed. For instance, field studies focused on invertebrates are currently highly underrepresented in the literature. More studies including a wider variety of traits measured and species tested is needed to improve our understanding of trait-correlation patterns and generalities. We studied nine behavioural traits, in the damselfly Calopteryx splendens, from an array of three experiments: (i) courtship, (ii) aggressiveness and (iii) boldness, and calculated their repeatability. The behaviours were measured twice, in two different contexts: (i) undisturbed territory and (ii) partially deteriorated territory. All behavioural traits measured, except for two, were repeatable across the two contexts. This work demonstrates, for the first time, the presence of within population personality differences in an adult damselfly in the wild. We further propose Calopteryx splendens as a promising model species for testing personality in the wild under highly controlled environmental conditions.

scholarly journals Transcriptional landscape of human microglia reveals robust gene expression signatures that implicates age, sex and APOE-related immunometabolic pathway perturbations

2021 ◽  
Author(s):  
Tulsi Patel ◽  
Troy P Carnwath ◽  
Xue Wang ◽  
Mariet Allen ◽  
Sarah J Lincoln ◽  
...  
Keyword(s):  
Single Cell ◽  
Genetic Factors ◽  
Disease Genes ◽  
Human Microglia ◽  
Bulk Data ◽  
Network Modules ◽  
Health And Disease ◽  
Transcriptome Resource ◽  
Carbohydrate Metabolism Genes ◽  
Transcriptional Landscape

Microglia have fundamental roles in health and disease, however effects of age, sex and genetic factors on human microglia have not been fully explored. We applied bulk and single cell approaches to comprehensively characterize human microglia transcriptomes and their associations with age, sex and APOE. We identified a novel microglial signature, characterized its expression in bulk data from 1,306 brain samples across 6 regions and in single cell microglia transcriptome. We discovered microglial co-expression network modules associated with age, sex and APOE-ε4 that are enriched for lipid and carbohydrate metabolism genes. Integrated analyses of modules with single cell transcriptomes revealed significant overlap between age-associated module genes and both pro-inflammatory and disease-associated microglial clusters. These modules and clusters harbor known neurodegenerative disease genes including APOE, PLCG2 and BIN1. These data represent a well-characterized human microglial transcriptome resource; and highlight age, sex and APOE-related microglial immunometabolism perturbations with potential relevance in neurodegeneration.

scholarly journals Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Ying Yan ◽  
Xyrus X. Maurer-Alcalá ◽  
Rob Knight ◽  
Sergei L. Kosakovsky Pond ◽  
Laura A. Katz
Keyword(s):  
Molecular Evolution ◽  
Gene Family ◽  
Single Cell ◽  
Genome Evolution ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Genome Architecture ◽  
Eukaryotic Genes ◽  
Ciliate Species ◽  
Transcript Diversity

ABSTRACT Ciliates, a eukaryotic clade that is over 1 billion years old, are defined by division of genome function between transcriptionally inactive germline micronuclei and functional somatic macronuclei. To date, most analyses of gene family evolution have been limited to cultivable model lineages (e.g., Tetrahymena, Paramecium, Oxytricha, and Stylonychia). Here, we focus on the uncultivable Karyorelictea and its understudied sister class Heterotrichea, which represent two extremes in genome architecture. Somatic macronuclei within the Karyorelictea are described as nearly diploid, while the Heterotrichea have hyperpolyploid somatic genomes. Previous analyses indicate that genome architecture impacts ciliate gene family evolution as the most diverse and largest gene families are found in lineages with extensively processed somatic genomes (i.e., possessing thousands of gene-sized chromosomes). To further assess ciliate gene family evolution, we analyzed 43 single-cell transcriptomes from 33 ciliate species representing 10 classes. Focusing on conserved eukaryotic genes, we use estimates of transcript diversity as a proxy for the number of paralogs in gene families among four focal clades: Karyorelictea, Heterotrichea, extensive fragmenters (with gene-size somatic chromosomes), and non-extensive fragmenters (with more traditional somatic chromosomes), the latter two within the subphylum Intramacronucleata. Our results show that (i) the Karyorelictea have the lowest average transcript diversity, while Heterotrichea are highest among the four groups; (ii) proteins in Karyorelictea are under the highest functional constraints, and the patterns of selection in ciliates may reflect genome architecture; and (iii) stop codon reassignments vary among members of the Heterotrichea and Spirotrichea but are conserved in other classes. IMPORTANCE To further our understanding of genome evolution in eukaryotes, we assess the relationship between patterns of molecular evolution within gene families and variable genome structures found among ciliates. We combine single-cell transcriptomics with bioinformatic tools, focusing on understudied and uncultivable lineages selected from across the ciliate tree of life. Our analyses show that genome architecture correlates with patterns of protein evolution as lineages with more canonical somatic genomes, such as the class Karyorelictea, have more conserved patterns of molecular evolution compared to other classes. This study showcases the power of single-cell transcriptomics for investigating genome architecture and evolution in uncultivable microbial lineages and provides transcriptomic resources for further research on genome evolution.

Single-cell approaches to understand genome organisation throughout the cell cycle

2019 ◽  
Vol 63 (2) ◽  
pp. 209-216
Author(s):  
Sarah E. McClelland
Keyword(s):  
Cell Cycle ◽  
Single Cell ◽  
Biological Data ◽  
Genome Architecture ◽  
Chromosome Architecture ◽  
Current State ◽  
Topologically Associated Domains ◽  
Mammalian Genomes ◽  
A Cell ◽  
Cell Variation

Abstract Mammalian genomes are ordered at several scales, ranging from nucleosomes (beads on a string), to topologically associated domains (TADs), laminar associated domains (LADs), and chromosome territories. These are described briefly below and we refer the reader to some recent comprehensive reviews on genome architecture summarising the current state of knowledge of the organisational principles of the nucleus [1,2]. Biological observations from populations of millions of individual cells can reveal consensus behaviour. New methods to study and interpret biological data at the single-cell level have recently been instrumental in revealing new understanding of cell-to-cell variation and novel biology. Here we will summarise the recent advances in single-cell technology that have provided insights into the behaviour of the mammalian genome during a cell cycle. We will focus on the interphase domain structure of chromosomes, including TADs and LADs, and how chromosome architecture changes during the cell cycle. The role of genome architecture relating to gene expression has been reviewed elsewhere [3].

Sign in / Sign up

Export Citation Format

Share Document