scholarly journals Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

2019 ◽  
Author(s):  
Yuanmeng Zhang ◽  
Jason Williams ◽  
Andrea Lucky
Keyword(s):  
Time Scales ◽  
Population Level ◽  
Deep Time ◽  
Ultraconserved Elements ◽  
Background Theory ◽  
Promising Tool ◽  
Probe Selection ◽  
Wet Lab ◽  
Phylogenomic Analyses ◽  
Targeted Enrichment

Targeted enrichment of ultraconserved elements (UCEs) has emerged as a promising tool for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and phylogeographic questions at deep time scales to population level studies at shallow time scales. However, UCEs are underutilized in arthropod phylogenomics, and the methodology can be daunting for beginners. Our goal is to introduce UCEs phylogenomics to a wider audience by summarizing recent advances in UCE phylogenomics in arthropod research to familiarize readers with background theory and steps involved in UCEs phylogenomics. We define terminology used in association with the UCE approach, evaluate current laboratory and bioinformatic methods and limitations, and finally provide a roadmap of steps in the UCEs pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. The UCEs pipeline can be divided into the following steps: 1) probe selection and design 2) wet lab work and sequencing, 3) bioinformatics, and 4) phylogenomic analyses. we provide quality-control tips to ensure that best results in data collection and downstream analyses. Our hope is to encourage increased adoption of UCEs in phylogenomics studies, deepen our understanding of the function of UCEs themselves across widely divergent taxa, and toward increased understanding of the tree of life.

scholarly journals Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

2019 ◽  
Vol 3 (5) ◽  
Author(s):  
Y Miles Zhang ◽  
Jason L Williams ◽  
Andrea Lucky
Keyword(s):  
Time Scales ◽  
Evolutionary History ◽  
Population Level ◽  
Tree Of Life ◽  
Deep Time ◽  
Ultraconserved Elements ◽  
Background Theory ◽  
Promising Tool ◽  
Recent Advances ◽  
Targeted Enrichment

Abstract Targeted enrichment of ultraconserved elements (UCEs) has emerged as a promising tool for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and biogeographic questions at deep time scales to population level studies at shallow time scales. However, the methodology can be daunting for beginners. Our goal is to introduce UCE phylogenomics to a wider audience by summarizing recent advances in arthropod research, and to familiarize readers with background theory and steps involved. We define terminology used in association with the UCE approach, evaluate current laboratory and bioinformatic methods and limitations, and, finally, provide a roadmap of steps in the UCE pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. By facilitating increased adoption of UCEs in phylogenomics studies that deepen our comprehension of the function of these markers across widely divergent taxa, we aim to ultimately improve understanding of the arthropod tree of life.

scholarly journals Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

2019 ◽  
Author(s):  
Yuanmeng Zhang ◽  
Jason Williams ◽  
Andrea Lucky
Keyword(s):  
Time Scales ◽  
Evolutionary History ◽  
Population Level ◽  
Tree Of Life ◽  
Deep Time ◽  
Ultraconserved Elements ◽  
Background Theory ◽  
Promising Tool ◽  
Recent Advances ◽  
Targeted Enrichment

Targeted enrichment of ultraconserved elements (UCE) has emerged as a promising tool for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and phylogeographic questions at deep time scales to population level studies at shallow time scales. However, the methodology can be daunting for beginners. Our goal is to introduce UCE phylogenomics to a wider audience by summarizing recent advances in arthropod research, and to familiarize readers with background theory and steps involved. We define terminology used in association with the UCE approach, evaluate current laboratory and bioinformatic methods and limitations, and, finally, provide a roadmap of steps in the UCE pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. By facilitating increased adoption of UCE in phylogenomics studies that deepen our comprehension of the function of these markers across widely divergent taxa, we aim to ultimately improve understanding of the arthropod tree of life.

EMERGING PROPERTIES IN POPULATION DYNAMICS WITH DIFFERENT TIME SCALES

1995 ◽  
Vol 03 (02) ◽  
pp. 591-602 ◽  
Author(s):  
PIERRE AUGER ◽  
JEAN-CHRISTOPHE POGGIALE
Keyword(s):  
Differential Equations ◽  
Time Scales ◽  
Time Scale ◽  
Population Level ◽  
Nonlinear Process ◽  
Linear Process ◽  
Fast Time ◽  
Slow Part ◽  
Spatial Patches ◽  
Different Time Scales

The aim of this work is to show that at the population level, emerging properties may occur as a result of the coupling between the fast micro-dynamics and the slow macrodynamics. We studied a prey-predator system with different time scales in a heterogeneous environment. A fast time scale is associated to the migration process on spatial patches and a slow time scale is associated to the growth and the interactions between the species. Preys go on the spatial patches on which some resources are located and can be caught by the predators on them. The efficiency of the predators to catch preys is patch-dependent. Preys can be more easily caught on some spatial patches than others. Perturbation theory is used in order to aggregate the initial system of ordinary differential equations for the patch sub-populations into a macro-system of two differential equations governing the total populations. Firstly, we study the case of a linear process of migration for which the aggregated system is formally identical to the slow part of the full system. Then, we study an example of a nonlinear process of migration. We show that under these conditions emerging properties appear at the population level.

scholarly journals Implementation of methane cycling for deep time, global warming simulations with the DCESS Earth System Model (Version 1.2)

2017 ◽  
Author(s):  
Gary Shaffer ◽  
Esteban Fernández Villanueva ◽  
Roberto Rondanelli ◽  
Jens Olaf Pepke Pedersen ◽  
Steffen Malskær Olsen ◽  
...  
Keyword(s):  
Global Warming ◽  
Time Scales ◽  
Sediment Cores ◽  
Earth System Model ◽  
System Model ◽  
Earth System ◽  
Deep Time ◽  
Methane Cycling ◽  
Model Version ◽  
Ocean Atmosphere

Abstract. Geological records reveal a number of ancient, large and rapid negative excursions of carbon-13 isotope. Such excursions can only be explained by massive injections of depleted carbon to the Earth System over a short duration. These injections may have forced strong global warming events, sometimes accompanied by mass extinctions, for example the Triassic-Jurassic and End-Permian extinctions, 201 and 252 million years ago. In many cases evidence points to methane as the dominant form of injected carbon, whether as thermogenic methane, formed by magma intrusions through overlying carbon-rich sediment, or from warming-induced dissociation of methane hydrate, a solid compound of methane and water found in ocean sediments. As a consequence of the ubiquity and importance of methane in major Earth events, Earth System models should include a comprehensive treatment of methane cycling but such a treatment has often been lacking. Here we implement methane cycling in the Danish Center for Earth System Science (DCESS) model, a simplified but well-tested Earth System Model of Intermediate Complexity. We use a generic methane input function that allows variation of input type, size, time scale and ocean-atmosphere partition. To be able to treat such massive inputs more correctly, we extend the model to deal with ocean suboxic/anoxic conditions and with radiative forcing and methane lifetimes appropriate for high atmospheric methane concentrations. With this new model version, we carried out an extensive set of simulations for methane inputs of various sizes, time scales and ocean-atmosphere partitions to probe model behaviour. We find that larger methane inputs over shorter time scales with more methane dissolving in the ocean lead to ever-increasing ocean anoxia with consequences for ocean life and global carbon cycling. Greater methane input directly to the atmosphere leads to more warming and, for example, greater carbon dioxide release from land soils. Analysis of synthetic sediment cores from the simulations provides guidelines for the interpretation of real sediment cores spanning the warming events. With this improved DCESS model version and paleo-reconstructions, we are now better armed to gauge the amounts, types, time scales and locations of methane injections driving specific, observed deep time, global warming events.

Multiple and variant time scales in dynamic information processing

2001 ◽  
Vol 24 (5) ◽  
pp. 814-814
Author(s):  
Hubert R. Dinse
Keyword(s):  
Information Processing ◽  
Receptive Field ◽  
Single Cell ◽  
Time Scales ◽  
Activity Pattern ◽  
Sensory Information ◽  
Population Level ◽  
Dynamic Information ◽  
Sensory Information Processing ◽  
Spatio Temporal

Single cell receptive field dynamics characterized by highly complicated spatio-temporal activity distributions observable during sensory information processing transforms into much simpler spatio-temporal activity pattern at a population level, indicating a qualitative transformational step of time-variant processing from microscopic to mesoscopic levels. As these dynamics are subject to significant modifications during learning, dynamic information processing is in a permanent state of use-dependent fluctuations.

scholarly journals Cellular memory enhances bacterial chemotactic navigation in rugged environments

2019 ◽  
Author(s):  
Adam Gosztolai ◽  
Mauricio Barahona
Keyword(s):  
Time Scales ◽  
Population Level ◽  
Analytical Approximation ◽  
Biochemical Networks ◽  
Cellular Memory ◽  
Gradient Sensing ◽  
Environmental Correlations ◽  
Heterogeneous Landscapes ◽  
Cellular Behaviour ◽  
External Signals

The response of microbes to external signals is mediated by biochemical networks with intrinsic time scales. These time scales give rise to a memory that impacts cellular behaviour. Here we study theoretically the role of cellular memory in Escherichia coli chemotaxis. Using an agent-based model, we show that cells with memory navigating rugged chemoattractant landscapes can enhance their drift speed by extracting information from environmental correlations. Maximal advantage is achieved when the memory is comparable to the time scale of fluctuations as perceived during swimming. We derive an analytical approximation for the drift velocity in rugged landscapes that explains the enhanced velocity, and recovers standard Keller-Segel gradient-sensing results in the limits when memory and fluctuation time scales are well separated. Our numerics also show that cellular memory can induce bet-hedging at the population level resulting in long-lived multi-modal distributions in heterogeneous landscapes.

scholarly journals Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?

2019 ◽  
Author(s):  
Angela McGaughran
Keyword(s):  
Museum Specimens ◽  
Library Preparation ◽  
Targeted Ngs ◽  
Wet Lab ◽  
Next Generation Sequencing Ngs ◽  
Sample Age ◽  
Ngs Data ◽  
The Relationship ◽  
Targeted Enrichment

Abstract Background Next generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wet-lab protocols and determining the effects of sample age on NGS library quality are therefore of vital importance. Here, I examine the relationship between sample age and various indicators of library quality following targeted NGS sequencing of ~1,300 loci using 271 samples of pinned moth specimens ( Helicoverpa armigera ) ranging in age from 4 to 116 years . Results I find that older samples have lower DNA concentrations following extraction and thus require a higher number of indexing PCR cycles during library preparation. When sequenced reads are aligned to a reference genome or to only the targeted region, older samples have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library sizes, while the percentage of adapters in sequenced reads increases significantly as samples become older. Older samples also show the poorest capture success, with lower enrichment and a higher improved coverage anticipated from further sequencing. Conclusions Sample age has significant, measurable impacts on the quality of NGS data following targeted enrichment. However, incorporating a uracil-removing enzyme into the blunt end-repair step during library preparation could help to remove and repair DNA damage, and using a method that prevents adapter-dimer formation may result in improved data yields.

scholarly journals Multispecies coalescent analysis unravels the non-monophyly and controversial relationships of Hexapoda

2017 ◽  
Author(s):  
Lucas A. Freitas ◽  
Beatriz Mello ◽  
Carlos G. Schrago
Keyword(s):  
Phylogenetic Relationships ◽  
Gene Tree ◽  
Genomic Data ◽  
Population Level ◽  
Phylogenetic Inference ◽  
Evolutionary Relationships ◽  
Effective Population ◽  
Multispecies Coalescent ◽  
Population Sizes ◽  
Phylogenomic Analyses

AbstractWith the increase in the availability of genomic data, sequences from different loci are usually concatenated in a supermatrix for phylogenetic inference. However, as an alternative to the supermatrix approach, several implementations of the multispecies coalescent (MSC) have been increasingly used in phylogenomic analyses due to their advantages in accommodating gene tree topological heterogeneity by taking account population-level processes. Moreover, the development of faster algorithms under the MSC is enabling the analysis of thousands of loci/taxa. Here, we explored the MSC approach for a phylogenomic dataset of Insecta. Even with the challenges posed by insects, due to large effective population sizes coupled with short deep internal branches, our MSC analysis could recover several orders and evolutionary relationships in agreement with current insect systematics. However, some phylogenetic relationships were not recovered by MSC methods. Most noticeable, a remiped crustacean was positioned within the Insecta. Additionally, the interordinal relationships within Polyneoptera and Neuropteroidea contradicted recent works, by suggesting the non-monophyly of Neuroptera. We notice, however, that these phylogenetic arrangements were also poorly supported by previous analyses and that they were sensitive to gene sampling.

scholarly journals A Method to sort heterogenous cell populations based on migration in 2D and 3D environments

2020 ◽  
Author(s):  
Aditya Arora ◽  
Jorge Luis Galeano Niño ◽  
Myint Zu Myaing ◽  
Bakya Arasi ◽  
Ruby Yun-Ju Huang ◽  
...  
Keyword(s):  
Population Level ◽  
Live Cells ◽  
Migratory Behaviour ◽  
Functional Tests ◽  
3D Environments ◽  
A Cell ◽  
Spontaneous Migration ◽  
2D And 3D ◽  
Targeted Enrichment

ABSTRACTWhereas phenotypic assays such as Boyden chambers and wound healing assays can easily be employed to characterize the migratory potential of cells at the population level, few methods exist that can sort subpopulations of cells based on their migratory behaviour from an initial heterogeneous pool. In this paper, we present an approach to sort migratory cancer and immune cells based on their spontaneous migration in 2D and 3D microenvironments. Using this method, which is easy to implement and readily scalable, millions of live cells can be sorted based on their migratory characteristics and then subjected to downstream genomic, molecular and functional tests. We reveal that enrichment of the most migratory cytotoxic T lymphocytes yields a pool of cells with enhanced cytotoxicity against cancer cells. This new functional sorting method opens new avenues for the precise characterization of the mechanisms underlying hitherto unexplained heterogeneities in migratory phenotypes within a cell population, and for the targeted enrichment of the most potent migratory leukocytes in immunotherapies.

scholarly journals Motion analysis for better understanding of psychomotor skills in laparoscopy: objective assessment-based simulation training using animal organs

2020 ◽  
Author(s):  
Koki Ebina ◽  
Takashige Abe ◽  
Madoka Higuchi ◽  
Jun Furumido ◽  
Naoya Iwahara ◽  
...  
Keyword(s):  
Path Length ◽  
Objective Assessment ◽  
Principal Component ◽  
Surgical Instruments ◽  
Psychomotor Skills ◽  
Surgical Experience ◽  
Promising Tool ◽  
Surgical Expertise ◽  
Objective Feedback ◽  
Wet Lab

Abstract Background Our aim was to characterize the motions of multiple laparoscopic surgical instruments among participants with different levels of surgical experience in a series of wet-lab training drills, in which participants need to perform a range of surgical procedures including grasping tissue, tissue traction and dissection, applying a Hem-o-lok clip, and suturing/knotting, and digitize the level of surgical competency. Methods Participants performed tissue dissection around the aorta, dividing encountered vessels after applying a Hem-o-lok (Task 1), and renal parenchymal closure (Task 2: suturing, Task 3: suturing and knot-tying), using swine cadaveric organs placed in a box trainer under a motion capture (Mocap) system. Motion-related metrics were compared according to participants’ level of surgical experience (experts: 50 ≤ laparoscopic surgeries, intermediates: 10–49, novices: 0–9), using the Kruskal–Wallis test, and significant metrics were subjected to principal component analysis (PCA). Results A total of 15 experts, 12 intermediates, and 18 novices participated in the training. In Task 1, a shorter path length and faster velocity/acceleration/jerk were observed using both scissors and a Hem-o-lok applier in the experts, and Hem-o-lok-related metrics markedly contributed to the 1st principal component on PCA analysis, followed by scissors-related metrics. Higher-level skills including a shorter path length and faster velocity were observed in both hands of the experts also in tasks 2 and 3. Sub-analysis showed that, in experts with 100 ≤  cases, scissors moved more frequently in the “close zone (0  ≤ to < 2.0 cm from aorta)” than those with 50–99 cases. Conclusion Our novel Mocap system recognized significant differences in several metrics in multiple instruments according to the level of surgical experience. “Applying a Hem-o-lok clip on a pedicle” strongly reflected the level of surgical experience, and zone-metrics may be a promising tool to assess surgical expertise. Our next challenge is to give completely objective feedback to trainees on-site in the wet-lab.

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