Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae

2021 ◽  
Author(s):  
Sonja I. Repetti ◽  
Cintia Iha ◽  
Kavitha Uthanumallian ◽  
Christopher J. Jackson ◽  
Yibi Chen ◽  
...  
Keyword(s):  
Green Algae ◽  
Common Ancestor ◽  
Nuclear Genome ◽  
Genomic Diversity ◽  
Biological Functions ◽  
High Quality ◽  
The Core ◽  
Homologous Genes ◽  
Intermediate Size ◽  
Selection For

The genomic diversity underpinning high ecological and species diversity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the Core Chlorophyta. We generated a high-quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the Core Chlorophyta, and incorporated this genome in a comparative analysis with 25 other genomes from diverse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most early-diverging prasinophytes and the remainder of the Core Chlorophyta. Our results suggest positive selection for genome streamlining in Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after divergence from their common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. These results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising prior to diversification in the UTC clade, which may underpin the success of this species-rich clade in a diversity of habitats.

scholarly journals Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Seth Commichaux ◽  
Kiran Javkar ◽  
Padmini Ramachandran ◽  
Niranjan Nagarajan ◽  
Denis Bertrand ◽  
...  
Keyword(s):  
Public Health ◽  
Public Health Response ◽  
High Quality ◽  
Short Read ◽  
Short Reads ◽  
The Core ◽  
Long Reads ◽  
Health Response ◽  
Long Read ◽  
Core Genes

Abstract Background Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower accuracy than short reads. Results We evaluated the accuracy of Listeria monocytogenes assemblies from enrichments (quasimetagenomes) of naturally-contaminated ice cream using long read (Oxford Nanopore) and short read (Illumina) sequencing data. Accuracy of ten assembly approaches, over a range of sequencing depths, was evaluated by comparing sequence similarity of genes in assemblies to a complete reference genome. Long read assemblies reconstructed a circularized genome as well as a 71 kbp plasmid after 24 h of enrichment; however, high error rates prevented high fidelity gene assembly, even at 150X depth of coverage. Short read assemblies accurately reconstructed the core genes after 28 h of enrichment but produced highly fragmented genomes. Hybrid approaches demonstrated promising results but had biases based upon the initial assembly strategy. Short read assemblies scaffolded with long reads accurately assembled the core genes after just 24 h of enrichment, but were highly fragmented. Long read assemblies polished with short reads reconstructed a circularized genome and plasmid and assembled all the genes after 24 h enrichment but with less fidelity for the core genes than the short read assemblies. Conclusion The integration of long and short read sequencing of quasimetagenomes expedited the reconstruction of a high quality pathogen genome compared to either platform alone. A new and more complete level of information about genome structure, gene order and mobile elements can be added to the public health response by incorporating long read analyses with the standard short read WGS outbreak response.

scholarly journals A High Rigidity and Precision Scanning Tunneling Microscope with Decoupled XY and Z Scans

Scanning ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-7
Author(s):  
Xu Chen ◽  
Tengfei Guo ◽  
Yubin Hou ◽  
Jing Zhang ◽  
Wenjie Meng ◽  
...  
Keyword(s):  
Scanning Tunneling Microscope ◽  
Atomic Resolution ◽  
Scanning Tunneling ◽  
Electronic Noise ◽  
High Quality ◽  
Tunneling Microscope ◽  
The Core ◽  
High Rigidity ◽  
The Common ◽  
The Impact

A new scan-head structure for the scanning tunneling microscope (STM) is proposed, featuring high scan precision and rigidity. The core structure consists of a piezoelectric tube scanner of quadrant type (for XY scans) coaxially housed in a piezoelectric tube with single inner and outer electrodes (for Z scan). They are fixed at one end (called common end). A hollow tantalum shaft is coaxially housed in the XY-scan tube and they are mutually fixed at both ends. When the XY scanner scans, its free end will bring the shaft to scan and the tip which is coaxially inserted in the shaft at the common end will scan a smaller area if the tip protrudes short enough from the common end. The decoupled XY and Z scans are desired for less image distortion and the mechanically reduced scan range has the superiority of reducing the impact of the background electronic noise on the scanner and enhancing the tip positioning precision. High quality atomic resolution images are also shown.

Wild Yeasts Selection for High-Quality Patagonian Wines

2016 ◽  
pp. 277-300
Author(s):  
Silvana María del Mónaco ◽  
Yolanda Leticia Curilén ◽  
Sebastián Mario Ezequiel Bravo ◽  
Adriana Beatriz Simes ◽  
Viviana Andrea Carreño ◽  
...  
Keyword(s):  
High Quality ◽  
Wild Yeasts ◽  
Selection For

scholarly journals The Molding Influence

1999 ◽  
Vol 121 (10) ◽  
pp. 70-72
Author(s):  
Hutchinson Harry
Keyword(s):  
Design Process ◽  
Cad Model ◽  
Test Program ◽  
High Quality ◽  
The Core ◽  
The One ◽  
Beta Testing ◽  
Standard Components ◽  
Beta Test

This article presents study that shows beta testing shapes software to the users’ hands so the product will fit the marketplace. MoldWizard is intended to reduce the time necessary to design complex mold tooling, such as this mold used to manufacture the plastic housings for high-quality nail guns. Depending on the complexity of a mold and its eventual use, the design process can require as many as 50 different steps, including tasks such as importing and cleaning up the CAD model of the part, adjusting its size for shrinkage, separating the core and cavity, generating mold bases, and adding sliders, inserts, and other standard components. Minco Tool & Mold uses Unigraphics to design molds like the one shown in the article for an automobile hubcap. Minco participated in the MoldWizard beta test program. A news group at the website let the test users communicate directly with each other. When beta testers had questions about how to use the program, they posted them in the news group and other testers would respond.

scholarly journals Introgression from Gorilla caused the Human-Chimpanzee split

2018 ◽  
Author(s):  
Johan Nygren
Keyword(s):  
Common Ancestor ◽  
Nuclear Genome ◽  
Genome Project ◽  
Lineage Sorting ◽  
Chromosome 5 ◽  
Speciation Model ◽  
Introgression Event ◽  
The Common

ABSTRACT: The Gorilla Genome Project (Scally, 2012) showed that 30% of the gorilla genome introgressed into the ancestor of humans and chimpanzees, and that the two species diverged through lineage sorting with 15% ending up in Pan and another 15% in Homo. That introgression is the Pan-Homo split, hybridization, which led to speciation as the new hybrid lineages became reproductively isolated from one another. The NUMT on chromosome 5 (“ps5”) (Popadin, 2017) fits perfectly with the introgression speciation model, it was formed from mtDNA that had diverged from the common ancestor of Pan-Homo for 1.8 Myr at the time of insertion into the nuclear genome, and originated in the Gorilla lineage. The ps5 pseudogene was transferred to Pan and Homo during the introgression event that led to the Pan-Homo split, 6 million years ago.

scholarly journals Amplifiers and the origin of animal signals

2016 ◽  
Vol 283 (1832) ◽  
pp. 20160324 ◽  
Author(s):  
Laurens Bogaardt ◽  
Rufus A. Johnstone
Keyword(s):  
Signal Detection ◽  
Female Choice ◽  
Signal Detection Theory ◽  
Animal Communication ◽  
Detection Theory ◽  
Direct Selection ◽  
Simple Explanation ◽  
Male Quality ◽  
High Quality ◽  
Selection For

In 1989, Hasson introduced the concept of an ‘amplifier’ within animal communication. This display reduces errors in the assessment of traits for which there is direct selection and renders differences in quality among animals more obvious. Amplifiers can evolve to fixation via the benefit they confer on high-quality animals. However, they also impose a cost on low-quality animals by revealing their lower quality, potentially leading these to refrain from amplifying. Hence, it was suggested that, if the level of amplification correlates with quality, direct choice for the amplifying display might emerge. Using the framework of signal detection theory, this article shows that, if the use of an amplifier is observable, direct choice for the amplifying display can indeed evolve. Consequently, low-quality animals may choose to amplify to some extent as well, even though this reveals their lower quality. In effect, the amplifier evolves to become a signal in its own right. We show that, as amplifiers can evolve without direct female choice and are likely to become correlated with male quality, selection for quality-dependent amplification provides a simple explanation for the origin of reliable signals in the absence of pre-existing preferences.

scholarly journals Mechanism of Action of Bu-Fei-Yi-Shen Formula in Treating Chronic Obstructive Pulmonary Disease Based on Network Pharmacology Analysis and Molecular Docking Validation

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Longchuan Wu ◽  
Yu Chen ◽  
Jiao Yi ◽  
Yi Zhuang ◽  
Lei Cui ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Mechanism Of Action ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Chronic Obstructive ◽  
Biological Functions ◽  
Active Ingredients ◽  
Obstructive Pulmonary Disease ◽  
The Core ◽  
Target Network

Objective. To explore the mechanism of action of Bu-Fei-Yi-Shen formula (BFYSF) in treating chronic obstructive pulmonary disease (COPD) based on network pharmacology analysis and molecular docking validation. Methods. First of all, the pharmacologically active ingredients and corresponding targets in BFYSF were mined by the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, the analysis platform, and literature review. Subsequently, the COPD-related targets (including the pathogenic targets and known therapeutic targets) were identified through the TTD, CTD, DisGeNet, and GeneCards databases. Thereafter, Cytoscape was employed to construct the candidate component-target network of BFYSF in the treatment of COPD. Moreover, the cytoHubba plug-in was utilized to calculate the topological parameters of nodes in the network; then, the core components and core targets of BFYSF in the treatment of COPD were extracted according to the degree value (greater than or equal to the median degree values for all nodes in the network) to construct the core network. Further, the Autodock vina software was adopted for molecular docking study on the core active ingredients and core targets, so as to verify the above-mentioned network pharmacology analysis results. Finally, the Omicshare database was applied in enrichment analysis of the biological functions of core targets and the involved signaling pathways. Results. In the core component-target network of BFYSF in treating COPD, there were 30 active ingredients and 37 core targets. Enrichment analysis suggested that these 37 core targets were mainly involved in the regulation of biological functions, such as response to biological and chemical stimuli, multiple cellular life processes, immunity, and metabolism. Besides, multiple pathways, including IL-17, Toll-like receptor (TLR), TNF, and HIF-1, played certain roles in the effect of BFYSF on treating COPD. Conclusion. BFYSF can treat COPD through the multicomponent, multitarget, and multipathway synergistic network, which provides basic data for intensively exploring the mechanism of action of BFYSF in treating COPD.

Mesoamerican Polyhedral Cores and Prismatic Blades

1968 ◽  
Vol 33 (4) ◽  
pp. 446-478 ◽  
Author(s):  
Don E. Crabtree
Keyword(s):  
High Speed ◽  
Large Series ◽  
High Speed Photography ◽  
High Quality ◽  
Pressure Method ◽  
The Core ◽  
Quality Material ◽  
Muscular Coordination

AbstractThis paper deals with the results of the author"s attempts to replicate the obsidian polyhedral cores and prismatic blades of Mesoamerica. Blades have been produced by the direct percussion, indirect percussion, and pressure methods. The pressure method using a chest crutch and a clamp produces cores and blades which are true replicas of aboriginal specimens. The importance of preforming the core and of platform preparation is stressed, and it is pointed out that, usually, actual removal of the blade offers few problems. However, to produce exhausted cores which show the perfection of aboriginal specimens and a large series of nearly identical blades requires good muscular coordination, high quality material, the establishment of patterns or rhythms of motor habits, and the absence of distractions. The author also discusses the difficulties of recovering from mistakes in manufacture.High-speed photography of prismatic blade removal, at 5,000 frames per second, has helped illustrate the behavior of the material and of the stoneworker. These photographs also indicate that under the present experimental and photographic conditions the author (Crabtree) is able to remove a prismatic blade from a core in about 1,250th of a second.

In depth analysis of kinase cross screening data to identify chemical starting points for inhibition of the nek family of kinases

2017 ◽  
Author(s):  
Carrow I. Wells ◽  
Nirav R. Kapadia ◽  
Rafael M. Couñago ◽  
David H. Drewry
Keyword(s):  
Drug Discovery ◽  
Small Molecules ◽  
Small Molecule ◽  
Kinase Inhibitors ◽  
Biological Functions ◽  
Chemical Probes ◽  
High Quality ◽  
Depth Analysis ◽  
Number Of Citations ◽  
Shed Light

AbstractPotent, selective, and cell active small molecule kinase inhibitors are useful tools to help unravel the complexities of kinase signaling. As the biological functions of individual kinases become better understood, they can become targets of drug discovery efforts. The small molecules used to shed light on function can also then serve as chemical starting points in these drug discovery efforts. The Nek family of kinases has received very little attention, as judged by number of citations in PubMed, yet they appear to play many key roles and have been implicated in disease. Here we present our work to identify high quality chemical starting points that have emerged due to the increased incidence of broad kinome screening. We anticipate that this analysis will allow the community to progress towards the generation of chemical probes and eventually drugs that target members of the Nek family.

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