scholarly journals Contributions of single-cell genomics to our understanding of planktonic marine archaea

2019 ◽  
Vol 374 (1786) ◽  
pp. 20190096 ◽  
Author(s):  
A. E. Santoro ◽  
M. Kellom ◽  
S. M. Laperriere
Keyword(s):  
Single Cell ◽  
Population Level ◽  
Systematic Investigation ◽  
Marine Microbes ◽  
Specific Group ◽  
Single Cell Genomics ◽  
Marine Microbiology ◽  
Genome Screening ◽  
The Impact ◽  
Marine Archaea

Single-cell genomics has transformed many fields of biology, marine microbiology included. Here, we consider the impact of single-cell genomics on a specific group of marine microbes—the planktonic marine archaea. Despite single-cell enabled discoveries of novel metabolic function in the marine thaumarchaea, population-level investigations are hindered by an overall lower than expected recovery of thaumarchaea in single-cell studies. Metagenome-assembled genomes have so far been a more useful method for accessing genome-resolved insights into the Marine Group II euryarchaea. Future progress in the application of single-cell genomics to archaeal biology in the ocean would benefit from more targeted sorting approaches, and a more systematic investigation of potential biases against archaea in single-cell workflows including cell lysis, genome amplification and genome screening. This article is part of a discussion meeting issue ‘Single cell ecology’.

scholarly journals Distinct Characteristics of Correlation Analysis at the Single-Cell and the Population Level

2020 ◽  
Author(s):  
Guoyu Wu ◽  
Yuchao Li
Keyword(s):  
Correlation Analysis ◽  
Single Cell ◽  
Biological Networks ◽  
Single Cells ◽  
Correlation Coefficients ◽  
Population Level ◽  
Single Cell Level ◽  
Cell Level ◽  
Biological Studies ◽  
The Impact

Abstract Background:Correlation analysis is widely used in biological studies to infer molecular relationships within biological networks. Recently, single-cell analysis has drawn tremendous interests, for its ability to obtain high-resolution molecular phenotypes. It turns out that there is little overlap of co-expressed genes identified in single-cell level investigations with that of population level investigations. However, the nature of the relationship of correlations between single-cell and population levels remains unclear. In this manuscript, we aimed to unveil the origin of the differences between the correlation coefficients at the single-cell level and that at the population level, and bridge the gap between them. Results:Through developing formulations to link correlations at the single-cell and the population level, we illustrated that aggregated correlations could be stronger, weaker or equal to the corresponding individual correlations, depending on the variations and the correlations within the population. When the correlation-within is weaker than the individual correlation, the correlation at the population level is stronger than that at the single-cell level. Through a bottom-up approach to model interactions between molecules in a signaling cascade or a multi-regulator controlled gene expression, we surprisingly found that the existence of interaction between two components could not be excluded simply based on their low correlation coefficients, suggesting a reconsideration of connectivity within biological networks which was derived solely from correlation analysis. We also investigated the impact of technical random measurement errors on the correlation coefficients for the single-cell level and the population level. The results indicate that the aggregated correlation is relatively robust and less affected.Conclusions:Because of the heterogeneity among single cells, correlation coefficients calculated based on data of the single-cell level might be different from that of the population level. Depending on the specific question we are asking, proper sampling and normalization procedure should be done before we draw any conclusions.

scholarly journals Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol

2020 ◽  
Vol 21 (19) ◽  
pp. 7366
Author(s):  
Chiara Carretta ◽  
Selene Mallia ◽  
Elena Genovese ◽  
Sandra Parenti ◽  
Sebastiano Rontauroli ◽  
...  
Keyword(s):  
Single Cell ◽  
Whole Genome Amplification ◽  
Clonal Evolution ◽  
Genomic Analysis ◽  
Response To Therapy ◽  
Whole Genome ◽  
Hematopoietic Stem ◽  
Single Cell Genomics ◽  
Genome Amplification ◽  
The Impact

Single-cell genomics has become the method of choice for the study of heterogeneous cell populations and represents an elective application in defining the architecture and clonal evolution in hematological neoplasms. Reconstructing the clonal evolution of a neoplastic population therefore represents the main way to understand more deeply the pathogenesis of the neoplasm, but it is also a potential tool to understand the evolution of the tumor population with respect to its response to therapy. Pre-analytical phase for single-cell genomics analysis is crucial to obtain a cell population suitable for single-cell sorting, and whole genome amplification is required to obtain the necessary amount of DNA from a single cell in order to proceed with sequencing. Here, we evaluated the impact of different methods of cellular immunostaining, fixation and whole genome amplification on the efficiency and yield of single-cell sequencing.

scholarly journals Impact of Influent Carbon to Phosphorus Ratio on Performance and Phenotypic Dynamics in Enhanced Biological Phosphorus Removal (EBPR) System - Insights into Carbon Distribution, Intracellular Polymer Stoichiometry and Pathways Shifts

2019 ◽  
Author(s):  
Nehreen Majed ◽  
April Z. Gu
Keyword(s):  
Single Cell ◽  
Batch Reactor ◽  
Reducing Power ◽  
Population Level ◽  
Tca Cycle ◽  
Biological Phosphorus Removal ◽  
Metabolic Functions ◽  
Glycolysis Pathway ◽  
The Impact ◽  
Biological Phosphorus

AbstractThis study investigated the impact of influent carbon to phosphorus (P) ratio on the variation in P-removal performance and associated intracellular polymers dynamics in key functionally relevant microbial populations, namely, PAOs and GAOs, at both individual and populations levels, in laboratory scale sequencing batch reactor-EBPR systems. Significant variations and dynamics were evidenced for the formation, utilization and stoichiometry of intracellular polymers, namely polyphosphate, glycogen and Polyhydroxyalkanoates in PAOs and GAOs in the EBPR systems that were operated with influent C/P ranged from 20 to 50, presumably as results of phylogenetic diversity changes and, or metabolic functions shifts in these two populations at different influent C/P ratios. Single cell Raman micro-spectroscopy enabled quantification of differentiated polymer inclusion levels in PAOs and GAOs and, showed that as the influent rbCOD/P ratio increases, the excessive carbon beyond stoichiometric requirement for PAOs would be diverted into GAOs. Our results also evidenced that when condition becomes more P limiting at higher rbCOD/P ratios, both energy and reducing power generation required for acetate uptake and PHB formation might shift from relying on both polyP hydrolysis and glycolysis pathway, to more enhancement and dependence on glycolysis in addition to partial/reverse TCA cycle. These findings provided new insights into the metabolic elasticity of PAOs and GAOs and their population-level parameters for mechanistic EBPR modeling. This study also demonstrated the potential of application of single cell Raman micro-spectroscopy method as a powerful tool for studying phenotypic dynamics in ecological systems such as EBPR.

Use of Nutrition Information and Understanding of “Percent Daily Value” on Nutrition Facts Tables: Evaluating the Impact of a National Public Education Campaign among Youth and Young Adults in Canada

2019 ◽  
Vol 80 (4) ◽  
pp. 200-204 ◽  
Author(s):  
Brittany Cormier ◽  
Lana Vanderlee ◽  
David Hammond
Keyword(s):  
Population Level ◽  
Correct Recall ◽  
Nutrition Information ◽  
Education Campaign ◽  
Knowledge Based ◽  
Public Education Campaign ◽  
Youth And Young Adults ◽  
Campaign Message ◽  
Health Canada ◽  
The Impact

Purpose: In 2010, Health Canada implemented a national campaign to improve understanding of “percent daily value” (%DV) in Nutrition Facts Tables (NFTs). This study examined sources of nutrition information and knowledge of %DV information communicated in the campaign. Methods: Respondents aged 16–30 years completed the Canada Food Study in 2016 (n = 2665). Measures included sources of nutrition information, NFT use, and %DV knowledge based on the campaign message (“5% DV or less is a little; 15% DV or more is a lot”). A logistic regression examined correlates of providing “correct” responses to %DV questions related to the campaign messaging. Results: Overall, 7.2% (n = 191) respondents correctly indicated that 5% is “a little”, and 4.3% (n = 115) correctly indicated 15% DV was “a lot”. Only 4.0% (n = 107) correctly answered both. Correct recall of %DV amounts was not associated with number of information sources reported, but was greater among those who were female, were younger, and reported greater NFT understanding and serving size information use (P < 0.05 for all). Conclusions: Results show low awareness of messaging from the Nutrition Facts Education Campaign among young Canadians. Such a mass media campaign may be insufficient on its own to enhance population-level understanding of %DV.

scholarly journals Understanding and responding to COVID-19 in Wales: protocol for a privacy-protecting data platform for enhanced epidemiology and evaluation of interventions

BMJ Open ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. e043010
Author(s):  
Jane Lyons ◽  
Ashley Akbari ◽  
Fatemeh Torabi ◽  
Gareth I Davies ◽  
Laura North ◽  
...  
Keyword(s):  
Policy Development ◽  
Healthcare Utilisation ◽  
Population Data ◽  
Population Level ◽  
Risk Groups ◽  
Service Utilisation ◽  
Natural Experiments ◽  
Spread Of Infection ◽  
The Impact

IntroductionThe emergence of the novel respiratory SARS-CoV-2 and subsequent COVID-19 pandemic have required rapid assimilation of population-level data to understand and control the spread of infection in the general and vulnerable populations. Rapid analyses are needed to inform policy development and target interventions to at-risk groups to prevent serious health outcomes. We aim to provide an accessible research platform to determine demographic, socioeconomic and clinical risk factors for infection, morbidity and mortality of COVID-19, to measure the impact of COVID-19 on healthcare utilisation and long-term health, and to enable the evaluation of natural experiments of policy interventions.Methods and analysisTwo privacy-protecting population-level cohorts have been created and derived from multisourced demographic and healthcare data. The C20 cohort consists of 3.2 million people in Wales on the 1 January 2020 with follow-up until 31 May 2020. The complete cohort dataset will be updated monthly with some individual datasets available daily. The C16 cohort consists of 3 million people in Wales on the 1 January 2016 with follow-up to 31 December 2019. C16 is designed as a counterfactual cohort to provide contextual comparative population data on disease, health service utilisation and mortality. Study outcomes will: (a) characterise the epidemiology of COVID-19, (b) assess socioeconomic and demographic influences on infection and outcomes, (c) measure the impact of COVID-19 on short -term and longer-term population outcomes and (d) undertake studies on the transmission and spatial spread of infection.Ethics and disseminationThe Secure Anonymised Information Linkage-independent Information Governance Review Panel has approved this study. The study findings will be presented to policy groups, public meetings, national and international conferences, and published in peer-reviewed journals.

Household and Population-Level Behavioural Changes Due to COVID-19 Pandemic: A Smart Thermostat Based Comparative Data Analysis

2021 ◽  
Vol 10 (1) ◽  
pp. 1-6
Author(s):  
Kirti Sundar Sahu ◽  
Arlene Oetomo ◽  
Niloofar Jalali ◽  
Plinio P. Morita
Keyword(s):  
Data Analysis ◽  
Population Level ◽  
World Health ◽  
Motion Sensors ◽  
Household Level ◽  
Work From Home ◽  
Significant Difference ◽  
Health Organization ◽  
Smart Thermostat ◽  
The Impact

The World Health Organization declared the coronavirus outbreak as a pandemic on March 11, 2020. To inhibit the spread of COVID-19, governments around the globe, including Canada, have implemented physical distancing and lockdown measures, including a work-from-home policy. Canada in 2020 has developed a 24-Hour Movement Guideline for all ages laying guidance on the ideal amount of physical activity, sedentary behaviour, and sleep (PASS) for an individual in a day. The purpose of this study was to investigate changes on the household and population-level in lifestyle behaviours (PASS) and time spent indoors at the household level, following the implementation of physical distancing protocols and stay-at-home guidelines. For this study, we used 2019 and 2020 data from ecobee, a Canadian smart Wi-Fi thermostat company, through the Donate Your Data (DYD) program. Using motion sensors data, we quantified the amount of sleep by using the absence of movement, and similarly, increased sensor activation to show a longer duration of household occupancy. The key findings of this study were; during the COVID-19 pandemic, overall household-level activity increased significantly compared to pre-pandemic times, there was no significant difference between household-level behaviours between weekdays and weekends during the pandemic, average sleep duration has not changed, but the pattern of sleep behaviour significantly changed, specifically, bedtime and wake up time delayed, indoor time spent has been increased and outdoor time significantly reduced. Our data analysis shows the feasibility of using big data to monitor the impact of the COVID-19 pandemic on the household and population-level behaviours and patterns of change.

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