scholarly journals A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 667 ◽  
Author(s):  
Ling Deng ◽  
Ronalds Silins ◽  
Josué L. Castro-Mejía ◽  
Witold Kot ◽  
Leon Jessen ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Large Scale ◽  
Metagenomic Sequencing ◽  
High Input ◽  
Human Gut ◽  
Specific Host ◽  
Substantial Progress ◽  
Low Volume ◽  
Made In

The human gut microbiome (GM) plays an important role in human health and diseases. However, while substantial progress has been made in understanding the role of bacterial inhabitants of the gut, much less is known regarding the viral component of the GM. Bacteriophages (phages) are viruses attacking specific host bacteria and likely play important roles in shaping the GM. Although metagenomic approaches have led to the discoveries of many new viruses, they remain largely uncultured as their hosts have not been identified, which hampers our understanding of their biological roles. Existing protocols for isolation of viromes generally require relatively high input volumes and are generally more focused on extracting nucleic acids of good quality and purity for down-stream analysis, and less on purifying viruses with infective capacity. In this study, we report the development of an efficient protocol requiring low sample input yielding purified viromes containing phages that are still infective, which also are of sufficient purity for genome sequencing. We validated the method through spiking known phages followed by plaque assays, qPCR, and metagenomic sequencing. The protocol should facilitate the process of culturing novel viruses from the gut as well as large scale studies on gut viromes.

scholarly journals A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples

2019 ◽  
Author(s):  
Ling Deng ◽  
Ronalds Silins ◽  
Josue Leonardo Castro Mejia ◽  
Witold Kot ◽  
Leon Jessen ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Large Scale ◽  
Metagenomic Sequencing ◽  
High Input ◽  
Human Gut ◽  
Specific Host ◽  
Substantial Progress ◽  
Low Volume ◽  
Made In

The human gut microbiome (GM) plays an important role in human health and diseases. However, while substantial progress has been made in understanding the role of bacterial inhabitants of the gut, much less is known regarding the viral component of the GM. Bacteriophages (phages) are viruses attacking specific host bacteria and likely play important roles in shaping the GM. Although metagenomic approaches have led to the discoveries of many new viruses, they largely remain uncultured as their hosts have not been identified, which hampers our understanding of their biological roles. Existing protocols for isolation of viromes generally require relatively high input volumes and are generally more focused on extracting nucleic acids of good quality and purity for down-stream analysis and less on purification of still infective viruses. Here we report the development of an efficient protocol requiring low sample input yielding purified viromes containing still infective phages which also are of sufficient purity for genome sequencing. We validated the method through spiking of known phages followed by plaque assays, qPCR and metagenomic sequencing. The protocol should facilitate the culturing of novel viruses from the gut as well as large scale studies on gut viromes.

scholarly journals Cosmic Inflation, Quantum Information and the Pioneering Role of John S Bell in Cosmology

Universe ◽  
2019 ◽  
Vol 5 (4) ◽  
pp. 92 ◽  
Author(s):  
Jérôme Martin
Keyword(s):  
Quantum Mechanics ◽  
Quantum Information ◽  
Large Scale ◽  
Gravitational Instability ◽  
Cosmic Inflation ◽  
Large Scale Structures ◽  
Scale Structures ◽  
Accuracy Data ◽  
Made In

According to the theory of cosmic inflation, the large scale structures observed in our Universe (galaxies, clusters of galaxies, Cosmic Background Microwave—CMB—anisotropy...) are of quantum mechanical origin. They are nothing but vacuum fluctuations, stretched to cosmological scales by the cosmic expansion and amplified by gravitational instability. At the end of inflation, these perturbations are placed in a two-mode squeezed state with the strongest squeezing ever produced in Nature (much larger than anything that can be made in the laboratory on Earth). This article studies whether astrophysical observations could unambiguously reveal this quantum origin by borrowing ideas from quantum information theory. It is argued that some of the tools needed to carry out this task have been discussed long ago by J. Bell in a, so far, largely unrecognized contribution. A detailled study of his paper and of the criticisms that have been put forward against his work is presented. Although J. Bell could not have realized it when he wrote his letter since the quantum state of cosmological perturbations was not yet fully characterized at that time, it is also shown that Cosmology and cosmic inflation represent the most interesting frameworks to apply the concepts he investigated. This confirms that cosmic inflation is not only a successful paradigm to understand the early Universe. It is also the only situation in Physics where one crucially needs General Relativity and Quantum Mechanics to derive the predictions of a theory and, where, at the same time, we have high-accuracy data to test these predictions, making inflation a playground of utmost importance to discuss foundational issues in Quantum Mechanics.

Role of autophagy in cancer prevention, development and therapy

2013 ◽  
Vol 55 ◽  
pp. 133-151 ◽  
Author(s):  
G. Vignir Helgason ◽  
Tessa L. Holyoake ◽  
Kevin M. Ryan
Keyword(s):  
Quality Control ◽  
Clinical Trials ◽  
Cancer Prevention ◽  
Mammalian Cells ◽  
Physiological Role ◽  
Anticancer Therapy ◽  
Substantial Progress ◽  
Health And Disease ◽  
Made In

Autophagy is a process that takes place in all mammalian cells and ensures homoeostasis and quality control. The term autophagy [self (auto)-eating (phagy)] was first introduced in 1963 by Christian de Duve, who discovered the involvement of lysosomes in the autophagy process. Since then, substantial progress has been made in understanding the molecular mechanism and signalling regulation of autophagy and several reviews have been published that comprehensively summarize these findings. The role of autophagy in cancer has received a lot of attention in the last few years and autophagy modulators are now being tested in several clinical trials. In the present chapter we aim to give a brief overview of recent findings regarding the mechanism and key regulators of autophagy and discuss the important physiological role of mammalian autophagy in health and disease. Particular focus is given to the role of autophagy in cancer prevention, development and in response to anticancer therapy. In this regard, we also give an updated list and discuss current clinical trials that aim to modulate autophagy, alone or in combination with radio-, chemo- or targeted therapy, for enhanced anticancer intervention.

scholarly journals Structural plasticity of actin-spectrin membrane skeleton and functional role of actin and spectrin in axon degeneration

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Guiping Wang ◽  
David J Simon ◽  
Zhuhao Wu ◽  
Deanna M Belsky ◽  
Evan Heller ◽  
...  
Keyword(s):  
Potential Role ◽  
Structural Plasticity ◽  
Membrane Skeleton ◽  
Retrograde Signaling ◽  
Axon Degeneration ◽  
Protein Loss ◽  
Connectivity Patterns ◽  
Substantial Progress ◽  
Made In

Axon degeneration sculpts neuronal connectivity patterns during development and is an early hallmark of several adult-onset neurodegenerative disorders. Substantial progress has been made in identifying effector mechanisms driving axon fragmentation, but less is known about the upstream signaling pathways that initiate this process. Here, we investigate the behavior of the actin-spectrin-based Membrane-associated Periodic Skeleton (MPS), and effects of actin and spectrin manipulations in sensory axon degeneration. We show that trophic deprivation (TD) of mouse sensory neurons causes a rapid disassembly of the axonal MPS, which occurs prior to protein loss and independently of caspase activation. Actin destabilization initiates TD-related retrograde signaling needed for degeneration; actin stabilization prevents MPS disassembly and retrograde signaling during TD. Depletion of βII-spectrin, a key component of the MPS, suppresses retrograde signaling and protects axons against degeneration. These data demonstrate structural plasticity of the MPS and suggest its potential role in early steps of axon degeneration.

scholarly journals Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data

2018 ◽  
Author(s):  
Janko Tackmann ◽  
João Frederico Matias Rodrigues ◽  
Christian von Mering
Keyword(s):  
Graphical Models ◽  
Large Scale ◽  
Study Data ◽  
Microbial Interactions ◽  
Data Sets ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Data Set ◽  
Seamless Integration

AbstractThe recent explosion of metagenomic sequencing data opens the door towards the modeling of microbial ecosystems in unprecedented detail. In particular, co-occurrence based prediction of ecological interactions could strongly benefit from this development. However, current methods fall short on several fronts: univariate tools do not distinguish between direct and indirect interactions, resulting in excessive false positives, while approaches with better resolution are so far computationally highly limited. Furthermore, confounding variables typical for cross-study data sets are rarely addressed. We present FlashWeave, a new approach based on a flexible Probabilistic Graphical Models framework to infer highly resolved direct microbial interactions from massive heterogeneous microbial abundance data sets with seamless integration of metadata. On a variety of benchmarks, FlashWeave outperforms state-of-the-art methods by several orders of magnitude in terms of speed while generally providing increased accuracy. We apply FlashWeave to a cross-study data set of 69 818 publicly available human gut samples, resulting in one of the largest and most diverse models of microbial interactions in the human gut to date.

scholarly journals Building a collaborative Psychological Science: Lessons learned from ManyBabies 1

2019 ◽  
Author(s):  
Krista Byers-Heinlein ◽  
Christina Bergmann ◽  
Catherine Davies ◽  
Michael C. Frank ◽  
Kiley Hamlin ◽  
...  
Keyword(s):  
Large Scale ◽  
Organizational Structures ◽  
Open Science ◽  
Lessons Learned ◽  
Psychological Science ◽  
Difficult Challenge ◽  
Implementation Data ◽  
Successes And Challenges ◽  
Made In

The field of infancy research faces a difficult challenge: some questions require samples that are simply too large for any one lab to recruit and test. ManyBabies aims to address this problem by forming large-scale collaborations on key theoretical questions in developmental science, while promoting the uptake of Open Science practices. Here, we look back on the first project completed under the ManyBabies umbrella – ManyBabies 1 – which tested the development of infant-directed speech preference. Our goal is to share the lessons learned over the course of the project and to articulate our vision for the role of large-scale collaborations in the field. First, we consider the decisions made in scaling up experimental research for a collaboration involving 100+ researchers and 70+ labs. Next, we discuss successes and challenges over the course of the project, including: protocol design and implementation, data analysis, organizational structures and collaborative workflows, securing funding, and encouraging broad participation in the project. Finally, we discuss the benefits we see both in ongoing ManyBabies projects and in future large-scale collaborations in general, with a particular eye towards developing best practices and increasing growth and diversity in infancy research and psychological science in general. Throughout the paper, we include first-hand narrative experiences, in order to illustrate the perspectives of researchers playing different roles within the project. While this project focused on the unique challenges of infant research, many of the insights we gained can be applied to large-scale collaborations across the broader field of psychology.

scholarly journals Irrigation in the Ili River Basin of Central Asia: From Ditches to Dams and Diversion

Water ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 1650 ◽  
Author(s):  
Steven Pueppke ◽  
Qingling Zhang ◽  
Sabir Nurtazin
Keyword(s):  
Iron Age ◽  
Large Scale ◽  
New Technologies ◽  
18Th Century ◽  
Irrigated Agriculture ◽  
Ili River Basin ◽  
The 1960S ◽  
The 19Th Century ◽  
Made In

Central Asia’s Ili River is fed by mountain streams that flow down into an isolated and arid basin that today is shared by Kazakhstan and China. Agriculture in the basin is dependent upon irrigation, which was practiced as long ago as the Iron Age, when early pastoralists constructed ditches to channel water from streams onto nearby fields. Irrigation had become much more common by the 18th century, when the region was controlled by the Dzungarian Khanate. The khanate was toppled by the Qing Chinese in the 1750s in the first of a series of confrontations that destroyed and then rebuilt the basin’s agricultural economy. The region has since been dominated by a succession of Chinese and Russian (and later Soviet and independent Kazakh) governments, each of which recognized the essential role of irrigated agriculture in maintaining control. Thus every cycle of destruction led to reclamation of new lands, resettlement of farmers and upgrading of infrastructure to expand irrigation. This allowed an impressive diversity of fruits, vegetables and field crops to be grown, especially on loess soils of the more fertile upper basin, where tributaries could be easily tapped by gravity flow. Many of these tributaries were entirely diverted by the 19th century, so that they no longer reached the Ili. Large scale irrigation commenced in the 1960s, when the Soviets built Kapchagai dam and reservoir in the lower part of the basin and installed pumps to raise water from the Ili River onto nearby reclaimed sierozem soils, mostly for cultivation of rice. China later constructed a cluster of small- and medium-sized dams that enabled expansion of agriculture in the upper part of the basin. Many irrigated areas along the lower reaches of the Ili in Kazakhstan have been abandoned, but irrigation in the upper basin continues to expand. Declining soil fertility, salinization, pollution, insufficient inflows and adverse economic conditions currently challenge irrigation across the entire basin. Investments are being made in new technologies as a means to sustain irrigated agriculture in the basin, but it remains to be seen if these strategies will be successful.

Reducing the Role of Government -- The Chinese Experiment

2008 ◽  
Vol 3 ◽  
pp. 1-37
Author(s):  
Vivienne Bath
Keyword(s):  
Role Of Government ◽  
Substantial Progress ◽  
The Law ◽  
The Government ◽  
Administrative Licensing ◽  
Made In

AbstractChina has taken an original and adventurous approach to the issue of over-regulation through the promulgation of the Administrative Licensing Law, which attempts to limit the number and type of licences and approvals which citizens and enterprises are obliged to obtain from the government. The Administrative Licensing Law has now been in effect for 3 years, and it is therefore an appropriate time to look at licensing and approvals in China. The article focuses on issues relating to the establishment and reduction of licensing requirements, including the actions taken by government to reduce them, the existence of “non-administrative” licensing and approval requirements and issues relating to enforcement. It concludes that although substantial progress has been made, improvements could be made in terms of dealing with the complexity of the system and providing new avenues for enforcement, and that a long-term on-going effort will be required to implement the law fully.

scholarly journals Landscape Level Interactions Among Ungulates, Vegetation, and Large-Scale Fires in Northern Yellowstone National Park

1990 ◽  
Vol 14 ◽  
pp. 179-181
Author(s):  
Monica Turner ◽  
William Romme ◽  
Linda Wallace
Keyword(s):  
Populus Tremuloides ◽  
Large Scale ◽  
National Laboratory ◽  
Model Development ◽  
Field Studies ◽  
Full Time ◽  
Oak Ridge ◽  
The Past ◽  
Substantial Progress ◽  
Made In

Substantial progress has been made in both the modeling and field studies during the first six months of research funding. Yegang Wu, Jennifer O'Hara, and Michael O'Hara all began working full time for the project on September 1, 1990. Wu is based at Oak Ridge National Laboratory (ORNL) and is working primarily on model development and analyses using the geographic information system (GIS) located in Yellowstone. The O'Hara's are based in Yellowstone and are working full time on the field studies. Here we describe our progress during the past six months for each main area of the proposed work: 1. field studies, including aspen (Populus tremuloides) and grassland sampling, and 2. model development and GIS analyses.

scholarly journals Entrepreneurship through Micro Finance in North East India: A Comprehensive Review of Existing Literature

2012 ◽  
Vol 4 (4) ◽  
pp. 168-184 ◽  
Author(s):  
Sanjay Kanti Das
Keyword(s):  
Large Scale ◽  
Small Scale ◽  
Secondary Sources ◽  
North East India ◽  
North East ◽  
Rapid Industrialization ◽  
Unemployed Youth ◽  
Distribution Of Income ◽  
Made In

Entrepreneurship on small scale is the only solution to the problems of unemployment and proper utilization of both human and non-human resources and improving the living conditions of the poor masses. The basic rationale of developing these industries are that they provide immediate large scale employment, ensure more equitable distribution of income, encourage decentralization of industries and eradicate poverty and unemployment. During the last three decades, many countries of the world have experienced the need and importance of entrepreneurship has been accepted as a strategy to achieve the twin objectives of promotion of entrepreneurship, particularly among the educated unemployed youth and also for rapid industrialization in the economy. The main object of this paper is to study the existing literature on entrepreneurship through Micro finance-SHG linkage in India in general and NER in particular. The analysis of this study is based on secondary sources. Efforts are also made in this paper to analyze the role of micro finance through SHGs in the promotion and development of entrepreneurship. This paper examines the different approaches of entrepreneurship and also explains the different key areas of micro enterprise development. Finally, this paper highlights the problems of micro, rural and women entrepreneurs and also suggested some specific measures based on the survey of existing literature, for the promotion of these industries in the country.

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