scholarly journals Evaluation of Two Approaches for Assessing the Genetic Similarity of Virioplankton Populations as Defined by Genome Size

2012 ◽  
Vol 78 (24) ◽  
pp. 8773-8783 ◽  
Author(s):  
Sanchita Jamindar ◽  
Shawn W. Polson ◽  
Sharath Srinivasiah ◽  
Lisa Waidner ◽  
K. Eric Wommack
Keyword(s):  
Genome Size ◽  
Spatial Scales ◽  
Low Cost ◽  
Geographic Location ◽  
Host Interactions ◽  
Pcr Fingerprinting ◽  
Rapd Pcr ◽  
Turn Over ◽  
Viral Host Interactions ◽  
Dna Pcr

ABSTRACTViral production estimates show that virioplankton communities turn over rapidly in aquatic ecosystems. Thus, it is likely that the genetic identity of viral populations comprising the virioplankton also change over temporal and spatial scales, reflecting shifts in viral-host interactions. However, there are few approaches that can provide data on the genotypic identity of viral populations at low cost and with the sample throughput necessary to assess dynamic changes in the virioplankton. This study examined two of these approaches—T4-like major capsid protein (g23) gene polymorphism and randomly amplified polymorphic DNA-PCR (RAPD-PCR) fingerprinting—to ask how well each technique could track differences in virioplankton populations over time and geographic location. Seasonal changes in overall virioplankton composition were apparent from pulsed-field gel electrophoresis (PFGE) analysis. T4-like phages containing similar g23 proteins were found within both small- and large-genome populations, including populations from different geographic locations and times. The surprising occurrence of T4-like g23 within small genomic groups (23 to 64 kb) indicated that the genome size range of T4-like phages may be broader than previously believed. In contrast, RAPD-PCR fingerprinting detected high genotypic similarity within PFGE bands from the same location, time, and genome size class without the requirement for DNA sequencing. Unlike g23 polymorphism, RAPD-PCR fingerprints showed a greater temporal than geographic variation. Thus, while polymorphism in a viral signature gene, such as g23, can be a powerful tool for inferring evolutionary relationships, the degree to which this approach can capture fine-scale variability within virioplankton populations is less clear.

scholarly journals Characterization of verocytotoxin-producingEscherichia coliO157 isolates from patients with haemolytic uraemic syndrome in Western Europe

1995 ◽  
Vol 115 (1) ◽  
pp. 1-3 ◽  
Author(s):  
A. E. Heuvelink ◽  
N. C. A. J. van de Kar ◽  
J. F. G. M. Meis ◽  
L. A. H. Monnens ◽  
W. J. G. Melchers
Keyword(s):  
Haemolytic Uraemic Syndrome ◽  
Western Europe ◽  
Random Amplified Polymorphic Dna ◽  
E Coli ◽  
Pcr Fingerprinting ◽  
Phage Types ◽  
Rapd Pcr ◽  
Typing Methods ◽  
Dna Pcr

SummaryFifty verocytotoxin (VT)-producingEscherichia coli(VTEC) strains of serogroup O157 were characterized by phage typing, polymerase chain reaction (PCR) for VT genes and theE. coliattaching and effacing (eae) gene, and random amplified polymorphic DNA–PCR (RAPD–PCR) fingerprinting. The collection represented isolates obtained from patients with diarrhoea-associated haemolytic-uraemic syndrome (D+ HUS) and their family contacts, isolated in the Netherlands, Belgium and Germany between 1989 and 1993. Based on isolates from separate families (n= 27) seven different phage types were identified, types 2 (44%) and 4 (33%) were predominant. Eighty-five percent of the strains contained only VT2 gene sequences and 15% both VT1 and VT2. All strains of the dominant phage types 2 and 4 carried the VT2 gene. Strains that belonged to the minor phage types 8, 14, 32 carried both VT1 and VT2 genes, with the exception of two isolates identified as phage types 49 and 54 which contained only VT2 genes. All O157 VTEC strains possessed the chromosomally-locatedeaegene, which indicates its usefulness as virulence marker. RAPD–PCR fingerprinting identified four distinct banding patterns, with one profile found among 79% of the strains. Based on the combined results of all typing methods used in this study, the collection of 50 O157 VTEC strains could be divided into nine distinct groups. Strains isolated from different persons within one family could not be distinguished by any of these methods. The data suggest that O157 VTEC strains are members of one clone that has become widely distributed.

scholarly journals Chikungunya and Zika Viruses: Co-Circulation and the Interplay between Viral Proteins and Host Factors

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 448
Author(s):  
Sineewanlaya Wichit ◽  
Nuttamonpat Gumpangseth ◽  
Rodolphe Hamel ◽  
Sakda Yainoy ◽  
Siwaret Arikit ◽  
...  
Keyword(s):  
Antiviral Drug ◽  
Virus Transmission ◽  
Antiviral Agent ◽  
Viral Proteins ◽  
Targeted Therapeutics ◽  
Limited Information ◽  
Mosquito Vectors ◽  
Host Proteins ◽  
Host Interactions ◽  
Viral Host Interactions

Chikungunya and Zika viruses, both transmitted by mosquito vectors, have globally re-emerged over for the last 60 years and resulted in crucial social and economic concerns. Presently, there is no specific antiviral agent or vaccine against these debilitating viruses. Understanding viral–host interactions is needed to develop targeted therapeutics. However, there is presently limited information in this area. In this review, we start with the updated virology and replication cycle of each virus. Transmission by similar mosquito vectors, frequent co-circulation, and occurrence of co-infection are summarized. Finally, the targeted host proteins/factors used by the viruses are discussed. There is an urgent need to better understand the virus–host interactions that will facilitate antiviral drug development and thus reduce the global burden of infections caused by arboviruses.

scholarly journals A low-cost technique to measure bank erosion proces ses along middle-size river reaches

2018 ◽  
Author(s):  
Gonzalo Duró ◽  
Alessandra Crosato ◽  
Maarten G. Kleinhans ◽  
Wim S. J. Uijttewaal
Keyword(s):  
Laser Scanning ◽  
Spatial Scales ◽  
Low Cost ◽  
Bank Erosion ◽  
Water Levels ◽  
Small Scale ◽  
Observation Distance ◽  
River Bank ◽  
Erosion Processes ◽  
Rtk Gps

Abstract. Diverse methods are currently available to measure river bank erosion at broad-ranging temporal and spatial scales. Yet, no technique provides low-cost and high-resolution to survey small-scale bank processes along a river reach. We investigate the capabilities of Structure-from-Motion photogrammetry applied with imagery from an Unmanned Aerial Vehicle (UAV) to describe the evolution of riverbank profiles in middle-size rivers. The bank erosion cycle is used as a reference to assess the applicability of different techniques. We surveyed 1.2 km of a restored bank of the Meuse River eight times within a year, combining different photograph perspectives and overlaps to identify an efficient UAV flight to monitor banks. The accuracy of the Digital Surface Models (DSMs) was evaluated compared with RTK GPS points and an Airborne Laser Scanning (ALS) of the whole reach. An oblique perspective with eight photo overlaps was sufficient to achieve the highest relative precision to observation distance of ~1:1400, with 10 cm error range. A complementary nadiral view increased coverage behind bank toe vegetation. The DSM and ALS had comparable accuracies except on banks, where the latter overestimates elevations. Sequential DSMs captured signatures of the erosion cycle such as mass failures, slump-block deposition, and bank undermining. Although this technique requires low water levels and banks without dense vegetation, it is a low-cost method to survey reach-scale riverbanks in sufficient resolution to quantify bank retreat and identify morphological features of the bank failure and erosion processes.

scholarly journals Novel approach to enhance coastal habitat and biotope mapping with drone aerial imagery analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
João Gama Monteiro ◽  
Jesús L. Jiménez ◽  
Francesca Gizzi ◽  
Petr Přikryl ◽  
Jonathan S. Lefcheck ◽  
...  
Keyword(s):  
Anthropogenic Impacts ◽  
Spatial Scales ◽  
Low Cost ◽  
Human Populations ◽  
Coastal Habitat ◽  
Coastal Monitoring ◽  
Monitoring Programs ◽  
Novel Approach ◽  
Aerial Platforms ◽  
Rocky Habitats

AbstractUnderstanding the complex factors and mechanisms driving the functioning of coastal ecosystems is vital towards assessing how organisms, ecosystems, and ultimately human populations will cope with the ecological consequences of natural and anthropogenic impacts. Towards this goal, coastal monitoring programs and studies must deliver information on a range of variables and factors, from taxonomic/functional diversity and spatial distribution of habitats, to anthropogenic stress indicators such as land use, fisheries use, and pollution. Effective monitoring programs must therefore integrate observations from different sources and spatial scales to provide a comprehensive view to managers. Here we explore integrating aerial surveys from a low-cost Remotely Piloted Aircraft System (RPAS) with concurrent underwater surveys to deliver a novel approach to coastal monitoring. We: (i) map depth and substrate of shallow rocky habitats, and; (ii) classify the major biotopes associated with these environmental axes; and (iii) combine data from i and ii to assess the likely distribution of common sessile organismal assemblages over the survey area. Finally, we propose a general workflow that can be adapted to different needs and aerial platforms, which can be used as blueprints for further integration of remote-sensing with in situ surveys to produce spatially-explicit biotope maps.

scholarly journals Diversity, pathogenicity and pandemic potential of Henipavirus: an interview with Benhur Lee

2019 ◽  
Vol 14 (7) ◽  
pp. 449-451
Author(s):  
Benhur Lee
Keyword(s):  
Advisory Committee ◽  
Recombinant Dna ◽  
International Committee ◽  
University Of Pennsylvania ◽  
Yale University ◽  
Postdoctoral Training ◽  
Host Interactions ◽  
School Of Medicine ◽  
The University ◽  
Viral Host Interactions

Biography Dr Benhur Lee is a Professor of Microbiology at the Icahn School of Medicine at Mount Sinai (ISMMS, NY, USA). He obtained his MD from Yale University School of Medicine (1995) and completed his clinical/postdoctoral training at the University of Pennsylvania (1995–2001). He was a Professor in the Department of Microbiology, Immunology & Molecular Genetics at the David Geffen School of Medicine at UCLA (2001–2013). Dr Lee is an appointed member of the NIH Novel and Exceptional Technology and Research Advisory Committee (NExTRAC), formerly known as the recombinant DNA Advisory committee (RAC). He is also on the International Committee on Taxonomy of Viruses (ICTV, paramyxovirus study group). Dr Lee has a special interest in emerging RNA viruses and HIV with a focus on molecular viral-host interactions that govern virus entry and budding.

Apoptosis and autophagy as a turning point in viral–host interactions: the case of human norovirus and its surrogates

2020 ◽  
Author(s):  
Sean Kennedy ◽  
Mélanie M Leroux ◽  
Alexis Simons ◽  
Brice Malve ◽  
Marc Devocelle ◽  
...  
Keyword(s):  
Viral Entry ◽  
Turning Point ◽  
Infection Process ◽  
Host Interactions ◽  
Antiviral Therapies ◽  
Leading Role ◽  
Host Interaction ◽  
Major Response ◽  
Causes Of Disease ◽  
Viral Host Interactions

Human gastroenteritis viruses are amid the major causes of disease worldwide, responsible for more than 2 million deaths per year. Human noroviruses play a leading role in the gastroenteritis outbreaks and the continuous emergence of new strains contributes to the significant morbidity and mortality. Many aspects of the viral entry and infection process remain unclear, including the major response of the host cell to the virus, which is the trigger of several programmed cell death related mechanisms. In this review, we assessed apoptosis and autophagy at various stages in the infection process to provide better understanding of the viral–host interaction. This brings us closer to fully understanding how noroviruses work, thus allowing the development of specific antiviral therapies.

scholarly journals Twelfth International Foamy Virus Conference—Meeting Report

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 134 ◽  
Author(s):  
Ottmar Herchenröder ◽  
Martin Löchelt ◽  
Florence Buseyne ◽  
Antoine Gessain ◽  
Marcelo A. Soares ◽  
...  
Keyword(s):  
Viral Vectors ◽  
Foamy Virus ◽  
Meeting Report ◽  
Virus Structure ◽  
Host Interactions ◽  
Research Areas ◽  
Current State ◽  
Foamy Viruses ◽  
Viral Host Interactions ◽  
Human Primate

The 12th International Foamy Virus Conference took place on August 30–31, 2018 at the Technische Universität Dresden, Dresden, Germany. The meeting included presentations on current research on non-human primate and non-primate foamy viruses (FVs; also called spumaretroviruses) as well as keynote talks on related research areas in retroviruses. The taxonomy of foamy viruses was updated earlier this year to create five new genera in the subfamily, Spumaretrovirinae, based on their animal hosts. Research on viruses from different genera was presented on topics of potential relevance to human health, such as natural infections and cross-species transmission, replication, and viral-host interactions in particular with the immune system, dual retrovirus infections, virus structure and biology, and viral vectors for gene therapy. This article provides an overview of the current state-of-the-field, summarizes the meeting highlights, and presents some important questions that need to be addressed in the future.

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