scholarly journals Virus-Host Infection Dynamics of Marine Single-Celled Eukaryotes Resolved from Metatranscriptomics

2016 ◽  
Author(s):  
Mohammad Moniruzzaman ◽  
Louie L. Wurch ◽  
Harriet Alexander ◽  
Sonya T. Dyhrman ◽  
Christopher J. Gobler ◽  
...  
Keyword(s):  
Viral Infections ◽  
Global Scale ◽  
Narragansett Bay ◽  
Brown Tide ◽  
Virus Infections ◽  
Natural Systems ◽  
Eukaryotic Diversity ◽  
Host Relationships ◽  
Host Infection

AbstractMetatranscriptomics has emerged as a tool in microbial ecology that can resolve the functional landscape of both prokaryotes and eukaryotes within a community. In this study, we extend the potential of metatranscriptomics to probe active virus infections and virus-host relationships in marine systems. Polyadenylation-selected RNA-seq data were examined from microbial communities in two productive marine environments: a brown tide bloom event dominated by Aureococcus anophagefferens in Quantuck Bay, NY, and a diatom-dominated plankton community in Narragansett Bay, RI. Active infections by diverse giant viruses (NCLDVs) of algal and non-algal hosts were found at both sites. Ongoing infections of A. anophagefferens by a known Mimiviridae (AaV) were observed during both the peak and decline of the bloom. Bloom decline was also accompanied by increased activity for viruses other than AaV, including (+) ssRNA viruses. In Narragansett Bay, increased temporal reso’lution revealed active NCLDVs with both ‘boom-and-bust’ as well as ‘steady-state infection’-like ecologies. Statistical co-occurrence examinations of the dsDNA, ssRNA and dsRNA markers within the data revealed a broad spectrum of statistically strong and significant virus-host relationships that included both known as well as novel interactions. Our approach offers a method for screening the diversity and dynamics of active viral infections in natural systems and develops links between viruses and their potential hosts in situ.SignificanceViruses are important partners in ecosystem scale ecology, yet their study to date is primarily limited to single virus-host infection models in the laboratory or limited to “potential-actions” derived from metagenomics analyses. Using metatranscriptomic sequences from polyadenylated-RNA selected samples, we have simultaneously captured information regarding eukaryotic diversity and active infection by viruses with dsDNA genomes, resulting in a statistical opportunity to predict “who is infecting whom”. This approach further provides concurrent insight regarding viruses with ssRNA and dsRNA genomes, capturing dynamics for the communities of viruses infecting single-celled eukaryotes. Given the central role of these plankton in global scale processes, our efforts result in a transformational step-forward regarding the study of in situ virus-host interactions.

Detection of Nucleic Acids in Cells or Tissue Sections Using In situ Polymerase Chain Reaction (PCR)

1996 ◽  
Vol 54 ◽  
pp. 16-17
Author(s):  
J. R. Hully ◽  
K. R. Luehrsen ◽  
K. Aoyagi ◽  
C. Shoemaker ◽  
R. Abramson
Keyword(s):  
Nucleic Acids ◽  
Viral Infections ◽  
Anatomical Location ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
Cellular Source ◽  
Gene Transcripts ◽  
Initial Description ◽  
In Cells

The development of PCR technology has greatly accelerated medical research at the genetic and molecular levels. Until recently, the inherent sensitivity of this technique has been limited to isolated preparations of nucleic acids which lack or at best have limited morphological information. With the obvious exception of cell lines, traditional PCR or reverse transcription-PCR (RT-PCR) cannot identify the cellular source of the amplified product. In contrast, in situ hybridization (ISH) by definition, defines the anatomical location of a gene and/or it’s product. However, this technique lacks the sensitivity of PCR and cannot routinely detect less than 10 to 20 copies per cell. Consequently, the localization of rare transcripts, latent viral infections, foreign or altered genes cannot be identified by this technique. In situ PCR or in situ RT-PCR is a combination of the two techniques, exploiting the sensitivity of PCR and the anatomical definition provided by ISH. Since it’s initial description considerable advances have been made in the application of in situ PCR, improvements in protocols, and the development of hardware dedicated to in situ PCR using conventional microscope slides. Our understanding of the importance of viral latency or viral burden in regards to HIV, HPV, and KSHV infections has benefited from this technique, enabling detection of single viral copies in cells or tissue otherwise thought to be normal. Clearly, this technique will be useful tool in pathobiology especially carcinogenesis, gene therapy and manipulations, the study of rare gene transcripts, and forensics.

Therapeutic Exploitation of Viral Interference

2020 ◽  
Vol 20 (4) ◽  
pp. 423-432 ◽  
Author(s):  
Imre Kovesdi ◽  
Tibor Bakacs
Keyword(s):  
Broad Spectrum ◽  
Viral Infections ◽  
Viral Vector ◽  
Antiviral Treatment ◽  
Type I ◽  
Virus Infections ◽  
Emerging Viruses ◽  
Viral Interference ◽  
Pathogenic Virus ◽  
Hepatitis C Rna

: Viral interference, originally, referred to a state of temporary immunity, is a state whereby infection with a virus limits replication or production of a second infecting virus. However, replication of a second virus could also be dominant over the first virus. In fact, dominance can alternate between the two viruses. Expression of type I interferon genes is many times upregulated in infected epithelial cells. Since the interferon system can control most, if not all, virus infections in the absence of adaptive immunity, it was proposed that viral induction of a nonspecific localized temporary state of immunity may provide a strategy to control viral infections. Clinical observations also support such a theory, which gave credence to the development of superinfection therapy (SIT). SIT is an innovative therapeutic approach where a non-pathogenic virus is used to infect patients harboring a pathogenic virus. : For the functional cure of persistent viral infections and for the development of broad- spectrum antivirals against emerging viruses a paradigm shift was recently proposed. Instead of the virus, the therapy should be directed at the host. Such a host-directed-therapy (HDT) strategy could be the activation of endogenous innate immune response via toll-like receptors (TLRs). Superinfection therapy is such a host-directed-therapy, which has been validated in patients infected with two completely different viruses, the hepatitis B (DNA), and hepatitis C (RNA) viruses. SIT exerts post-infection interference via the constant presence of an attenuated non-pathogenic avian double- stranded (ds) RNA viral vector which boosts the endogenous innate (IFN) response. SIT could, therefore, be developed into a biological platform for a new “one drug, multiple bugs” broad-spectrum antiviral treatment approach.

scholarly journals Innate Immunity in Children and the Role of ACE2 Expression in SARS-CoV-2 Infection

2021 ◽  
Vol 13 (3) ◽  
pp. 363-382
Author(s):  
Mario Dioguardi ◽  
Angela Pia Cazzolla ◽  
Claudia Arena ◽  
Diego Sovereto ◽  
Giorgia Apollonia Caloro ◽  
...  
Keyword(s):  
Innate Immunity ◽  
Viral Infections ◽  
Respiratory Infections ◽  
Viral Disease ◽  
Receptor Expression ◽  
Virus Infections ◽  
Search Terms ◽  
Bibliographic Search ◽  
Meta Analyses

COVID-19 (Coronavirus Disease 2019) is an emerging viral disease caused by the coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which leads to severe respiratory infections in humans. The first reports came in December 2019 from the city of Wuhan in the province of Hubei in China. It was immediately clear that children developed a milder disease than adults. The reasons for the milder course of the disease were attributed to several factors: innate immunity, difference in ACE2 (angiotensin-converting enzyme II) receptor expression, and previous infections with other common coronaviruses (CovH). This literature review aims to summarize aspects of innate immunity by focusing on the role of ACE2 expression and viral infections in children in modulating the antibody response to SARS-CoV-2 infection. This review was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Articles deemed potentially eligible were considered, including those dealing with COVID-19 in children and providing more up-to-date and significant data in terms of epidemiology, prognosis, course, and symptoms, focusing on the etiopathogenesis of SARS-CoV-2 disease in children. The bibliographic search was conducted using the search engines PubMed and Scopus. The following search terms were entered in PubMed and Scopus: COVID-19 AND ACE2 AND Children; COVID-19 AND Immunity innate AND children. The search identified 857 records, and 18 studies were applicable based on inclusion and exclusion criteria that addressed the issues of COVID-19 concerning the role of ACE2 expression in children. The scientific literature agrees that children develop milder COVID-19 disease than adults. Milder symptomatology could be attributed to innate immunity or previous CovH virus infections, while it is not yet fully understood how the differential expression of ACE2 in children could contribute to milder disease.

scholarly journals Methods for Estimating Gene Frequencies and Detecting Selection in Bacterial Populations

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 499-508 ◽  
Author(s):  
Bruce Rannala ◽  
Wei-Gang Qiu ◽  
Daniel E Dykhuizen
Keyword(s):  
Ixodes Scapularis ◽  
Balancing Selection ◽  
Surface Protein ◽  
Allele Frequencies ◽  
Gene Frequencies ◽  
Bacterial Populations ◽  
Polymerase Chain ◽  
Host Infection ◽  
Infinite Alleles Model

Abstract Recent breakthroughs in molecular technology, most significantly the polymerase chain reaction (PCR) and in situ hybridization, have allowed the detection of genetic variation in bacterial communities without prior cultivation. These methods often produce data in the form of the presence or absence of alleles or genotypes, however, rather than counts of alleles. Using relative allele frequencies from presence-absence data as estimates of population allele frequencies tends to underestimate the frequencies of common alleles and overestimate those of rare ones, potentially biasing the results of a test of neutrality in favor of balancing selection. In this study, a maximum-likelihood estimator (MLE) of bacterial allele frequencies designed for use with presence-absence data is derived using an explicit stochastic model of the host infection (or bacterial sampling) process. The performance of the MLE is evaluated using computer simulation and a method is presented for evaluating the fit of estimated allele frequencies to the neutral infinite alleles model (IAM). The methods are applied to estimate allele frequencies at two outer surface protein loci (ospA and ospC) of the Lyme disease spirochete, Borrelia burgdorferi, infecting local populations of deer ticks (Ixodes scapularis) and to test the fit to a neutral IAM.

scholarly journals Virus infections of honeybees Apis Mellifera

2015 ◽  
Vol 4 (3) ◽  
Author(s):  
Giuseppina Tantillo ◽  
Marilisa Bottaro ◽  
Angela Di Pinto ◽  
Vito Martella ◽  
Pietro Di Pinto ◽  
...  
Keyword(s):  
Viral Infections ◽  
Control Strategies ◽  
Future Research ◽  
Virus Infections ◽  
Deformed Wing Virus ◽  
Starting Point ◽  
Invasive Organisms ◽  
Queen Cell ◽  
Kashmir Bee Virus ◽  
Paralysis Virus

The health and vigour of honeybee colonies are threatened by numerous parasites (such as <em>Varroa destructor</em> and <em>Nosema</em> spp.) and pathogens, including viruses, bacteria, protozoa. Among honeybee pathogens, viruses are one of the major threats to the health and wellbeing of honeybees and cause serious concern for researchers and beekeepers. To tone down the threats posed by these invasive organisms, a better understanding of bee viral infections will be of crucial importance in developing effective and environmentally benign disease control strategies. Here we summarize recent progress in the understanding of the morphology, genome organization, transmission, epidemiology and pathogenesis of eight honeybee viruses: Deformed wing virus (DWV) and Kakugo virus (KV); Sacbrood virus (SBV); Black Queen cell virus (BQCV); Acute bee paralysis virus (ABPV); Kashmir bee virus (KBV); Israeli Acute Paralysis Virus (IAPV); Chronic bee paralysis virus (CBPV). The review has been designed to provide researchers in the field with updated information about honeybee viruses and to serve as a starting point for future research.

scholarly journals Two decades of in-situ temperature measurements in the upper troposphere and lowermost stratosphere from IAGOS long-term routine observation

2017 ◽  
Author(s):  
Florian Berkes ◽  
Patrick Neis ◽  
Martin G. Schultz ◽  
Ulrich Bundke ◽  
Susanne Rohs ◽  
...  
Keyword(s):  
Weather Forecast ◽  
Global Scale ◽  
Temperature Trend ◽  
Data Set ◽  
Medium Range Weather Forecast ◽  
Upper Troposphere ◽  
Temperature Trends ◽  
Geographical Regions

Abstract. Despite several studies on temperature trends in the tropopause region, a comprehensive understanding of the evolution of temperatures in this climate-sensitive region of the atmosphere remains elusive. Here we present a unique global-scale, long-term data set of high-resolution in-situ temperature data measured aboard passenger aircraft within the European Research Infrastructure IAGOS (In-service Aircraft for a Global Observing System, www.iagos.org). This data set is used to investigate temperature trends within the global upper troposphere and lowermost stratosphere (UTLS) for the period 1995 to 2012 in different geographical regions and vertical layers of the UTLS. The largest amount of observations is available over the North Atlantic. Here, a neutral temperature trend is found within the lowermost stratosphere. This contradicts the temperature trend in the European Centre for Medium Range Weather Forecast (ECMWF) ERA-Interim reanalysis, where a significant (95 % confidence) temperature increase of +0.56 K/decade is obtained. Differences between trends derived from observations and reanalysis data can be traced back to changes in the temperature bias between observation and model data over the studied period. This study demonstrates the value of the IAGOS temperature observations as anchor point for the evaluation of reanalyses and its suitability for independent trend analyses.

Clinical use of Antiviral Drugs

1987 ◽  
Vol 21 (5) ◽  
pp. 399-405 ◽  
Author(s):  
Milap C. Nahata
Keyword(s):  
Influenza A ◽  
Viral Infections ◽  
Antiviral Agent ◽  
Antiviral Drugs ◽  
Investigational Drug ◽  
Virus Infections ◽  
Herpes Encephalitis ◽  
Herpes Simplex Viruses ◽  
Varicella Zoster ◽  
Syncytial Virus

Remarkable progress has been made in antiviral chemotherapy. Six approved antiviral drugs are now available for the treatment of various viral infections. Trifluridine, idoxuridine and vidarabine are all effective in patients with herpes keratitis; trifluridine is preferred due to its low toxicity. Acyclovir is the drug of choice in patients with infections due to herpes simplex viruses, including genital herpes, herpes encephalitis, and neonatal herpes, and infections due to varicella-zoster virus. Amantadine is the only drug currently available for prophylaxis and treatment of influenza A, but an investigational drug, rimantadine, appears to be equally effective and less toxic than amantadine. Ribavirin is the most recently approved antiviral agent for the treatment of respiratory syncytial virus infections. Numerous antiviral drugs are being studied in patients with acquired immunodeficiency syndrome. Although currently available drugs have improved our ability to manage a variety of viral illnesses, much needs to be learned about specific dosage guidelines based on the studies of pharmacokinetics, pharmacodynamics, potential adverse effects and viral resistance, and the role of combination therapy to optimize therapy.

scholarly journals Virus-mediated archaeal hecatomb in the deep seafloor

2016 ◽  
Vol 2 (10) ◽  
pp. e1600492 ◽  
Author(s):  
Roberto Danovaro ◽  
Antonio Dell’Anno ◽  
Cinzia Corinaldesi ◽  
Eugenio Rastelli ◽  
Ricardo Cavicchioli ◽  
...  
Keyword(s):  
Viral Infection ◽  
Deep Sea ◽  
Viral Infections ◽  
Biogeochemical Cycles ◽  
Global Scale ◽  
Viral Lysis ◽  
Group I ◽  
Global Biogeochemical Cycles ◽  
Bacterial Genes ◽  
The Impact

Viruses are the most abundant biological entities in the world’s oceans, and they play a crucial role in global biogeochemical cycles. In deep-sea ecosystems, archaea and bacteria drive major nutrient cycles, and viruses are largely responsible for their mortality, thereby exerting important controls on microbial dynamics. However, the relative impact of viruses on archaea compared to bacteria is unknown, limiting our understanding of the factors controlling the functioning of marine systems at a global scale. We evaluate the selectivity of viral infections by using several independent approaches, including an innovative molecular method based on the quantification of archaeal versus bacterial genes released by viral lysis. We provide evidence that, in all oceanic surface sediments (from 1000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria. We also found that, within deep-sea benthic archaea, the impact of viruses was mainly directed at members of specific clades of Marine Group I Thaumarchaeota. Although archaea represent, on average, ~12% of the total cell abundance in the top 50 cm of sediment, virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of ~0.3 to 0.5 gigatons of carbon per year globally. Our results indicate that viral infection represents a key mechanism controlling the turnover of archaea in surface deep-sea sediments. We conclude that interactions between archaea and their viruses might play a profound, previously underestimated role in the functioning of deep-sea ecosystems and in global biogeochemical cycles.

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