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1. Temporal profiling resolves the drivers of microbial nitrogen cycling variability in coastal sediments

Author:
Helen L. Hayden,   et al.   ; Alexis J. Marshall; Lori Phillips; Andrew Longmore; Karla B. Heidelberg; Caixian Tang; Pauline Mele;     Show all 7 Authors
Source:
Science of the total environment 2023 v.856 pp. 159057
ISSN:
0048-9697
Subject:
Archaea; DNA; RNA; ammonium; anaerobic ammonium oxidation; coastal zone management; detection limit; environment; genes; microbial activity; microbial nitrogen; nitrates; nitrites; nitrogen fixation; oxidation; phylogeny; seasonal variation; sediments; Australia
Abstract:
... Here we describe the potential for sediment microbial nitrogen-cycling gene (DNA) and activity (RNA) abundances to spatially resolve coastal areas impacted by seasonal variability in external nutrient inputs. Three sites were chosen within a nitrogen-limited embayment, Port Phillip Bay (PPB), Australia that reflect variability in both proximity to external nutrient inputs and the dominant form of ...
DOI:
10.1016/j.scitotenv.2022.159057

2. Transmission of mushroom virus X and the impact of virus infection on the transcriptomes and proteomes of different strains of Agaricus bisporus

Author:
Helen Grogan,   et al.   ; Eoin O'Connor; Sean Doyle; Aniça Amini; David A. Fitzpatrick;     Show all 5 Authors
Source:
Fungal biology 2021 v.125 no.9 pp. 704-717
ISSN:
1878-6146
Subject:
Agaricus bisporus; Myoviridae; RNA; color; food crops; fruits; gene expression; gene expression regulation; horticulture; hyphae; industry; mycelium; mycology; pathogens; physiological transport; proteome; proteomics; transcriptome; transcriptomics; viruses
Abstract:
... Cultivation of Agaricus bisporus is a large horticultural industry for many countries worldwide, where a single variety is almost grown exclusively. Mushroom virus X (MVX), a complex of multiple positive-sense single stranded RNA (ss(+)RNA) viruses, is a major pathogen of typical A. bisporus crops. MVX can manifest a variety of symptoms in crops and is highly infective and difficult to eradicate o ...
DOI:
10.1016/j.funbio.2021.04.005

3. Propidium monoazide for viable Salmonella enterica detection by PCR and LAMP assays in comparison to RNA‐based RT‐PCR, RT‐LAMP, and culture‐based assays

Author:
Doris Helen D'Souza,   et al.   ; Chayapa Techathuvanan;     Show all 2 Author
Source:
Journal of food science 2020 v.85 no.10 pp. 3509-3516
ISSN:
0022-1147
Subject:
DNA; RNA; Salmonella Enteritidis; agar; autoclaving; cell viability; food industry; heat; lysine; propidium; reverse transcription loop-mediated isothermal amplification; ultraviolet radiation; xylose
Abstract:
... Rapid and sensitive detection of live/infectious foodborne pathogens is urgently needed in order to prevent outbreaks and food recalls. This study aimed to (1) evaluate the incorporation of propidium monoazide (PMA) into PCR or LAMP assays to selectively detect viable Salmonella Enteritidis following sublethal heat or UV treatment, and autoclave sterilization; and (2) compare the detection of PMA‐ ...
DOI:
10.1111/1750-3841.15459

4. Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments

Author:
Helen Ibeawuchi,   et al.   ; Prashant N. M.; Hongyu Liu; Christian Dillard; Turkey Alsaeedy; Hang Chan; Anelia Dafinova Horvath;     Show all 7 Authors
Source:
Genes 2021 v.12 no.10 pp. -
ISSN:
2073-4425
Subject:
RNA; barcoding; cell lines; evolution; genomics; somatic mutation; stop codon
Abstract:
... Currently, the detection of single nucleotide variants (SNVs) from 10 x Genomics single-cell RNA sequencing data (scRNA-seq) is typically performed on the pooled sequencing reads across all cells in a sample. Here, we assess the gaining of information regarding SNV assessments from individual cell scRNA-seq data, wherein the alignments are split by cellular barcode prior to the variant call. We al ...
DOI:
10.3390/genes12101558

5. The diverse structural landscape of quadruplexes

Author:
Helen L. Lightfoot,   et al.   ; Timo Hagen; Natalie J. Tatum; Jonathan Hall;     Show all 4 Authors
Source:
FEBS letters 2019 v.593 no.16 pp. 2083-2102
ISSN:
0014-5793
Subject:
DNA; RNA; landscapes; nucleic acid conformation; therapeutics
Abstract:
... G‐quadruplexes are secondary structures formed in G‐rich sequences in DNA and RNA. Considerable research over the past three decades has led to in‐depth insight into these unusual structures in DNA. Since the more recent exploration into RNA G‐quadruplexes, such structures have demonstrated their in cellulo existence, function and roles in pathology. In comparison to Watson‐Crick‐based secondary s ...
DOI:
10.1002/1873-3468.13547

6. Explaining Pathogenicity of Congenital Zika and Guillain–Barré Syndromes: Does Dysregulation of RNA Editing Play a Role?

Author:
Helen Piontkivska,   et al.   ; Noel‐Marie Plonski; Michael M. Miyamoto; Marta L. Wayne;     Show all 4 Authors
Source:
BioEssays 2019 v.41 no.6 pp. e1800239
ISSN:
0265-9247
Subject:
RNA; RNA editing; Zika virus; adenosine deaminase; adults; adverse effects; autophagy; cell proliferation; infants; neurotoxicity; pathogenesis; pathogenicity; signs and symptoms (animals and humans)
Abstract:
... Previous studies of Zika virus (ZIKV) pathogenesis have focused primarily on virus‐driven pathology and neurotoxicity, as well as host‐related changes in cell proliferation, autophagy, immunity, and uterine function. It is now hypothesized that ZIKV pathogenesis arises instead as an (unintended) consequence of host innate immunity, specifically, as the side effect of an otherwise well‐functioning ...
DOI:
10.1002/bies.201800239
PubMed:
31106880
PubMed Central:
PMC6699488

7. Surveillance along the Rio Grande during the 2020 Vesicular Stomatitis Outbreak Reveals Spatio-Temporal Dynamics of and Viral RNA Detection in Black Flies

Author:
Helen K. Vessels,   et al.   ; Katherine I. Young; Federico Valdez; Christina Vaquera; Carlos Campos; Lawrence Zhou; J. Kevin Moulton; Barbara S. Drolet; Paula Rozo-Lopez; Angela M. Pelzel-McCluskey; Debra C. Peters; Luis L. Rodriguez; Kathryn A. Hanley;     Show all 13 Authors
Source:
Pathogens 2021 v.10 no.10 pp. -
ISSN:
2076-0817
Subject:
RNA; Simulium; Vesiculovirus; ecology; invertebrates; livestock; monitoring; normalized difference vegetation index; temperature; vegetation; vesicular stomatitis; Mexico; New Mexico
Abstract:
... Vesicular stomatitis virus (VSV) emerges periodically from its focus of endemic transmission in southern Mexico to cause epizootics in livestock in the US. The ecology of VSV involves a diverse, but largely undefined, repertoire of potential reservoir hosts and invertebrate vectors. As part of a larger program to decipher VSV transmission, we conducted a study of the spatiotemporal dynamics of Sim ...
DOI:
10.3390/pathogens10101264

8. Evidence of Immune Modulators in the Secretome of the Equine Tapeworm Anoplocephala perfoliata

Author:
Helen C. Phillips,   et al.   ; Boontarikaan Wititkornkul; Benjamin J. Hulme; John J. Tomes; Nathan R. Allen; Chelsea N. Davis; Sarah D. Davey; Alan R. Cookson; Matthew J. Hegarty; Martin T. Swain; Peter M. Brophy; Ruth E. Wonfor; Russell M. Morphew;     Show all 13 Authors
Source:
Pathogens 2021 v.10 no.7 pp. -
ISSN:
2076-0817
Subject:
Anoplocephala perfoliata; RNA; adults; gel chromatography; horses; host-parasite relationships; proteomics; tapeworms; transcriptome; transcriptomics
Abstract:
... Anoplocephala perfoliata is a neglected gastro-intestinal tapeworm, commonly infecting horses worldwide. Molecular investigation of A. perfoliata is hampered by a lack of tools to better understand the host–parasite interface. This interface is likely influenced by parasite derived immune modulators released in the secretome as free proteins or components of extracellular vesicles (EVs). Therefore ...
DOI:
10.3390/pathogens10070912

9. Generation of small molecule-binding RNA arrays and their application to fluorogen-binding RNA aptamers

Author:
Helen A. Vincent,   et al.   ; Charlotte A. Henderson; Callum A. Rail; Louise E. Butt; Anastasia J. Callaghan;     Show all 5 Authors
Source:
Methods 2019 v.167 pp. 39-53
ISSN:
1046-2023
Subject:
RNA; biosensors; engineering; image analysis; malachite; malachite green; metabolites; nucleotide aptamers; screening; spinach
Abstract:
... The discovery and engineering of more and more functions of RNA has highlighted the utility of RNA-targeting small molecules. Recently, several fluorogen-binding RNA aptamers have been developed that have been applied to live cell imaging of RNA and metabolites as RNA tags or biosensors, respectively. Although the design and application of these fluorogen-binding RNA aptamer-based devices is strai ...
DOI:
10.1016/j.ymeth.2019.04.021
PubMed:
31055072
PubMed Central:
PMC7068705

10. Effect of pancreas disease caused by SAV 2 on protein and fat digestion in Atlantic salmon

Author:
Åse Helen Garseth,   et al.   ; Magnus Vikan Røsæg; Espen Rimstad; Arne Guttvik; Bård Skjelstad; Eldar Åsgard Bendiksen;     Show all 6 Authors
Source:
Journal of fish diseases 2019 v.42 no.1 pp. 97-108
ISSN:
0140-7775
Subject:
Alphavirus; RNA; Salmo salar; body length; digestion; digestive enzymes; fish; histopathology; lipid metabolism; pancreas; pancreas disease; viral load; viruses
Abstract:
... Salmonid alphavirus (SAV) causes pancreas disease (PD) in farmed Atlantic salmon (Salmo salar L.), and exocrine pancreas tissue is a primary target of the virus. Digestive enzymes secreted by the exocrine pancreas break down macromolecules in feed into smaller molecules that can be absorbed. The effect of SAV infection on digestion has been poorly studied. In this study, longitudinal observations ...
DOI:
10.1111/jfd.12914

11. Neurological pathophysiology of SARS‐CoV‐2 and pandemic potential RNA viruses: a comparative analysis

Author:
Helen Lavretsky,   et al.   ; Nikhil Chakravarty; Thrisha Senthilnathan; Sophia Paiola; Priya Gyani; Sebastian Castillo Cario; Estrella Urena; Akash Jeysankar; Prakash Jeysankar; Joseph Ignatius Irudayam; Sumathi Natesan Subramanian; Shantanu Joshi; Gustavo Garcia Jr.; Arunachalam Ramaiah; Vaithilingaraja Arumugaswami;     Show all 15 Authors
Source:
FEBS letters 2021 v.595 no.23 pp. 2854-2871
ISSN:
0014-5793
Subject:
COVID-19 infection; Nipah henipavirus; RNA; Severe acute respiratory syndrome coronavirus 2; Zika virus; blood-brain barrier; brain; magnetism; pandemic; pathophysiology
Abstract:
... SARS‐CoV‐2 has infected hundreds of millions of people with over four million dead, resulting in one of the worst global pandemics in recent history. Neurological symptoms associated with COVID‐19 include anosmia, ageusia, headaches, confusion, delirium, and strokes. These may manifest due to viral entry into the central nervous system (CNS) through the blood–brain barrier (BBB) by means of ill‐de ...
DOI:
10.1002/1873-3468.14227

12. Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection

Author:
Helen E. Everett,   et al.   ; Fabian Z. X. Lean; Alexander M. P. Byrne; Pauline M. van Diemen; Shelley Rhodes; Joe James; Benjamin Mollett; Vivien J. Coward; Paul Skinner; Caroline J. Warren; Kevin R. Bewley; Samantha Watson; Shellene Hurley; Kathryn A. Ryan; Yper Hall; Hugh Simmons; Alejandro Núñez; Miles W. Carroll; Ian H. Brown; Sharon M. Brookes;     Show all 20 Authors
Source:
Viruses 2021 v.13 no.1 pp. -
ISSN:
1999-4915
Subject:
RNA; Severe acute respiratory syndrome coronavirus 2; antibodies; ferrets; fur; human diseases; humans; humoral immunity; inoculum; microscopy; models; mucosa; neurons; nose; nucleoproteins; nucleotide sequences; sequence analysis
Abstract:
... Ferrets were experimentally inoculated with SARS-CoV-2 (severe acute respiratory syndrome (SARS)-related coronavirus 2) to assess infection dynamics and host response. During the resulting subclinical infection, viral RNA was monitored between 2 and 21 days post-inoculation (dpi), and reached a peak in the upper respiratory cavity between 4 and 6 dpi. Viral genomic sequence analysis in samples fro ...
DOI:
10.3390/v13010113

13. Piscine orthoreovirus‐3 is prevalent in wild seatrout (Salmo trutta L.) in Norway

Author:
Åse Helen Garseth,   et al.   ; Torfinn Moldal; Siri Kristine Gåsnes; Monika Jankowska Hjortaas; Vegard Pedersen Sollien; Anne‐Gerd Gjevre;     Show all 6 Authors
Source:
Journal of fish diseases 2019 v.42 no.3 pp. 391-396
ISSN:
0140-7775
Subject:
Oncorhynchus kisutch; Oncorhynchus mykiss; RNA; Salmo salar; Salmo trutta; Salvelinus alpinus; anadromous fish; freshwater; indigenous species; marine environment; nucleotide sequences; pathogens; polymerase chain reaction; rivers; salmon; surveys; trout; viruses; Chile; Norway
Abstract:
... In 2017, a PCR‐based survey for Piscine orthoreovirus‐3 (PRV‐3) was conducted in wild anadromous and non‐anadromous salmonids in Norway. In seatrout (anadromous Salmo trutta L.), the virus was present in 16.6% of the fish and in 15 of 21 investigated rivers. Four of 221 (1.8%) Atlantic salmon (Salmo salar L.) from three of 15 rivers were also PCR‐positive, with Ct‐values indicating low amounts of ...
DOI:
10.1111/jfd.12943
PubMed:
30659618
PubMed Central:
PMC6850415

14. Mineral Waste Containing High Levels of Iron from an Environmental Disaster (Bento Rodrigues, Mariana, Brazil) is Associated with Higher Titers of Enteric Viruses

Author:
Helen Treichel,   et al.   ; Gislaine Fongaro; Aline Viancelli; Deyse A. dos Reis; Aníbal F. Santiago; Marta Hernández; Willian Michellon; Maria Célia da Silva Lanna; David Rodríguez-Lázaro;     Show all 9 Authors
Source:
Food and environmental virology 2019 v.11 no.2 pp. 178-183
ISSN:
1867-0334
Subject:
DNA; Mastadenovirus; RNA; bacteria; biosynthesis; disasters; heavy metals; hepatitis A; iron; mining; models; pathogenicity; quantitative polymerase chain reaction; risk; rivers; salts; sanitation; viruses; wastes; water pollution; Atlantic Ocean; Brazil
Abstract:
... Although the effects of heavy metals on the behavior, including infectivity, of bacteria have been studied, little information is available about their effects on enteric viruses. We report an investigation of effects on the biosynthesis of human adenoviruses (HAdV) and hepatitis A (HAV) of waters contaminated with mineral waste following an environmental disaster in Mariana City, Minas Gerais Sta ...
DOI:
10.1007/s12560-019-09373-5

15. Biochemical composition and fatty acid profile in a strain of the lineage ‘Nevada’, belonging to the Brachionus plicatilis (Rotifera) complex, fed different diets

Author:
Helen Miliou,   et al.   ; Venetia Kostopoulou; George Verriopoulos;     Show all 3 Authors
Source:
Aquaculture research 2015 v.46 no.4 pp. 813-824
ISSN:
1355-557X
Subject:
Brachionus plicatilis; DNA; RNA; bakers yeast; diet; diurnal variation; docosahexaenoic acid; eicosapentaenoic acid; embryogenesis; fatty acid composition; highly unsaturated fatty acids; lipid content; monounsaturated fatty acids; omega-3 fatty acids; parthenogenesis; population structure; protein content; reproductive performance; Nevada
Abstract:
... A strain of the lineage Brachionus ‘Nevada’ was batch cultured with two diets, differing in biochemical composition: baker's yeast (treatment 1), which has higher protein:lipid ratio compared with CULTURE SELCO (treatment 2). The biochemical composition (DNA, RNA, lipid, protein content) and fatty acid profile of rotifers of both treatments was analysed and related to previously published populati ...
DOI:
10.1111/are.12232

16. Stable level of HIV transmitted drug resistance in Estonia despite significant scale-up of antiretroviral therapy

Author:
Helen Lepa,   et al.   ; Pilleriin Soodla; Kristi Huik; Merit Pauskar; Lize Cuypers; Kristel Van Laethem; Heli Rajasaar; Eveli Kallas; Anna Velts-Lindh; Ene-Ly Jõgeda; Irja Lutsar; Radko Avi;     Show all 12 Authors
Source:
Infection, genetics, and evolution 2019 v.75 pp. 103901
ISSN:
1567-1348
Subject:
HIV infections; Human immunodeficiency virus 1; RNA; RNA-directed DNA polymerase; antiretroviral agents; databases; drug resistance; drugs; enzyme inhibitors; monitoring; mutation; observational studies; patients; phylogeny; proteinases; risk factors; screening; therapeutics; Eastern European region; Estonia
Abstract:
... Due to the widespread use of non-nucleoside reverse transcriptase inhibitors (NNRTI) as part of first-line therapies to curb the human immunodeficiency virus (HIV) epidemic in Eastern-European countries, transmitted drug resistance (TDR) is of serious concern in this region. Therefore, TDR and its associated risk factors were investigated among newly diagnosed HIV-1 subjects in Estonia.This nation ...
DOI:
10.1016/j.meegid.2019.05.019

17. Statistical modelling of data showing pandemic H1N1 2009 swine influenza A virus infection kinetics in vaccinated pigs

Author:
Helen E. Everett,   et al.   ; Laetitia Canini; Mario Aramouni; Vivien Coward; Andrew Ramsay; Michael Kelly; Sophie Morgan; Elma Tchilian; Sarah Gilbert; Bryan Charleston; Ian H. Brown; Sharon M. Brookes; Mark E.J. Woolhouse;     Show all 13 Authors
Source:
Data in Brief 2019 v.27 pp. 104576
ISSN:
2352-3409
Subject:
Influenza A virus; RNA; nose; pandemic; swine; swine influenza; viruses
Abstract:
... A swine influenza A pandemic 2009 H1N1 (pH1N1) virus was used in a pig challenge model to investigate the efficacy of whole inactivated vaccines homologous or heterologous to the challenge virus as well as a commercial vaccine. Nasal shedding of viral RNA was monitored daily by real-time, quantitative RT-PCR (RRT-qPCR) as detailed (1). Here we report the statistical modelling of the viral RNA shed ...
DOI:
10.1016/j.dib.2019.104576

18. Interscapular and Perivascular Brown Adipose Tissue Respond Differently to a Short-Term High-Fat Diet

Author:
Helen Budge,   et al.   ; Peter Aldiss; Jo E. Lewis; David J. Boocock; Amanda K. Miles; Ian Bloor; Francis J. P. Ebling; Michael E. Symonds;     Show all 8 Authors
Source:
Nutrients 2019 v.11 no.5 pp. -
ISSN:
2072-6643
Subject:
RNA; Toll-like receptors; apoptosis; biochemical pathways; blood serum; brown adipose tissue; cell adhesion; free fatty acids; gene expression; gene expression regulation; genes; glucagon; high fat diet; histones; insulin; laboratory animals; lipid content; lipid metabolism; nucleosomes; nutrient excess; peroxisome proliferator-activated receptors; proteome; rats; signal transduction; weight gain
Abstract:
... Brown adipose tissue (BAT) function may depend on its anatomical location and developmental origin. Interscapular BAT (iBAT) regulates acute macronutrient metabolism, whilst perivascular BAT (PVAT) regulates vascular function. Although phenotypically similar, whether these depots respond differently to acute nutrient excess is unclear. Given their distinct anatomical locations and developmental or ...
DOI:
10.3390/nu11051065
PubMed:
31086124
PubMed Central:
PMC6566556

19. Protein induced fluorescence enhancement (PIFE) for probing protein–nucleic acid interactions

Author:
Helen Hwang,   et al.   ; Sua Myong;     Show all 2 Author
Source:
Chemical Society reviews 2014 v.43 no.4 pp. 1221-1229
ISSN:
1460-4744
Subject:
DNA; RNA; dyes; fluorescence
Abstract:
... Single molecule studies of protein–nucleic acid interactions shed light on molecular mechanisms and kinetics involved in protein binding, translocation, and unwinding of DNA and RNA substrates. In this review, we provide an overview of a single molecule fluorescence method, termed “protein induced fluorescence enhancement” (PIFE). Unlike FRET where two dyes are required, PIFE employs a single dye ...
DOI:
10.1039/c3cs60201j
PubMed:
24056732
PubMed Central:
PMC4142350

20. Differential detection of classical swine fever virus challenge strains in C-strain vaccinated pigs

Author:
Helen E Everett; Helen R Crooke,   et al.   ; Bentley S Crudgington; Olubukola Sosan-Soulé;     Show all 4 Authors
Source:
BMC veterinary research 2014 v.10 no.1 pp. 281
ISSN:
1746-6148
Subject:
Classical swine fever virus; RNA; biosecurity; blood; disease control; disease transmission; farms; genetic variation; herds; hog cholera; reverse transcriptase polymerase chain reaction; risk; swine; tonsils; vaccination; vaccines; viremia; viruses
Abstract:
... BACKGROUND: Control of classical swine fever (CSF) by vaccination ideally requires that field strain infection can be detected irrespective of the vaccination status of the herd. To inform on the usefulness of molecular tests compatible with genetic Differentiation of Infected from Vaccinated Animals (DIVA) principles when using live-attenuated vaccines, tonsil homogenates from a vaccination-chall ...
DOI:
10.1186/s12917-014-0281-9
PubMed:
25495277
PubMed Central:
PMC4280032

21. Rapid detection of Grapevine leafroll-associated virus type 3 using a reverse transcription loop-mediated amplification method

Author:
Helen Ann Walsh,   et al.   ; Gerhard Pietersen;     Show all 2 Author
Source:
Journal of virological methods 2013 v.194 no.1-2 pp. 308-316
ISSN:
0166-0934
Subject:
Grapevine leafroll-associated virus; RNA; Vitis; autumn; color; culling (plants); cultivars; enzyme-linked immunosorbent assay; equipment; genes; insecticides; planting; polymerase chain reaction; population; rapid methods; reverse transcription; reverse transcription loop-mediated isothermal amplification; vector control; vines; vineyards; South Africa
Abstract:
... Grapevine leafroll disease (GLD) is the most important disease of Grapevines in South Africa. Grapevine leafroll-associated virus type 3 (GLRaV-3) has a close association with the disease and is prevalent in South African vineyards. GLD can be controlled using a combination of virus-free planting material, systemic insecticides to control vector populations and removal of infected vines by roguing ...
DOI:
10.1016/j.jviromet.2013.08.030

22. Sex-lethal enables germline stem cell differentiation by down-regulating Nanos protein levels during Drosophila oogenesis

Author:
Helen K. Salz,   et al.   ; Johnnie Chau; Laura Shapiro Kulnane;     Show all 3 Authors
Source:
Proceedings of the National Academy of Sciences of the United States of America 2012 v.109 no.24 pp. 9465-9470
ISSN:
0027-8424
Subject:
Drosophila; RNA; RNA-binding proteins; X chromosome; adults; animal ovaries; binding sites; cell differentiation; females; gene expression regulation; germ cells; males; oogenesis; regulator genes; sex determination; somatic cells; stem cells
Abstract:
... Drosophila ovarian germ cells require Sex-lethal (Sxl) to exit from the stem cell state and to enter the differentiation pathway. Sxl encodes a female-specific RNA binding protein and in somatic cells serves as the developmental switch gene for somatic sex determination and X-chromosome dosage compensation. None of the known Sxl target genes are required for germline differentiation, leaving open ...
DOI:
10.1073/pnas.1120473109
PubMed:
22645327
PubMed Central:
PMC3386055

23. Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity

Author:
Hwang, Helen,   et al.   ; Kim, Hajin; Myong, Sua;     Show all 3 Authors
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.18 pp. 7414-7418
ISSN:
0027-8424
Subject:
RNA; acids; binding proteins; fluorescence; fluorescent dyes; monitoring; single-stranded DNA
Abstract:
... Single-molecule FRET has been widely used for monitoring protein-nucleic acids interactions. Direct visualization of the interactions, however, often requires a site-specific labeling of the protein, which can be circuitous and inefficient. In addition, FRET is insensitive to distance changes in the 0-3-nm range. Here, we report a systematic calibration of a single molecule fluorescence assay term ...
DOI:
10.1073/pnas.1017672108
PubMed:
21502529
PubMed Central:
PMC3088603

24. Synchrotron- and focal plane array-based Fourier-transform infrared spectroscopy differentiates the basalis and functionalis epithelial endometrial regions and identifies putative stem cell regions of human endometrial glands

Author:
Helen F. Stringfellow,   et al.   ; Georgios Theophilou; Camilo L. M. Morais; Diane E. Halliwell; Kássio M. G. Lima; Josephine Drury; Pierre L. Martin-Hirsch; Dharani K. Hapangama; Francis L. Martin;     Show all 9 Authors
Source:
Analytical and bioanalytical chemistry 2018 v.410 no.18 pp. 4541-4554
ISSN:
1618-2642
Subject:
DNA; Fourier transform infrared spectroscopy; RNA; carcinogenesis; endometrium; epithelium; humans; mitosis; multivariate analysis; spectral analysis; stem cells; vibration
Abstract:
... The cyclical process of regeneration of the endometrium suggests that it may contain a cell population that can provide daughter cells with high proliferative potential. These cell lineages are clinically significant as they may represent clonogenic cells that may also be involved in tumourigenesis as well as endometriotic lesion development. To determine whether the putative stem cell location wi ...
DOI:
10.1007/s00216-018-1111-x
PubMed:
29740671
PubMed Central:
PMC6021468

25. Comparison of Reverse Transcriptase PCR, Reverse Transcriptase Loop-Mediated Isothermal Amplification, and Culture-Based Assays for Salmonella Detection from Pork Processing Environments

Author:
Helen D'Souza,   et al.   ; Chayapa Techathuvanan; Frances Ann Draughon;     Show all 3 Authors
Source:
Journal of food protection 2011 v.74 no.2 pp. 294-301
ISSN:
0362-028X
Subject:
RNA; RNA-directed DNA polymerase; Salmonella Typhimurium; agar; autoclaving; bags; detection limit; filters; gel electrophoresis; labor; lysine; melting; peptones; pork; pork industry; reverse transcriptase polymerase chain reaction; reverse transcription loop-mediated isothermal amplification; screening; xylose
Abstract:
... Novel rapid Salmonella detection assays without the need for sophisticated equipment or labor remain in high demand. Real-time reverse transcriptase PCR (RT-PCR) assays, though rapid and sensitive, require expensive thermocyclers, while a novel RT loop-mediated isothermal amplification (RT-LAMP) method requires only a simple water bath. Our objective was to compare the detection sensitivity of Sal ...
DOI:
10.4315/0362-028X.JFP-10-306

26. Nucleic acid separations using superficially porous silica particles

Author:
Helen Wood,   et al.   ; Elizabeth D. Close; Alison O. Nwokeoji; Dafydd Milton; Ken Cook; Darsha M. Hindocha; Elliot C. Hook; Mark J. Dickman;     Show all 8 Authors
Source:
Journal of chromatography 2016 v.1440 pp. 135-144
ISSN:
0021-9673
Subject:
DNA; RNA; mass spectrometry; molecular weight; oligoribonucleotides; porosity; porous media; reversed-phase liquid chromatography; ribonucleases; silica; therapeutics
Abstract:
... Ion pair reverse-phase liquid chromatography has been widely employed for nucleic acid separations. A wide range of alternative stationary phases have been utilised in conjunction with ion pair reverse-phase chromatography, including totally porous particles, non-porous particles, macroporous particles and monolithic stationary phases. In this study we have utilised superficially porous silica par ...
DOI:
10.1016/j.chroma.2016.02.057
PubMed:
26948761
PubMed Central:
PMC4801196

27. A generic real-time TaqMan assay for specific detection of lapinized Chinese vaccines against classical swine fever

Author:
Helen Everett; Helen Crooke,   et al.   ; Lihong Liu; Hongyan Xia; Olubukola Sosan; Alexandra Meindl-Böhmer; Hua-Ji Qiu; Volker Moennig; Sándor Belák; Frederik Widén;     Show all 10 Authors
Source:
Journal of virological methods 2011 v.175 no.2 pp. 170-174
ISSN:
0166-0934
Subject:
RNA; detection limit; disease control; financial economics; genes; genotype; hog cholera; industry; reverse transcriptase polymerase chain reaction; swine; vaccination; viral vaccines; viruses; Philippines
Abstract:
... Classical swine fever (CSF) is a highly contagious disease, causing severe economic losses in the pig industry worldwide. Vaccination of pigs with lapinized Chinese vaccines is still practised in some regions of the world, where the virus is enzootic, in order to prevent and control the disease. However, a single real-time assay that can detect all lapinized Chinese vaccines used widely, namely, L ...
DOI:
10.1016/j.jviromet.2011.05.003

28. Toxicogenomics and Cancer Susceptibility: Advances with Next-Generation Sequencing

Author:
Helen Deng,   et al.   ; Baitang Ning; Zhenqiang Su; Nan Mei; Huixiao Hong; Leming Shi; James C. Fuscoe; William H. Tolleson;     Show all 8 Authors
Source:
Journal of environmental science and health 2014 v.32 no.2 pp. 121-158
ISSN:
1532-4095
Subject:
DNA damage; DNA replication; RNA; alleles; carcinogenesis; environmental exposure; environmental factors; environmental science; epigenetics; gene expression; genetic disorders; genetic variation; germ cells; high-throughput nucleotide sequencing; humans; mutagenicity; public health; risk; somatic mutation; therapeutics; toxicogenomics
Abstract:
... The aim of this review is to comprehensively summarize the recent achievements in the field of toxicogenomics and cancer research regarding genetic-environmental interactions in carcinogenesis and detection of genetic aberrations in cancer genomes by next-generation sequencing technology. Cancer is primarily a genetic disease in which genetic factors and environmental stimuli interact to cause gen ...
DOI:
10.1080/10590501.2014.907460
PubMed:
24875441
PubMed Central:
PMC5712441

29. Quantitative label-free mass spectrometry using contralateral and adjacent breast tissues reveal differentially expressed proteins and their predicted impacts on pathways and cellular functions in breast cancer

Author:
Talita Helen Bombardelli Gomig,   et al.   ; Iglenir João Cavalli; Ricardo Lehtonen Rodrigues de Souza; Evelyn Vieira; Aline Castro Rodrigues Lucena; Michel Batista; Kelly Cavalcanti Machado; Fabricio Klerynton Marchini; Fabio Albuquerque Marchi; Rubens Silveira Lima; Cícero de Andrade Urban; Luciane Regina Cavalli; Enilze Maria de Souza Fonseca Ribeiro;     Show all 13 Authors
Source:
Journal of proteomics 2019 v.199 pp. 1-14
ISSN:
1874-3919
Subject:
RNA; biomarkers; breast neoplasms; breasts; carcinogenesis; carcinoma; endothelial nitric oxide synthase; fatty acid metabolism; gene expression regulation; lymph nodes; mass spectrometry; metastasis; nitric oxide; oxidative stress; patients; protein synthesis; proteins; proteome; proteomics; signal transduction
Abstract:
... Proteins play an essential role in the biological processes associated with cancer. Their altered expression levels can deregulate critical cellular pathways and interactive networks. In this study, the mass spectrometry-based label-free quantification followed by functional annotation was performed to investigate the most significant deregulated proteins among tissues of primary breast tumor (PT) ...
DOI:
10.1016/j.jprot.2019.02.007

30. Detection of nine respiratory RNA viruses using three multiplex RT-PCR assays incorporating a novel RNA internal control transcript

Author:
Helen Auburn,   et al.   ; Mark Zuckerman; Simon Broughton; Anne Greenough; Melvyn Smith;     Show all 5 Authors
Source:
Journal of virological methods 2011 v.176 no.1-2 pp. 9-13
ISSN:
0166-0934
Subject:
RNA; chimerism; fluorescent antibody technique; infants; mixed infection; plasmids; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; viruses
Abstract:
... Real-time PCR is a significant improvement over viral isolation and immunofluorescence for routinely detecting respiratory viruses. We developed three real-time internally controlled multiplex RT-PCR assays for detecting nine respiratory viruses. An internal control transcript consisting of a chimeric plasmid was synthesised and incorporated into each multiplex to monitor amplification efficiency, ...
DOI:
10.1016/j.jviromet.2011.05.017

31. TRANSVAC workshop on standardisation and harmonisation of analytical platforms for HIV, TB and malaria vaccines: ‘How can big data help?’

Author:
Helen A. Fletcher,   et al.   ; Céline Dutruel; Jelle Thole; Mark Geels; Hans-Joachim Mollenkopf; Tom Ottenhoff; Carlos A. Guzman; Odile Leroy; Stefan H.E. Kaufmann;     Show all 9 Authors
Source:
Vaccine 2014 v.32 no.35 pp. 4365-4368
ISSN:
0264-410X
Subject:
Human immunodeficiency virus; RNA; clinical trials; data collection; experts; immunity; infectious diseases; infrastructure; malaria vaccines; protein synthesis
Abstract:
... High-throughput analyses of RNA and protein expression are increasingly used for better understanding of vaccine-induced immunity and protection against infectious disease. With an increasing number of vaccine candidates in clinical development, it is timely to consider standardisation and harmonisation of sample collection, storage and analysis to ensure results of highest quality from these prec ...
DOI:
10.1016/j.vaccine.2014.06.014

32. Use of a highly sensitive strand-specific quantitative PCR to identify abortive replication in the mouse model of respiratory syncytial virus disease

Author:
Helen Bright,   et al.   ; Richard Bannister; Deborah Rodrigues; Edward J Murray; Carl Laxton; Mike Westby;     Show all 6 Authors
Source:
Virology journal 2010 v.7 no.1 pp. 250
ISSN:
1743-422X
Subject:
RNA; Respiratory syncytial virus; genome; humans; inoculum; lungs; mice; quantitative polymerase chain reaction; therapeutics; virus replication; viruses
Abstract:
... BACKGROUND: The BALB/c mouse is commonly used to study RSV infection and disease. However, despite the many advantages of this well-characterised model, the inoculum is large, viral replication is restricted and only a very small amount of virus can be recovered from infected animals. A key question in this model is the fate of the administered virus. Is replication really being measured or is the ...
DOI:
10.1186/1743-422X-7-250

33. Changes in immune cell populations in the periphery and liver of GBV-B-infected and convalescent tamarins (Saguinus labiatus)

Author:
Helen Bright,   et al.   ; Simon P. Hood; Edward T. Mee; Hannah Perkins; Ori Bowen; Jessica M. Dale; Neil M. Almond; Peter Karayiannis; Neil J. Berry; Nicola J. Rose;     Show all 10 Authors
Source:
Virus research 2014 v.179 pp. 93-101
ISSN:
0168-1702
Subject:
CD4-positive T-lymphocytes; Hepatitis C virus; RNA; Saguinus; animal models; cell-mediated immunity; liver; phenotype; viremia; virus replication
Abstract:
... Flaviviruses related to hepatitis C virus (HCV) in suitable animal models may provide further insight into the role that cellular immunity contributes to spontaneous clearance of HCV. We characterised changes in lymphocyte populations in tamarins with an acute GBV-B infection, a hepatitis virus of the flaviviridae. Major immune cell populations were monitored in peripheral and intra-hepatic lympho ...
DOI:
10.1016/j.virusres.2013.11.006
PubMed:
24246306
PubMed Central:
PMC3969288

34. Glioma progression is shaped by genetic evolution and microenvironment interactions

Author:
Helen Wheeler,   et al.   ; Frederick S. Varn; Kevin C. Johnson; Jan Martinek; Jason T. Huse; MacLean P. Nasrallah; Pieter Wesseling; Lee A.D. Cooper; Tathiane M. Malta; Taylor E. Wade; Thais S. Sabedot; Daniel Brat; Peter V. Gould; Adelheid Wöehrer; Kenneth Aldape; Azzam Ismail; Santhosh K. Sivajothi; Floris P. Barthel; Hoon Kim; Emre Kocakavuk; Nazia Ahmed; Kieron White; Indrani Datta; Hyo-Eun Moon; Steven Pollock; Christine Goldfarb; Ga-Hyun Lee; Luciano Garofano; Kevin J. Anderson; Djamel Nehar-Belaid; Jill S. Barnholtz-Sloan; Spyridon Bakas; Annette T. Byrne; Fulvio D’Angelo; Hui K. Gan; Mustafa Khasraw; Simona Migliozzi; D. Ryan Ormond; Sun Ha Paek; Erwin G. Van Meir; Annemiek M.E. Walenkamp; Colin Watts; Tobias Weiss; Michael Weller; Karolina Palucka; Lucy F. Stead; Laila M. Poisson; Houtan Noushmehr; Antonio Iavarone; Roel G.W. Verhaak; Kristin D. Alfaro; Samirkumar B. Amin; David M. Ashley; Christoph Bock; Andrew Brodbelt; Ketan R. Bulsara; Ana Valeria Castro; Jennifer M. Connelly; Joseph F. Costello; John F. de Groot; Gaetano Finocchiaro; Pim J. French; Anna Golebiewska; Ann C. Hau; Chibo Hong; Craig Horbinski; Kasthuri S. Kannan; Mathilde CM. Kouwenhoven; Anna Lasorella; Peter S. LaViolette; Keith L. Ligon; Allison K. Lowman; Shwetal Mehta; Hrvoje Miletic; Annette M. Molinaro; Ho Keung Ng; Simone P. Niclou; Johanna M. Niers; Joanna J. Phillips; Raul Rabadan; Ganesh Rao; Guido Reifenberger; Nader Sanai; Susan C. Short; Peter Sillevis Smitt; Andrew E. Sloan; Marion Smits; James M. Snyder; Hiromichi Suzuki; Ghazaleh Tabatabai; Georgette Tanner; William H. Tomaszewski; Michael Wells; Bart A. Westerman; Jichun Xie; W.K. Alfred Yung; Gelareh Zadeh; Junfei Zhao; Roel GW. Verhaak; The GLASS Consortium;     Show all 100 Authors
Source:
Cell 2022 v.185 no.12 pp. 2184-2199.e16
ISSN:
0092-8674
Subject:
DNA; RNA; adults; disease progression; evolution; glioma; histology; isocitrate dehydrogenase; mutation; neurons; therapeutics
Abstract:
... The factors driving therapy resistance in diffuse glioma remain poorly understood. To identify treatment-associated cellular and genetic changes, we analyzed RNA and/or DNA sequencing data from the temporally separated tumor pairs of 304 adult patients with isocitrate dehydrogenase (IDH)-wild-type and IDH-mutant glioma. Tumors recurred in distinct manners that were dependent on IDH mutation status ...
DOI:
10.1016/j.cell.2022.04.038

35. Sample Collection Protocol Effects on Quantification of Gene Expression in Potato Leaf Tissue

Author:
Tai, Helen,   et al.   ; Luo, Sainan; Zebarth, Bernie; Li, Xiu-Qing; Millard, Pete; De Koeyer, David; Xiong, Xingyao;     Show all 7 Authors
Source:
Plant molecular biology reporter 2011 v.29 no.2 pp. 369-378
ISSN:
0735-9640
Subject:
RNA; field experimentation; freezing; gene expression; genes; ice; leaves; nitrogen; plant tissues; potatoes; statistical analysis; temperature
Abstract:
... New platforms allow quantification of gene expression from large, replicated experiments but current sampling protocols for plant tissue using immediate flash freezing in liquid nitrogen are a barrier to these high-throughput studies. In this study, we compared four sampling methods for RNA extraction for gene expression analysis: (1) the standard sampling method of flash freezing whole leaves in ...
DOI:
10.1007/s11105-010-0239-4

36. Host gene expression changes in cattle infected with Alcelaphine herpesvirus 1

Author:
Helen Todd,   et al.   ; George C. Russell; Julio Benavides; Dawn M. Grant; Jackie Thomson; Vipul Puri; Mintu Nath; David M. Haig;     Show all 8 Authors
Source:
Virus research 2012 v.169 no.1 pp. 246-254
ISSN:
0168-1702
Subject:
T-lymphocytes; enzymes; cytotoxicity; interferon-gamma; malignant catarrhal fever; inflammation; microarray technology; pathogenesis; steers; genes; lymph nodes; immune response; kidneys; Alcelaphine gammaherpesvirus 1; viruses; RNA; gene expression regulation; chemokines; tissues
Abstract:
... Malignant catarrhal fever is a lymphoproliferative disease of cattle and other ungulates caused by infection with gamma-herpesviruses of the genus Macavirus. These viruses do not establish a productive infection but instead replicate in a cell-associated fashion in T lymphocytes, leading to systemic immune dysregulation and a generally fatal outcome. Despite significant progress in understanding t ...
DOI:
10.1016/j.virusres.2012.08.011
PubMed:
22925730
PubMed Central:
PMC3657188

37. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

Author:
Neil, Helen,   et al.   ; Malabat, Christophe; d'Aubenton-Carafa, Yves; Xu, Zhenyu; Steinmetz, Lars M.; Jacquier, Alain;     Show all 6 Authors
Source:
Nature 2009 v.457 no.7232 pp. 1038-1042
ISSN:
0028-0836
Subject:
Saccharomyces cerevisiae; yeasts; promoter regions; transcription (genetics); gene expression; RNA; degradation
Abstract:
... Pervasive and hidden transcription is widespread in eukaryotes, but its global level, the mechanisms from which it originates and its functional significance are unclear. Cryptic unstable transcripts (CUTs) were recently described as a principal class of RNA polymerase II transcripts in Saccharomyces cerevisiae 5. These transcripts are targeted for degradation immediately after synthesis by the ac ...
DOI:
10.1038/nature07747

38. Total RNA isolation fromPicea mariana dry seed

Author:
Helen H. Tai,   et al.   ; Céline Pelletier; Tannis Beardmore;     Show all 3 Authors
Source:
Plant molecular biology reporter 2004 v.22 no.1 pp. 93
ISSN:
0735-9640
Subject:
Picea mariana; RNA; conifers; lithium chloride; mice; seeds
Abstract:
... Isolating RNA from dry conifer seeds can be difficult because of a number of interfering compounds present in seeds. We describe a protocol for total RNA isolation from black spruce dry seeds, which is an adaptation of a method used for mouse myeloma tissues. The extraction relies on selective precipitation of RNA by using lithium chloride. ...
DOI:
10.1007/BF02773357

39. Characterization of Vibrio cholerae Hfq Provides Novel Insights into the Role of the Hfq C-Terminal Region

Author:
Helen A. Vincent,   et al.   ; Charlotte A. Henderson; Timothy J. Ragan; Acely Garza-Garcia; Peter D. Cary; Darren M. Gowers; Marc Malfois; Paul C. Driscoll; Frank Sobott; Anastasia J. Callaghan;     Show all 10 Authors
Source:
Journal of molecular biology 2012 v.420 no.1-2 pp. 56-69
ISSN:
0022-2836
Subject:
Escherichia coli; RNA; RNA-binding proteins; Vibrio cholerae; X-radiation; dissociation; genes; mass spectrometry; polyacrylamide gel electrophoresis; virulence
Abstract:
... Hfq is a bacterial RNA binding protein that facilitates small RNA-mediated posttranscriptional gene regulation. In Vibrio cholerae, Hfq and four Hfq-dependent small RNAs are essential for the expression of virulence genes, but little is known about this mechanism at the molecular level. To better understand V. cholerae Hfq structure and mechanism, we characterized the protein, alongside Escherichi ...
DOI:
10.1016/j.jmb.2012.03.028
PubMed:
22484176
PubMed Central:
PMC3477312

40. Ecotoxicogenomics: Microarray interlaboratory comparability

Author:
Helen Poynton,   et al.   ; Doris E. Vidal-Dorsch; Steven M. Bay; Shelly Moore; Blythe Layton; Alvine C. Mehinto; Chris D. Vulpe; Marianna Brown-Augustine; Alex Loguinov; Natàlia Garcia-Reyero; Edward J. Perkins; Lynn Escalon; Nancy D. Denslow; Colli-Dula R. Cristina; Tri Doan; Shweta Shukradas; Joy Bruno; Lorraine Brown; Graham Van Agglen; Paula Jackman; Megan Bauer;     Show all 21 Authors
Source:
Chemosphere 2016 v.144 pp. 193-200
ISSN:
0045-6535
Subject:
Amphipoda; RNA; ecotoxicology; estuaries; gene expression; gene expression regulation; genes; microarray technology; monitoring; risk assessment; sediments; toxicity; transcriptomics
Abstract:
... Transcriptomic analysis can complement traditional ecotoxicology data by providing mechanistic insight, and by identifying sub-lethal organismal responses and contaminant classes underlying observed toxicity. Before transcriptomic information can be used in monitoring and risk assessment, it is necessary to determine its reproducibility and detect key steps impacting the reliable identification of ...
DOI:
10.1016/j.chemosphere.2015.08.019

41. Suppression of Avian Influenza Transmission in Genetically Modified Chickens

Author:
Sang, Helen,   et al.   ; Lyall, Jon; Irvine, Richard M.; Sherman, Adrian; McKinley, Trevelyan J.; Núñez, Alejandro; Purdie, Auriol; Outtrim, Linzy; Brown, Ian H.; Rolleston-Smith, Genevieve; Tiley, Laurence;     Show all 11 Authors
Source:
Science 2011 v.331 no.6014 pp. 223-226
ISSN:
0036-8075
Subject:
Influenza A virus; RNA; avian influenza; biosecurity; chickens; human health; poultry production; transgenic animals; vaccination; viruses
Abstract:
... Infection of chickens with avian influenza virus poses a global threat to both poultry production and human health that is not adequately controlled by vaccination or by biosecurity measures. A novel alternative strategy is to develop chickens that are genetically resistant to infection. We generated transgenic chickens expressing a short-hairpin RNA designed to function as a decoy that inhibits a ...
DOI:
10.1126/science.1198020

42. Building Programmable Jigsaw Puzzles with RNA

Author:
Hansma, Helen G.,   et al.   ; Chworos, Arkadiusz; Severcan, Isil; Koyfman, Alexey Y.; Weinkam, Patrick; Oroudjev, Emin; Jaeger, Luc;     Show all 7 Authors
Source:
Science 2004 v.306 no.5704 pp. 2068-2072
ISSN:
0036-8075
Subject:
RNA; chemistry; fabrics; geometry; prediction; topology
Abstract:
... One challenge in supramolecular chemistry is the design of versatile, self-assembling building blocks to attain total control of arrangement of matter at a molecular level. We have achieved reliable prediction and design of the three-dimensional structure of artificial RNA building blocks to generate molecular jigsaw puzzle units called tectosquares. They can be programmed with control over their ...
DOI:
10.1126/science.1104686