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Publication
Journal: Scientific Reports
May/16/2017
Abstract
Cis-acting RNA structures in the genomes of RNA viruses play critical roles in viral infection, yet their importance in the bipartite genomes of the picorna-like, plant-infecting comoviruses has not been carefully investigated. We previously characterized SLC, a stem-loop structure in the 5' untranslated region (UTR) of the bean pod mottle comovirus (BPMV) RNA2, and found it to be essential for RNA2 accumulation in infected cells. Here we report the identification of SL1, a similar cis-acting element in the other BPMV genome segment - RNA1. SL1 encompasses a portion of RNA1 5' UTR but extends into the coding sequence for nine nucleotides, thus was missed in the previous study. While the stems of SL1 and SLC share little sequence similarity, their end loops are of the same size and identical for 11 of 15 nucleotides. Importantly, SL1 and SLC are functionally interchangeable, and separate exchanges of the stem and loop portions were likewise well tolerated. By contrast, the conserved loop sequence tolerated minimal perturbations. Finally, stem-loop structures with similar configurations were identified in two other comoviruses. Therefore, SL1 and SLC are likely essential comoviral RNA structures that play a conserved function in viral infection cycles.
Publication
Journal: Journal of Animal Breeding and Genetics
January/3/2017
Abstract
We studied the effect of including GWAS results on the accuracy of single- and multipopulation genomic predictions. Phenotypes (backfat thickness) and genotypes of animals from two sire lines (SL1, n = 1146 and SL3, n = 1264) were used in the analyses. First, GWAS were conducted for each line and for a combined data set (both lines together) to estimate the genetic variance explained by each SNP. These estimates were used to build matrices of weights (D), which was incorporated into a GBLUP method. Single population evaluated with traditional GBLUP had accuracies of 0.30 for SL1 and 0.31 for SL3. When weights were employed in GBLUP, the accuracies for both lines increased (0.32 for SL1 and 0.34 for SL3). When a multipopulation reference set was used in GBLUP, the accuracies were higher (0.36 for SL1 and 0.32 for SL3) than in single-population prediction. In addition, putting together the multipopulation reference set and the weights from the combined GWAS provided even higher accuracies (0.37 for SL1, and 0.34 for SL3). The use of multipopulation predictions and weights estimated from a combined GWAS increased the accuracy of genomic predictions.
Publication
Journal: Molekulyarnaya Biologiya
November/7/2017
Abstract
Proteins of the Piwi family and short Piwi-interacting RNAs (piRNAs) ensure the protection of the genome from transposable elements. We have previously shown that nuclear Piwi protein tends to concentrate in the nucleoli of the cells of Drosophila melanogaster ovaries. It could be hypothesized that the function of Piwi in the nucleolus is associated with the repression of R1 and R2 retrotransposons inserted into the rDNA cluster. Here, we show that Piwi participates in recruiting Udd protein to nucleoli. Udd is a component of the conserved Selectivity Factor I-like (SL1-like) complex, which is required for transcription initiation by RNA polymerase I. We found that Udd localization depends on Piwi in germline cells, but not in somatic cells of the ovaries. In contrast, knockdowns of the SL1-like components (Udd or TAF1b) do not disrupt Piwi localization. We also observed that the absence of Udd or TAF1b in germline cells, as well as the impairment of Piwi nuclear localization lead to the accumulation of late stage egg chambers in the ovaries, which could be explained by reduced rRNA transcription. These results allow us to propose for the first time a role for Piwi in the nucleolus that is not directly associated with transposable element repression.
Publication
Journal: Progres en Urologie
May/24/1993
Abstract
Fifteen paraplegic patients all presenting with vesico-sphincteric dyssynergia underwent, between January and September 1990, a urodynamic and electromyographic examination combined with pre-voiding or voiding transrectal ultrasonography. The ultrasound apparatus used was a Siemens Sonoline SL1 with a MHz linear intracavitary probe giving a strictly longitudinal plane of section. The urodynamic apparatus used was a Wiest 6000 with a Böhler 7 F urethral catheter and an electromyography needle-electrode implanted in the striated sphincter. This type of ultrasonography provided a precise and dynamic image of the bladder neck, prostatic urethra and external striated sphincter during the phases of filling and voiding. Spastic contractions of the striated sphincter during detrusor contraction were observed in 8 patients with an intermittent and jerky urinary stream. In 7 patients, the striated sphincter remained closed during detrusor contraction and only opened briefly as soon as detrusor contraction decreased, allowing only a weak and transient flow. By allowing the direct visualisation of the sphincteric obstruction during voiding, dynamic transrectal ultrasonography clearly confirmed the diagnosis of vesico-sphincteric dyssynergia. In contrast with classical voiding cystourethrography, this is a non-invasive, inexpensive and, most importantly, repeatable technique, as it does not require any irradiation. It is therefore suitable for drug evaluation trials, particularly of alpha-blockers and to assess one of the many treatments proposed in vesico-sphincteric dyssynergia.
Publication
Journal: Frontiers in Neural Circuits
March/21/2019
Abstract
Little is known about the molecular and cellular mechanisms involved in the formation of the cranial peripheral sensory system in vertebrates. To identify genes involved in the formation of these circuits, we performed a forward genetic screen utilizing a transgenic zebrafish line (p2rx3.2:gfpsl1) that expresses green fluorescent protein (gfp) in sensory neurons of the Vth, VIIth, IXth and Xth cranial ganglia. Here, we describe a novel zebrafish mutant in which a missense mutation in the adam19b gene selectively affects the epibranchial sensory circuits.
Publication
Journal: Revista Cubana de Medicina Tropical
June/15/1999
Abstract
The biological characteristics of 11 HIV-1 strains isolated from patients with a fast clinical evolution to AIDS were studied. The viral isolates were classified according to their replication kinetics and cell tropism. Taking into account these criteria, it was observed that 8 of the isolated strains (72.7%) were of rapid high growth (RH) or slow low 3 (SL3) with preferential tropism to the lymphocytic stock, as it corresponds to AIDS patients. 3 (27.3%) had characteristics of slow low 1 (SL1). The cytopathogenicity of the strains was studied in the MT4 cellular line, and it was observed that most of them (72.7%) were syncytium-inducing strains (SI), which allowed to prove the in vivo and in vitro relation of the biological properties. It was not so in 3 of the cultures (27.3%) that behaved as non-syncytium inducers.
Publication
Journal: Microbiology Resource Announcements
January/14/2019
Abstract
Halomonas sp. strain SL1, a halophilic gammaproteobacterium, was isolated from samples from the Great Salt Lake in Utah. We report here the draft genome sequence of SL1, which has an estimated total sequence length of 3.6 Mb.
Publication
Journal: Journal of Biomolecular NMR
March/6/2002
Abstract
The cross-peaks of 1H-NOESY spectra at different time delays are compared to a mode-coupling diffusion (MCD) calculation, including the evaluation of the full 1H relaxation matrix, in the case of a 23 nucleotide fragment of the stem-loop SL1 domain of HIV-1Lai genomic RNA mutated in a single position. The MCD theory gives significant agreement with 1H relaxation experiments enabling a thorough understanding of the differential local dynamics along the sequence and particularly of the dynamics of nucleotides in the stem and in the loop. The differential dynamics of this hairpin structure is important in directing the dimerization of the retroviral genome, a fundamental step in the infectious process. The demonstration of a reliable use of time dependent NOE cross-peaks, largely available from NMR solution structure determination, coupled to MCD analysis, to probe the local dynamics of biological macromolecules, is a result of general interest of this paper.
Publication
Journal: Aquatic Toxicology
September/25/2011
Abstract
We evaluated the effects of 17(-ethinylestradiol (EE(2)) on sexual differentiation in transgenic olvas-GFP/STII-YI medaka (Oryzias latipes) in terms of the proliferative activity of germ cells. This strain contains the green fluorescent protein (GFP) gene fused to the regulatory region of the medaka vasa gene, and germ cell-specific expression of GFP can be visualized in living (transparent) individuals. From 0 days post-hatch (0 dph) onwards, juveniles were exposed to graded concentrations of EE(2) (25.2-1710 ng/L) for 35 days. The gonads of live specimens were monitored by measuring their size and calculating their GFP-fluorescence area. GFP-fluorescent area in control females was about 10 times that in control males at 10 days posthatch (dph) whereas the gonadal size of 10 dph males that had been exposed to 158 ng/L of EE(2) significantly increased up to twice the size of control males, indicating that abnormal sexual differentiation towards female might occur in these individuals. Histological examination and identification of the sex-linked marker SL1 indicated that male to female sex reversal occurred at EE(2) exposure ≥45.1 ng/L at 35 dph. These results suggest that observation of proliferative activity of germ cells in the olvas-GFP/STII-YI strain could be applied to facilitated screening fish model to detect adverse effects on sexual differentiation as early as 10 dph juveniles.
Publication
Journal: RNA Biology
February/18/2019
Abstract
The Mason-Pfizer monkey virus (MPMV) genomic RNA (gRNA) packaging signal is a highly-structured element with several stem-loops held together by two phylogenetically conserved long-range interactions (LRIs) between U5 and gag complementary sequences. These LRIs play a critical role in maintaining the structure of the 5´ end of the MPMV gRNA. Thus, one could hypothesize that the overall RNA secondary structure of this region is further architecturally held together by three other stem loops (SL3, Gag SL1, and Gag SL2) comprising of sequences from the distal parts of the 5´untranslated region (5' UTR) to ~ 120 nucleotides into gag, excluding gag sequences involved in forming the U5-Gag LRIs. To provide functional evidence for the biological significance of these stem loops during gRNA encapsidation, these structural motifs were mutated and their effects on MPMV RNA packaging and propagation were tested in a single round trans-complementation assay. The mutant RNA structures were further studied by high throughput SHAPE (hSHAPE) assay. Our results reveal that sequences involved in forming these three stem loops do not play crucial roles at an individual level during MPMV gRNA packaging or propagation. Further structure-function analysis indicates that the U5-Gag LRIs have a more important architectural role in stabilizing the higher order structure of the 5´ UTR than the three stem loops which have a more secondary and perhaps indirect role in stabilizing the overall RNA secondary structure of the region. Our work provides a better understanding of the molecular interactions that take place during MPMV gRNA packaging.
Publication
Journal: Nucleic Acids Research
October/23/2017
Abstract
In bacteria, small non-coding RNAs (sRNAs) could function in gene regulations under variable stress responses. DsrA is an ∼90-nucleotide Hfq-dependent sRNA found in Escherichia coli. It regulates the translation and degradation of multiple mRNAs, such as rpoS, hns, mreB and rbsD mRNAs. However, its functional structure and particularly how it regulates multiple mRNAs remain obscure. Using NMR, we investigated the solution structures of the full-length and isolated stem-loops of DsrA. We first solved the NMR structure of the first stem-loop (SL1), and further studied the melting process of the SL1 induced by the base-pairing with the rpoS mRNA and the A-form duplex formation of the DsrA/rpoS complex. The secondary structure of the second stem-loop (SL2) was also determined, which contains a lower stem and an upper stem with distinctive stability. Interestingly, two conformational states of SL2 in dynamic equilibrium were observed in our NMR spectra, suggesting that the conformational selection may occur during the base-pairing between DsrA and mRNAs. In summary, our study suggests that the conformational plasticity of DsrA may represent a special mechanism sRNA employed to deal with its multiple regulatory targets of mRNA.
Publication
Journal: The Journal of the Association of Physicians of India
March/14/1994
Abstract
We have evaluated the immediate heart rate response to standing and lying and in 100 Diabetic subjects aged 43 +/- 10 years who underwent five other cardiovascular autonomic tests. Using a specially devised scoring system the patients were divided into three groups: a) 58 subjects without autonomic neuropathy, b) 15 borderliners, c) 27 with autonomic neuropathy. The results were compared with 50, sex and age matched controls. We studied SL1 = ratio between R-R mean before lying and R-R maximum between the 20th to 25th beat and R-R minimum over the first 5 beats after lying. In controls SL1 was 1.35 +/- 0.18 and SL2 was 1.52 +/- 0.23. In diabetic subjects without autonomic neuropathy SL1 was 1.20 +/- 0.86 (p < 0.01), SL2 1.50 +/- 0.02 (p < 0.001). In the group with autonomic neuropathy SL1 was 1.04 +/- 0.02 (p < 0.001) and SL2 was 1.20 +/- 0.09 (p < 0.001). We propose that the lowest normal and highest abnormal limits of SL1 are 1.12 and 1.08 respectively and that normal and highest abnormal limits of SL2 are 1.23 and 1.18 respectively. We suggest the use of SL1 as a pure parasympathetic test and SL2 as a mixed but predominantly sympathetic test in the diagnosis of autonomic neuropathy.
Publication
Journal: Nucleic Acids Research
November/12/2018
Abstract
The 3'X tail is a functionally essential 98-nt sequence located at the 3'-end of the hepatitis C virus (HCV) RNA genome. The domain contains two absolutely conserved dimer linkage sequence (DLS) and k nucleotide segments involved in viral RNA dimerization and in a distal base-pairing interaction with stem-loop 5BSL3.2, respectively. We have previously shown that domain 3'X forms an elongated structure comprising two coaxially stacked SL1' and SL2' stem-loops. This conformation favors RNA dimerization by exposing a palindromic DLS segment in an apical loop, but buries in the upper stem of hairpin SL2' the k nucleotides involved in the distal contact with 5BSL3.2. Using nuclear magnetic resonance spectroscopy and gel electrophoresis experiments, here we show that the establishment of the complex between domain 3'X and stem-loop 5BSL3.2 only requires a rearrangement of the nucleotides forming the upper region of subdomain SL2'. The results indicate that the interaction does not occur through a canonical kissing loop mechanism involving the unpaired nucleotides of two terminal loops, but rather involves a base-paired stem and an apical loop and may result in a kissing three-way junction. On the basis of this information we suggest how the 3'X tail switches between monomer, homodimer and heterodimer states to regulate the HCV viral cycle.
Related with
Publication
Journal: Nigerian postgraduate medical journal, The
January/21/2009
Abstract
OBJECTIVE
To document sonographically identifiable causes of vaginal bleeding in secondarily amenorrhoeic women of child bearing age.
METHODS
A retrospective study of ultrasonographic findings among 102 secondarily amenorrhoeic women of childbearing age with vaginal bleeding was carried out. Ultrasound scan was carried using Siemens Sonoline SL1 equipment with 3.5MHz and 5.0MHz transducers
RESULTS
75(73.2%) patients had pregnancy-related conditions, 14(13.7%) had normal, non-pregnant uteri while the remaining 13 (12.8%) had other gynaecological conditions namely pelvic inflammatory disease (PID), uterine fibroids and ovarian masses. Though pregnancy-related conditions are the major causes of vaginal bleeding in amenorrhoeic women of childbearing age, PID, fibroids and ovarian masses are possible findings.
CONCLUSIONS
Ultrasound examination is vital in the elucidation of vaginal bleeding in amenorrhoeic women. Pregnancy related conditions are not the only significant cause of amenorrhoea complicated by vaginal bleeding.
Publication
Journal: Minerva Medica
July/17/1985
Abstract
33 subjects belonging to I.G.T. class according to N.D.D.G. criteria and controlled in our ambulatory, have been studied for the response to the tests usually employed for the investigation of parasympathetic and sympathetic cardiovascular innervation. We have found pathological values for the SL1 test and borderline values for SL2 and LS tests; on the contrary all the other tests presented normal values. The Authors conclude that signs of deterioration of cardiac and vascular innervation, especially regarding the parasympathetic nervous system, can be present also in the subjects showing a small glucose metabolism alteration. This subclinical alterations do not depend on factors which can interfere with the responses to the tests (as age, boyd weight, sex and presence or absence of diabetic familiarity) but on glucose metabolism alteration. Hence also the subjects with I.G.T. have to be considered as a at risk population, like the neuropathic diabetics.
Publication
Journal: Mobile Genetic Elements
February/19/2017
Abstract
Replication of retroviruses and transposition of endogenous retroelements exploits a unique mechanism of post-transcriptional regulation as a means of exporting their incompletely-spliced mRNAs (which serve as both the genomic RNA and the template for protein synthesis). Following discovery of the Rev response element (RRE) that mediates nucleocytoplasmic export of the full-length and singly-spliced human immunodeficiency virus type 1 (HIV-1) genome, equivalent cis-acting regulatory elements have been characterized for both complex and simple retroviruses and retroelements, together with the obligate viral and host proteins with which they interact. The exception to this is the gammaretrovirus family of simple retroviruses, exemplified by reticuloendotheliosis virus (REV), murine leukemia virus (MLV) and xenotropic MLV-related retrovirus (XMRV). In this commentary, we discuss our recent data that reported structural and functional data on the MLV/XMRV post-transcriptional regulatory element (designated the PTE). The PTE was characterized by a highly-structured region of multiple stem-loops (SL1 - SL7) overlapping the pro and 5' portion of the pol open reading frames, comprising a bipartite export signal whose structures are separated by ∼1400 nt. In addition, structural probing suggested that SL3 nucleotides were involved in pseudoknot formation. These data, when compared with RNA transport elements of complex retroviruses (HIV) and simple murine retrotransposons (musD), collectively present an emerging picture that long-range tertiary interactions are critical mediators of their biological function.
Publication
Journal: Journal of Environmental Management
May/11/2020
Abstract
The Soil and Water Assessment Tool (SWAT) is a physical model designed to predict the hydrological processes that could characterize natural and anthropized watersheds. The model can be forced using input data of climate prediction models, soil characteristics and land use scenarios to forecast their effect on hydrological processes. In this study, the SWAT model has been applied in the Aspio basin, a small watershed, highly anthropized and characterized by a short runoff generation. Three simulations setup, named SL1, SL2 and SL3, were investigated using different soil resolution to identify the best model performance. An increase of space requirement and calibration time has been registered in conjunction with the increasing soil resolution. Among all simulations, SL1 has been chosen as the best one in describing watershed streamflow, despite it was characterized by the lower soil resolution. A map of susceptibility to runoff for the entire basin was so created reclassifying the runoff amount of four years in five classes of susceptibility, from very low to very high. Eleven sub-basins, coinciding with the main urban settlements, were identified as highly susceptible to runoff generation. Considering future climate predictions, a slight increase of runoff has been forecasted during summer and autumn. The map of susceptibility successfully identified as highly prone to runoff those sub-basins where extreme flood events were yet recorded in the past, remarking the reliability of the proposed assessment and suggesting that this methodology could represent a useful tool in flood managing plan.
Publication
Journal: Biomolecular NMR Assignments
August/27/2021
Abstract
The stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7-33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses. SL1 is present in genomic SARS-CoV-2 RNA as well as in all subgenomic mRNA species produced by the virus during replication, thus representing a ubiquitous cis-regulatory RNA with potential functions at all stages of the viral life cycle. We present here the 1H, 13C and 15N chemical shift assignment of the 29 nucleotides-RNA construct 5_SL1, which denotes the native 27mer SL1 stabilized by an additional terminal G-C base-pair.
Keywords: 5'-UTR; COVID19-NMR; SARS-CoV-2; SL1; Solution NMR spectroscopy.
Publication
Journal: DNA sequence : the journal of DNA sequencing and mapping
December/21/1993
Abstract
The structure of an esterase gene from Caenorhabditis elegans has been determined by comparison of the sequences in genomic and cDNA clones. The gene was mapped close to the center of chromosome V (1.7 centimorgans to the left of dpy-11) and is therefore distinct from the gut esterase gene ges-1. It possessed 7 short introns. The 5' splice site of intron 3 presented the sequence GC instead of the usual GT that was found in the other six introns. The cDNA was trans-spliced with the short leader SL1. The open reading frame indicated that a protein of 557 aminoacids was encoded. The deduced aminoacid sequence did not present a signal peptide at the N-terminal but a potential N-myristoylation site (GXXXS) provided that the initiator methionine was removed. This protein should therefore remain intracellular. Comparison of this C. elegans sequence to other protein sequences in databases, as well as the analysis of the secondary structure in the protein showed that it belongs to the subgroup of esterases in the alpha/beta hydrolase fold family.
Publication
Journal: Dalton Transactions
December/5/2007
Abstract
The 2,2'-dipicolylamine (DPA)-tethered thioglycoside ligand, N,N-bis(2-pyridylmethyl)-2-aminoethyl 1-deoxy-1-thio-2,3,4,6-tetra-O-acetyl-beta-d-glucopyranoside (sL1), has been prepared and its copper(II) complex synthesized. Using copper(II) chloride, the copper complex was isolated as a chloride-bound species formulated as [Cu(sL1)Cl(ClO(4))](1). The corresponding O-glycoside complex ([Cu(L1)Cl](ClO(4)), 2) was also prepared using L1 (N,N-bis(2-pyridylmethyl)-2-aminoethyl 2,3,4,6-tetra-O-acetyl-beta-d-glucopyranoside), and both complexes were characterized and compared by means of X-ray crystallography, cyclic voltammetry, electronic absorption and circular dichroism (CD) spectra. Although both complexes exhibited similar copper coordination geometries, the absolute configuration of the O/S chiral center generated by the copper coordination was inverted. The electronic and CD spectra of acetonitrile solutions of 1 and 2 were different likely due to the presence of a copper-sulfur charge-transfer band for 1. Complex also exhibits a large Cotton effect around 700 nm. The corresponding d-d transition of the copper(II) center reveals that the asymmetric copper-sulfur (oxygen) coordination remains even in solution.
Publication
Journal: Biorheology
April/18/1999
Abstract
A filtrometer is described for measuring the flow of fluids through microfilters. The flow of Newtonian fluids through the filters can be predicted from the diameter, length and number of pores. There are no physical artefacts such as turbulent flow or a significant lag period before steady-state flow is achieved. The instrument has been used as a viscometer and has been used to record and analyse the flow of undiluted blood through 5 microns polycarbonate filters. The calculated viscosity of Newtonian fluids agrees well with those measured by a more conventional viscometer (Ostwald). Flow profiles of blood have been analysed to give both the numbers and the flow properties of a small population of slow leukocytes which equate numerically with the monocytes. They are subdivided into three distinct sub-populations, according to their rheological properties, and these are termed SL1, SL2 and PB. The concentration of these cells, in blood, are 0.12 +/- 0.02 x 10(6) ml-1, 0.11 +/- 0.02 x 10(6) ml-1, 0.09 +/- 0.02 x 10(6) ml-1 in young females aged about 25 years. The transit time of these cells, through 5 microns pores, is 34.8 +/- 1.4 s, 147.5 +/- 2.5 s and>> 300 s, respectively. Analysis of blood from older men (53-79 years) gives essentially the same results although the concentration of SL1 is slightly higher at 0.19 +/- 0.09 x 10(6) ml-1.
Publication
Journal: RNA
October/8/2015
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that use partial base-pairing to recognize and regulate the expression of messenger RNAs (mRNAs). Mature miRNAs arise from longer primary transcripts (pri-miRNAs) that are processed to a shorter hairpin precursor miRNA (pre-miRNA) by the Microprocessor complex. In Caenorhabditis elegans the primary let-7 (pri-let-7) transcript undergoes trans-splicing, where pri-let-7 is cleaved at a 3' splice site and the splice-leader-1 (SL1) sequence is appended at the 5' end. Here we investigate the role of this splicing event in the biogenesis of let-7 miRNA. We hypothesized that splicing changes the secondary structure of the pri-let-7 transcript, creating a more favorable substrate for recognition by the Microprocessor. Supporting this idea, we detected conspicuous structural differences between unspliced and SL1-spliced pri-let-7 transcripts using in vitro ribonuclease (RNase) assays. Through the generation of transgenic worm strains, we found that the RNA secondary structure produced by splicing, as opposed to the act of splicing itself, optimizes processing of pri-let-7 by the Microprocessor in vivo. We also observed that the endogenous spliced, but not the unspliced, pri-let-7 transcripts bind to the Microprocessor and accumulate upon its depletion. We conclude that splicing is a key step in generating pri-let-7 transcripts with a structure that enables downstream processing events to produce appropriate levels of mature let-7.
Publication
Journal: Journal of Biomolecular Structure and Dynamics
August/17/2011
Abstract
Viral maturation of HIV-1 involves refolding of its genomic RNA, which is believed to include a rearrangement of the SL1 stem-loop from a metastable conformation called kissing loop dimer (KD) to a stable one termed extended dimer (ED). To investigate this rearrangement in vitro we have studied the thermal melting of the RNA dimers formed by slightly modified 23-nucleotide SL1 RNA of HIV-1 Mal. Local structural changes in the RNA dimers during the melting were monitored by changes in the fluorescence of 2-aminopurine (2AP) incorporated in predetermined positions of RNA. We have shown that the stem regions of both preformed KD and ED melt in the temperature interval from 75 ° C to 90 ° C. Kissing loop interface of the KD RNA is found to be disrupted at lower temperatures from 20 ° C to 55 ° C, at which the stem regions remain intact. Conversion of the preformed KD to ED overcoming the kinetic barrier occurs between 55 ° C and 65 ° C. The melting of "loop-loop" regions in both preformed and newly formed EDs takes place around 70 ° C. Our finding that thermoinduced KD-to-ED conversion is preceded by transient dissociation of loop-loop interface disagrees with a common idea of strand exchange without disruption of loop-loop-contact.
Publication
Journal: Journal of Applied Microbiology
August/3/2020
Abstract
Aims: This study compared the bag-mediated filtration system (BMFS) and standard WHO two-phase separation methods for poliovirus (PV) environmental surveillance, examined factors impacting PV detection, and monitored Sabin-like (SL) PV type 2 presence with withdrawal of oral polio vaccine type 2 (OPV2) in April 2016.
Methods and results: Environmental samples were collected in Nairobi, Kenya (Sept 2015-Feb 2017), concentrated via BMFS and two-phase separation methods, then assayed using the WHO PV isolation algorithm and intratypic differentiation diagnostic screening kit. SL1, SL2, and SL3 were detected at higher rates in BMFS than two-phase samples (p<0.05). In BMFS samples, SL PV detection did not significantly differ with volume filtered, filtration time, or filter shipment time (p>0.05), while SL3 was detected less frequently with higher shipment temperatures (p=0.027). SL2 was detected more frequently before OPV2 withdrawal in BMFS and two-phase samples (p<1x10-5 ).
Conclusions: PV was detected at higher rates with the BMFS, a method that includes a secondary concentration step, than using the standard WHO two-phase method. SL2 disappearance from the environment was commensurate with OPV2 withdrawal.
Significance and impact of the study: The BMFS offers comparable or improved PV detection under the conditions in this study, relative to the two-phase method.
Keywords: Kenya; Poliovirus; ViroCap; enteric viruses; environmental surveillance; filtration; wastewater.
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