scholarly journals Modular Evolution of Coronavirus Genomes

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1270
Author(s):  
Yulia Vakulenko ◽  
Andrei Deviatkin ◽  
Jan Felix Drexler ◽  
Alexander Lukashev
Keyword(s):  
Phylogenetic Signal ◽  
Formal Analysis ◽  
Genetic Distances ◽  
Pairwise Distance ◽  
Spike Gene ◽  
Modular Evolution ◽  
Deviation Matrix ◽  
Alpha Beta ◽  
Low Incidence ◽  
Set Up

The viral family Coronaviridae comprises four genera, termed Alpha-, Beta-, Gamma-, and Deltacoronavirus. Recombination events have been described in many coronaviruses infecting humans and other animals. However, formal analysis of the recombination patterns, both in terms of the involved genome regions and the extent of genetic divergence between partners, are scarce. Common methods of recombination detection based on phylogenetic incongruences (e.g., a phylogenetic compatibility matrix) may fail in cases where too many events diminish the phylogenetic signal. Thus, an approach comparing genetic distances in distinct genome regions (pairwise distance deviation matrix) was set up. In alpha, beta, and delta-coronaviruses, a low incidence of recombination between closely related viruses was evident in all genome regions, but it was more extensive between the spike gene and other genome regions. In contrast, avian gammacoronaviruses recombined extensively and exist as a global cloud of genes with poorly corresponding genetic distances in different parts of the genome. Spike, but not other structural proteins, was most commonly exchanged between coronaviruses. Recombination patterns differed between coronavirus genera and corresponded to the modular structure of the spike: recombination traces were more pronounced between spike domains (N-terminal and C-terminal parts of S1 and S2) than within domains. The variability of possible recombination events and their uneven distribution over the genome suggest that compatibility of genes, rather than mechanistic or ecological limitations, shapes recombination patterns in coronaviruses.

scholarly journals K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology

Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Peio Ziarsolo ◽  
Tomas Hasing ◽  
Rebeca Hilario ◽  
Victor Garcia-Carpintero ◽  
Jose Blanca ◽  
...  
Keyword(s):  
Cost Effective ◽  
Genetic Distances ◽  
Set Design ◽  
Special Equipment ◽  
Genetic Studies ◽  
Set Up ◽  
Genomic Regions ◽  
Biology Laboratory ◽  
Genotyping Technology ◽  
Genetic Results

Abstract Background K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. Results As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%. Conclusion K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies.

scholarly journals Real time surveillance of COVID-19 space and time clusters during the summer 2020 in Spain

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Nicolás Rosillo ◽  
Javier Del-Águila-Mejía ◽  
Ayelén Rojas-Benedicto ◽  
María Guerrero-Vadillo ◽  
Marina Peñuelas ◽  
...  
Keyword(s):  
Real Time ◽  
Scan Statistic ◽  
Cluster Aggregation ◽  
Space And Time ◽  
Spatial Trends ◽  
Community Transmission ◽  
Low Incidence ◽  
Set Up ◽  
And Control ◽  
Time Scan

Abstract Background On June 21st de-escalation measures and state-of-alarm ended in Spain after the COVID-19 first wave. New surveillance and control strategy was set up to detect emerging outbreaks. Aim To detect and describe the evolution of COVID-19 clusters and cases during the 2020 summer in Spain. Methods A near-real time surveillance system to detect active clusters of COVID-19 was developed based on Kulldorf’s prospective space-time scan statistic (STSS) to detect daily emerging active clusters. Results Analyses were performed daily during the summer 2020 (June 21st – August 31st) in Spain, showing an increase of active clusters and municipalities affected. Spread happened in the study period from a few, low-cases, regional-located clusters in June to a nationwide distribution of bigger clusters encompassing a higher average number of municipalities and total cases by end-August. Conclusion STSS-based surveillance of COVID-19 can be of utility in a low-incidence scenario to help tackle emerging outbreaks that could potentially drive a widespread transmission. If that happens, spatial trends and disease distribution can be followed with this method. Finally, cluster aggregation in space and time, as observed in our results, could suggest the occurrence of community transmission.

The demand for psychiatric services as a result of the Gulf war

1991 ◽  
Vol 15 (4) ◽  
pp. 201-203
Author(s):  
Jacqueline M. Atkinson
Keyword(s):  
Medical Officer ◽  
Gulf War ◽  
Subsequent Treatment ◽  
Psychiatric Services ◽  
Military Hospital ◽  
Royal Navy ◽  
Post Traumatic Stress ◽  
Low Incidence ◽  
Set Up

Despite the brevity of the Gulf war, there is still the strong possibility that it will leave long-term problems for psychiatric services within the NHS. The low incidence of acute psychiatric problems in the Falklands conflict does not obviate long-term problems. Surgeon-Commander O'Connell of the Royal Navy, reported informally in the newspapers (Guardian, 7 May 1990) that up to 30% of the 28,000 Falklands veterans are still suffering from post-traumatic stress disorder (PTSD). Hughes (1990), medical officer with 2nd Paratroop Regiment at Goose Green, described his realisation that he had PTSD, his subsequent treatment by the NHS and transfer to a military hospital. The Royal Navy still has a counselling service, set up in 1987, but it is clear that military services cannot deal with all the current problems, let alone those to come. The advice of the Ministry of Defence is that the initial onus to recognise a problem lies with the family and that sufferers should seek treatment through their GP.

scholarly journals Quantitative functional outcomes of the conservative management of partial segmental thrombosis of the corpus cavernosum

2015 ◽  
Vol 97 (7) ◽  
pp. e108-e111 ◽  
Author(s):  
H Gresty ◽  
S Tadtayev ◽  
N Arumainayagam ◽  
S Patel ◽  
C King ◽  
...  
Keyword(s):  
Sexual Function ◽  
Conservative Management ◽  
Erectile Function ◽  
Functional Outcomes ◽  
Case Reports ◽  
Formal Analysis ◽  
Corpus Cavernosum ◽  
Complete Recovery ◽  
Low Incidence

The low incidence of partial segmental thrombosis of the corpus cavernosum (PSTCC) means its management is guided by isolated case reports. Erectile function is an important outcome that has not been described quantitatively in the literature. We present two cases of PSTCC managed conservatively. Although both patients reported resolution of local symptoms, formal analysis of sexual function at follow-up review has revealed that only one achieved complete recovery.

A programme for the inventory, characterisation, evaluation, conservation and utilisation of European rabbit (Oryctolagus cuniculus) genetic resources

1999 ◽  
Vol 25 ◽  
pp. 57-70 ◽  
Author(s):  
G. Bolet ◽  
M. Monnerot ◽  
C. Arnal ◽  
J. Arnold ◽  
D. Bell ◽  
...  
Keyword(s):  
Data Bank ◽  
Genetic Distances ◽  
European Rabbit ◽  
Focal Points ◽  
Genetic Characteristics ◽  
Frozen Embryos ◽  
Rabbit Meat ◽  
Set Up ◽  
European Programme ◽  
Data Banks

SummaryIn Europe, more than 60 breeds are described by the national associations of rabbit breeders. However, these breeds are scarcely used in the commercial production of rabbit meat in Europe, which is based mainly on commercial strains. A European programme, coordinated by the I. N. R. A., has been initiated to realise the inventory of all these breeds and to evaluate the zootechnical value and the genetic characteristics of some of them. Through the European association of rabbit breeders and the FAO national focal points, all the European countries have been asked to fill out a questionnaire describing their populations of rabbits. A data bank is being set up, which will be included in the FAO (DAD-IS) and EAAP data banks. A sample of 10 breeds has been chosen (Flemish Giant, French Lop, Belgian Hare, Vienna White, Champagne Argente, Thuringer, Fauve de Bourgogne, Chinchilla, Himalayan, British). Their zootechnical value (reproduction, growth and carcass traits) is being evaluated on three experimental farms, in comparison with a control breed. At the same time, their genetic polymorphism and the genetic distances between these 10 breeds are calculated on the basis of microsatellites, mitochondrial DNA, other genetic markers and protein polymorphism. Finally, a bank of frozen embryos from these 10 breeds is being constituted.

scholarly journals Echovirus type 6 transmission clusters and the role of environmental surveillance in early warning, the Netherlands, 2007 to 2016

2018 ◽  
Vol 23 (45) ◽  
Author(s):  
Susana Monge ◽  
Kimberley Benschop ◽  
Loes Soetens ◽  
Roan Pijnacker ◽  
Susan Hahné ◽  
...  
Keyword(s):  
The Netherlands ◽  
Early Warning ◽  
Clinical Case ◽  
Sewage Water ◽  
Genetic Distances ◽  
Pairwise Distance ◽  
Environmental Surveillance ◽  
Phylogenetic Cluster ◽  
Echovirus Type

Background In the Netherlands, echovirus type 6 (E6) is identified through clinical and environmental enterovirus surveillance (CEVS and EEVS). Aim We aimed to identify E6 transmission clusters and to assess the role of EEVS in surveillance and early warning of E6. Methods We included all E6 strains from CEVS and EEVS from 2007 through 2016. CEVS samples were from patients with enterovirus illness. EEVS samples came from sewage water at pre-specified sampling points. E6 strains were defined by partial VP1 sequence, month and 4-digit postcode. Phylogenetic E6 clusters were detected using pairwise genetic distances. We identified transmission clusters using a combined pairwise distance in time, place and phylogeny dimensions. Results E6 was identified in 157 of 3,506 CEVS clinical episodes and 92 of 1,067 EEVS samples. Increased E6 circulation was observed in 2009 and from 2014 onwards. Eight phylogenetic clusters were identified; five included both CEVS and EEVS strains. Among these, identification in EEVS did not consistently precede CEVS. One phylogenetic cluster was dominant until 2014, but genetic diversity increased thereafter. Of 14 identified transmission clusters, six included both EEVS and CEVS; in two of them, EEVS identification preceded CEVS identification. Transmission clusters were consistent with phylogenetic clusters, and with previous outbreak reports. Conclusion Algorithms using combined time–place–phylogeny data allowed identification of clusters not detected by any of these variables alone. EEVS identified strains circulating in the population, but EEVS samples did not systematically precede clinical case surveillance, limiting EEVS usefulness for early warning in a context where E6 is endemic.

scholarly journals Detecting impaired language processing in MCI patients using around-the-ear cEEgrid electrodes

2021 ◽  
Author(s):  
K. Segaert ◽  
C. Poulisse ◽  
R. Markiewicz ◽  
L. Wheeldon ◽  
D. Marchment ◽  
...  
Keyword(s):  
Language Processing ◽  
Language Comprehension ◽  
Daily Living ◽  
Lexical Retrieval ◽  
Clinical Tool ◽  
Cognitive Domains ◽  
Non Invasive ◽  
Word Onset ◽  
Alpha Beta ◽  
Set Up

AbstractMild cognitive impairment (MCI) is the term used to identify those individuals with subjective and objective cognitive decline but with preserved activities of daily living and an absence of dementia. While MCI can impact functioning in different cognitive domains, most notably episodic memory, relatively little is known about the comprehension of language in MCI. In this study we used around-the-ear electrodes (cEEGrids) to identify impairments during language comprehension in MCI patients. In a group of 23 MCI patients and 23 age-matched controls, language comprehension was tested in a two-word phrase paradigm. We examined the oscillatory changes following word onset as a function of lexical retrieval (e.g. swrfeq versus swift) and semantic binding (e.g. horse preceded by swift versus preceded by swrfeq). Electrophysiological signatures (as measured by the cEEGrids) were significantly different between MCI patients and controls. In controls lexical retrieval was associated with a rebound in the alpha/beta range and semantic binding was associated with a post-word alpha/beta suppression. In contrast, both the lexical retrieval and semantic binding signatures were absent in the MCI group. The signatures observed using cEEGrids in controls were comparable to those signatures obtained with a full-cap EEG set-up. Importantly, our findings suggest that MCI patients have impaired electrophysiological signatures for comprehending single-words and multi-word phrases. Moreover, cEEGrids set-ups provide a non-invasive and sensitive clinical tool for detecting early impairments in language comprehension in MCI.

The Use of Standard Alpha and Beta Surface Scintillation Contamination Monitors to Confirm the Contamination Fingerprint and to Check on Source Quality

2011 ◽  
Author(s):  
Pete Burgess
Keyword(s):  
Count Rate ◽  
Surface Condition ◽  
Surface Contamination ◽  
Ratio Method ◽  
Channel Ratio ◽  
Alpha Channel ◽  
Channel Analysis ◽  
Alpha Beta ◽  
Set Up ◽  
Counting Window

Normally, beta and alpha surface contamination monitors are used with a simple counting threshold, i.e. any pulse over a predetermined amplitude is counted. This is very different from gamma monitoring, where the use of counting windows is very popular and the use of full multi-channel analysis is common. Many current surface contamination ratemeters have the capacity to drive dual phosphor detectors and can be set up to provide beta and alpha channels. Effectively, the beta channel is a counting window, i.e. all pulses which are bigger than the threshold and smaller than the alpha threshold are counted. Larger pulses go into the alpha channel. This paper addresses how this can be used with beta only and alpha only detectors to provide information on the source. The detector is set up conventionally to a defined point for the lowest beta energy anticipated. The instrument is then switched to alpha + beta mode and the alpha threshold set to 3 times the beta threshold. With this set up, the alpha to beta channel count rate ratio varies smoothly by a factor of 14 between Y-90 (Emax 2.27 MeV) and C-14 (Emax 0.16 MeV). Hence the instrument can be used to estimate the energy of an unknown beta contaminant or to confirm that a mixed beta fingerprint has essentially the same mix. The same approach can be used with alpha probes to confirm the source quality. The main worry with alpha monitoring is the surface condition. A poor surface condition will lead to a low count rate. Using the channel ratio method will identify grubby sources. The resulting ratio can be used either as a go/no trigger, i.e. any surface with a low ratio will be treated as untrustworthy, or alternatively the ratio can be used to correct the reading to give a better estimate of surface activity.

Prospective study of post-ESWL infections of the urinary tract

1992 ◽  
Vol 59 (1_suppl) ◽  
pp. 134-136
Author(s):  
G. Zanetti ◽  
E. Montanari ◽  
A. Guarneri ◽  
M. Seveso ◽  
A. Trinchieri ◽  
...  
Keyword(s):  
Antibiotic Therapy ◽  
Prospective Study ◽  
Renal Stones ◽  
Post Treatment ◽  
Maximum Diameter ◽  
Symptomatic Infection ◽  
Before And After ◽  
Low Incidence ◽  
Set Up ◽  
A Prospective Study

Throughout the world ESWL is nowadays the treatment of choice in renoureteral stones and ever smaller stones can be treated. We have undertaken the present study to evaluate post treatment infective complications in low-risk patients. A prospective study has been performed on 150 non-infected patients before ESWL treated for renal stones whose maximum diameter was less than 15 mm. None out of this group underwent pretreatment manoeuvres. Urinecultures were checked before and after treatment (3 days – 30 days). Out of 150 third day urine cultures 11 were positive but only 5 patients presented a symptomatic infection. All patients whose urineculture was positive received antibiotic treatment. All urinecultures were negative at the 30 days follow-up. The low incidence of urinary symptomatic and asymptomatic infections in our series and the rapid cure by antibiotic therapy suggest performing ESWL treatment in selected patients without any antibiotic prophylaxis. Antibiotic therapy will be set up just in symptomatic or asymptomatic post-treatment infections.

Contribution of DNA-typing to bushmeat surveys: assessment of a roadside market in south-western Nigeria

2011 ◽  
Vol 38 (8) ◽  
pp. 696 ◽  
Author(s):  
Ayodeji Olayemi ◽  
Akinlabi Oyeyiola ◽  
Agostinho Antunes ◽  
Céline Bonillo ◽  
Corinne Cruaud ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Secondary Forest ◽  
Dna Typing ◽  
Central Africa ◽  
Genetic Distances ◽  
Morphological Identification ◽  
Cryptic Taxa ◽  
Conservation Concern ◽  
Set Up ◽  
Bushmeat Trade

Context Following recent socioeconomic transformations in western and central Africa, the volume of bushmeat hunting, a traditional source of proteins and revenue for rural populations, has reached unsustainable levels. The morphological identification of species sold on bushmeat market stalls may be challenging because of the presence of cryptic taxa and smoked or processed carcasses. Aims To assess the contribution of DNA-typing to traditional bushmeat surveys. We conducted a case study at a roadside bushmeat market in Asejire, south-western Nigeria, to characterise the mammalian diversity and sketch out the dynamics of the bushmeat trade. Methods We generated a 402-bp Cytochrome b fragment using a ‘universal’ mitochondrial primer pair that successfully amplified across five mammalian orders, and used assignment procedures to assess the taxonomic identification of the traded species. We combined DNA-typing with morphological-based market surveys and questionnaires to half (n = 20) of the market stakeholders. Key results Our combined morphological–DNA-based survey revealed a total of 17 species, representing seven mammalian orders (Rodentia, Lagomorpha, Primates, Hyracoidea, Carnivora, Pholidota and Artiodactyla). DNA-typing allowed identifying the Walter’s duiker, a cryptic, newly described species from the Dahomey Gap, and diagnosing an unidentified primate as the white-throated monkey, Cercopithecus erythrogaster, a species of high conservation concern in Nigeria. K2P pairwise genetic distances among all species exceeded the 11% threshold, indicative of species-level distinction. The most hunted species were the Walter’s duiker and, to a lesser extent, the greater cane rat, Thryonomys swinderianus. Questionnaires to traders revealed that the Asejire roadside market was a straightforward trader–hunter system centralising off-takes from distant hunting sites. Conclusions We showed how mitochondrial DNA-typing combined with assignment procedures improved the characterisation of the mammalian diversity sold on bushmeat markets. The hunted mammalian community consisted of versatile, small- to medium-sized secondary forest species characteristic of the Dahomey Gap assemblage; their sustainable management is in doubt because of the lack of conservation and health awareness within the traders’ community. Implications Given the utility of mitochondrial DNA-typing in identifying species sold in bushmeat markets, we argue in favour of multi-entry investigations to reach a comprehensive characterisation of the bushmeat trade. The building of a web-accessible mtDNA database covering the spectrum of the species hunted for bushmeat would appear to be a valuable diagnostic tool that may help Nigeria and neighbouring countries to set up a rigorous monitoring of wildlife extirpation.

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