Simple low-cost production of DNA MS2 virus-like particles as molecular diagnostic controls

Suitable controls are integral for the validation and continued quality assurance of diagnostic workflows. Plasmids, DNA, or in vitro transcribed RNA are often used to validate novel diagnostic workflows, however, they are poorly representative of clinical samples. RNA phage virus-like particles (VLPs) packaged with exogenous RNA have been used in clinical diagnostics as workflow controls, serving as surrogates for infectious viral particles. Comparable controls for DNA viruses are more challenging to produce, with analogous DNA phages being infectious and packaging of DNA within RNA phages requiring complex purification procedures and expensive chemical linkers. We present a simple and inexpensive method to produce Emesvirus zinderi (MS2) VLPs, packaged with DNA, that makes use of affinity chromatography for purification and enzymatic production of exogenous DNA suitable for packaging. The produced VLPs were packaged with hepatitis B virus DNA and were then quantified using droplet digital PCR and calibrated against the WHO international standard using a commercial assay in an accredited clinical laboratory

Improving file distribution performance by grouping in peer-to-peer networks

It has been shown that the peer-to-peer paradigm is more efficient than the traditional client-server model for file sharing among a large number of users. Given a group of leechers who wants to download a single file and a group of seeds who possesses the whole file, the minimum time needed for distributing the file to all users can be calculated based on their bandwidth availabilities. A scheduling algorithm has been developed so that every leecher can obtain the file within this minimum time. Unfortunately, this mechanism is not optimal with regard to the average download time among the peers. In this paper, we study how to reduce the average download time without prolonging the time needed for all leechers to obtain the file from a theoretical perspective. Based on the bandwidth capacities, the seeds and leechers are divided into different groups. We identify the necessary conditions for grouping to bring about benefits. We also study the impact on performance when leechers leave the system before the downloading process is complete. To evaluate our mechanism, we conduct extensive simulations and compare the performance with a BitTorrentlike file sharing algorithm. The results show that our grouping protocol successfully reduces the average download time over a wide range of system configurations. © 2009 IEEE.published_or_final_versio

Super-Yang-Mills and M5-branes

We uplift 5-dimensional super-Yang-Mills theory to a 6-dimensional gauge theory with the help of a space-like constant vector $\eta^M$, whose norm determines the Yang-Mills coupling constant. After the localization of $\eta^M$ the 6D gauge theory acquires Lorentzian invariance as well as scale invariance. We discuss KK states, instantons and the flux quantization. The 6D theory admits extended solutions like 1/2 BPS `strings' and monopoles.Comment: 15 pages; minor changes, to appear in JHE

The effects of dog management on Echinococcus spp. prevalence in villages on the eastern Tibetan Plateau, China

Background The pastoral area of the eastern Tibetan plateau is a very important human echinococcosis endemic region. Domestic dogs are the main definitive host for the transmission of Echinococcus granulosus sensu lato (s.1.) and E. multilocularis to humans. To control the infection risks, a national-level canine echinococcosis prevention and control program has been implemented since 2015 in Shiqu County, Sichuan, China, The objective of this investigation was to evaluate its effect on Echinococcus spp. prevalence in dogs. Methods We surveyed 69 households with 84 owned dogs, for dog keeping information in the villages of Rizha and Eduoma. A total of 105 dog fecal samples, consisting of 75 from owned dogs and 30 unknown dog fecal samples were collected between 2015 and 2017 to determine Echinococcus spp. prevalence using copro-PCR. Eight variables based on household surveys were included into a logistic regression model for significantly relevant factors to canine echinococcosis prevalence in dogs. Results The overall Echinococcus spp. copro-DNA prevalence decreased significantly in dogs from 51.2% (2015) to 20.0% (2017) in Rizha, and insignificantly from 11.5% (2016) to 4.3% (2017) in Eduoma. Echinococcus multilocularis was the most prevalent species continually detected during the entire research period, while E. granulosus was rare and not detected in 2017. Echinococcus shiquicus prevalence was as high as E. multilocularis , although only detected in 2015 in Rizha. Unleashed dog feces were mainly collected in Rizha Village in 2015. Although 93.2% of owned dogs were leashed, and the monthly praziquantel dosing rate reached 97%, E. multilocularis infection could still be detected in 11.1% of owned dogs in 2017. Monthly deworming, leashing dogs 24h per day, and the avoidance of dogs feeding on livestock viscera are significant measures to prevent canine echinococcosis infection in owned dogs. Conclusion Carrying out a canine echinococcosis prevention and control program can significantly decrease the Echinococcus prevalence. The potential contact between leashed dogs and wild small mammals is still a risk to re-infect owned dogs. This study shows that the long term application of regular dog dosing in the vast remote echinococcosis endemic areas of west China is still challenging

Temporal inabilities and decision-making capacity in depression

We report on an interview-based study of decision-making capacity in two classes of patients suffering from depression. Developing a method of second-person hermeneutic phenomenology, we articulate the distinctive combination of temporal agility and temporal inability characteristic of the experience of severely depressed patients. We argue that a cluster of decision-specific temporal abilities is a critical element of decision-making capacity, and we show that loss of these abilities is a risk factor distinguishing severely depressed patients from mildly/moderately depressed patients. We explore the legal and clinical consequences of this result

Pseudomonas aeruginosa biofilm disruption using microbial surfactants.

AIMS: To establish the ability of the rhamnolipids biosurfactants from Pseudomonas aeruginosa, in the presence and absence of caprylic acid and ascorbic acid, to disrupt bacterial biofilms, compared with the anionic alkyl sulphate surfactant Sodium dodecyl sulphate (SDS). METHODS AND RESULTS: Pseudomonas aeruginosa ATCC 15442 biofilms were disrupted by rhamnolipids at concentrations between 0·5 and 0·4 g l(-1) and with SDS at 0·8 g l(-1) . The combination of rhamnolipids 0·4 g l(-1) and caprylic acid at 0·1 g l(-1) showed a remarkable effect on biofilm disruption and cell killing. After 30 min of treatment most of the biofilm was disrupted and cell viability was significantly reduced. Neither caprylic acid nor ascorbic acid has any effect on biofilm disruption at 0·1 g l(-1) . SDS is an effective antimicrobial agent; however, in the presence of caprylic acid its effect was neutralized. CONCLUSIONS: The results show that rhamnolipids at low concentration in the presence of caprylic acid are promising molecules for inhibition/disruption of biofilms formed by Ps. aeruginosa ATCC 15442. SIGNIFICANCE AND IMPACT OF THE STUDY: The disruption of biofilms has major significance in many industrial and domestic cleaning applications and in medical situations

The fragilis interferon-inducible gene family of transmembrane proteins is associated with germ cell specification in mice.

BACKGROUND: Specification of primordial germ cells in mice depends on instructive signalling events, which act first to confer germ cell competence on epiblast cells, and second, to impose a germ cell fate upon competent precursors. fragilis, an interferon-inducible gene coding for a transmembrane protein, is the first gene to be implicated in the acquisition of germ cell competence. RESULTS: Here, we describe four additional fragilis-related genes, fragilis2-5, which are clustered within a 68 kb region in the vicinity of the fragilis locus on Chr 7. These genes exist in a number of mammalian species, which in the human are also clustered on the syntenic region on Chr 11. In the mouse, fragilis2 and fragilis3, which are proximate to fragilis, exhibit expression that overlaps with the latter in the region of specification of primordial germ cells. Using single cell analysis, we confirm that all these three fragilis-related genes are predominant in nascent primordial germ cells, as well as in gonadal germ cells. CONCLUSION: The Fragilis family of interferon-inducible genes is tightly associated with germ cell specification in mice. Furthermore, its evolutionary conservation suggests that it probably plays a critical role in all mammals. Detailed analysis of these genes may also elucidate the role of interferons as signalling molecules during development

Location and associated carbon storage of erosional escarpments of seagrass Posidonia mats

Seagrasses of the genus Posidonia can form an irregular seascape due to erosional processes exposing thick walls of organic matter-rich soils. However, little is known about the location and characteristics of these particular formations. Here we provide comprehensive estimates of organic carbon (Corg) storage in Posidonia oceanica and Posidonia australis meadows, while providing insight into their location and mechanisms of formation, and highlighting future research directions. Erosional reef escarpments are restricted to shallow highly productive P. oceanica meadows from the Mediterranean Sea and P. australis meadows from the Indian Ocean, and sustain the existence of Corg-rich deposits in surrounding meadows. The thickness of the mat escarpments can reach up to 3 m and their length can vary from few to hundreds of meters. Mechanisms of formation appear to differ among sites, from naturally-induced escarpments by wave action and/or tidal flow to human-induced escarpments by dredging activities. The inter-twined remains of seagrass shoots within the sediment matrix consolidate the sandy substrate and hold the exposed Posidonia mat escarpments together, maintaining a semi-rigid structure. This phenomenon is unusual but of exceptional importance in marine biogeochemical cycles, revealing the largest Corg sinks among seagrasses worldwide (ranging from 15 to 176 kg Corg m−2 in 2 m-thick mats accumulated at 2–249 g Corg m−2 yr−1 over 300–3000 yr)

Rapid identification of mutations in GJC2 in primary lymphoedema using whole exome sequencing combined with linkage analysis with delineation of the phenotype.

Background: Primary lymphoedema describes a chronic, frequently progressive, failure of lymphatic drainage. This disorder is frequently genetic in origin, and a multigenerational family in which eight individuals developed postnatal lymphoedema of all four limbs was ascertained from the joint Lymphoedema/Genetic clinic at St George's Hospital. Methods: Linkage analysis was used to determine a locus, and exome sequencing was employed to look for causative variants. Results: Linkage analysis revealed cosegregation of a 16.1 Mb haplotype on chromosome 1q42 that contained 173 known or predicted genes. Whole exome sequencing in a single affected individual was undertaken, and the search for the causative variant was focused to within the linkage interval. This approach revealed two novel non-synonymous single nucleotide substitutions within the chromosome 1 locus, in NVL and GJC2. NVL and GJC2 were sequenced in an additional cohort of individuals with a similar phenotype and non-synonymous variants were found in GJC2 in four additional families. Conclusion: This report demonstrates the power of exome sequencing efficiently applied to a traditional positional cloning pipeline in disease gene discovery, and suggests that the phenotype produced by GJC2 mutations is predominantly one of 4 limb lymphoedema

Intracluster age gradients in numerous young stellar clusters

This is the final version of the article.Available from Oxford University Press via the DOI in this record.The pace and pattern of star formation leading to rich young stellar clusters is quite uncertain. In this context, we analyse the spatial distribution of ages within 19 young (median t ≲ 3 Myr on the Siess et al. time-scale), morphologically simple, isolated, and relatively rich stellar clusters. Our analysis is based on young stellar object (YSO) samples from the Massive Young Star-Forming Complex Study in Infrared and X-ray and Star Formation in Nearby Clouds surveys, and a new estimator of pre-main sequence (PMS) stellar ages, AgeJX, derived from X-ray and near-infrared photometric data. Median cluster ages are computed within four annular subregions of the clusters. We confirm and extend the earlier result of Getman et al. (2014): 80 per cent of the clusters show age trends where stars in cluster cores are younger than in outer regions. Our cluster stacking analyses establish the existence of an age gradient to high statistical significance in several ways. Time-scales vary with the choice of PMS evolutionary model; the inferred median age gradient across the studied clusters ranges from 0.75 to 1.5 Myr pc−1. The empirical finding reported in the present study – late or continuing formation of stars in the cores of star clusters with older stars dispersed in the outer regions – has a strong foundation with other observational studies and with the astrophysical models like the global hierarchical collapse model of Vázquez-Semadeni et al.The MYStIX project is now supported by the Chandra archive grant AR7-18002X. The SFiNCs project is supported at Penn State by NASA grant NNX15AF42G, Chandra GO grant SAO AR5-16001X, Chandra GO grant GO2-13012X, Chandra GO grant GO3-14004X, Chandra GO grant GO4-15013X, and the Chandra ACIS Team contract SV474018 (G. Garmire & L. Townsley, Principal Investigators), issued by the Chandra X-ray Center, which is operated by the Smithsonian Astrophysical Observatory for and on behalf of NASA under contract NAS8-03060. The Guaranteed Time Observations (GTO) data used here were selected by the ACIS Instrument Principal Investigator, Gordon P. Garmire, of the Huntingdon Institute for X-ray Astronomy, LLC, which is under contract to the Smithsonian Astrophysical Observatory; Contract SV2-82024. This research has made use of NASA's Astrophysics Data System Bibliographic Services and SAOImage DS9 software developed by Smithsonian Astrophysical Observatory