Demonstration of a novel technique to quantitatively assess inflammatory mediators and cells in rat knee joints

<p>Abstract</p> <p>Background</p> <p>The inflammation that accompanies the pain and swelling associated with osteo- and rheumatoid arthritis is mediated by complex interactions of inflammatory mediators. Cytokines play a pivotal role in orchestrating many of these processes, including inflammatory cell recruitment, adhesion and activation. In addition, prostaglandins are secreted into the synovial cavity and are involved in perpetuation of local inflammation, vasodilatation and vasoconstriction, and also with bone resorption. Pre-clinical models have been developed in order to correlate to the human disease and principle among these is the adjuvant-induced arthritis model in the rat.</p> <p>Methods</p> <p>We have developed a technique to quantitatively assess the contents of synovial fluid samples from rat joints. Two needles joined together are inserted into the knee joint of anaesthetised rats and connected to a Watson-Marlow perfusion pump. Sterile saline is infused and withdrawn at 100 μl min^-1until a 250 μl sample is collected.</p> <p>Results</p> <p>Our results demonstrate up to 125 fold increases in synovial IL1α and IL1β concentrations, approximately 30 fold increases in levels of IL6 and IL10 and a 200–300 fold elevation in synovial concentrations of TNFα during FCA-induced experimental arthritis. Finally, this novel technique has demonstrated a dose-response relationship between FCA and the total cell counts of synovial perfusates.</p> <p>Conclusion</p> <p>In summary, this new technique provides a robust method for quantifying inflammatory mediators and cells from the synovial cavity itself, thereby detailing the inflammatory processes from within the capsule and excluding those processes occurring in other tissues surrounding the entire articulation.</p

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

An RNA-seq experiment with 48 biological replicates in each of 2 conditions was performed to determine the number of biological replicates ($n_r$) required, and to identify the most effective statistical analysis tools for identifying differential gene expression (DGE). When $n_r=3$, seven of the nine tools evaluated give true positive rates (TPR) of only 20 to 40 percent. For high fold-change genes ($|log_{2}(FC)|\gt2$) the TPR is $\gt85$ percent. Two tools performed poorly; over- or under-predicting the number of differentially expressed genes. Increasing replication gives a large increase in TPR when considering all DE genes but only a small increase for high fold-change genes. Achieving a TPR $\gt85$% across all fold-changes requires $n_r\gt20$. For future RNA-seq experiments these results suggest $n_r\gt6$, rising to $n_r\gt12$ when identifying DGE irrespective of fold-change is important. For $6 \lt n_r \lt 12$, superior TPR makes edgeR the leading tool tested. For $n_r \ge12$, minimizing false positives is more important and DESeq outperforms the other tools.Comment: 21 Pages and 4 Figures in main text. 9 Figures in Supplement attached to PDF. Revision to correct a minor error in the abstrac

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment

High-throughput RNA sequencing (RNA-seq) is now the standard method to determine differential gene expression. Identifying differentially expressed genes crucially depends on estimates of read count variability. These estimates are typically based on statistical models such as the negative binomial distribution, which is employed by the tools edgeR, DESeq and cuffdiff. Until now, the validity of these models has usually been tested on either low-replicate RNA-seq data or simulations. A 48-replicate RNA-seq experiment in yeast was performed and data tested against theoretical models. The observed gene read counts were consistent with both log-normal and negative binomial distributions, while the mean-variance relation followed the line of constant dispersion parameter of ~0.01. The high-replicate data also allowed for strict quality control and screening of bad replicates, which can drastically affect the gene read-count distribution. RNA-seq data have been submitted to ENA archive with project ID PRJEB5348.Comment: 15 pages 6 figure

'Choosing shoes': a preliminary study into the challenges facing clinicians in assessing footwear for rheumatoid patients

Background: Footwear has been accepted as a therapeutic intervention for the foot affected by rheumatoid arthritis (RA). Evidence relating to the objective assessment of footwear in patients with RA is limited. The aims of this study were to identify current footwear styles, footwear characteristics, and factors that influence footwear choice experienced by patients with RA. Methods: Eighty patients with RA were recruited from rheumatology clinics during the summer months. Clinical characteristics, global function, and foot impairment and disability measures were recorded. Current footwear, footwear characteristics and the factors associated with choice of footwear were identified. Suitability of footwear was recorded using pre-determined criteria for assessing footwear type, based on a previous study of foot pain. Results: The patients had longstanding RA with moderate-to severe disability and impairment. The foot and ankle assessment demonstrated a low-arch profile with both forefoot and rearfoot structural deformities. Over 50% of shoes worn by patients were opentype footwear. More than 70% of patients’ footwear was defined as being poor. Poor footwear characteristics such as heel rigidity and sole hardness were observed. Patients reported comfort (17%) and fit (14%) as important factors in choosing their own footwear. Only five percent (5%) of patients wore therapeutic footwear. Conclusions: The majority of patients with RA wear footwear that has been previously described as poor. Future work needs to aim to define and justify the specific features of footwear that may be of benefit to foot health for people with RA

The broad-spectrum antiviral drug arbidol inhibits foot-and-mouth disease virus genome replication

Arbidol (ARB, also known as umifenovir) is used clinically in several countries as an anti-influenza virus drug. ARB inhibits multiple enveloped viruses in vitro and the primary mode of action is inhibition of virus entry and/or fusion of viral membranes with intracellular endosomal membranes. ARB is also an effective inhibitor of non-enveloped poliovirus types 1 and 3. In the current report, we evaluate the antiviral potential of ARB against another picornavirus, foot-and-mouth disease virus (FMDV), a member of the genus Aphthovirus and an important veterinary pathogen. ARB inhibits the replication of FMDV RNA sub-genomic replicons. ARB inhibition of FMDV RNA replication is not a result of generalized inhibition of cellular uptake of cargo, such as transfected DNA, and ARB can be added to cells up to 3 h post-transfection of FMDV RNA replicons and still inhibit FMDV replication. ARB prevents the recovery of FMDV replication upon withdrawal of the replication inhibitor guanidine hydrochloride (GuHCl). Although restoration of FMDV replication is known to require de novo protein synthesis upon GuHCl removal, ARB does not suppress cellular translation or FMDV internal ribosome entry site (IRES)-driven translation. ARB also inhibits infection with the related Aphthovirus, equine rhinitis A virus (ERAV). Collectively, the data demonstrate that ARB can inhibit some non-enveloped picornaviruses. The data are consistent with inhibition of picornavirus genome replication, possibly via the disruption of intracellular membranes on which replication complexes are located

Haplotype tagging reveals parallel formation of hybrid races in two butterfly species.

Genetic variation segregates as linked sets of variants or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. Yet, genomic data often omit haplotype information due to constraints in sequencing technologies. Here, we present "haplotagging," a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species, the geographic clines for the major wing-pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the center of the hybrid zone. We propose that shared warning signaling (Müllerian mimicry) may couple the cline shifts seen in both species and facilitate the parallel coemergence of a novel hybrid morph in both comimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations

Pre-cooling for endurance exercise performance in the heat: a systematic review.

PMCID: PMC3568721The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1741-7015/10/166. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Endurance exercise capacity diminishes under hot environmental conditions. Time to exhaustion can be increased by lowering body temperature prior to exercise (pre-cooling). This systematic literature review synthesizes the current findings of the effects of pre-cooling on endurance exercise performance, providing guidance for clinical practice and further research

Model experiment of magnetic field amplification in laser-produced plasmas via the Richtmyer-Meshkov instability

A model experiment of magnetic field amplification (MFA) via the Richtmyer-Meshkov instability (RMI) in supernova remnants (SNRs) was performed using a high-power laser. In order to account for very-fast acceleration of cosmic rays observed in SNRs, it is considered that the magnetic field has to be amplified by orders of magnitude from its background level. A possible mechanism for the MFA in SNRs is stretching and mixing of the magnetic field via the RMI when shock waves pass through dense molecular clouds in interstellar media. In order to model the astrophysical phenomenon in laboratories, there are three necessary factors for the RMI to be operative: a shock wave, an external magnetic field, and density inhomogeneity. By irradiating a double-foil target with several laser beams with focal spot displacement under influence of an external magnetic field, shock waves were excited and passed through the density inhomogeneity. Radiative hydrodynamic simulations show that the RMI evolves as the density inhomogeneity is shocked, resulting in higher MFA