Post-transcriptional regulation in the nucleus and cytoplasm: study of mean time to threshold (MTT) and narrow escape problem

Messenger RNAs (mRNAs) can be repressed and degraded by small non-coding RNA molecules. In this paper, we formulate a coarsegrained Markov-chain description of the post-transcriptional regulation of mRNAs by either small interfering RNAs (siRNAs) or microRNAs (miRNAs). We calculate the probability of an mRNA escaping from its domain before it is repressed by siRNAs/miRNAs via calculation of the mean time to threshold: when the number of bound siRNAs/miRNAs exceeds a certain threshold value, the mRNA is irreversibly repressed. In some cases, the analysis can be reduced to counting certain paths in a reduced Markov model. We obtain explicit expressions when the small RNA bind irreversibly to the mRNA and we also discuss the reversible binding case. We apply our models to the study of RNA interference in the nucleus, examining the probability of mRNAs escaping via small nuclear pores before being degraded by siRNAs. Using the same modelling framework, we further investigate the effect of small, decoy RNAs (decoys) on the process of post-transcriptional regulation, by studying regulation of the tumor suppressor gene, PTEN: decoys are able to block binding sites on PTEN mRNAs, thereby reducing the number of sites available to siRNAs/miRNAs and helping to protect it from repression. We calculate the probability of a cytoplasmic PTEN mRNA translocating to the endoplasmic reticulum before being repressed by miRNAs. We support our results with stochastic simulations.

Hydrodynamic dispersion within porous biofilms

Many microorganisms live within surface-associated consortia, termed biofilms, that can form intricate porous structures interspersed with a network of fluid channels. In such systems, transport phenomena, including flow and advection, regulate various aspects of cell behavior by controlling nutrient supply, evacuation of waste products, and permeation of antimicrobial agents. This study presents multiscale analysis of solute transport in these porous biofilms. We start our analysis with a channel-scale description of mass transport and use the method of volume averaging to derive a set of homogenized equations at the biofilm-scale in the case where the width of the channels is significantly smaller than the thickness of the biofilm. We show that solute transport may be described via two coupled partial differential equations or telegrapher's equations for the averaged concentrations. These models are particularly relevant for chemicals, such as some antimicrobial agents, that penetrate cell clusters very slowly. In most cases, especially for nutrients, solute penetration is faster, and transport can be described via an advection-dispersion equation. In this simpler case, the effective diffusion is characterized by a second-order tensor whose components depend on (1) the topology of the channels' network; (2) the solute's diffusion coefficients in the fluid and the cell clusters; (3) hydrodynamic dispersion effects; and (4) an additional dispersion term intrinsic to the two-phase configuration. Although solute transport in biofilms is commonly thought to be diffusion dominated, this analysis shows that hydrodynamic dispersion effects may significantly contribute to transport.

A multi-method evaluation of a training course on dual diagnosis

A training course on dual diagnosis was developed within the Irish forensic mental health service, to bridge the gap in the lack of training on dual diagnosis in Ireland. The course was designed for service providers within mental health and addiction services. Twenty participants involving nursing, social work, police and social welfare disciplines attended the first training course. A mixed methodology research design was adapted to describe participants' evaluation of the training course. Data were collected using multiple methods: pre- and post-test, daily evaluation and focus group interviews. Quantitative data were analysed using the spss Version 16.0 and qualitative data were analysed thematically. Findings from the pre- and post-test suggest an increase in participants' knowledge of dual diagnosis and an increase in confidence in conducting groups. Daily evaluation indicates that the course content largely met participants' needs. Finally, three themes emerged from the focus group interview: increased confidence, the training course/teaching methods and personal/organizational challenges. This study implies that service providers within mental health and addiction services benefit from inter-professional, needs and skills based courses incorporating a variety of teaching methods. The way forward for future dual diagnosis training course developments would be working in partnership with service users and carers.

Healthcare-associated infection in Irish long-term care facilities: results from the First National Prevalence Study

BACKGROUND

Prevalence of healthcare-associated infection (HCAI) and antimicrobial use in Irish long-term care facilities (LTCFs) has never been studied.

AIM

To collect baseline data on HCAI prevalence and antibiotic use in Irish LTCFs to inform national LTCF policy and plan future HCAI prevention programmes.

METHODS

A prevalence study of HCAI and antibiotic use was undertaken in Irish LTCFs. Participation was voluntary. Data on HCAI risk factors, signs and symptoms of infection and antimicrobial use were collected prospectively on a single day in each institution.

FINDINGS

Sixty-nine Irish LTCFs participated and 4170 eligible residents were surveyed; 472 (11.3%) had signs/symptoms of infection (266, 6.4%) and/or were on antibiotics (426, 10.2%). A third of residents (1430, 34.3%) were aged ≥85 years and more than half disorientated (2110, 50.6%) with impaired mobility (2101, 50.4%). HCAI prevalence was 3.7% (range: 0-22.2%). The most common HCAI was urinary tract infection (UTI) (62 residents, 40% of HCAI). Presence of a urinary catheter was associated with UTI (P < 0.0000001). Antibiotics were prescribed for treatment (262 residents, 57.8%) and prophylaxis (182 residents, 40.2%) of infection. The most common indication for prophylaxis was UTI prevention (35.8% of total prescriptions). Fourteen (10.2%) residents on UTI prophylaxis had a urinary catheter. The most common indications for therapy included respiratory tract infections (35.1%), UTI (32.1%) and skin infection (21.8%).

CONCLUSION

This study highlights the frequency of prophylactic antimicrobial prescribing and provides an important baseline to inform future preventive strategies.

Studies on the effect of temperature and pH on the inactivation of fish viral and bacterial pathogens

Disposal of fish by-products in the European Community must comply with Regulation (EC) No 1069/2009 which categorizes animal by-products according to risk, and specifies methods of disposal of by-products according to that risk. There is provision under the regulation for composting or ensiling to be used for by-products from aquatic animals. Biosecurity considerations require knowledge of the parameters of time and temperature, or time and pH, required to inactivate any fish pathogens that may be present. To provide those data, we undertook laboratory studies on the inactivation of a number of fish pathogenic viruses and bacteria at 60 °C, pH 4.0 and pH 12.0 as a preliminary to conducting subsequent trials with the most resistant viruses and bacteria in fish tissues. The most resistant bacterium to 60 °C, pH 4.0 as well as pH 12.0 was Lactococcus garvieae. Its concentration was reduced to the level of sensitivity of the test after 24-48 h exposure to 60 °C, but it survived for at least 7 days at pH 4.0 and 14 days at pH 12.0. The most resistant virus to 60 °C was infectious pancreatic necrosis virus, and to pH 12.0 was infectious salmon anaemia virus. The majority of the viruses tested survived exposure to pH 4.0 for up to 28 days. The results suggest that the process of acid ensiling alone is not an effective method for the inactivation of many viral and bacterial pathogens, and fish by-products would need further treatment by a method approved under the regulation following ensiling, whereas alkaline or heat treatment are likely to provide an increased degree of biosecurity for on-farm processing of mortalities.

A model of cell migration within the extracellular matrix based on a phenotypic switching mechanism

Cell migration involves different mechanisms in different cell types and tissue environments. Changes in migratory behaviour have been observed experimentally and associated with phenotypic switching in various situations, such as the migration-proliferation dichotomy of glioma cells, the epithelial-mesenchymal transition or the mesenchymal-amoeboid transition of fibrosarcoma cells in the extracellular matrix (ECM). In the present study, we develop a modelling framework to account for changes in migratory behaviour associated with phenotypic switching. We take into account the influence of the ECM on cell motion and more particularly the alignment process along the fibers. We use a mesoscopic description to model two cell populations with different migratory properties. We derive the corresponding continuum (macroscopic) model by appropriate rescaling, which leads to a generic reaction-diffusion system for the two cell phenotypes. We investigate phenotypic adaptation to dense and sparse environments and propose two complementary transition mechanisms. We study these mechanisms by using a combination of linear stability analysis and numerical simulations. Our investigations reveal that when the cell migratory ability is reduced by a crowded environment, a diffusive instability may appear and lead to the formation of aggregates of cells of the same phenotype. Finally, we discuss the importance of the results from a biological perspective.

Calciphylaxis: calcific uraemic arteriolopathy--a case study

Having worked in nephrology for more than 20 years, and never encountering this condition before, we came across three patients who had been diagnosed with calciphylaxis in the space of 12 months. This condition is also known as calcific uraemic arteriolopathy and is a syndrome of medical calcification of the small arteries, which leads to painful ischaemia of the surrounding subcubitis and skin (1). Prevalence of 1-4% has been estimated in various haemodialysis populations. Also 1% per year in dialysis patients has also been suggested (3). The mortality rate for distal lesions is 23%, whilst the mortality for proximal lesions is 63% (4). The pathogenesis of this condition remains uncertain. However, vascular calcium deposition is thought to be important, and raised serum phosphate levels were associated with a substantially increased risk of calciphylaxis. Although PTH levels were high, plasma PTH was not consistently higher in patients with calciphylaxis than controls (5). The important aspect of the condition for the patients is the sheer pain and distress suffered, as well as the high mortality rate. Therefore, the implications for nurses are early detection, to allow speedy treatment to take place and involvement of the multidisciplinary team to enhance care and provide as much support as possible, thus facilitating optimal outcome and comfort.

Neonatal transportation: the effects of a national neonatal transportation programme

BACKGROUND

The transport of critically ill newborns by specialised transport teams has been shown to be associated with a significant improvement in their clinical condition on arrival at the receiving hospital.

AIM

To determine if the National Neonatal Transport Programme introduced in 2001 improved clinical condition of newborns at the end of transfer.

METHODS

A retrospective study of all 176 patients transported by the National Neonatal Transport Programme between March 2001 and March 2002.

RESULTS

Before transfer, 17% of patients were hypothermic, 2% hypoglycaemic and 11% acidotic as were 7%, 3% and 5% respectively at the end of transfer. A review of 172 neonatal transports between 1987 and 1989 revealed that 21% of patients were hypothermic, 13% hypoglycaemic and 20% acidotic at the end of transfer.

CONCLUSIONS

The National Neonatal Transport Programme has resulted in improved clinical condition of newborns at the end of transfer when compared to their condition before transfer and compared to outcomes prior to the introduction of the programme.