RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs

RNAs assume sophisticated structures that are active in myriad cellular processes. In this review, we highlight newly identified ribozymes, riboswitches, and small RNAs, some of which control the function of cellular metabolic and gene expression networks. We then examine recent developments in genome-wide RNA structure probing technologies that are yielding new insights into the structural landscape of the transcriptome. Finally, we discuss how these RNA ‘structomic’ methods can address emerging questions in RNA systems biology, from the mechanisms behind long non-coding RNAs to new bases for human diseases

The Cardiorespiratory Demands of Treadmill Walking with and without the Use of Ekso GT™ within Able-Bodied Participants: A Feasibility Study

Individuals with neurological impairments tend to lead a predominantly sedentary lifestyle due to impaired gait function and mobility. This may be detrimental to health by negatively impacting cardiorespiratory fitness and muscular strength, and increasing the risk of developing secondary health problems. Powered exoskeletons are assistive devices that may aid neurologically impaired individuals in achieving the World Health Organisation’s (WHO) physical activity (PA) guidelines for health. Increased PA should elicit a sufficient cardiorespiratory stimulus to provide health benefits to exoskeleton users. This study examined the cardiorespiratory demands of treadmill walking with and without the Ekso GT™ among able-bodied participants. The Ekso GT™ is a powered exoskeleton that enables individuals with neurological impairments to walk by supporting full body mass with motors attached at the hip and knee joints to generate steps. This feasibility study consisted of one group of healthy able-bodied individuals (n = 8). Participants completed two 12 min treadmill walking assessments, one with and one without the Ekso GT™ at the same fixed speed. Throughout each walking bout, various cardiorespiratory parameters, namely, volume of oxygen per kilogram (kg) of body mass ([Formula: see text] O(2)·kg(−1)), volume of carbon dioxide per kg of body mass ([Formula: see text] CO(2)·kg(−1)), respiratory exchange ratio (RER), ventilation ([Formula: see text] (E)), heart rate (HR), and rate of perceived exertion (RPE), were recorded. Treadmill walking with Ekso GT™ elevated all recorded measurements to a significantly greater level (p ≤ 0.05) (except RER at 1 km·h(–1); p = 0.230) than treadmill walking without the Ekso GT™ did at the same fixed speed. An increased cardiorespiratory response was recorded during treadmill walking with the exoskeleton. Exoskeleton walking may, therefore, be an effective method to increase PA levels and provide sufficient stimulus in accordance with the PA guidelines to promote cardiorespiratory fitness and subsequently enhance overall health

Visual short-term memory binding deficit with age-related hearing loss in cognitively normal older adults

Age-related hearing loss (ARHL) has been posited as a possible modifiable risk factor for neurocognitive impairment and dementia. Measures sensitive to early neurocognitive changes associated with ARHL would help to elucidate the mechanisms underpinning this relationship. We hypothesized that ARHL might be associated with decline in visual short-term memory binding (VSTMB), a potential biomarker for preclinical dementia due to Alzheimer’s disease (AD). We examined differences in accuracy between older adults with hearing loss and a control group on the VSTMB task from a single feature (shapes) condition to a feature binding (shapes-colors) condition. Hearing loss was associated with a weaker capacity to process bound features which appeared to be accounted for by a weaker sensitivity for change detection (A’). Our findings give insight into the neural mechanisms underpinning neurocognitive decline with ARHL and its temporal sequence

What matters in Cardiovascular Research? Scientific discovery driving clinical delivery

No abstract available

Epidemiological study of E. coli O157:H7 isolated in Northern Ireland using pulsed-field gel electrophoresis (PFGE)

In Northern Ireland over the last 7 years, there is a mean of 41.9 laboratory reports per annum of human gastrointestinal infection (range 19-54) caused by Escherichia coli O157:H7. In the preceding years 1992-1996, reports were 5.4 per annum, whereas in 1997-2000, reports increased from 30 to 54 per annum. This high level has continued on an annual basis to date. The aim of this study was therefore to retrospectively examine this period of exponential increase in reports to help ascertain the genetic relatedness of strains employing pulsed-field gel electrophoresis (PFGE), as no data on the molecular epidemiology of E. coli O157:H7 in Northern Ireland has yet been published. Clinical isolates (n=84) were PFGE typed employing Xba I digestion and resulting band profiles demonstrated the presence of 13, 9 and 16 clonal types, for 1997, 1998 and 1999, respectively. In 1998, five clonal types remained from 1997 with the introduction of 4 new clonal types, whereas in 1999, 10 new clonal types were observed, accounting for over half (58%) of the E. coli O157 isolates for that year. These data suggest that, unlike gastrointestinal infections due to thermophilic campylobacters, there was considerable genetic evolution of PFGE clonal types of E. coli O157, through the displacement and emergence of genotypes. Further studies are now required to find the environmental reservoirs of these common clonal types of clinical E. coli O157:H7 in Northern Ireland to help define sources and routes of transmission of this infection locally

Complex thermal expansion properties in a molecular honeycomb lattice

[FeL3][BF4]2·xH2O (L = 3-(pyrazinyl)-1H-pyrazole) shows negative thermal expansion between 150–240 K but positive thermal expansion at 240–300 K, linked to rearrangement of anions and water molecules within pores in the lattice.</p

Improving tumor budding reporting in colorectal cancer : a Delphi consensus study

Tumor budding is a long-established independent adverse prognostic marker in colorectal cancer, yet methods for its assessment have varied widely. In an effort to standardize its reporting, a group of experts met in Bern, Switzerland, in 2016 to reach consensus on a single, international, evidence-based method for tumor budding assessment and reporting (International Tumor Budding Consensus Conference [ITBCC]). Tumor budding assessment using the ITBCC criteria has been validated in large cohorts of cancer patients and incorporated into several international colorectal cancer pathology and clinical guidelines. With the wider reporting of tumor budding, new issues have emerged that require further clarification. To better inform researchers and health-care professionals on these issues, an international group of experts in gastrointestinal pathology participated in a modified Delphi process to generate consensus and highlight areas requiring further research. This effort serves to re-affirm the importance of tumor budding in colorectal cancer and support its continued use in routine clinical practice.Peer reviewe

A randomized, embedded trial of pre-notification of trial participation did not increase recruitment rates to a falls prevention trial

Objectives: To design and evaluate the effectiveness of a pre-notification leaflet about research to increase recruitment to a randomised controlled trial (RCT). Methods: A methodological, two arm, randomised controlled trial was conducted, embedded within an existing cohort RCT (REFORM). Participants were randomised for the embedded trial, using a 1:2 (intervention:control) allocation ratio, prior to being randomised for the REFORM RCT. Controls received a trial recruitment pack. The intervention group received an additional pre-notification leaflet 2 to 3 weeks before the recruitment pack. Primary and secondary analyses were conducted using relative risk, the Cox Proportional Hazards Model and Incremental Cost Effectiveness Ratios. Results: Of the 1,436 intervention group participants, 73 (5.1%) were randomised into the REFORM trial compared to 126 (4.4%) of the 2,878 control group participants. The associated relative risk (1.16) was not statistically significant (95% CI 0.88 - 1.56). The leaflet did not significantly increase return rate (RR 1.10, 95% CI 0.92 -1.28) or decrease time to return (Hazard Ratio: 1.11, 95% CI 0.93 -1.33). Incremental Cost Effectiveness Ratios indicated that the intervention may be cost-effective if the true estimate of effect were close to the upper bound of the associated 95% CI. Conclusion: A pre-notification leaflet to potential trial participants demonstrated a small difference in favour of the intervention with regards randomisation (0.7% difference) and return rates (1.1% difference).Results should however be interpreted with caution as confidence intervals for these estimates cross the point of no effect. Nevertheless, this research enhances existing evidence for pre-notification to increase recruitment rates, with further development and assessment of this potentially cost-effective intervention being recommended

Corticotroph Aggressive Pituitary Tumors and Carcinomas Frequently Harbor ATRX Mutations

Context: Aggressive pituitary tumors (APTs) are characterized by unusually rapid growth and lack of response to standard treatment. About 1% to 2% develop metastases being classified as pituitary carcinomas (PCs). For unknown reasons, the corticotroph tumors are overrepresented among APTs and PCs. Mutations in the alpha thalassemia/mental retardation syndrome X-linked (ATRX) gene, regulating chromatin remodeling and telomere maintenance, have been implicated in the development of several cancer types, including neuroendocrine tumors. Objective: To study ATRX protein expression and mutational status of the ATRX gene in APTs and PCs. Design: We investigated ATRX protein expression by using immunohistochemistry in 30 APTs and 18 PCs, mostly of Pit-1 and T-Pit cell lineage. In tumors lacking ATRX immunolabeling, mutational status of the ATRX gene was explored. Results: Nine of the 48 tumors (19%) demonstrated lack of ATRX immunolabelling with a higher proportion in patients with PCs (5/18; 28%) than in those with APTs (4/30;13%). Lack of ATRX was most common in the corticotroph tumors, 7/22 (32%), versus tumors of the Pit-1 lineage, 2/24 (8%). Loss-of-function ATRX mutations were found in all 9 ATRX immunonegative cases: nonsense mutations (n = 4), frameshift deletions (n = 4), and large deletions affecting 22-28 of the 36 exons (n = 3). More than 1 ATRX gene defect was identified in 2 PCs. Conclusion: ATRX mutations occur in a subset of APTs and are more common in corticotroph tumors. The findings provide a rationale for performing ATRX immunohistochemistry to identify patients at risk of developing aggressive and potentially metastatic pituitary tumors.Peer reviewe