A novel regulatory interplay between atypical B12 riboswitches and uORF translation in Mycobacterium tuberculosis

Vitamin B12 is an essential cofactor in all domains of life and B12-sensing riboswitches are some of the most widely distributed riboswitches. Mycobacterium tuberculosis, the causative agent of tuberculosis, harbours two B12-sensing riboswitches. One controls expression of metE, encoding a B12-independent methionine synthase, the other controls expression of ppe2 of uncertain function. Here, we analysed ligand sensing, secondary structure and gene expression control of the metE and ppe2 riboswitches. Our results provide the first evidence of B12 binding by these riboswitches and show that they exhibit different preferences for individual isoforms of B12, use distinct regulatory and structural elements and act as translational OFF switches. Based on our results, we propose that the ppe2 switch represents a new variant of Class IIb B12-sensing riboswitches. Moreover, we have identified short translated open reading frames (uORFs) upstream of metE and ppe2, which modulate the expression of their downstream genes. Translation of the metE uORF suppresses MetE expression, while translation of the ppe2 uORF is essential for PPE2 expression. Our findings reveal an unexpected regulatory interplay between B12-sensing riboswitches and the translational machinery, highlighting a new level of cis-regulatory complexity in M. tuberculosis. Attention to such mechanisms will be critical in designing next-level intervention strategies.

Assessment of the Adverse Health Effects of Aflatoxin Exposure from Unpackaged Peanut Oil in Guangdong, China

Aflatoxins are liver carcinogens and are common contaminants in unpackaged peanut (UPP) oil. However, the health risks associated with consuming aflatoxins in UPP oil remain unclear. In this study, aflatoxin contamination in 143 UPP oil samples from Guangdong Province were assessed via liquid chromatography-tandem mass spectrometry (LC-MS). We also recruited 168 human subjects, who consumed this oil, to measure their liver functions and lipid metabolism status. Aflatoxin B1 (AFB1) was detected in 79.72% of the UPP oil samples, with levels ranging from 0.02 to 174.13 μg/kg. The average daily human intake of AFB1 from UPP oil was 3.14 ng/kg·bw/day; therefore, the incidence of liver cancer, caused by intake of 1 ng/kg·bw/day AFB1, was estimated to be 5.32 cases out of every 100,000 persons per year. Meanwhile, Hepatitis B virus (HBV) infection and AFB1 exposure exerted a synergistic effect to cause liver dysfunction. In addition, the triglycerides (TG) abnormal rate was statistically significant when using AFB1 to estimate daily intake (EDI) quartile spacing grouping (p = 0.011). In conclusion, high aflatoxin exposure may exacerbate the harmful effects of HBV infection on liver function. Contamination of UPP oil with aflatoxins in Guangdong urgently requires more attention, and public health management of the consumer population is urgently required.

Identification of different MRI atrophy progression trajectories in epilepsy by subtype and stage inference

Artificial intelligence (AI)-based tools are widely employed, but their use for diagnosis and prognosis of neurological disorders is still evolving. Here we analyse a cross-sectional multicentre structural MRI dataset of 696 people with epilepsy and 118 control subjects. We use an innovative machine-learning algorithm, Subtype and Stage Inference, to develop a novel data-driven disease taxonomy, whereby epilepsy subtypes correspond to distinct patterns of spatiotemporal progression of brain atrophy.In a discovery cohort of 814 individuals, we identify two subtypes common to focal and idiopathic generalized epilepsies, characterized by progression of grey matter atrophy driven by the cortex or the basal ganglia. A third subtype, only detected in focal epilepsies, was characterized by hippocampal atrophy. We corroborate external validity via an independent cohort of 254 people and confirm that the basal ganglia subtype is associated with the most severe epilepsy.Our findings suggest fundamental processes underlying the progression of epilepsy-related brain atrophy. We deliver a novel MRI- and AI-guided epilepsy taxonomy, which could be used for individualized prognostics and targeted therapeutics.

Recruiting a skeleton crew-Methods for simulating and augmenting paleoanthropological data using Monte Carlo based algorithms

OBJECTIVES

Data collection is a major hindrance in many types of analyses in human evolutionary studies. This issue is fundamental when considering the scarcity and quality of fossil data. From this perspective, many research projects are impeded by the amount of data available to perform tasks such as classification and predictive modeling.

MATERIALS AND METHODS

Here we present the use of Monte Carlo based methods for the simulation of paleoanthropological data. Using two datasets containing cross-sectional biomechanical information and geometric morphometric 3D landmarks, we show how synthetic, yet realistic, data can be simulated to enhance each dataset, and provide new information with which to perform complex tasks with, in particular classification. We additionally present these algorithms in the form of an R library; AugmentationMC. We also use a geometric morphometric dataset to simulate 3D models, and emphasize the power of Machine Teaching, as opposed to Machine Learning.

RESULTS

Our results show how Monte Carlo based algorithms, such as the Markov Chain Monte Carlo, are useful for the simulation of morphometric data, providing synthetic yet highly realistic data that has been tested statistically to be equivalent to the original data. We additionally provide a critical overview of bootstrapping techniques, showing how Monte Carlo based methods perform better than bootstrapping as the data simulated is not an exact copy of the original sample.

DISCUSSION

While synthetic datasets should never replace large and real datasets, this can be considered an important advance in how paleoanthropological data can be handled.

Utilisation and costs of mental health-related service use among adolescents

Background

The high level of care needs for adolescents with mental health conditions represents a challenge to the public sector, especially in low and middle-income countries. We estimated the costs to the public purse of health, education, criminal justice and social care service use associated with psychiatric conditions among adolescents in Brazil; and examined whether the trajectory of psychopathology and its impact on daily life, and parental stigma towards mental illness, was associated with service utilisation and costs.

Methods

Data on reported service use among adolescents from a prospective community cohort (n = 1,400) were combined with Brazilian unit costs. Logistic regression and generalised linear models were used to examine factors associated with service use and associated costs, respectively.

Results

Twenty-two percent of those who presented with a psychiatric disorder used some type of service for their mental health in the previous twelve months. Higher odds of service use were associated with having a diagnosed mental disorder (either incident, [OR = 2.49, 95%CI = 1.44–4.30, p = 0.001], remittent [OR = 2.16, 95%CI = 1.27–3.69, p = 0.005] or persistent [OR = 3.01, 95%CI = 1.69–5.36, p<0.001]), higher impact of symptoms on adolescent’s life (OR = 1.32, 95%CI = 1.19–1.47, p<0.001) and lower parental stigma toward mental illness (OR = 1.12, 95%CI = 1.05–1.20, p = 0.001). Average annual cost of service use was 527.14 USD (s.d. = 908.10). Higher cost was associated with higher disorder impact (β = 0.25, 95%CI = 0.12–0.39, p<0.001), lower parental stigma (β = 0.12, 95%CI = 0.02–0.23, p = 0.020) and white ethnicity (β = 0.55, 95%CI = 0.04–1.07, p = 0.036).

Conclusion

The impact of mental health problems on adolescents’ daily lives and parental stigmatising attitudes toward mental illness were the main predictors of both service use and costs.

Childhood individual and family modifiable risk factors for criminal conviction: a 7-year cohort study from Brazil

Crime is a major public problem in low- and middle-income countries (LMICs) and its preventive measures could have great social impact. The extent to which multiple modifiable risk factors among children and families influence juvenile criminal conviction in an LMIC remains unexplored; however, it is necessary to identify prevention targets. This study examined the association between 22 modifiable individual and family exposures assessed in childhood (5-14 years, n = 2511) and criminal conviction at a 7-year follow-up (13-21 years, n = 1905, 76% retention rate) in a cohort of young people in Brazil. Population attributable risk fraction (PARF) was computed for significant risk factors. Criminal convictions were reported for 81 (4.3%) youths. Although most children living in poverty did not present criminal conviction (89%), poverty at baseline was the only modifiable risk factor significantly associated with crime (OR 4.14, 99.8% CI 1.38-12.46) with a PARF of 22.5% (95% CI 5.9-36.1%). It suggests that preventing children's exposure to poverty would reduce nearly a quarter of subsequent criminal convictions. These findings highlight the importance of poverty in criminal conviction, as it includes several deprivations and suggest that poverty eradication interventions during childhood may be crucial for reducing crime among Brazilian youth.

Decadal shift in foraging strategy of a migratory southern ocean predator

Rapid anthropogenic environmental change is expected to impact a host of ecological parameters in Southern Ocean ecosystems. Of critical concern are the consequences of these changes on the range of species that show fidelity to migratory destinations, as philopatry is hypothesized to help or hinder adaptation to climate change depending on the circumstances. Many baleen whales show philopatry to feeding grounds and are also capital breeders that meet migratory and reproductive costs through seasonal energy intake. Southern right whales (Eubalaena australis, SRWs) are capital breeders that have a strong relationship between reproductive output and foraging success. The population dynamics of South Africa's population of SRWs are characterized by two distinct periods: the 1990s, a period of high calving rates; and the late 2010s, a period associated with lowered calving rates. Here we use analyses of stable carbon (δ13 C) and nitrogen (δ15 N) isotope values from SRW biopsy samples (n = 122) collected during these two distinct periods to investigate foraging ecology of the South African population of SRWs over a time period coincident with the demographic shift. We show that South African SRWs underwent a dramatic northward shift, and diversification, in foraging strategy from 1990s to 2010s. Bayesian mixing model results suggest that during the 1990s, South African SRWs foraged on prey isotopically similar to South Georgia/Islas Georgias del Sur krill. In contrast, in the 2010s, South African SRWs foraged on prey isotopically consistent with the waters of the Subtropical Convergence, Polar Front and Marion Island. We hypothesize that this shift represents a response to changes in preferred habitat or prey, for example, the decrease in abundance and southward range contraction of Antarctic krill. By linking reproductive decline to changing foraging strategies for the first time in SRWs, we show that altering foraging strategies may not be sufficient to adapt to a changing ocean.

Accuracy of circulating histones in predicting persistent organ failure and mortality in patients with acute pancreatitis

BACKGROUND

Early prediction of acute pancreatitis severity remains a challenge. Circulating levels of histones are raised early in mouse models and correlate with disease severity. It was hypothesized that circulating histones predict persistent organ failure in patients with acute pancreatitis.

METHODS

Consecutive patients with acute pancreatitis fulfilling inclusion criteria admitted to Royal Liverpool University Hospital were enrolled prospectively between June 2010 and March 2014. Blood samples were obtained within 48 h of abdominal pain onset and relevant clinical data during the hospital stay were collected. Healthy volunteers were enrolled as controls. The primary endpoint was occurrence of persistent organ failure. The predictive values of circulating histones, clinical scores and other biomarkers were determined.

RESULTS

Among 236 patients with acute pancreatitis, there were 156 (66·1 per cent), 57 (24·2 per cent) and 23 (9·7 per cent) with mild, moderate and severe disease respectively, according to the revised Atlanta classification. Forty-seven healthy volunteers were included. The area under the receiver operating characteristic (ROC) curve (AUC) for circulating histones in predicting persistent organ failure and mortality was 0·92 (95 per cent c.i. 0·85 to 0·99) and 0·96 (0·92 to 1·00) respectively; histones were at least as accurate as clinical scores or biochemical markers. For infected pancreatic necrosis and/or sepsis, the AUC was 0·78 (0·62 to 0·94). Histones did not predict or correlate with local pancreatic complications, but correlated negatively with leucocyte cell viability (r = -0·511, P = 0·001).

CONCLUSION

Quantitative assessment of circulating histones in plasma within 48 h of abdominal pain onset can predict persistent organ failure and mortality in patients with acute pancreatitis. Early death of immune cells may contribute to raised circulating histone levels in acute pancreatitis.