An efficient and robust approach to Mendelian randomization with measured pleiotropic effects in a high-dimensional setting.

Valid estimation of a causal effect using instrumental variables requires that all of the instruments are independent of the outcome conditional on the risk factor of interest and any confounders. In Mendelian randomization studies with large numbers of genetic variants used as instruments, it is unlikely that this condition will be met. Any given genetic variant could be associated with a large number of traits, all of which represent potential pathways to the outcome which bypass the risk factor of interest. Such pleiotropy can be accounted for using standard multivariable Mendelian randomization with all possible pleiotropic traits included as covariates. However, the estimator obtained in this way will be inefficient if some of the covariates do not truly sit on pleiotropic pathways to the outcome. We present a method that uses regularization to identify which out of a set of potential covariates need to be accounted for in a Mendelian randomization analysis in order to produce an efficient and robust estimator of a causal effect. The method can be used in the case where individual-level data are not available and the analysis must rely on summary-level data only. It can be used where there are any number of potential pleiotropic covariates up to the number of genetic variants less one. We show the results of simulation studies that demonstrate the performance of the proposed regularization method in realistic settings. We also illustrate the method in an applied example which looks at the causal effect of urate plasma concentration on coronary heart disease

Noise-augmented directional clustering of genetic association data identifies distinct mechanisms underlying obesity.

Funder: NIHR Cambridge Biomedical Research CentreClustering genetic variants based on their associations with different traits can provide insight into their underlying biological mechanisms. Existing clustering approaches typically group variants based on the similarity of their association estimates for various traits. We present a new procedure for clustering variants based on their proportional associations with different traits, which is more reflective of the underlying mechanisms to which they relate. The method is based on a mixture model approach for directional clustering and includes a noise cluster that provides robustness to outliers. The procedure performs well across a range of simulation scenarios. In an applied setting, clustering genetic variants associated with body mass index generates groups reflective of distinct biological pathways. Mendelian randomization analyses support that the clusters vary in their effect on coronary heart disease, including one cluster that represents elevated body mass index with a favourable metabolic profile and reduced coronary heart disease risk. Analysis of the biological pathways underlying this cluster identifies inflammation as potentially explaining differences in the effects of increased body mass index on coronary heart disease

Pleiotropy robust methods for multivariable Mendelian randomization

Abstract: Mendelian randomization is a powerful tool for inferring the presence, or otherwise, of causal effects from observational data. However, the nature of genetic variants is such that pleiotropy remains a barrier to valid causal effect estimation. There are many options in the literature for pleiotropy robust methods when studying the effects of a single risk factor on an outcome. However, there are few pleiotropy robust methods in the multivariable setting, that is, when there are multiple risk factors of interest. In this article we introduce three methods which build on common approaches in the univariable setting: MVMR‐Robust; MVMR‐Median; and MVMR‐Lasso. We discuss the properties of each of these methods and examine their performance in comparison to existing approaches in a simulation study. MVMR‐Robust is shown to outperform existing outlier robust approaches when there are low levels of pleiotropy. MVMR‐Lasso provides the best estimation in terms of mean squared error for moderate to high levels of pleiotropy, and can provide valid inference in a three sample setting. MVMR‐Median performs well in terms of estimation across all scenarios considered, and provides valid inference up to a moderate level of pleiotropy. We demonstrate the methods in an applied example looking at the effects of intelligence, education and household income on the risk of Alzheimer's disease

Otolithic receptor mechanisms for vestibular-evoked myogenic potentials: A review

Air-conducted sound and bone-conduced vibration activate otolithic receptors and afferent neurons in both the utricular and saccular maculae, and trigger small electromyographic (EMG) responses [called vestibular-evoked myogenic potentials (VEMPs)] in various muscle groups throughout the body. The use of these VEMPs for clinical assessment of human otolithic function is built on the following logical steps: (1) that high-frequency sound and vibration at clinically effective stimulus levels activate otolithic receptors and afferents, rather than semicircular canal afferents, (2) that there is differential anatomical projection of otolith afferents to eye muscles and neck muscles, and (3) that isolated stimulation of the utricular macula induces short latency responses in eye muscles, and that isolated stimulation of the saccular macula induces short latency responses in neck motoneurons. Evidence supports these logical steps, and so VEMPs are increasingly being used for clinical assessment of otolith function, even differential evaluation of utricular and saccular function. The proposal, originally put forward by Curthoys in 2010, is now accepted: that the ocular vestibular-evoked myogenic potential reflects predominantly contralateral utricular function and the cervical vestibular-evoked myogenic potential reflects predominantly ipsilateral saccular function. So VEMPs can provide differential tests of utricular and saccular function, not because of stimulus selectivity for either of the two maculae, but by measuring responses which are predominantly determined by the differential neural projection of utricular as opposed to saccular neural information to various muscle groups. The major question which this review addresses is how the otolithic sensory system, with such a high density otoconial layer, can be activated by individual cycles of sound and vibration and show such tight locking of the timing of action potentials of single primary otolithic afferents to a particular phase angle of the stimulus cycle even at frequencies far above 1,000 Hz. The new explanation is that it is due to the otoliths acting as seismometers at high frequencies and accelerometers at low frequencies. VEMPs are an otolith-dominated response, but in a particular clinical condition, semicircular canal dehiscence, semicircular canal receptors are also activated by sound and vibration, and act to enhance the otolith-dominated VEMP responses

Transformation of Environmental Bacillus subtilis Isolates by Transiently Inducing Genetic Competence

Domesticated laboratory strains of Bacillus subtilis readily take up and integrate exogenous DNA. In contrast, “wild” ancestors or Bacillus strains recently isolated from the environment can only be genetically modified by phage transduction, electroporation or protoplast transformation. Such methods are laborious, have a variable yield or cannot efficiently be used to alter chromosomal DNA. A major disadvantage of using laboratory strains is that they have often lost, or do not display ecologically relevant physiologies such as the ability to form biofilms. Here we present a method that allows genetic transformation by natural competence in several environmental isolates of B. subtilis. Competence in these strains was established by expressing the B. subtilis competence transcription factor ComK from an IPTG-inducible promoter construct present on an unstable plasmid. This transiently activates expression of the genes required for DNA uptake and recombination in the host strain. After transformation, the comK encoding plasmid is lost easily because of its intrinsic instability and the transformed strain returns to its wild state. Using this method, we have successfully generated mutants and introduced foreign DNA into a number of environmental isolates and also B. subtilis strain NCIB3610, which is widely used to study biofilm formation. Application of the same method to strains of B. licheniformis was unsuccessful. The efficient and rapid approach described here may facilitate genetic studies in a wider array of environmental B. subtilis strains

MendelianRandomization v0.5.0: updates to an R package for performing Mendelian randomization analyses using summarized data.

The MendelianRandomization package is a software package written for the R software environment that implements methods for Mendelian randomization based on summarized data. In this manuscript, we describe functions that have been added to the package or updated in recent years. These features can be divided into four categories: robust methods for Mendelian randomization, methods for multivariable Mendelian randomization, functions for data visualization, and the ability to load data into the package seamlessly from the PhenoScanner web-resource. We provide examples of the graphical output produced by the data visualization commands, as well as syntax for obtaining suitable data and performing a Mendelian randomization analysis in a single line of code

Uso de un consorcio bacteriano extremo-halotolerante para la biodegradación de crudo en ambientes salinos

Results of the application of a novel bacterial consortium extremely-halotolerant for the biodegradation of crude oil using free and immobilized cell systems, in media with salinities ranged from zero to 220 g/L, are described. Its effectiveness increased when the cells were immobilized on polyurethane foam, polypropylene fibers, scourers and Celatom and the salinity of the culture medium surpassed 20 g/L. Four of the microorganisms belonging to the consortium grew in media with salinities varying from zero to 320 g/L and are amongst the most halotolerant microorganisms described up to now. Se describen resultados de la aplicación de un nuevo consorcio bacteriano extremo-halotolerante para la biodegradación de crudos en medios con salinidades desde cero hasta 220 g/L, en sistemas con células libres e inmovilizadas sobre diferentes soportes. Su efectividad se incrementó cuando el consorcio se inmovilizó sobre espuma de poliuretano, fibras de polipropileno, scourers y Celatom, y la salinidad del medio superó los 20 g/L. Cuatro de los microorganismos que conforman el consorcio bacteriano crecieron en medios con salinidades desde cero hasta 320 g/L y se encuentran entre los de mayor halotolerancia reportados hasta la fecha.

Genetically predicted vegetable intake and cardiovascular diseases and risk factors: an investigation with Mendelian randomization

Background: The associations between vegetable intake and cardiovascular diseases have been demonstrated in observational studies, but less sufficiently in randomized trials. Mendelian randomization has been considered a promising alternative in causal inference. The separate effects of cooked and raw vegetable intake remain unclear. This study aimed to investigate the associations between cooked and raw vegetable intake with cardiovascular outcomes using MR. Methods: We identified 15 and 28 genetic variants statistically and biologically associated with cooked and raw vegetable intake, respectively, from previous genome-wide association studies, which were used as instrumental variables to estimate associations with coronary heart disease (CHD), stroke, heart failure (HF), and atrial fibrillation (AF). The independent effects of genetically predicted cooked and raw vegetable intake were examined using multivariable MR analysis. We performed one-sample and two-sample MR analyses and combined their results using meta-analysis. Bonferroni correction was applied for multiple comparisons. We performed two-sample MR analysis for cardiometabolic risk factors (serum lipids, blood pressure, body mass index, and glycemic traits) to explore the potential mechanisms. Results: In the MR meta-analysis of 1.2 million participants, we found null evidence for associations between genetically predicted cooked and raw vegetable intake with CHD, HF, or AF. Raw vegetable intake was nominally associated with stroke (odds ratio [95% confidence interval] 0.82 [0.69–0.98] per 1 daily serving increase, p = 0.03), but this association did not pass the corrected significance level. We found consistently null evidence for associations with serum lipids, blood pressure, body mass index, or glycemic traits. Conclusions: We found null evidence for associations between genetically predicted vegetable intake with CHD, AF, HF, or cardiometabolic risk factors in this MR study. Raw vegetable intake may reduce risk of stroke, but this warrants more research. True associations between vegetable intake and CVDs cannot be completely ruled out, and future investigations are required for causal inference in nutritional research