MTHFD1 controls DNA methylation in Arabidopsis.

DNA methylation is an epigenetic mechanism that has important functions in transcriptional silencing and is associated with repressive histone methylation (H3K9me). To further investigate silencing mechanisms, we screened a mutagenized Arabidopsis thaliana population for expression of SDCpro-GFP, redundantly controlled by DNA methyltransferases DRM2 and CMT3. Here, we identify the hypomorphic mutant mthfd1-1, carrying a mutation (R175Q) in the cytoplasmic bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (MTHFD1). Decreased levels of oxidized tetrahydrofolates in mthfd1-1 and lethality of loss-of-function demonstrate the essential enzymatic role of MTHFD1 in Arabidopsis. Accumulation of homocysteine and S-adenosylhomocysteine, genome-wide DNA hypomethylation, loss of H3K9me and transposon derepression indicate that S-adenosylmethionine-dependent transmethylation is inhibited in mthfd1-1. Comparative analysis of DNA methylation revealed that the CMT3 and CMT2 pathways involving positive feedback with H3K9me are mostly affected. Our work highlights the sensitivity of epigenetic networks to one-carbon metabolism due to their common S-adenosylmethionine-dependent transmethylation and has implications for human MTHFD1-associated diseases

Correlación clínica y ultrasonográfica de las alteraciones en el esqueleto axial equino y las cojeras torácicas y pélvicas detectadas mediante evaluación objetiva

Cervical and thoracolumbar changes are commonly found in sports animals and may be related to biomechanical alterations, driving movement, and the type of saddle used. The objective of this study was to characterize the correlation between clinical and ultrasonographic findings of the equine axial skeleton with objective evaluation lameness in the thoracic or pelvic limbs. A total of 76 horses of the mounted cavalry with an average of ten years of age, divided between castrated males and females of indeterminate breeds, were submitted to clinical, ultrasonographic and objective evaluations. The evaluated variables were classified in scores from 0 to 4, for later statistical analysis spearman correlation through the RStudio® software. The animals were classified into six groups according to the objective, clinical and ultrasonographic changes. A weak positive correlation was observed between the objective evaluation variable in relation to the clinical (r = 0.1, p > 0,05) and ultrasonographic (r = 0.1, p > 0,05) evaluation variables. In the present study, it was impossible to consider the correlations statistically significant since the p-value was higher than the significance level of 5%. Therefore, the associated evaluation of the axial and appendicular skeleton is of fundamental importance in the clinical routine to investigate musculoskeletal changes. This was demonstrated in the present study, where 68.42% (n=52) presented both clinical and ultrasonographic changes of the axial skeleton concomitantly with thoracic and/or pelvic lameness.As alterações cervicais e toracolombares são comumente encontradas em animais de esporte e podem estar relacionadas a alterações biomecânicas, movimento de condução e ao tipo de sela utilizada. O objetivo deste estudo foi caracterizar a correlação entre os achados clínicos e ultrassonográficos do esqueleto axial equino com a avaliação objetiva de claudicação nos membros torácicos ou pélvicos. Um total de 76 cavalos da cavalaria montada, com uma média de dez anos de idade, divididos entre machos castrados e fêmeas de raças indeterminadas, foram submetidos a avaliações clínicas, ultrassonográficas e objetivas. As variáveis avaliadas foram classificadas em escores de 0 a 4, para posterior análise estatística de correlação de Spearman por meio do software RStudio®. Os animais foram classificados em seis grupos de acordo com as alterações na avaliações objetiva, clínica e ultrassonográfica. Foi observada uma correlação positiva fraca entre a variável de avaliação objetiva em relação às variáveis de avaliação clínica (r = 0,1, p > 0,05) e ultrassonográfica (r = 0,1, p > 0,05). No presente estudo, não foi possível considerar as correlações estatisticamente significativas, uma vez que o valor de p foi superior ao nível de significância de 5%. Portanto, a avaliação associada do esqueleto axial e apendicular é de fundamental importância na rotina clínica para investigar alterações musculoesqueléticas. Isso foi demonstrado no presente estudo, onde 68,42% (n=52) apresentaram tanto alterações clínicas quanto ultrassonográficas no esqueleto axial concomitantemente com claudicação torácica e/ou pélvica.Las alteraciones cervicales y toracolumbares son comunes en animales deportivos y pueden estar relacionadas con cambios biomecánicos, el movimiento de conducción y el tipo de silla utilizada. El objetivo de este estudio fue caracterizar la correlación entre los hallazgos clínicos y ultrasonográficos del esqueleto axial equino con la evaluación objetiva de la cojera en las extremidades torácicas o pélvicas. Un total de 76 caballos de la caballería montada, con una media de diez años de edad, divididos entre machos castrados y hembras de razas indeterminadas, se sometieron a evaluaciones clínicas, ultrasonográficas y objetivas. Las variables evaluadas se clasificaron en puntuaciones del 0 al 4, para un posterior análisis estadístico de correlación de Spearman mediante el software RStudio®. Los animales se clasificaron en seis grupos de acuerdo con las alteraciones en las evaluaciones objetivas, clínicas y ultrasonográficas. Se observó una correlación positiva débil entre la variable de evaluación objetiva en relación con las variables de evaluación clínica (r = 0,1, p > 0,05) y ultrasonográfica (r = 0,1, p > 0,05). En el presente estudio, no fue posible considerar las correlaciones estadísticamente significativas, ya que el valor de p fue superior al nivel de significancia del 5%. Por lo tanto, la evaluación conjunta del esqueleto axial y apendicular es de fundamental importancia en la rutina clínica para investigar las alteraciones musculoesqueléticas. Esto se demostró en el presente estudio, donde el 68,42% (n=52) presentó tanto alteraciones clínicas como ultrasonográficas en el esqueleto axial de manera concomitante con la cojera torácica y/o pélvica

Simplified risk stratification criteria for identification of patients with MRSA bacteremia at low risk of infective endocarditis: implications for avoiding routine transesophageal echocardiography in MRSA bacteremia

The aim of this study was to identify patients with methicillin-resistant Staphylococcus aureus (MRSA) bacteremia with low risk of infective endocarditis (IE) who might not require routine trans-esophageal echocardiography (TEE). We retrospectively evaluated 398 patients presenting with MRSA bacteremia for the presence of the following clinical criteria: intravenous drug abuse (IVDA), long-term catheter, prolonged bacteremia, intra-cardiac device, prosthetic valve, hemodialysis dependency, vertebral/nonvertebral osteomyelitis, cardio-structural abnormality. IE was diagnosed using the modified Duke criteria. Of 398 patients with MRSA bacteremia, 26.4 % of cases were community-acquired, 56.3 % were health-care-associated, and 17.3 % were hospital-acquired. Of the group, 44 patients had definite IE, 119 had possible IE, and 235 had a rejected diagnosis. Out of 398 patients, 231 were evaluated with transthoracic echocardiography (TTE) or TEE. All 44 patients with definite IE fulfilled at least one criterion (sensitivity 100 %). Finally, a receiver operator characteristic (ROC) curve was obtained to evaluate the total risk score of our proposed criteria as a predictor of the presence of IE, and this was compared to the ROC curve of a previously proposed criteria. The area under the ROC curve for our criteria was 0.710, while the area under the ROC curve for the criteria previously proposed was 0.537 (p < 0.001). The p-value for comparing those 2 areas was less than 0.001, indicating statistical significance. Patients with MRSA bacteremia without any of our proposed clinical criteria have very low risk of developing IE and may not require routine TEE

Dropout in a longitudinal, cohort study of urologic disease in community men

BACKGROUND: Reasons for attrition in studies vary, but may be a major concern in long-term studies if those who drop out differ systematically from those who continue to participate. Factors associated with dropout were evaluated in a twelve-year community-based, prospective cohort study of urologic disease in men. METHODS: During 1989–1991, 2,115 randomly selected Caucasian men, ages 40–79 years from Olmsted County, Minnesota were enrolled and followed with questionnaires biennially; 332 men were added in follow-up. A random subset (~25%) received a urologic examination. Baseline characteristics including age, benign prostatic hyperplasia (BPH) symptoms, comorbidities, and socioeconomic factors were compared between subjects who did and did not participate after the twelfth year of follow-up. RESULTS: Of the 2,447 men, 195 died and were excluded; 682 did not participate in 2002. Compared with men in the 40–49 year age group, men ≥ 70 years of age at baseline had a greater relative odds of dropout, 2.65 (95% CI: 1.93, 3.63). In age-adjusted analyses, relative to men without stroke, men who had suffered a stroke had a higher odds of dropout, age-adjusted OR 3.07 (95% CI: 1.49, 6.33). Presence of at least one BPH symptom was not associated with dropout, (age-adjusted OR 1.12 (95% CI: 0.93, 1.36)). CONCLUSION: These results provide assurance that dropout was not related to primary study outcomes. However, factors associated with dropout should be taken into account in analyses where they may be potential confounders

A Fokker-Planck formalism for diffusion with finite increments and absorbing boundaries

Gaussian white noise is frequently used to model fluctuations in physical systems. In Fokker-Planck theory, this leads to a vanishing probability density near the absorbing boundary of threshold models. Here we derive the boundary condition for the stationary density of a first-order stochastic differential equation for additive finite-grained Poisson noise and show that the response properties of threshold units are qualitatively altered. Applied to the integrate-and-fire neuron model, the response turns out to be instantaneous rather than exhibiting low-pass characteristics, highly non-linear, and asymmetric for excitation and inhibition. The novel mechanism is exhibited on the network level and is a generic property of pulse-coupled systems of threshold units.Comment: Consists of two parts: main article (3 figures) plus supplementary text (3 extra figures

Eosinophils Are Important for Protection, Immunoregulation and Pathology during Infection with Nematode Microfilariae

Eosinophil responses typify both allergic and parasitic helminth disease. In helminthic disease, the role of eosinophils can be both protective in immune responses and destructive in pathological responses. To investigate whether eosinophils are involved in both protection and pathology during filarial nematode infection, we explored the role of eosinophils and their granule proteins, eosinophil peroxidase (EPO) and major basic protein-1 (MBP-1), during infection with Brugia malayi microfilariae. Using eosinophil-deficient mice (PHIL), we further clarify the role of eosinophils in clearance of microfilariae during primary, but not challenge infection in vivo. Deletion of EPO or MBP-1 alone was insufficient to abrogate parasite clearance suggesting that either these molecules are redundant or eosinophils act indirectly in parasite clearance via augmentation of other protective responses. Absence of eosinophils increased mast cell recruitment, but not other cell types, into the broncho-alveolar lavage fluid during challenge infection. In addition absence of eosinophils or EPO alone, augmented parasite-induced IgE responses, as measured by ELISA, demonstrating that eosinophils are involved in regulation of IgE. Whole body plethysmography indicated that nematode-induced changes in airway physiology were reduced in challenge infection in the absence of eosinophils and also during primary infection in the absence of EPO alone. However lack of eosinophils or MBP-1 actually increased goblet cell mucus production. We did not find any major differences in cytokine responses in the absence of eosinophils, EPO or MBP-1. These results reveal that eosinophils actively participate in regulation of IgE and goblet cell mucus production via granule secretion during nematode-induced pathology and highlight their importance both as effector cells, as damage-inducing cells and as supervisory cells that shape both innate and adaptive immunity

Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach

<p>Abstract</p> <p>Background</p> <p>For heterogeneous tissues, such as blood, measurements of gene expression are confounded by relative proportions of cell types involved. Conclusions have to rely on estimation of gene expression signals for homogeneous cell populations, e.g. by applying micro-dissection, fluorescence activated cell sorting, or <it>in-silico </it>deconfounding. We studied feasibility and validity of a non-negative matrix decomposition algorithm using experimental gene expression data for blood and sorted cells from the same donor samples. Our objective was to optimize the algorithm regarding detection of differentially expressed genes and to enable its use for classification in the difficult scenario of reversely regulated genes. This would be of importance for the identification of candidate biomarkers in heterogeneous tissues.</p> <p>Results</p> <p>Experimental data and simulation studies involving noise parameters estimated from these data revealed that for valid detection of differential gene expression, quantile normalization and use of non-log data are optimal. We demonstrate the feasibility of predicting proportions of constituting cell types from gene expression data of single samples, as a prerequisite for a deconfounding-based classification approach.</p> <p>Classification cross-validation errors with and without using deconfounding results are reported as well as sample-size dependencies. Implementation of the algorithm, simulation and analysis scripts are available.</p> <p>Conclusions</p> <p>The deconfounding algorithm without decorrelation using quantile normalization on non-log data is proposed for biomarkers that are difficult to detect, and for cases where confounding by varying proportions of cell types is the suspected reason. In this case, a deconfounding ranking approach can be used as a powerful alternative to, or complement of, other statistical learning approaches to define candidate biomarkers for molecular diagnosis and prediction in biomedicine, in realistically noisy conditions and with moderate sample sizes.</p

Histological validation of a type 1 diabetes clinical diagnostic model for classification of diabetes

This is the final version. Available on open access from Wiley via the DOI in this recordAims: Misclassification of diabetes is common due to an overlap in the clinical features of type 1 and type 2 diabetes. Combined diagnostic models incorporating clinical and biomarker information have recently been developed that can aid classification, but they have not been validated using pancreatic pathology. We evaluated a clinical diagnostic model against histologically defined type 1 diabetes. Methods: We classified cases from the Network for Pancreatic Organ donors with Diabetes (nPOD) biobank as type 1 (n = 111) or non-type 1 (n = 42) diabetes using histopathology. Type 1 diabetes was defined by lobular loss of insulin-containing islets along with multiple insulin-deficient islets. We assessed the discriminative performance of previously described type 1 diabetes diagnostic models, based on clinical features (age at diagnosis, BMI) and biomarker data [autoantibodies, type 1 diabetes genetic risk score (T1D-GRS)], and singular features for identifying type 1 diabetes by the area under the curve of the receiver operator characteristic (AUC-ROC). Results: Diagnostic models validated well against histologically defined type 1 diabetes. The model combining clinical features, islet autoantibodies and T1D-GRS was strongly discriminative of type 1 diabetes, and performed better than clinical features alone (AUC-ROC 0.97 vs. 0.95; P = 0.03). Histological classification of type 1 diabetes was concordant with serum C-peptide [median < 17 pmol/l (limit of detection) vs. 1037 pmol/l in non-type 1 diabetes; P < 0.0001]. Conclusions: Our study provides robust histological evidence that a clinical diagnostic model, combining clinical features and biomarkers, could improve diabetes classification. Our study also provides reassurance that a C-peptide-based definition of type 1 diabetes is an appropriate surrogate outcome that can be used in large clinical studies where histological definition is impossible. Parts of this study were presented in abstract form at the Network for Pancreatic Organ Donors Conference, Florida, USA, 19–22 February 2019 and Diabetes UK Professional Conference, Liverpool, UK, 6–8 March 2019.Diabetes UKNational Institutes of Health (NIH)National Institute for Health Research (NIHR)JDRFHelmsley Charitable Trus