Methods used to investigate a possible environmental source of Mycobacterium avium-intracellulare-scrofulaceum (MAIS) infection in farmed deer

Dissecting myogenin-mediated retinoid X receptor signaling in myogenic differentiation

Deciphering the molecular mechanisms underpinning myoblast differentiation is a critical step in developing the best strategy to promote muscle regeneration in patients suffering from muscle-related diseases. We have previously established that a rexinoid x receptor (RXR)-selective agonist, bexarotene, enhances the differentiation and fusion of myoblasts through a direct regulation of MyoD expression, coupled with an augmentation of myogenin protein. Here, we found that RXR signaling associates with the distribution of myogenin at poised enhancers and a distinct E-box motif. We also found an association of myogenin with rexinoid-responsive gene expression and identified an epigenetic signature related to histone acetyltransferase p300. Moreover, RXR signaling augments residue-specific histone acetylation at enhancers co-occupied by p300 and myogenin. Thus, genomic distribution of transcriptional regulators is an important designate for identifying novel targets as well as developing therapeutics that modulate epigenetic landscape in a selective manner to promote muscle regeneration.

Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing

Tissue-specific gene expression requires coordinated control of gene-proximal and -distal cis-regulatory elements (CREs), yet functional analysis of gene-distal CREs such as enhancers remains challenging. Here we describe CRISPR/dCas9-based enhancer-targeting epigenetic editing systems, enCRISPRa and enCRISPRi, for efficient analysis of enhancer function in situ and in vivo. Using dual effectors capable of re-writing enhancer-associated chromatin modifications, we show that enCRISPRa and enCRISPRi modulate gene transcription by remodeling local epigenetic landscapes at sgRNA-targeted enhancers and associated genes. Comparing with existing methods, the improved systems display more robust perturbations of enhancer activity and gene transcription with minimal off-targets. Allele-specific targeting of enCRISPRa to oncogenic TAL1 super-enhancer modulates TAL1 expression and cancer progression in xenotransplants. Single or multi-loci perturbations of lineage-specific enhancers using an enCRISPRi knock-in mouse establish in vivo evidence for lineage-restricted essentiality of developmental enhancers during hematopoiesis. Hence, enhancer-targeting CRISPR epigenetic editing provides opportunities for interrogating enhancer function in native biological contexts.

Analysis of possible factors affecting the specificity of the gamma interferon test in tuberculosis-free cattle herds

Bovine tuberculosis (TB) is still a zoonotic problem in the world. Despite the fact that eradication programs for bovine TB are being implemented in many countries, it remains a public health problem. These programs are mainly based on a single intradermal tuberculin test using bovine tuberculin purified protein derivative (PPD), isolation, and slaughtering of infected animals. The aim of this study was to assess the specificity of the gamma interferon (IFN-gamma) test in TB-free cattle herds, by using not only Australian tuberculins but also tuberculins produced at our institute, and to correlate the response with the type of production (beef cattle, dairy cattle, and a dual-purpose breed), the housing system, and the age of the animals. We studied 800 animals selected from 20 TB- and paratuberculosis-free herds. The animals were tested in parallel, after stimulation with Australian tuberculins and tuberculins produced at our institute, by using the skin test and two IFN-gamma assays. The results of this trial showed that the specificity of the IFN-gamma test is higher than that of the skin test (96.8%) and ranges from 97.3% (using only Australian tuberculins) to 98.6% (using tuberculins produced at our institute). We found that different categories of cattle could influence the specificity of the skin test but that these differences tended to be reduced in the IFN-gamma assay, especially when Italian PPDs were used.

Evaluation of the specificity of the gamma-interferon test in Italian bovine tuberculosis-free herds

We investigated the specificity of the gamma-interferon test for bovine tuberculosis (TB) in 1,557 cattle in 30 paratuberculosis-free and officially certified TB-free dairy herds, located in three provinces of the Lombardy Region in Northern Italy. The TB-free status of the herds under examination was further confirmed by the tuberculin skin test, by an antibody assay and by post mortem examination of animals culled from the herds during the study period. The specificity of the gamma-interferon tests after a single test and a double sampling scheme were 88.8% and 95.4%, respectively. After a single test, 11.7% of dubious reactors were also detected, while most cattle (47.4%) were shown to be avian reactors, probably due to contamination from infected birds and/or forage. There was strong evidence that the specificity of the test could be related to the animals' interaction with environmental mycobacteria and/or ageing. To reduce the percentage of nonspecific bovine reactors under alleged TB-free conditions, test procedures might involve the use of more specific antigens and/or different reaction thresholds.