Insm1 regulates mTEC development and immune tolerance.

The expression of self-antigens in medullary thymic epithelial cells (mTECs) is essential for the establishment of immune tolerance, but the regulatory network that controls the generation and maintenance of the multitude of cell populations expressing self-antigens is poorly understood. Here, we show that Insm1, a zinc finger protein with known functions in neuroendocrine and neuronal cells, is broadly coexpressed with an autoimmune regulator (Aire) in mTECs. Insm1 expression is undetectable in most mimetic cell populations derived from mTECs but persists in neuroendocrine mimetic cells. Mutation of Insm1 in mice downregulated Aire expression, dysregulated the gene expression program of mTECs, and altered mTEC subpopulations and the expression of tissue-restricted antigens. Consistent with these findings, loss of Insm1 resulted in autoimmune responses in multiple peripheral tissues. We found that Insm1 regulates gene expression in mTECs by binding to chromatin. Interestingly, the majority of the Insm1 binding sites are co-occupied by Aire and enriched in superenhancer regions. Together, our data demonstrate the important role of Insm1 in the regulation of the repertoire of self-antigens needed to establish immune tolerance.

DeepTag: A General Framework for Fiducial Marker Design and Detection.

A fiducial marker system usually consists of markers, a detection algorithm, and a coding system. The appearance of markers and the detection robustness are generally limited by the existing detection algorithms, which are hand-crafted with traditional low-level image processing techniques. Furthermore, a sophisticatedly designed coding system is required to overcome the shortcomings of both markers and detection algorithms. To improve the flexibility and robustness in various applications, we propose a general deep learning based framework, DeepTag, for fiducial marker design and detection. DeepTag not only supports detection of a wide variety of existing marker families, but also makes it possible to design new marker families with customized local patterns. Moreover, we propose an effective procedure to synthesize training data on the fly without manual annotations. Thus, DeepTag can easily adapt to existing and newly-designed marker families. To validate DeepTag and existing methods, beside existing datasets, we further collect a new large and challenging dataset where markers are placed in different view distances and angles. Experiments show that DeepTag well supports different marker families and greatly outperforms the existing methods in terms of both detection robustness and pose accuracy. Both code and dataset are available at https://herohuyongtao.github.io/research/publications/deep-tag/.

Primacy of mouth over eyes to perceive audiovisual Mandarin lexical tones.

The visual cues of lexical tones are more implicit and much less investigated than consonants and vowels, and it is still unclear what facial areas contribute to facial tones identification. This study investigated Chinese and English speakers' eye movements when they were asked to identify audiovisual Mandarin lexical tones. The Chinese and English speakers were presented with an audiovisual clip of Mandarin monosyllables (for instance, /a/, /à/, /i/, /ì/) and were asked to identify whether the syllables were a dipping tone (/a/, / i/) or a falling tone (/ à/, /ì/). These audiovisual syllables were presented in clear, noisy and silent (absence of audio signal) conditions. An eye-tracker recorded the participants' eye movements. Results showed that the participants gazed more at the mouth than the eyes. In addition, when acoustic conditions became adverse, both the Chinese and English speakers increased their gaze duration at the mouth rather than at the eyes. The findings suggested that the mouth is the primary area that listeners utilise in their perception of audiovisual lexical tones. The similar eye movements between the Chinese and English speakers imply that the mouth acts as a perceptual cue that provides articulatory information, as opposed to social and pragmatic information.

DNA G-quadruplex structure participates in regulation of lipid metabolism through acyl-CoA binding protein.

G-quadruplex structure (G4) is a type of DNA secondary structure that widely exists in the genomes of many organisms. G4s are believed to participate in multiple biological processes. Acyl-CoA binding protein (ACBP), a ubiquitously expressed and highly conserved protein in eukaryotic cells, plays important roles in lipid metabolism by transporting and protecting acyl-CoA esters. Here, we report the functional identification of a G4 in the promoter of the ACBP gene in silkworm and human cancer cells. We found that G4 exists as a conserved element in the promoters of ACBP genes in invertebrates and vertebrates. The BmACBP G4 bound with G4-binding protein LARK regulated BmACBP transcription, which was blocked by the G4 stabilizer pyridostatin (PDS) and G4 antisense oligonucleotides. PDS treatment with fifth instar silkworm larvae decreased the BmACBP expression and triacylglycerides (TAG) level, resulting in reductions in fat body mass, body size and weight and growth and metamorphic rates. PDS treatment and knocking out of the HsACBP G4 in human hepatic adenocarcinoma HepG2 cells inhibited the expression of HsACBP and decreased the TAG level and cell proliferation. Altogether, our findings suggest that G4 of the ACBP genes is involved in regulation of lipid metabolism processes in invertebrates and vertebrates.

Large-scale screening of i-motif binding compounds in the silkworm, Bombyx mori.

DNA secondary structure i-motif involves in gene transcription and considered as a novel target for cancer gene therapy. I-motif-binding compounds can either stabilize or destroy the structure, resulting in change in target gene transcription. In this study, a large-scale screening of binding compounds was conducted using the i-motif structure of BmPOUM2, a transcription factor in silkworm, Bombyx mori. Surface plasmon resonance imaging (SPRi) high-throughput binding screening of 3642 compounds found 60 compounds with an binding affinity Kd of 10-7-10-6 M. SPRi and circular dichroism (CD) double screening demonstrated that the BmPOUM2 i-motif structure bound the compounds IF1, IF3, IF4, IF6 and IF7 with Kd of 10-7 M, and the compounds IF2 and tetrakis (4-N-methylpyridyl) porphine (TMPyP4) with a Kd of 10-8 M. Interestingly, IF2, IF3, IF4, IF6 and IF7 promoted the binding of the i-motif-binding protein BmILF with the i-motif structure, whereas TMPyP4 inhibited the binding. This study provided a list of compounds that have potential applications in functional analysis of i-motif structure and in pesticide and drug development through gene transcription regulation by i-motif structure.

Identification of binding domains and key amino acids involved in the interaction between BmLARK and G4 structure in the BmPOUM2 promoter in Bombyx mori.

It has been found that the non-B form DNA structures, like G-quadruplex (G4) and i-motif, are involved in many important biological processes. Our previous study showed that the silkworm transcription factor BmLARK binds to the G4 structure in the promoter of the transcription factor BmPOUM2 and regulates its promoter activity. However, the binding mechanism between BmLARK and BmPOUM2 G4 structure remains unclear. In this study, binding domains and key amino acid residues involved in the interaction between BmLARK and BmPOUM2 G4 were studied. The electrophoretic mobility shift assay results indicated that the two RNA-recognition motifs (RRM) of BmLARK are simultaneously required for the binding with the G4 structure. Either RRM1 or RRM2 alone could not bind with the G4 structure. The zinc-finger motif was not involved in the binding. A series of mutant proteins with specific amino acid mutations were expressed and used to identify the key amino acid residues involving the interaction. The results indicated that ß sheets, especially the ß1 and ß3 sheets, in the RRM domains of BmLARK played critical roles in the binding with the G4 structure. Several amino acid mutations of RRM1/2 in ribonucleoprotein domain 1 (RNP1) (motif in ß3 strand) and RNP2 (motif in ß1 strand) caused loss of binding ability, indicating that these amino acids are the key sites for the binding. All the results suggest that RRM domains, particularly their the RNP1 and RNP2 motifs, play important roles not only in RNA recognition, but also in the G4 structure binding.

TopoTag: A Robust and Scalable Topological Fiducial Marker System.

Fiducial markers have been playing an important role in augmented reality (AR), robot navigation, and general applications where the relative pose between a camera and an object is required. Here we introduce TopoTag, a robust and scalable topological fiducial marker system, which supports reliable and accurate pose estimation from a single image. TopoTag uses topological and geometrical information in marker detection to achieve higher robustness. Topological information is extensively used for 2D marker detection, and further corresponding geometrical information for ID decoding. Robust 3D pose estimation is achieved by taking advantage of all TopoTag vertices. Without sacrificing bits for higher recall and precision like previous systems, TopoTag can use full bits for ID encoding. TopoTag supports tens of thousands unique IDs and easily extends to millions of unique tags resulting in massive scalability. We collected a large test dataset including in total 169,713 images for evaluation, involving in-plane and out-of-plane rotation, image blur, different distances, and various backgrounds, etc. Experiments on the dataset and real indoor and outdoor scene tests with a rolling shutter camera both show that TopoTag significantly outperforms previous fiducial marker systems in terms of various metrics, including detection accuracy, vertex jitter, pose jitter and accuracy, etc. In addition, TopoTag supports occlusion as long as the main tag topological structure is maintained and allows for flexible shape design where users can customize internal and external marker shapes. Code for our marker design/generation, marker detection, and dataset are available at http://herohuyongtao.github.io/research/publications/topo-tag/.

In vivo visualization of the i-motif DNA secondary structure in the Bombyx mori testis.

BACKGROUND: A large number of in vitro experiments have confirmed that DNA molecules can form i-motif advanced structure when multiple cytosines exist in the sequence. However, whether these structures are present in vivo environment still lacks sufficient experimental evidence. RESULTS: In this paper, we report the in vivo visualization of i-motif structures in the nuclei and chromosomes of the testis of the invertebrate Bombyx mori using immunofluorescence staining with an antibody specifically recognizing the endogenous transcription factor BmILF, which binds i-motif structure with high specificity. The number of i-motif structures observed in the genome increased when the pH was changed from basic to acidic and decreased under treatment with an i-motif inhibitor, the porphyrin compound TMPyP4. The pH change affected the transcription of genes that contain i-motif sequences. Moreover, there were more i-motif structures observed in the testis cells in interphase than in any other cell cycle stage. CONCLUSIONS: In this study, the i-motif structures in invertebrates were detected for the first time at the cell and organ levels. The formation of the structures depended on cell cycle and pH and affected gene expression.