-
Current Protocols Jul 2021The intricate folding of chromatin enables living organisms to store genomic material in an extremely small volume while facilitating proper cell function. Hi-C is a...
The intricate folding of chromatin enables living organisms to store genomic material in an extremely small volume while facilitating proper cell function. Hi-C is a chromosome conformation capture (3C)-based technology to detect pair-wise chromatin interactions genome-wide, and has become a benchmark tool to study genome organization. In Hi-C, chromatin conformation is first captured by chemical cross-linking of cells. Cells are then lysed and subjected to restriction enzyme digestion, before the ends of the resulting fragments are marked with biotin. Fragments within close 3D proximity are ligated, and the biotin label is used to selectively enrich for ligated junctions. Finally, isolated ligation products are prepared for high-throughput sequencing, which enables the mapping of pair-wise chromatin interactions genome-wide. Over the past decade, "next-generation" sequencing has become cheaper and easier to perform, enabling more interactions to be sampled to obtain higher resolution in chromatin interaction maps. Here, we provide an in-depth guide to performing an up-to-date Hi-C procedure on mammalian cell lines. These protocols include recent improvements that increase the resolution potential of the assay, namely by enhancing cross-linking and using a restriction enzyme cocktail. These improvements result in a versatile Hi-C procedure that enables the detection of genome folding features at a wide range of distances. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Fixation of nuclear conformation Basic Protocol 2: Chromosome conformation capture Basic Protocol 3: Hi-C sequencing library preparation.
Topics: Animals; Chromatin; Chromosomes; Genome; High-Throughput Nucleotide Sequencing; Nucleic Acid Conformation
PubMed: 34286910
DOI: 10.1002/cpz1.198 -
Nature Microbiology Oct 2022The ancient, ongoing coevolutionary battle between bacteria and their viruses, bacteriophages, has given rise to sophisticated immune systems including...
The ancient, ongoing coevolutionary battle between bacteria and their viruses, bacteriophages, has given rise to sophisticated immune systems including restriction-modification and CRISPR-Cas. Many additional anti-phage systems have been identified using computational approaches based on genomic co-location within defence islands, but these screens may not be exhaustive. Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands. Additionally, our work indicates that intact prophages and mobile genetic elements are primary reservoirs and distributors of defence systems in E. coli, with defence systems typically carried in specific locations or hotspots. These hotspots encode dozens of additional uncharacterized defence system candidates. Our findings reveal an extended landscape of antiviral immunity in E. coli and provide an approach for mapping defence systems in other species.
Topics: Antiviral Agents; Bacteriophages; CRISPR-Cas Systems; Escherichia coli; Prophages
PubMed: 36123438
DOI: 10.1038/s41564-022-01219-4 -
Neurology Mar 2023Studies on tumefactive brain lesions in myelin oligodendrocyte glycoprotein-immunoglobulin G (IgG)-associated disease (MOGAD) are lacking. We sought to characterize the...
BACKGROUND AND OBJECTIVES
Studies on tumefactive brain lesions in myelin oligodendrocyte glycoprotein-immunoglobulin G (IgG)-associated disease (MOGAD) are lacking. We sought to characterize the frequency clinical, laboratory, and MRI features of these lesions in MOGAD and compare them with those in multiple sclerosis (MS) and aquaporin-4-IgG-positive neuromyelitis optica spectrum disorder (AQP4+NMOSD).
METHODS
We retrospectively searched 194 patients with MOGAD and 359 patients with AQP4+NMOSD with clinical/MRI details available from the Mayo Clinic databases and included those with ≥1 tumefactive brain lesion (maximum transverse diameter ≥2 cm) on MRI. Patients with tumefactive MS were identified using the Mayo Clinic medical record linkage system. Binary multivariable stepwise logistic regression identified independent predictors of MOGAD diagnosis; Cox proportional regression models were used to assess the risk of relapsing disease and gait aid in patients with tumefactive MOGAD vs those with nontumefactive MOGAD.
RESULTS
We included 108 patients with tumefactive demyelination (MOGAD = 43; AQP4+NMOSD = 16; and MS = 49). Tumefactive lesions were more frequent among those with MOGAD (43/194 [22%]) than among those with AQP4+NMOSD (16/359 [5%], < 0.001). Risk of relapse and need for gait aid were similar in tumefactive and nontumefactive MOGAD. Clinical features more frequent in MOGAD than in MS included headache (18/43 [42%] vs 10/49 [20%]; = 0.03) and somnolence (12/43 [28%] vs 2/49 [4%]; = 0.003), the latter also more frequent than in AQP4+NMOSD (0/16 [0%]; = 0.02). The presence of peripheral T2-hypointense rim, T1-hypointensity, diffusion restriction (particularly an arc pattern), ring enhancement, and Baló-like or cystic appearance favored MS over MOGAD ( ≤ 0.001). MRI features were broadly similar in MOGAD and AQP4+NMOSD, except for more frequent diffusion restriction in AQP4+NMOSD (10/15 [67%]) than in MOGAD (11/42 [26%], = 0.005). CSF analysis revealed less frequent positive oligoclonal bands in MOGAD (2/37 [5%]) than in MS (30/43 [70%], < 0.001) and higher median white cell count in MOGAD than in MS (33 vs 6 cells/μL, < 0.001). At baseline, independent predictors of MOGAD diagnosis were the presence of somnolence/headache, absence of T2-hypointense rim, lack of T1-hypointensity, and no diffusion restriction (Nagelkerke = 0.67). Tumefactive lesion resolution was more common in MOGAD than in MS or AQP4+NMOSD and improved model performance.
DISCUSSION
Tumefactive lesions are frequent in MOGAD but not associated with a worse prognosis. The clinical, MRI, and CSF attributes of tumefactive MOGAD differ from those of tumefactive MS and are more similar to those of tumefactive AQP4+NMOSD with the exception of lesion resolution, which favors MOGAD.
Topics: Humans; Neuromyelitis Optica; Multiple Sclerosis; Immunoglobulin G; Retrospective Studies; Sleepiness; Aquaporin 4; Myelin-Oligodendrocyte Glycoprotein; Recurrence; Autoantibodies
PubMed: 36690455
DOI: 10.1212/WNL.0000000000206820 -
Journal of the American Statistical... 2022Numerical embedding has become one standard technique for processing and analyzing unstructured data that cannot be expressed in a predefined fashion. It stores the main...
Numerical embedding has become one standard technique for processing and analyzing unstructured data that cannot be expressed in a predefined fashion. It stores the main characteristics of data by mapping it onto a numerical vector. An embedding is often unsupervised and constructed by transfer learning from large-scale unannotated data. Given an embedding, a downstream learning method, referred to as a two-stage method, is applicable to unstructured data. In this article, we introduce a novel framework of embedding learning to deliver a higher learning accuracy than the two-stage method while identifying an optimal learning-adaptive embedding. In particular, we propose a concept of -minimal sufficient learning-adaptive embeddings, based on which we seek an optimal one to maximize the learning accuracy subject to an embedding constraint. Moreover, when specializing the general framework to classification, we derive a graph embedding classifier based on a hyperlink tensor representing multiple hypergraphs, directed or undirected, characterizing multi-way relations of unstructured data. Numerically, we design algorithms based on blockwise coordinate descent and projected gradient descent to implement linear and feed-forward neural network classifiers, respectively. Theoretically, we establish a learning theory to quantify the generalization error of the proposed method. Moreover, we show, in linear regression, that the one-hot encoder is more preferable among two-stage methods, yet its dimension restriction hinders its predictive performance. For a graph embedding classifier, the generalization error matches up to the standard fast rate or the parametric rate for linear or nonlinear classification. Finally, we demonstrate the utility of the classifiers on two benchmarks in grammatical classification and sentiment analysis. Supplementary materials for this article are available online.
PubMed: 36936129
DOI: 10.1080/01621459.2020.1775614 -
PloS One 2021In genomics, optical mapping technology provides long-range contiguity information to improve genome sequence assemblies and detect structural variation. Originally a...
In genomics, optical mapping technology provides long-range contiguity information to improve genome sequence assemblies and detect structural variation. Originally a laborious manual process, Bionano Genomics platforms now offer high-throughput, automated optical mapping based on chips packed with nanochannels through which unwound DNA is guided and the fluorescent DNA backbone and specific restriction sites are recorded. Although the raw image data obtained is of high quality, the processing and assembly software accompanying the platforms is closed source and does not seem to make full use of data, labeling approximately half of the measured signals as unusable. Here we introduce two new software tools, independent of Bionano Genomics software, to extract and process molecules from raw images (OptiScan) and to perform molecule-to-molecule and molecule-to-reference alignments using a novel signal-based approach (OptiMap). We demonstrate that the molecules detected by OptiScan can yield better assemblies, and that the approach taken by OptiMap results in higher use of molecules from the raw data. These tools lay the foundation for a suite of open-source methods to process and analyze high-throughput optical mapping data. The Python implementations of the OptiTools are publicly available through http://www.bif.wur.nl/.
Topics: Chromosome Mapping; Genomics; High-Throughput Nucleotide Sequencing; Optical Restriction Mapping; Sequence Analysis, DNA
PubMed: 34591846
DOI: 10.1371/journal.pone.0253102 -
Methods in Molecular Biology (Clifton,... 2021Technology advance during the past decade has greatly expanded our understanding of the higher-order structure of the genome. The various chromosome conformation capture...
Technology advance during the past decade has greatly expanded our understanding of the higher-order structure of the genome. The various chromosome conformation capture (3C)-based techniques such as Hi-C have provided the most widely used tools for interrogating three-dimensional (3D) genome organization. We recently developed a Hi-C variant, DNase Hi-C, for characterizing 3D genome organization. DNase Hi-C employs DNase I for chromatin fragmentation, aiming to overcome restriction enzyme digestion-related limitations associated with traditional Hi-C methods. By combining DNase Hi-C with DNA capture technology, we further implemented a high-throughput approach, called targeted DNase Hi-C, which enables to map fine-scale chromatin architecture at exceptionally high resolution and thereby is an ideal tool for mapping the physical landscapes of cis-regulatory networks and for characterizing phenotype-associated chromatin 3D signatures. Here, I describe a detailed protocol of targeted DNase Hi-C library preparation, which covers experimental steps starting from cell cross-linking to library amplification.
Topics: Chromatin; Chromosomes; Deoxyribonucleases; Genome; Saccharomyces cerevisiae
PubMed: 32820399
DOI: 10.1007/978-1-0716-0664-3_5 -
Ultrasound in Obstetrics & Gynecology :... Jul 2022Doppler techniques are needed for the evaluation of the intraplacental circulation and can be of great value in the diagnosis of placental anomalies. Highly sensitive... (Review)
Review
Doppler techniques are needed for the evaluation of the intraplacental circulation and can be of great value in the diagnosis of placental anomalies. Highly sensitive Doppler techniques can differentiate between the maternal (spiral arteries) and fetal (intraplacental branches of the umbilical artery) components of the placental circulation and assist in the evaluation of the placental functional units. A reduced number of placental functional units can be associated with obstetric complications, such as fetal growth restriction. Doppler techniques can also provide information on decidual vessels and blood movement. Abnormal decidual circulation increases the risk of placenta accreta. Doppler evaluation of the placenta greatly contributes to the diagnosis and clinical management of placenta accreta, vasa previa, placental infarcts, placental infarction hematoma, maternal floor infarction, massive perivillous fibrin deposition and placental tumors. However, it has a limited role in the diagnosis and clinical management of placental abruption, placental hematomas, placental mesenchymal dysplasia and mapping of placental anastomoses in monochorionic twin pregnancies. © 2021 International Society of Ultrasound in Obstetrics and Gynecology.
Topics: Female; Fetal Growth Retardation; Humans; Infarction; Placenta; Placenta Accreta; Placenta Diseases; Pregnancy; Ultrasonography, Doppler; Ultrasonography, Prenatal
PubMed: 34806234
DOI: 10.1002/uog.24816 -
Interdisciplinary Sciences,... Mar 2021Gene sequencing technology has been playing an important role in many aspects, such as life science, disease medicine and health medicine, particularly in the extremely...
Gene sequencing technology has been playing an important role in many aspects, such as life science, disease medicine and health medicine, particularly in the extremely tough process of fighting against 2019-novel coronavirus. Drawing DNA restriction map is a particularly important technology in genetic biology. The simplified partial digestion method (SPDP), a biological method, has been widely used to cut DNA molecules into DNA fragments and obtain the biological information of each fragment. In this work, we propose an algorithm based on 0-1 planning for the location of restriction sites on a DNA molecule, which is able to solve the problem of DNA fragment reconstruction just based on data of fragments' length. Two specific examples are presented in detail. Furthermore, based on 1000 groups of original DNA sequences randomly generated, we define the coincidence rate and unique coincidence rate between the reconstructed DNA sequence and the original DNA sequence, and then analyze separately the effect of the number of fragments and the maximum length of DNA fragments on the coincidence rate and unique coincidence rate as defined. The effectiveness of the algorithm is proved. Besides, based on the existing optimization solution obtained, we simulate and discuss the influence of the error by computation method. It turns out that the error of position of one restriction site does not affect other restriction sites and errors of most restriction sites may lead to the failure of sequence reconstruction. Matlab 7.1 program is used to solve feasible solutions of the location of restriction sites, derive DNA fragment sequence and carry out the statistical analysis and error analysis. This paper focuses on basic computer algorithm implementation of rearrangement and sequencing rather than biochemical technology. The innovative application of the mathematical idea of 0-1 planning to DNA sequence mapping construction, to a certain extent, greatly simplifies the difficulty and complexity of calculation and accelerates the process of 'jigsaw' of DNA fragments.
Topics: Algorithms; Base Sequence; Models, Theoretical; Sequence Analysis, DNA; Statistics as Topic
PubMed: 33609237
DOI: 10.1007/s12539-021-00419-6 -
Nature Communications Dec 2023Telomere length (TL) shortening is a pivotal indicator of biological aging and is associated with many human diseases. The genetic determinates of human TL have been...
Telomere length (TL) shortening is a pivotal indicator of biological aging and is associated with many human diseases. The genetic determinates of human TL have been widely investigated, however, most existing studies were conducted based on adult tissues which are heavily influenced by lifetime exposure. Based on the analyses of terminal restriction fragment (TRF) length of telomere, individual genotypes, and gene expressions on 166 healthy placental tissues, we systematically interrogate TL-modulated genes and their potential functions. We discover that the TL in the placenta is comparatively longer than in other adult tissues, but exhibiting an intra-tissue homogeneity. Trans-ancestral TL genome-wide association studies (GWASs) on 644,553 individuals identify 20 newly discovered genetic associations and provide increased polygenic determination of human TL. Next, we integrate the powerful TL GWAS with placental expression quantitative trait locus (eQTL) mapping to prioritize 23 likely causal genes, among which 4 are functionally validated, including MMUT, RRM1, KIAA1429, and YWHAZ. Finally, modeling transcriptomic signatures and TRF-based TL improve the prediction performance of human TL. This study deepens our understanding of causal genes and transcriptomic determinants of human TL, promoting the mechanistic research on fine-grained TL regulation.
Topics: Adult; Humans; Female; Pregnancy; Genome-Wide Association Study; Placenta; Telomere Shortening; Telomere; Gene Expression Profiling
PubMed: 38129441
DOI: 10.1038/s41467-023-44355-z -
Radiologie (Heidelberg, Germany) Nov 2022The classification of cardiomyopathies used in Germany goes back to the European Society of Cardiology (ESC) classification of 2008. The cardiomyopathies are subdivided... (Review)
Review
BACKGROUND
The classification of cardiomyopathies used in Germany goes back to the European Society of Cardiology (ESC) classification of 2008. The cardiomyopathies are subdivided according to the phenotype, so that magnetic resonance imaging (MRI) is able to differentiate between the various cardiomyopathies.
IMAGING AND DIFFERENTIAL DIAGNOSTICS
The strength of MRI is the ability to differentiate nonischemic cardiomyopathies from other diseases with similar morphofunctional aspects, based on the possibilities of tissue differentiation. In the case of dilated cardiomyopathy (DCM), for example, a differentiation from inflammatory DCM is possible. In the case of hypertrophic cardiomyopathy (HCM), obstructive and nonobstructive forms can be differentiated analogously to the echo but amyloidosis or Fabry disease can also be detected. Evaluation of the right ventricular function is reliable in arrhythmogenic right ventricular cardiomyopathy (ARVC). The use of MRI is also able to directly detect the characteristic fibrofatty degeneration. In the rare restrictive cardiomyopathies (RCM), MRI can track restriction and, for example by means of T1, T2 and T2* mapping, detect sphingolipid accumulation in the myocardium in the context of Fabry disease or iron overload in the context of hemochromatosis.
INNOVATIONS
The quantitative methods of parametric mapping provide the possibility of treatment monitoring but the clinical relevance of this monitoring is still the subject of current research. The unclassified cardiomyopathies can present clinically with similar symptoms to ischemic or inflammatory diseases, so that in the case of myocardial infarction without obstructive coronary arteries (MINOCA) in cardiac catheterization, MRI is a decisive diagnostic tool to determine the actual underlying disease. Similarly, in new cardiomyopathies such as noncompaction cardiomyopathy, MRI can pave the way for a morphological disease definition.
Topics: Humans; Arrhythmogenic Right Ventricular Dysplasia; Cardiomyopathies; Cardiomyopathy, Dilated; Fabry Disease; Magnetic Resonance Imaging; Reproducibility of Results
PubMed: 36129478
DOI: 10.1007/s00117-022-01068-6