Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes

Explosive growth in the study of microbial epigenetics has revealed a diversity of chemical structures and biological functions of DNA modifications in restriction-modification (R-M) and basic genetic processes. Here, we describe the discovery of shared consensus sequences for two seemingly unrelated DNA modification systems, [superscript 6m]A methylation and phosphorothioation (PT), in which sulfur replaces a nonbridging oxygen in the DNA backbone. Mass spectrometric analysis of DNA from Escherichia coli B7A and Salmonella enterica serovar Cerro 87, strains possessing PT-based R-M genes, revealed d(G[subscript PS] [superscript 6m]A) dinucleotides in the G[subscript PS] [superscript 6m]AAC consensus representing ∼5% of the 1,100 to 1,300 PT-modified d(G[subscript PS] A) motifs per genome, with [superscript 6m]A arising from a yet-to-be-identified methyltransferase. To further explore PT and 6m A in another consensus sequence, G[subscript PS] [superscript 6m]ATC, we engineered a strain of E. coli HST04 to express Dnd genes from Hahella chejuensis KCTC2396 (PT in G[subscript PS] ATC) and Dam methyltransferase from E. coli DH10B ( [superscript 6m] A in G [superscript 6m] ATC). Based on this model, in vitro studies revealed reduced Dam activity in G PS ATC-containing oligonucleotides whereas single-molecule real-time sequencing of HST04 DNA revealed [superscript 6m] A in all 2,058 G[subscript PS] ATC sites (5% of 37,698 total GATC sites). This model system also revealed temperature-sensitive restriction by DndFGH in KCTC2396 and B7A, which was exploited to discover that [superscript 6m] A can substitute for PT to confer resistance to restriction by the DndFGH system. These results point to complex but unappreciated interactions between DNA modification systems and raise the possibility of coevolution of interacting systems to facilitate the function of each

Weak decays of heavy hadrons into dynamically generated resonances

In this paper, we present a review of recent works on weak decay of heavy mesons and baryons with two mesons, or a meson and a baryon, interacting strongly in the final state. The aim is to learn about the interaction of hadrons and how some particular resonances are produced in the reactions. It is shown that these reactions have peculiar features and act as filters for some quantum numbers which allow to identify easily some resonances and learn about their nature. The combination of basic elements of the weak interaction with the framework of the chiral unitary approach allow for an interpretation of results of many reactions and add a novel information to different aspects of the hadron interaction and the properties of dynamically generated resonances.We would like to thank C. Hanhart and S. Stone for valuable comments on the manuscript. One of us, E. O., wishes to acknowledge support from the Chinese Academy of Science in the Program of Visiting Professorship for Senior International Scientists (Grant No. 2013T2J0012). This work is partly supported by the Spanish Ministerio de Economia y Competitividad and European FEDER funds under the contract numbers FIS2011-28853-C02-01, FIS2011-28853-C02-02, FIS2014-57026-REDT, FIS2014-51948-C2-1-P, and FIS2014-51948-C2-2-P, and the Generalitat Valenciana in the program Prometeo II-2014/068. This work is also partly supported by the National Natural Science Foundation of China under Grant Nos. 11165005, 11565007, 11475227, 11375080 and 11575076. We acknowledge the support of the European Community-Research Infrastructure Integrating Activity Study of Strongly Interacting Matter (acronym HadronPhysics3, Grant Agreement n. 283286) under the Seventh Framework Programme of EU. It is also supported by the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (No. Y5KF151CJ1). M. D. gratefully acknowledges support from the NSF/PIF Grant No. PHY 1415459 and the NSF/Career grant No. 1452055.Peer reviewe

Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences

Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other PT functions. Here we report two novel, orthogonal technologies to map PTs across the genomes of B7A and FF75 with >90% agreement: single molecule, real-time sequencing and deep sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of G[subscript ps]AAC/G[subscript ps]TTC motifs, but with only 12% of 40,701 possible sites modified. In contrast, PT in FF75 occurs as a single-strand modification at C[subscript ps]CA, again with only 14% of 160,541 sites modified. Single-molecule analysis indicates that modification could be partial at any particular genomic site even with active restriction by DndF-H, with direct interaction of modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results point to highly unusual target selection by PT-modification proteins and rule out known R-M mechanisms.National Natural Science Foundation (China)Ministry of Science and Technology of the People's Republic of China (973 and 863 Programs)Shanghai Municipal Council of Science and Technology. Shanghai Pujiang ProgramNational Science Foundation (U.S.) (CHE-1019990)National Institute of Environmental Health Sciences (ES002109)Singapore. National Research Foundation (Singapore-MIT Alliance for Research and Technology

New discoveries in the field of metabolism by applying single-cell and spatial omics

Single-cell multi-Omics (SCM-Omics) and spatial multi-Omics (SM-Omics) technologies provide state-of-the-art methods for exploring the composition and function of cell types in tissues/organs. Since its emergence in 2009, single-cell RNA sequencing (scRNA-seq) has yielded many groundbreaking new discoveries. The combination of this method with the emergence and development of SM-Omics techniques has been a pioneering strategy in neuroscience, developmental biology, and cancer research, especially for assessing tumor heterogeneity and T-cell infiltration. In recent years, the application of these methods in the study of metabolic diseases has also increased. The emerging SCM-Omics and SM-Omics approaches allow the molecular and spatial analysis of cells to explore regulatory states and determine cell fate, and thus provide promising tools for unraveling heterogeneous metabolic processes and making them amenable to intervention. Here, we review the evolution of SCM-Omics and SM-Omics technologies, and describe the progress in the application of SCM-Omics and SM-Omics in metabolism-related diseases, including obesity, diabetes, nonalcoholic fatty liver disease (NAFLD) and cardiovascular disease (CVD). We also conclude that the application of SCM-Omics and SM-Omics approaches can help resolve the molecular mechanisms underlying the pathogenesis of metabolic diseases in the body and facilitate therapeutic measures for metabolism-related diseases. This review concludes with an overview of the current status of this emerging field and the outlook for its future

Engineering and modification of microbial chassis for systems and synthetic biology

Engineering and modifying synthetic microbial chassis is one of the best ways not only to unravel the fundamental principles of life but also to enhance applications in the health, medicine, agricultural, veterinary, and food industries. The two primary strategies for constructing a microbial chassis are the top-down approach (genome reduction) and the bottom-up approach (genome synthesis). Research programs on this topic have been funded in several countries. The ‘Minimum genome factory’ (MGF) project was launched in 2001 in Japan with the goal of constructing microorganisms with smaller genomes for industrial use. One of the best examples of the results of this project is E. coli MGF-01, which has a reduced-genome size and exhibits better growth and higher threonine production characteristics than the parental strain [1]. The ‘cell factory’ project was carried out from 1998 to 2002 in the Fifth Framework Program of the EU (European Union), which tried to comprehensively understand microorganisms used in the application field. One of the outstanding results of this project was the elucidation of proteins secreted by Bacillus subtilis, which was summarized as the ‘secretome’ [2]. The GTL (Genomes to Life) program began in 2002 in the United States. In this program, researchers aimed to create artificial cells both in silico and in vitro, such as the successful design and synthesis of a minimal bacterial genome by John Craig Venter's group [3]. This review provides an update on recent advances in engineering, modification and application of synthetic microbial chassis, with particular emphasis on the value of learning about chassis as a way to better understand life and improve applications. Keywords: Microbial chassis, Systems biology, Synthetic biolog

DNA phosphorothioate modification—a new multi-functional epigenetic system in bacteria

Synthetic phosphorothioate (PT) internucleotide linkages, in which a nonbridging oxygen is replaced by a sulphur atom, share similar physical and chemical properties with phosphodiesters but confer enhanced nuclease tolerance on DNA/RNA, making PTs a valuable biochemical and pharmacological tool. Interestingly, PT modification was recently found to occur naturally in bacteria in a sequence-selective and R P configuration-specific manner. This oxygen-sulphur swap is catalysed by the gene products of dndABCDE, which constitute a defence barrier with DndFGH in some bacterial strains that can distinguish and attack non-PT-modified foreign DNA, resembling DNA methylation-based restriction-modification (R-M) systems. Despite their similar defensive mechanisms, PT- and methylation-based R-M systems have evolved to target different consensus contexts in the host cell because when they share the same recognition sequences, the protective function of each can be impeded. The redox and nucleophilic properties of PT sulphur render PT modification a versatile player in the maintenance of cellular redox homeostasis, epigenetic regulation and environmental fitness. The widespread presence of dnd systems is considered a consequence of extensive horizontal gene transfer, whereas the lability of PT during oxidative stress and the susceptibility of PT to PT-dependent endonucleases provide possible explanations for the ubiquitous but sporadic distribution of PT modification in the bacterial world

A Novel and Effective Method for Congestive Heart Failure Detection and Quantification Using Dynamic Heart Rate Variability Measurement.

Risk assessment of congestive heart failure (CHF) is essential for detection, especially helping patients make informed decisions about medications, devices, transplantation, and end-of-life care. The majority of studies have focused on disease detection between CHF patients and normal subjects using short-/long-term heart rate variability (HRV) measures but not much on quantification. We downloaded 116 nominal 24-hour RR interval records from the MIT/BIH database, including 72 normal people and 44 CHF patients. These records were analyzed under a 4-level risk assessment model: no risk (normal people, N), mild risk (patients with New York Heart Association (NYHA) class I-II, P1), moderate risk (patients with NYHA III, P2), and severe risk (patients with NYHA III-IV, P3). A novel multistage classification approach is proposed for risk assessment and rating CHF using the non-equilibrium decision-tree-based support vector machine classifier. We propose dynamic indices of HRV to capture the dynamics of 5-minute short term HRV measurements for quantifying autonomic activity changes of CHF. We extracted 54 classical measures and 126 dynamic indices and selected from these using backward elimination to detect and quantify CHF patients. Experimental results show that the multistage risk assessment model can realize CHF detection and quantification analysis with total accuracy of 96.61%. The multistage model provides a powerful predictor between predicted and actual ratings, and it could serve as a clinically meaningful outcome providing an early assessment and a prognostic marker for CHF patients

Use of Mutual Information and Transfer Entropy to Assess Interaction between Parasympathetic and Sympathetic Activities of Nervous System from HRV

Obstructive sleep apnea (OSA) is a common sleep disorder that often associates with reduced heart rate variability (HRV) indicating autonomic dysfunction. HRV is mainly composed of high frequency components attributed to parasympathetic activity and low frequency components attributed to sympathetic activity. Although, time domain and frequency domain features of HRV have been used to sleep studies, the complex interaction between nonlinear independent frequency components with OSA is less known. This study included 30 electrocardiogram recordings (20 OSA patient recording and 10 healthy subjects) with apnea or normal label in 1-min segment. All segments were divided into three groups: N-N group (normal segments of normal subjects), P-N group (normal segments of OSA subjects) and P-OSA group (apnea segments of OSA subjects). Frequency domain indices and interaction indices were extracted from segmented RR intervals. Frequency domain indices included nuLF, nuHF, and LF/HF ratio; interaction indices included mutual information (MI) and transfer entropy (TE (H→L) and TE (L→H)). Our results demonstrated that LF/HF ratio was significant higher in P-OSA group than N-N group and P-N group. MI was significantly larger in P-OSA group than P-N group. TE (H→L) and TE (L→H) showed a significant decrease in P-OSA group, compared to P-N group and N-N group. TE (H→L) were significantly negative correlation with LF/HF ratio in P-N group (r = −0.789, p = 0.000) and P-OSA group (r = −0.661, p = 0.002). Our results indicated that MI and TE is powerful tools to evaluate sympathovagal modulation in OSA. Moreover, sympathovagal modulation is more imbalance in OSA patients while suffering from apnea event compared to free event