Direct detection of molecular intermediates from first-passage times

All natural phenomena are governed by energy landscapes. However, the direct measurement of this fundamen-tal quantity remains challenging, particularly in complex systems involving intermediate states. Here, we uncover key details of the energy landscapes that underpin a range of experimental systems through quantitative analysis of first-passage time distributions. By combined study of colloidal dynamics in confinement, transport through a biological pore, and the folding kinetics of DNA hairpins, we demonstrate conclusively how a short-time, power-law regime of the first-passage time distribution reflects the number of intermediate states associated with each of these processes, despite their differing length scales, time scales, and interactions. We thereby establish a powerful method for investigating the underlying mechanisms of complex molecular processes

Electric-field Control of Magnetism with Emergent Topological Hall Effect in SrRuO3 through Proton Evolution

Ionic substitution forms an essential pathway to manipulate the carrier density and crystalline symmetry of materials via ion-lattice-electron coupling, leading to a rich spectrum of electronic states in strongly correlated systems. Using the ferromagnetic metal SrRuO3 as a model system, we demonstrate an efficient and reversible control of both carrier density and crystalline symmetry through the ionic liquid gating induced protonation. The insertion of protons electron-dopes SrRuO3, leading to an exotic ferromagnetic to paramagnetic phase transition along with the increase of proton concentration. Intriguingly, we observe an emergent topological Hall effect at the boundary of the phase transition as the consequence of the newly-established Dzyaloshinskii-Moriya interaction owing to the breaking of inversion symmetry in protonated SrRuO3 with the proton compositional film-depth gradient. We envision that electric-field controlled protonation opens a novel strategy to design material functionalities

Impaired thymic iNKT cell differentiation at early precursor stage in murine haploidentical bone marrow transplantation with GvHD

IntroductionEarly recovery of donor-derived invariant natural killer T (iNKT) cells are associated with reduced risk of graft-versus-host disease (GvHD) and overall survival. Patients with severe GvHD, however, had much slower iNKT cell reconstitution relative to conventional T cells.MethodsTo characterize the delay of iNKT cell reconstitution and explore its possible causes, we used a haploidentical bone marrow transplantation (haplo-BMT) mouse model with GvHD. We found the delayed recovery of thymic and peripheral iNKT cell numbers with markedly decreased thymic NKT1 subset in GvHD mice. The defective generation of thymic iNKT precursors with egress capability contributed to the reduced peripheral iNKT cells in GvHD mice. We further identified intermediate NK1.1- NKT1 precursor subpopulations under steady-state conditions and found that the differentiation of these subpopulations was impaired in the thymi of GvHD mice. Detailed characterization of iNKT precursors and thymic microenvironment showed a close association of elevated TCR/co-stimulatory signaling provided by double positive thymocytes and macrophages with defective down-regulation of proliferation, metabolism, and NKT2 signature in iNKT precursor cells. Correspondingly, NKT2 but not NKT1 differentiation was favored in GvHD mice.DiscussionThese data underline the important roles of TCR and co-stimulatory signaling in the differentiation of thymic iNKT subsets under transplantation conditions

Reversible manipulation of the magnetic state in SrRuO3 through electric-field controlled proton evolution

Ionic substitution forms an essential pathway to manipulate the structural phase, carrier density and crystalline symmetry of materials via ion-electron-lattice coupling, leading to a rich spectrum of electronic states in strongly correlated systems. Using the ferromagnetic metal SrRuO3 as a model system, we demonstrate an efficient and reversible control of both structural and electronic phase transformations through the electric-field controlled proton evolution with ionic liquid gating. The insertion of protons results in a large structural expansion and increased carrier density, leading to an exotic ferromagnetic to paramagnetic phase transition. Importantly, we reveal a novel protonated compound of HSrRuO3 with paramagnetic metallic as ground state. We observe a topological Hall effect at the boundary of the phase transition due to the proton concentration gradient across the film-depth. We envision that electric-field controlled protonation opens up a pathway to explore novel electronic states and material functionalities in protonated material systems

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays.

Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.This work is part of the ‘‘SpatioTemporal Omics Consortium’’ (STOC) paper package. A list of STOC members is available at: http://sto-consortium.org. We would like to thank the MOTIC China Group, Rongqin Ke (Huaqiao University, Xiamen, China), Jiazuan Ni (Shenzhen University, Shenzhen, China), Wei Huang (Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China), and Jonathan S. Weissman (Whitehead Institute, Boston, USA) for their help. This work was supported by the grant of Top Ten Foundamental Research Institutes of Shenzhen, the Shenzhen Key Laboratory of Single-Cell Omics (ZDSYS20190902093613831), and the Guangdong Provincial Key Laboratory of Genome Read and Write (2017B030301011); Longqi Liu was supported by the National Natural Science Foundation of China (31900466) and Miguel A. Esteban’s laboratory at the Guangzhou Institutes of Biomedicine and Health by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16030502), National Natural Science Foundation of China (92068106), and the Guangdong Basic and Applied Basic Research Foundation (2021B1515120075).S

Single-molecule thiol-disulfide interchange

Thiol-disulfide interchange occurs widely in cellular processes including redox sensing and homeostasis, protein folding, cell signalling, and the regulation of apoptosis. Nature exploits this chemistry in a highly selective manner, which is challenging to recapitulate in vitro. In this thesis, we report site selective and regioselective thioldisulfide interchange on macromolecular disulfide substrates elongated within a protein nanoreactor, where they react with cysteine thiolates presented at different locations along the length of a β strand. Numerous individual reaction events were detected by promoting the substrate turnover. For each substrate, we defined the most reactive cysteines on the β strand and which sulfur atom in the disulfide was attacked and found that the chemistry can be controlled with atomic precision. We further applied our control over the selectivity of thiol-disulfide interchange to the development of a molecular machine. Intrigued by technological potential, scientists have long attempted to control molecular motion. We monitor the individual 0.7-nm steps of a single molecular hopper as it moves in an electric field along a track in a nanopore controlled by a chemical ratchet based on thiol-disulfide interchange. The hopper demonstrates characteristics desired in a moving molecule: defined start- and end-points, processivity, fuel autonomy, directional motion and external control. The hopper is readily functionalized to carry cargos. For example, DNA can be ratcheted along the track in either direction, a prerequisite for nanopore sequencing.</p

Single-molecule thiol-disulfide interchange

Thiol-disulfide interchange occurs widely in cellular processes including redox sensing and homeostasis, protein folding, cell signalling, and the regulation of apoptosis. Nature exploits this chemistry in a highly selective manner, which is challenging to recapitulate in vitro. In this thesis, we report site selective and regioselective thioldisulfide interchange on macromolecular disulfide substrates elongated within a protein nanoreactor, where they react with cysteine thiolates presented at different locations along the length of a β strand. Numerous individual reaction events were detected by promoting the substrate turnover. For each substrate, we defined the most reactive cysteines on the β strand and which sulfur atom in the disulfide was attacked and found that the chemistry can be controlled with atomic precision. We further applied our control over the selectivity of thiol-disulfide interchange to the development of a molecular machine. Intrigued by technological potential, scientists have long attempted to control molecular motion. We monitor the individual 0.7-nm steps of a single molecular hopper as it moves in an electric field along a track in a nanopore controlled by a chemical ratchet based on thiol-disulfide interchange. The hopper demonstrates characteristics desired in a moving molecule: defined start- and end-points, processivity, fuel autonomy, directional motion and external control. The hopper is readily functionalized to carry cargos. For example, DNA can be ratcheted along the track in either direction, a prerequisite for nanopore sequencing.</p

Expression, purification, crystallization and preliminary crystallographic study of the carboxyl-terminal domain of the human voltage-gated proton channel Hv1

Here, the C-terminal domain of the human voltage-gated proton channel Hv1 (C-Hv1) was overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method

Integrated Multi-Omics Perspective to Strengthen the Understanding of Salt Tolerance in Rice

Salt stress is one of the major constraints to rice cultivation worldwide. Thus, the development of salt-tolerant rice cultivars becomes a hotspot of current rice breeding. Achieving this goal depends in part on understanding how rice responds to salt stress and uncovering the molecular mechanism underlying this trait. Over the past decade, great efforts have been made to understand the mechanism of salt tolerance in rice through genomics, transcriptomics, proteomics, metabolomics, and epigenetics. However, there are few reviews on this aspect. Therefore, we review the research progress of omics related to salt tolerance in rice and discuss how these advances will promote the innovations of salt-tolerant rice breeding. In the future, we expect that the integration of multi-omics salt tolerance data can accelerate the solution of the response mechanism of rice to salt stress, and lay a molecular foundation for precise breeding of salt tolerance

The Relationship between Branched-Chain Amino Acid Related Metabolomic Signature and Insulin Resistance: A Systematic Review

Recent studies have shown the positive association between increased circulating BCAAs (valine, leucine, and isoleucine) and insulin resistance (IR) in obese or diabetic patients. However, results seem to be controversial in different races, diets, and distinct tissues. Our aims were to evaluate the relationship between BCAA and IR as well as later diabetes risk and explore the phenotypic and genetic factors influencing BCAA level based on available studies. We performed systematic review, searching MEDLINE, EMASE, ClinicalTrials.gov, the Cochrane Library, and Web of Science from inception to March 2016. After selection, 23 studies including 20,091 participants were included. Based on current evidence, we found that BCAA is a useful biomarker for early detection of IR and later diabetic risk. Factors influencing BCAA level can be divided into four parts: race, gender, dietary patterns, and gene variants. These factors might not only contribute to the elevated BCAA level but also show obvious associations with insulin resistance. Genes related to BCAA catabolism might serve as potential targets for the treatment of IR associated metabolic disorders. Moreover, these factors should be controlled properly during study design and data analysis. In the future, more large-scale studies with elaborate design addressing BCAA and IR are required