Weak Topological Insulators in PbTe/SnTe Superlattices

It is desirable to realize topological phases in artificial structures by engineering electronic band structures. In this paper, we investigate $(PbTe)_m(SnTe)_{2n-m}$ superlattices along [001] direction and find a robust weak topological insulator phase for a large variety of layer numbers m and 2n-m. We confirm this topologically non-trivial phase by calculating Z2 topological invariants and topological surface states based on the first-principles calculations. We show that the folding of Brillouin zone due to the superlattice structure plays an essential role in inducing topologically non-trivial phases in this system. This mechanism can be generalized to other systems in which band inversion occurs at multiple momenta, and gives us a brand-new way to engineer topological materials in artificial structures.Comment: 6 pages, 4 figures, another author adde

Towards a Topological Classification of Nonadiabaticity in Chemical Reactions

The application of topology, a branch of mathematics, to the study of electronic states in crystalline materials has had a revolutionary impact on the field of condensed matter physics. For example, the development of topological band theory has delivered new approaches and tools to characterize the electronic structure of materials, resulting in the discovery of new phases of matter with exotic properties. In the framework of topological band theory, the crossings between energy levels of electrons are characterized by topological invariants, which predict the presence of topological boundary states. Given the frequency of energy level crossings on the potential energy surface in molecules, the applicability of these concepts to molecular systems could be of great interest for our understanding of reaction dynamics. However, challenges arise due to differing quantum mechanical descriptions of solids and molecules. Out work aims to bridge the gap between topological band theory and molecular chemistry. We propose that the Euler Class, a topological invariant, can be used to categorize and analyse the distribution of nonadiabatic couplings on the potential energy surface. To exemplify this connection, we introduce a model system with two distinct regimes that are characterized by different values of the Euler Class, yet identical potential energy surfaces. Contrary to expectations set by the Born-Oppenheimer approximation, we propose that these two regimes don't exhibit identical dynamics, due to a qualitatively distinct distribution of nonadiabatic couplings

Advances in the application of co-culture strategies in organoids

As a good in vitro research model, organoids are more and more widely used in the biomedical field. By developing self-assembled 3D structures using various tissue culture techniques, organoids can rebuild the high complexity of cells in the inherent structure of the organ, and are therefore unanimously used to study mechanisms regulating body development and disease, high-throughput drug screening, and personalized treatment and so on. To better recapitulate cell-to-cell interactions within the microenvironment, co-culture strategies have been extended to more cell types, and their rapid development offers broader prospects for organoids and paves the way for the treatment of human diseases and regenerative medicine. This review discussed the role of co-culture strategies in organoid generation, and focused on the application of various cellular components and microorganisms in organoid construction, thereby providing reference and help for scholars to construct and develop organoids with a higher degree of in vivo simulation

End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data

RNA-seq protocols that focus on transcript termini are well suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this, we created the End Sequence Analysis Toolkit (ESAT). As a test, we first compared end-sequencing and bulk RNA-seq using RNA from dendritic cells stimulated with lipopolysaccharide (LPS). As predicted by the telescripting model for transcriptional bursts, ESAT detected an LPS-stimulated shift to shorter 3\u27-isoforms that was not evident by conventional computational methods. Then, droplet-based microfluidics was used to generate 1000 cDNA libraries, each from an individual pancreatic islet cell. ESAT identified nine distinct cell types, three distinct beta-cell types, and a complex interplay between hormone secretion and vascularization. ESAT, then, offers a much-needed and generally applicable computational pipeline for either bulk or single-cell RNA end-sequencing

Human Immune System Development and Rejection of Human Islet Allografts in Spontaneously Diabetic NOD-Rag1null IL2rγnull Ins2Akita Mice

OBJECTIVE: To create an immunodeficient mouse model that spontaneously develops hyperglycemia to serve as a diabetic host for human islets and stem cell-derived beta-cells in the absence or presence of a functional human immune system. RESEARCH DESIGN AND METHODS: We backcrossed the Ins2(Akita) mutation onto the NOD-Rag1(null) IL2rgamma(null) strain and determined 1) the spontaneous development of hyperglycemia, 2) the ability of human islets, mouse islets, and dissociated mouse islet cells to restore euglycemia, 3) the generation of a human immune system following engraftment of human hematopoietic stem cells, and 4) the ability of the humanized mice to reject human islet allografts. RESULTS: We confirmed the defects in innate and adaptive immunity and the spontaneous development of hyperglycemia conferred by the IL2rgamma(null), Rag1(null), and Ins2(Akita) genes in NOD-Rag1(null) IL2rgamma(null) Ins2(Akita) (NRG-Akita) mice. Mouse and human islets restored NRG-Akita mice to normoglycemia. Insulin-positive cells in dissociated mouse islets, required to restore euglycemia in chemically diabetic NOD-scid IL2rgamma(null) and spontaneously diabetic NRG-Akita mice, were quantified following transplantation via the intrapancreatic and subrenal routes. Engraftment of human hematopoietic stem cells in newborn NRG-Akita and NRG mice resulted in equivalent human immune system development in a normoglycemic or chronically hyperglycemic environment, with \u3e50% of engrafted NRG-Akita mice capable of rejecting human islet allografts. CONCLUSIONS: NRG-Akita mice provide a model system for validation of the function of human islets and human adult stem cell, embryonic stem cell, or induced pluripotent stem cell-derived beta-cells in the absence or presence of an alloreactive human immune system

Tracing evolutionary footprints to identify novel gene functional linkages.

Systematic determination of gene function is an essential step in fully understanding the precise contribution of each gene for the proper execution of molecular functions in the cell. Gene functional linkage is defined as to describe the relationship of a group of genes with similar functions. With thousands of genomes sequenced, there arises a great opportunity to utilize gene evolutionary information to identify gene functional linkages. To this end, we established a computational method (called TRACE) to trace gene footprints through a gene functional network constructed from 341 prokaryotic genomes. TRACE performance was validated and successfully tested to predict enzyme functions as well as components of pathway. A so far undescribed chromosome partitioning-like protein ro03654 of an oleaginous bacteria Rhodococcus sp. RHA1 (RHA1) was predicted and verified experimentally with its deletion mutant showing growth inhibition compared to RHA1 wild type. In addition, four proteins were predicted to act as prokaryotic SNARE-like proteins, and two of them were shown to be localized at the plasma membrane. Thus, we believe that TRACE is an effective new method to infer prokaryotic gene functional linkages by tracing evolutionary events

The proteomics of lipid droplets: structure, dynamics, and functions of the organelle conserved from bacteria to humans.

Lipid droplets are cellular organelles that consists of a neutral lipid core covered by a monolayer of phospholipids and many proteins. They are thought to function in the storage, transport, and metabolism of lipids, in signaling, and as a specialized microenvironment for metabolism in most types of cells from prokaryotic to eukaryotic organisms. Lipid droplets have received a lot of attention in the last 10 years as they are linked to the progression of many metabolic diseases and hold great potential for the development of neutral lipid-derived products, such as biofuels, food supplements, hormones, and medicines. Proteomic analysis of lipid droplets has yielded a comprehensive catalog of lipid droplet proteins, shedding light on the function of this organelle and providing evidence that its function is conserved from bacteria to man. This review summarizes many of the proteomic studies on lipid droplets from a wide range of organisms, providing an evolutionary perspective on this organelle

Emergent Spin Phenomena in Air-Stable, Atomically Thin Lead

A stable platform to synthesize ultrathin heavy metals, with a strong interfacial Rashba effect, could lead to high efficiency charge-to-spin conversion for next-generation spintronics. Here we report wafer-scale synthesis of air-stable, epitaxially registered monolayer Pb on SiC (0001) via confinement heteroepitaxy (CHet). The highly asymmetric interfacial bonding in this heavy metal system lends to strong Rashba spin-orbit coupling near the Fermi level. Additionally, the system's air stability enables ex-situ spin torque ferromagnetic resonance (ST-FMR) measurements that demonstrate charge-to-spin conversion in CHet-based 2D-Pb/ferromagnet heterostructures and a 1.5x increase in the effective field ratio compared to control samples.Comment: 17 pages, 4 figures. Supporting Information included (20 pages, 9 figures, 1 table

CHOP Mediates Endoplasmic Reticulum Stress-Induced Apoptosis in Gimap5-Deficient T Cells

Gimap5 (GTPase of the immunity-associated protein 5) has been linked to the regulation of T cell survival, and polymorphisms in the human GIMAP5 gene associate with autoimmune disorders. The BioBreeding diabetes-prone (BBDP) rat has a mutation in the Gimap5 gene that leads to spontaneous apoptosis of peripheral T cells by an unknown mechanism. Because Gimap5 localizes to the endoplasmic reticulum (ER), we hypothesized that absence of functional Gimap5 protein initiates T cell death through disruptions in ER homeostasis. We observed increases in ER stress-associated chaperones in T cells but not thymocytes or B cells from Gimap5−/− BBDP rats. We then discovered that ER stress-induced apoptotic signaling through C/EBP-homologous protein (CHOP) occurs in Gimap5−/− T cells. Knockdown of CHOP by siRNA protected Gimap5−/− T cells from ER stress-induced apoptosis, thereby identifying a role for this cellular pathway in the T cell lymphopenia of the BBDP rat. These findings indicate a direct relationship between Gimap5 and the maintenance of ER homeostasis in the survival of T cells