Composite Fermi Liquid at Zero Magnetic Field in Twisted MoTe_{2}.

The pursuit of exotic phases of matter outside of the extreme conditions of a quantizing magnetic field is a long-standing quest of solid state physics. Recent experiments have observed spontaneous valley polarization and fractional Chern insulators in zero magnetic field in twisted bilayers of MoTe_{2}, at partial filling of the topological valence band (ν=-2/3 and -3/5). We study the topological valence band at half filling, using exact diagonalization and density matrix renormalization group calculations. We discover a composite Fermi liquid (CFL) phase even at zero magnetic field that covers a large portion of the phase diagram near twist angle ∼3.6°. The CFL is a non-Fermi liquid phase with metallic behavior despite the absence of Landau quasiparticles. We discuss experimental implications including the competition between the CFL and a Fermi liquid, which can be tuned with a displacement field. The topological valence band has excellent quantum geometry over a wide range of twist angles and a small bandwidth that is, remarkably, reduced by interactions. These key properties stabilize the exotic zero field quantum Hall phases. Finally, we present an optical signature involving "extinguished" optical responses that detects Chern bands with ideal quantum geometry.

Untwisting Moiré Physics: Almost Ideal Bands and Fractional Chern Insulators in Periodically Strained Monolayer Graphene.

Moiré systems have emerged in recent years as a rich platform to study strong correlations. Here, we will propose a simple, experimentally feasible setup based on periodically strained graphene that reproduces several key aspects of twisted moiré heterostructures-but without introducing a twist. We consider a monolayer graphene sheet subject to a C_{2}-breaking periodic strain-induced pseudomagnetic field with period L_{M}≫a, along with a scalar potential of the same period. This system has almost ideal flat bands with valley-resolved Chern number ±1, where the deviation from ideal band geometry is analytically controlled and exponentially small in the dimensionless ratio (L_{M}/l_{B})^{2}, where l_{B} is the magnetic length corresponding to the maximum value of the pseudomagnetic field. Moreover, the scalar potential can tune the bandwidth far below the Coulomb scale, making this a very promising platform for strongly interacting topological phases. Using a combination of strong-coupling theory and self-consistent Hartree-Fock, we find quantum anomalous Hall states at integer fillings. At fractional filling, exact diagonaliztion reveals a fractional Chern insulator at parameters in the experimentally feasible range. Overall, we find that this system has larger interaction-induced gaps, smaller quasiparticle dispersion, and enhanced tunability compared to twisted graphene systems, even in their ideal limit.

MiYA, an efficient machine-learning workflow in conjunction with the YeastFab assembly strategy for combinatorial optimization of heterologous metabolic pathways in Saccharomyces cerevisiae.

Facing boosting ability to construct combinatorial metabolic pathways, how to search the metabolic sweet spot has become the rate-limiting step. We here reported an efficient Machine-learning workflow in conjunction with YeastFab Assembly strategy (MiYA) for combinatorial optimizing the large biosynthetic genotypic space of heterologous metabolic pathways in Saccharomyces cerevisiae. Using ß-carotene biosynthetic pathway as example, we first demonstrated that MiYA has the power to search only a small fraction (2-5%) of combinatorial space to precisely tune the expression level of each gene with a machine-learning algorithm of an artificial neural network (ANN) ensemble to avoid over-fitting problem when dealing with a small number of training samples. We then applied MiYA to improve the biosynthesis of violacein. Feed with initial data from a colorimetric plate-based, pre-screened pool of 24 strains producing violacein, MiYA successfully predicted, and verified experimentally, the existence of a strain that showed a 2.42-fold titer improvement in violacein production among 3125 possible designs. Furthermore, MiYA was able to largely avoid the branch pathway of violacein biosynthesis that makes deoxyviolacein, and produces very pure violacein. Together, MiYA combines the advantages of standardized building blocks and machine learning to accelerate the Design-Build-Test-Learn (DBTL) cycle for combinatorial optimization of metabolic pathways, which could significantly accelerate the development of microbial cell factories.

2-Hydroxyisobutyrylation on histone H4K8 is regulated by glucose homeostasis in Saccharomyces cerevisiae.

New types of modifications of histones keep emerging. Recently, histone H4K8 2-hydroxyisobutyrylation (H4K8hib) was identified as an evolutionarily conserved modification. However, how this modification is regulated within a cell is still elusive, and the enzymes adding and removing 2-hydroxyisobutyrylation have not been found. Here, we report that the amount of H4K8hib fluctuates in response to the availability of carbon source in Saccharomyces cerevisiae and that low-glucose conditions lead to diminished modification. The removal of the 2-hydroxyisobutyryl group from H4K8 is mediated by the histone lysine deacetylase Rpd3p and Hos3p in vivo. In addition, eliminating modifications at this site by alanine substitution alters transcription in carbon transport/metabolism genes and results in a reduced chronological life span (CLS). Furthermore, consistent with the glucose-responsive H4K8hib regulation, proteomic analysis revealed that a large set of proteins involved in glycolysis/gluconeogenesis are modified by lysine 2-hydroxyisobutyrylation. Cumulatively, these results established a functional and regulatory network among Khib, glucose metabolism, and CLS.

Engineering the ribosomal DNA in a megabase synthetic chromosome.

We designed and synthesized a 976,067-base pair linear chromosome, synXII, based on native chromosome XII in Saccharomyces cerevisiae SynXII was assembled using a two-step method, specified by successive megachunk integration and meiotic recombination-mediated assembly, producing a functional chromosome in S. cerevisiae. Minor growth defect "bugs" detected in synXII, caused by deletion of tRNA genes, were rescued by introducing an ectopic copy of a single tRNA gene. The ribosomal gene cluster (rDNA) on synXII was left intact during the assembly process and subsequently replaced by a modified rDNA unit used to regenerate rDNA at three distinct chromosomal locations. The signature sequences within rDNA, which can be used to determine species identity, were swapped to generate a Saccharomyces synXII strain that would be identified as Saccharomyces bayanus by standard DNA barcoding procedures.

YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae.

It is a routine task in metabolic engineering to introduce multicomponent pathways into a heterologous host for production of metabolites. However, this process sometimes may take weeks to months due to the lack of standardized genetic tools. Here, we present a method for the design and construction of biological parts based on the native genes and regulatory elements in Saccharomyces cerevisiae. We have developed highly efficient protocols (termed YeastFab Assembly) to synthesize these genetic elements as standardized biological parts, which can be used to assemble transcriptional units in a single-tube reaction. In addition, standardized characterization assays are developed using reporter constructs to calibrate the function of promoters. Furthermore, the assembled transcription units can be either assayed individually or applied to construct multi-gene metabolic pathways, which targets a genomic locus or a receiving plasmid effectively, through a simple in vitro reaction. Finally, using ß-carotene biosynthesis pathway as an example, we demonstrate that our method allows us not only to construct and test a metabolic pathway in several days, but also to optimize the production through combinatorial assembly of a pathway using hundreds of regulatory biological parts.

Biosynthesis of nucleotide sugars by a promiscuous UDP-sugar pyrophosphorylase from Arabidopsis thaliana (AtUSP).

Nucleotide sugars are activated forms of monosaccharides and key intermediates of carbohydrate metabolism in all organisms. The availability of structurally diverse nucleotide sugars is particularly important for the characterization of glycosyltransferases. Given that limited methods are available for preparation of nucleotide sugars, especially their useful non-natural derivatives, we introduced herein an efficient one-step three-enzyme catalytic system for the synthesis of nucleotide sugars from monosaccharides. In this study, a promiscuous UDP-sugar pyrophosphorylase (USP) from Arabidopsis thaliana (AtUSP) was used with a galactokinase from Streptococcus pneumoniae TIGR4 (SpGalK) and an inorganic pyrophosphatase (PPase) to effectively synthesize four UDP-sugars. AtUSP has better tolerance for C4-derivatives of Gal-1-P compared to UDP-glucose pyrophosphorylase from S. pneumoniae TIGR4 (SpGalU). Besides, the nucleotide substrate specificity and kinetic parameters of AtUSP were systematically studied. AtUSP exhibited considerable activity toward UTP, dUTP and dTTP, the yield of which was 87%, 85% and 84%, respectively. These results provide abundant information for better understanding of the relationship between substrate specificity and structural features of AtUSP.