The trajectory of carbon emissions and terrestrial carbon sinks at the provincial level in China.

Global greenhouse gas emission, major factor driving climate change, has been increasing since nineteenth century. STIRPAT and CEVSA models were performed to estimate the carbon emission peaks and terrestrial ecosystem carbon sinks at the provincial level in China, respectively. Utilizing the growth characteristics and the peak time criteria for the period 1997-2019, the patterns of energy consumption and CO emissions from 30 Chinese provinces are categorized into four groups: (i) one-stage increase (5 provinces), (ii) two-stage increase (10 provinces), (iii) maximum around 2013 (13 provinces), and (iv) maximum around 2017 (2 provinces).

Exploring the potential of clay catalysts in catalytic pyrolysis of mixed plastic waste for fuel and energy recovery.

Developing low-cost and high-activity catalysts is one of the keys to promoting the catalytic pyrolysis of waste plastics to fuels for plastic recycling. This work studied the effect of clay as the catalyst on mixed plastic pyrolysis for fuel and energy recovery. Four kinds of clay, including nanoclay, montmorillonite, kaolin, and hydrotalcite, were used as catalysts for the pyrolysis of mixed plastic consisted of polyethylene terephthalate, polystyrene, polypropylene, low-density polyethylene, and high-density polyethylene.

Coral-algal endosymbiosis characterized using RNAi and single-cell RNA-seq.

Corals form an endosymbiotic relationship with the dinoflagellate algae Symbiodiniaceae, but ocean warming can trigger algal loss, coral bleaching and death, and the degradation of ecosystems. Mitigation of coral death requires a mechanistic understanding of coral-algal endosymbiosis. Here we report an RNA interference (RNAi) method and its application to study genes involved in early steps of endosymbiosis in the soft coral Xenia sp.

A tubulin-binding protein that preferentially binds to GDP-tubulin and promotes GTP exchange.

α- and β-tubulin form heterodimers, with GTPase activity, that assemble into microtubules. Like other GTPases, the nucleotide-bound state of tubulin heterodimers controls whether the molecules are in a biologically active or inactive state. While α-tubulin in the heterodimer is constitutively bound to GTP, β-tubulin can be bound to either GDP (GDP-tubulin) or GTP (GTP-tubulin).

CscoreTool-M infers 3D sub-compartment probabilities within cell population.

Motivation: Computational inference of genome organization based on Hi-C sequencing has greatly aided the understanding of chromatin and nuclear organization in three dimensions (3D). However, existing computational methods fail to address the cell population heterogeneity. Here we describe a probabilistic-modeling-based method called CscoreTool-M that infers multiple 3D genome sub-compartments from Hi-C data.

Degradation strategies of pesticide residue: From chemicals to synthetic biology.

The past 50 years have witnessed a massive expansion in the demand and application of pesticides. However, pesticides are difficult to be completely degraded without intervention hence the pesticide residue could pose a persistent threat to non-target organisms in many aspects. To aim at the problem of the abuse of pesticide products and excessive pesticide residues in the environment, chemical and biological degradation methods are widely developed but are scaled and insufficient to solve such a pollution.

Nucleoplasmic lamin C rapidly accumulates at sites of nuclear envelope rupture with BAF and cGAS.

In mammalian cell nuclei, the nuclear lamina (NL) underlies the nuclear envelope (NE) to maintain nuclear structure. The nuclear lamins, the major structural components of the NL, are involved in the protection against NE rupture induced by mechanical stress. However, the specific role of the lamins in repair of NE ruptures has not been fully determined.

High quality mapping of chromatin at or near the nuclear lamina from small numbers of cells reveals cell cycle and developmental changes of chromatin at the nuclear periphery.

The chromatin associated with the nuclear lamina (NL) is referred to as lamina-associated domains (LADs). Here, we present an adaptation of the tyramide-signal amplification sequencing (TSA-seq) protocol, which we call chromatin pull down-based TSA-seq (cTSA-seq), that can be used to map chromatin regions at or near the NL from as little as 50 000 cells. The cTSA-seq mapped regions are composed of previously defined LADs and smaller chromatin regions that fall within the Hi-C defined B-compartment containing nuclear peripheral heterochromatin.

Nuclear lamin isoforms differentially contribute to LINC complex-dependent nucleocytoskeletal coupling and whole-cell mechanics.

The ability of a cell to regulate its mechanical properties is central to its function. Emerging evidence suggests that interactions between the cell nucleus and cytoskeleton influence cell mechanics through poorly understood mechanisms. Here we conduct quantitative confocal imaging to show that the loss of A-type lamins tends to increase nuclear and cellular volume while the loss of B-type lamins behaves in the opposite manner.

Phylogenetic convergence of phase separation and mitotic function in the disordered protein BuGZ.

Intrinsically disordered proteins (IDPs) effect biological function despite their sequence-encoded lack of preference for stable three-dimensional structure. Among their many functions, IDPs form membraneless cellular compartments through liquid-liquid phase separation (LLPS), also termed biomolecular condensation. The extent to which LLPS has been evolutionarily selected remains largely unknown, as the complexities of IDP evolution hamper progress.

Computational analyses reveal spatial relationships between nuclear pore complexes and specific lamins.

Nuclear lamin isoforms form fibrous meshworks associated with nuclear pore complexes (NPCs). Using datasets prepared from subpixel and segmentation analyses of 3D-structured illumination microscopy images of WT and lamin isoform knockout mouse embryo fibroblasts, we determined with high precision the spatial association of NPCs with specific lamin isoform fibers. These relationships are retained in the enlarged lamin meshworks of Lmna-/- and Lmnb1-/- fibroblast nuclei.

An APEX2 proximity ligation method for mapping interactions with the nuclear lamina.

The nuclear lamina (NL) is a meshwork found beneath the inner nuclear membrane. The study of the NL is hindered by the insolubility of the meshwork and has driven the development of proximity ligation methods to identify the NL-associated/proximal proteins, RNA, and DNA. To simplify and improve temporal labeling, we fused APEX2 to the NL protein lamin-B1 to map proteins, RNA, and DNA.

Lineage dynamics of the endosymbiotic cell type in the soft coral Xenia.

Many corals harbour symbiotic dinoflagellate algae. The algae live inside coral cells in a specialized membrane compartment known as the symbiosome, which shares the photosynthetically fixed carbon with coral host cells while host cells provide inorganic carbon to the algae for photosynthesis. This endosymbiosis-which is critical for the maintenance of coral reef ecosystems-is increasingly threatened by environmental stressors that lead to coral bleaching (that is, the disruption of endosymbiosis), which in turn leads to coral death and the degradation of marine ecosystems.

Isolation, Molecular Characterization and Antibiotic Susceptibility Pattern of from Aquatic Products in the Southern Fujian Coast, China.

is a major gastroenteritis-causing pathogen in many Asian countries. Antimicrobial resistance in has been recognized as a critical threat to food safety. In this study, we determined the prevalence and incidence of antimicrobial resistance in in the southern Fujian coast, China.

Regulation of zebrafish dorsoventral patterning by phase separation of RNA-binding protein Rbm14.

RNA-binding proteins with intrinsically disordered regions (IDRs) such as Rbm14 can phase separate in vitro. To what extent the phase separation contributes to their physiological functions is however unclear. Here we show that zebrafish Rbm14 regulates embryonic dorsoventral patterning through phase separation.

Protein phase separation in mitosis.

Through phase separation, some proteins form liquid-like condensates or droplets which can flow, fuse, and even deform when pressure is applied. In some cases, the condensates 'mature' to form gel or solid-like structure. Recent studies suggest that the liquid-like condensates form the structural basis for several membrane-less subcellular organelles such as stress granules and other subcellular structures.

aFARP-ChIP-seq, a convenient and reliable method for genome profiling in as few as 100 cells with a capability for multiplexing ChIP-seq.

Much effort has been devoted to understand how chromatin modification regulates development and disease. Despite recent progress, however, it remains difficult to obtain high-quality epigenomic maps using chromatin-immunoprecipitation-coupled deep sequencing (ChIP-seq) in samples with low-cell numbers. Here, we present an Atlantis dsDNase-based technology, aFARP-ChIP-seq, that provides accurate profiling of genome-wide histone modifications in as few as 100 cells.

Cell-type-specific role of lamin-B1 in thymus development and its inflammation-driven reduction in thymus aging.

Cellular architectural proteins often participate in organ development and maintenance. Although functional decay of some of these proteins during aging is known, the cell-type-specific developmental role and the cause and consequence of their subsequent decay remain to be established especially in mammals. By studying lamins, the nuclear structural proteins, we demonstrate that lamin-B1 functions specifically in the thymic epithelial cells (TECs) for proper thymus organogenesis.

Role of lamins in 3D genome organization and global gene expression.

Genome-wide mapping of lamin-B1-genome interactions has shown that gene-poor and transcriptionally inactive genomic regions are associated with the nuclear lamina. Numerous studies have suggested that lamins, the major structural components of the nuclear lamina, play a role in global chromatin organization and gene expression. How lamins could influence the 3D genome organization and transcription from the nuclear periphery has, however, remained unclear.

A Lamin-Binding Ligand Inhibits Homologous Recombination Repair of DNA Double-Strand Breaks.

Nuclear lamins are type V intermediate filament proteins. Lamins, including LA, LB1, LB2, and LC, are the major protein components forming the nuclear lamina to support the mechanical stability of the mammalian cell nucleus. Increasing evidence has shown that LA participates in homologous recombination (HR) repair of DNA double-strand breaks (DSBs) .

Lamins Organize the Global Three-Dimensional Genome from the Nuclear Periphery.

Lamins are structural components of the nuclear lamina (NL) that regulate genome organization and gene expression, but the mechanism remains unclear. Using Hi-C, we show that lamins maintain proper interactions among the topologically associated chromatin domains (TADs) but not their overall architecture. Combining Hi-C with fluorescence in situ hybridization (FISH) and analyses of lamina-associated domains (LADs), we reveal that lamin loss causes expansion or detachment of specific LADs in mouse ESCs.

CscoreTool: fast Hi-C compartment analysis at high resolution.

Summary: The genome-wide chromosome conformation capture (Hi-C) has revealed that the eukaryotic genome can be partitioned into A and B compartments that have distinctive chromatin and transcription features. Current Principle Component Analyses (PCA)-based method for the A/B compartment prediction based on Hi-C data requires substantial CPU time and memory. We report the development of a method, CscoreTool, which enables fast and memory-efficient determination of A/B compartments at high resolution even in datasets with low sequencing depth.

Aurora A activation in mitosis promoted by BuGZ.

Protein phase separation or coacervation has emerged as a potential mechanism to regulate biological functions. We have shown that coacervation of a mostly unstructured protein, BuGZ, promotes assembly of spindle and its matrix. BuGZ in the spindle matrix binds and concentrates tubulin to promote microtubule (MT) assembly.

Lamin B1 is required for mature neuron-specific gene expression during olfactory sensory neuron differentiation.

B-type lamins are major constituents of the nuclear lamina in all metazoan cells, yet have specific roles in the development of certain cell types. Although they are speculated to regulate gene expression in developmental contexts, a direct link between B-type lamins and developmental gene expression in an in vivo system is currently lacking. Here, we identify lamin B1 as a key regulator of gene expression required for the formation of functional olfactory sensory neurons.

VisMatchmaker: Cooperation of the User and the Computer in Centralized Matching Adjustment.

Centralized matching is a ubiquitous resource allocation problem. In a centralized matching problem, each agent has a preference list ranking the other agents and a central planner is responsible for matching the agents manually or with an algorithm. While algorithms can find a matching which optimizes some performance metrics, they are used as a black box and preclude the central planner from applying his domain knowledge to find a matching which aligns better with the user tasks.