Nature Communications

Một thành phần quan trọng trong việc diễn giải các nghiên cứu cấp hệ thống là suy diễn các con đường sinh học phong phú và các phức hợp protein có trong các tập dữ liệu OMICs. Việc phân tích thành công yêu cầu tích hợp một bộ dữ liệu sinh học hiện có rộng rãi và áp dụng một quy trình phân tích vững chắc để tạo ra các kết quả có thể diễn giải được. Metascape là một cổng thông tin dựa trên web được thiết kế để cung cấp một nguồn tài nguyên chú thích và phân tích danh sách gen toàn diện cho các nhà sinh học thực nghiệm. Về các tính năng thiết kế, Metascape kết hợp sự phong phú chức năng, phân tích互译, chú thích gen và tìm kiếm thành viên để tận dụng hơn 40 cơ sở kiến thức độc lập trong một cổng tích hợp duy nhất. Ngoài ra, nó còn tạo điều kiện cho việc phân tích so sánh các tập dữ liệu qua nhiều thí nghiệm độc lập và chính xác. Metascape cung cấp trải nghiệm người dùng đơn giản hóa một cách đáng kể thông qua giao diện phân tích nhanh một cú nhấp chuột để tạo ra các đầu ra có thể diễn giải được. Tóm lại, Metascape là một công cụ hiệu quả và tối ưu cho các nhà sinh học thực nghiệm để phân tích và diễn giải một cách toàn diện các nghiên cứu dựa trên OMICs trong kỷ nguyên dữ liệu lớn.

Wave-particle duality is an inherent peculiarity of the quantum world. The double-slit experiment has been frequently used for understanding different aspects of this fundamental concept. The occurrence of interference rests on the lack of which-way information and on the absence of decoherence mechanisms, which could scramble the wave fronts. Here, we report on the observation of two-center interference in the molecular-frame photoelectron momentum distribution upon ionization of the neon dimer by a strong laser field. Postselection of ions, which are measured in coincidence with electrons, allows choosing the symmetry of the residual ion, leading to observation of both, gerade and ungerade, types of interference.

Stimulated cells and cancer cells have widespread shortening of mRNA 3’-untranslated regions (3’UTRs) and switches to shorter mRNA isoforms due to usage of more proximal polyadenylation signals (PASs) in introns and last exons. U1 snRNP (U1), vertebrates’ most abundant non-coding (spliceosomal) small nuclear RNA, silences proximal PASs and its inhibition with antisense morpholino oligonucleotides (U1 AMO) triggers widespread premature transcription termination and mRNA shortening. Here we show that low U1 AMO doses increase cancer cells’ migration and invasion in vitro by up to 500%, whereas U1 over-expression has the opposite effect. In addition to 3’UTR length, numerous transcriptome changes that could contribute to this phenotype are observed, including alternative splicing, and mRNA expression levels of proto-oncogenes and tumor suppressors. These findings reveal an unexpected role for U1 homeostasis (available U1 relative to transcription) in oncogenic and activated cell states, and suggest U1 as a potential target for their modulation.

Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system’s technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system’s ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients.

The ice arches that usually develop at the northern and southern ends of Nares Strait play an important role in modulating the export of Arctic Ocean multi-year sea ice. The Arctic Ocean is evolving towards an ice pack that is younger, thinner, and more mobile and the fate of its multi-year ice is becoming of increasing interest. Here, we use sea ice motion retrievals from Sentinel-1 imagery to report on the recent behavior of these ice arches and the associated ice fluxes. We show that the duration of arch formation has decreased over the past 20 years, while the ice area and volume fluxes along Nares Strait have both increased. These results suggest that a transition is underway towards a state where the formation of these arches will become atypical with a concomitant increase in the export of multi-year ice accelerating the transition towards a younger and thinner Arctic ice pack.

Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop CellChat, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applying CellChat to mouse and human skin datasets shows its ability to extract complex signaling patterns. Our versatile and easy-to-use toolkit CellChat and a web-based Explorer (http://www.cellchat.org/) will help discover novel intercellular communications and build cell-cell communication atlases in diverse tissues.

Since 2002, beta coronaviruses (CoV) have caused three zoonotic outbreaks, SARS-CoV in 2002–2003, MERS-CoV in 2012, and the newly emerged SARS-CoV-2 in late 2019. However, little is currently known about the biology of SARS-CoV-2. Here, using SARS-CoV-2 S protein pseudovirus system, we confirm that human angiotensin converting enzyme 2 (hACE2) is the receptor for SARS-CoV-2, find that SARS-CoV-2 enters 293/hACE2 cells mainly through endocytosis, that PIKfyve, TPC2, and cathepsin L are critical for entry, and that SARS-CoV-2 S protein is less stable than SARS-CoV S. Polyclonal anti-SARS S1 antibodies T62 inhibit entry of SARS-CoV S but not SARS-CoV-2 S pseudovirions. Further studies using recovered SARS and COVID-19 patients’ sera show limited cross-neutralization, suggesting that recovery from one infection might not protect against the other. Our results present potential targets for development of drugs and vaccines for SARS-CoV-2.