《自然》（20190228出版）一周論文導讀

知識 03-02

翻譯 | 宗華

Nature, 28 FEBRUARY 2019, Vol. 566, No. 7745

《自然》2019年2月28日，第7745期566卷

《自然》（20190228出版）一周論文導讀

打開今日頭條，查看更多圖片

拓撲物理學Topological Physics

A complete catalogue of high-quality topological materials

對高質量拓撲材料的完整分類

作者：M. G. Vergniory, L. Elcoro, Claudia Felser, Nicolas Regnault, et al

鏈接：

https://www.nature.com/articles/s41586-019-0954-4

摘要：

利用最近發展起來的一種叫做拓撲量子化學的形式體系，我們在無機晶體結構資料庫中對「高質量」材料（其原子位置和結構已得到非常精確的測量）進行了高通量搜索，以識別新的拓撲相。

我們開發了代碼來計算26938種化學計量材料的所有對稱性的全部特徵，並找到了3307種拓撲絕緣體、4078種拓撲半金屬，但未發現脆弱相。對於這7385種材料，我們提供了電子帶結構，包括一些電子性質（帶隙和電子數）、對稱性指標和其他拓撲信息。我們的結果表明，自然界中超過27%的物質具有拓撲性質。

Abstract

Using a recently developed formalism called topological quantum chemistry, we perform a high-throughput search of 『high-quality』 materials (for which the atomic positions and structure have been measured very accurately) in the Inorganic Crystal Structure Database in order to identify new topological phases. We develop codes to compute all characters of all symmetries of 26,938 stoichiometric materials, and find 3,307 topological insulators, 4,078 topological semimetals and no fragile phases. For these 7,385 materials we provide the electronic band structure, including some electronic properties (bandgap and number of electrons), symmetry indicators, and other topological information. Our results show that more than 27 per cent of all materials in nature are topological.

Comprehensive search for topological materials using symmetry indicators

利用對稱性指標對拓撲材料進行全面搜索

作者：Feng Tang, Hoi Chun Po, Ashvin Vishwanath & Xiangang Wan

鏈接：

https://www.nature.com/articles/s41586-019-0937-5

摘要：

雖然理論上提出的一些拓撲材料已得到實驗證實，但由於缺乏能使微小費米表面態的干擾最小化的拓撲材料，對拓撲性質的廣泛實驗探索以及在實際器件中的應用受到了限制。在這裡，我們將對稱性指標的方法應用於全部230個可能的空間基團中所有合適的非磁性化合物。

資料庫搜索揭示了數千種候選拓撲材料，其中我們重點介紹了241種拓撲絕緣體和142種拓撲結晶絕緣體。這些絕緣體要麼具有明顯的全帶隙，要麼具有相當大的直接帶隙，並帶有微小的費米口袋。此外，我們列出了在費米能級附近擁有帶交叉點的692種拓撲半金屬材料。

Abstract

Although several theoretically proposed topological materials have been experimentally confirmed, extensive experimental exploration of topological properties, as well as applications in realistic devices, has been restricted by the lack of topological materials in which interference from trivial Fermi surface states is minimized. Here we apply our method of symmetry indicators to all suitable nonmagnetic compounds in all 230 possible space groups. A database search reveals thousands of candidate topological materials, of which we highlight 241 topological insulators and 142 topological crystalline insulators that have either noticeable full bandgaps or a considerable direct gap together with small trivial Fermi pockets. Furthermore, we list 692 topological semimetals that have band crossing points located near the Fermi level.

Catalogue of topological electronic materials

對拓撲電子材料的分類

作者：Tiantian Zhang, Yi Jiang, Zhida Song, He Huang, Yuqing He, Zhong Fang, Hongming Weng & Chen Fang

鏈接：

https://www.nature.com/articles/s41586-019-0944-6

摘要：

硒化鉍、砷化鉭、鉍鈉等拓撲電子材料大多表現出非常規的線性響應，並且在邊界處表現出異常的無間隙態。它們具有基礎和應用價值，在高性能電子和量子計算領域具有應用潛力。

但迄今為止，由於計算拓撲不變性質（或拓撲節點）存在困難，對它們的搜尋受到阻礙，因為這既需要材料方面的經驗，也需要使用先進理論工具的專業知識。在此，我們介紹了一種有效、高效和全自動的演算法，用於診斷大量非磁性材料中的非平凡能帶拓撲。我們的演算法基於最近開發的已佔用能帶的對稱表示和拓撲不變數之間的窮舉映射。

我們瀏覽了晶體資料庫中的39519種可用材料，發現其中多達8056種在拓撲結構上是非平凡的。所有結果都可以在具有互動式用戶界面的資料庫中獲得和搜索。

Abstract

Topological electronic materials such as bismuth selenide, tantalum arsenide and sodium bismuthide show unconventional linear response in the bulk, as well as anomalous gapless states at their boundaries. They are of both fundamental and applied interest, with the potential for use in high-performance electronics and quantum computing. But their detection has so far been hindered by the difficulty of calculating topological invariant properties (or topological nodes), which requires both experience with materials and expertise with advanced theoretical tools. Here we introduce an effective, efficient and fully automated algorithm that diagnoses the nontrivial band topology in a large fraction of nonmagnetic materials. Our algorithm is based on recently developed exhaustive mappings between the symmetry representations of occupied bands and topological invariants. We sweep through a total of 39,519 materials available in a crystal database, and find that as many as 8,056 of them are topologically nontrivial. All results are available and searchable in a database with an interactive user interface.

生物學Biology

The single-cell transcriptional landscape of mammalian organogenesis

哺乳動物器官形成的單細胞轉錄圖譜

作者：Junyue Cao, Malte Spielmann, Xiaojie Qiu, Xingfan Huang

鏈接：

https://www.nature.com/articles/s41586-019-0969-x

摘要：

哺乳動物的器官形成是一個不尋常的過程。在很短的時間內，三個胚層的細胞轉化成一個包括了大部分主要的內部和外部器官的胚胎。在這裡，我們在單細胞解析度的層面上研究了小鼠器官形成的轉錄動力學。

利用單細胞組合索引，我們在一項實驗中分析了來自61個胚胎的約200萬個細胞的轉錄組，這些胚胎在妊娠9.5~13.5天發育。由此產生的「小鼠器官形成細胞圖譜」（MOCA）提供了這一關鍵時期發育過程的全局視圖。我們使用Monocle 3識別了數百種細胞類型和56條軌跡，其中許多軌跡僅因為細胞覆蓋的深度而被檢測到，並共同定義了數千個相應的標記基因。

Abstract

Mammalian organogenesis is a remarkable process. Within a short timeframe, the cells of the three germ layers transform into an embryo that includes most of the major internal and external organs. Here we investigate the transcriptional dynamics of mouse organogenesis at single-cell resolution. Using single-cell combinatorial indexing, we profiled the transcriptomes of around 2 million cells derived from 61 embryos staged between 9.5 and 13.5 days of gestation, in a single experiment. The resulting 『mouse organogenesis cell atlas』 (MOCA) provides a global view of developmental processes during this critical window. We use Monocle 3 to identify hundreds of cell types and 56 trajectories, many of which are detected only because of the depth of cellular coverage, and collectively define thousands of corresponding marker genes.

A single-cell molecular map of mouse gastrulation and early organogenesis

小鼠原腸胚和早期器官形成的單細胞分子地圖

作者：Blanca Pijuan-Sala, Jonathan A. Griffiths, Carolina Guibentif

鏈接：

https://www.nature.com/articles/s41586-019-0933-9

摘要：

在整個動物王國中，原腸胚形成代表了一次關鍵的發育事件。其間，胚胎多能細胞分化成能產生成年生物體的譜系特異性前體。

在此，我們報告了來自小鼠胚胎的116312個單細胞的轉錄圖譜。這些細胞在受精後6.5~8.5天的9個連續時間點收集。我們構建了從多能性到所有主要胚胎譜系的細胞分化分子地圖，並且探尋了涉及內臟和原始條紋衍生內胚層相結合的複雜事件。

此外，我們利用單細胞分析表明，Tal1??/嵌合體胚胎在早期中胚層多樣化中表現出缺陷，並且因此展示了如何結合時間和轉錄信息闡明基因功能。

Abstract

Across the animal kingdom, gastrulation represents a key developmental event during which embryonic pluripotent cells diversify into lineage-specific precursors that will generate the adult organism. Here we report the transcriptional profiles of 116,312 single cells from mouse embryos collected at nine sequential time points ranging from 6.5 to 8.5 days post-fertilization. We construct a molecular map of cellular differentiation from pluripotency towards all major embryonic lineages, and explore the complex events involved in the convergence of visceral and primitive streak-derived endoderm. Furthermore, we use single-cell profiling to show that Tal1?/? chimeric embryos display defects in early mesoderm diversification, and we thus demonstrate how combining temporal and transcriptional information can illuminate gene function.

健康Health

Altered human oligodendrocyte heterogeneity in multiple sclerosis

多發性硬化症中被改變的人類少突膠質異質性

作者：Sarah J?kel, Eneritz Agirre, Ana Mendanha Falc?o, David van Bruggen, et al

鏈接：

https://www.nature.com/articles/s41586-019-0903-2

摘要：

在這裡，我們對多發性硬化症（MS）患者和未受影響對照組的死後人腦白質區域進行了單核RNA測序。我們確定了控制人類白質的少突膠質亞群，其中一些與小鼠相似，並為這些細胞狀態定義了新的標記。

值得注意的是，一些亞群在MS組織中代表性不足，而其他亞群更為普遍。這些成熟少突膠質細胞亞群內的差異可能表明MS病變中少突膠質細胞的功能狀態不同。

我們在正常白質中也發現了類似的變化，表明多發性硬化症是一種比局部脫髓鞘更廣泛的疾病。我們發現MS中少突膠質細胞異質性的改變，可能對了解該疾病惡化和開發治療方法有重要意義。

Abstract

Here we performed single-nucleus RNA sequencing from white matter areas of post-mortem human brain from patients with multiple sclerosis(MS) and from unaffected controls. We identified subclusters of oligodendroglia in control human white matter, some with similarities to mouse, and defined new markers for these cell states. Notably, some subclusters were underrepresented in MS tissue, whereas others were more prevalent. These differences in mature oligodendrocyte subclusters may indicate different functional states of oligodendrocytes in MS lesions. We found similar changes in normal-appearing white matter, showing that MS is a more diffuse disease than its focal demyelination suggests. Our findings of an altered oligodendroglial heterogeneity in MS may be important for understanding disease progression and developing therapeutic approaches.

Singlet molecular oxygen regulates vascular tone and blood pressure in inflammation

單線態分子氧調控炎症中的血管張力和血壓

作者：Christopher P. Stanley, Ghassan J. Maghzal, Anita Ayer, et al

鏈接：

https://www.nature.com/articles/s41586-019-0947-3

摘要：

單線態分子氧（¹O₂）在光合植物、細菌和真菌中已經有了明確的作用，但在哺乳動物中沒有。我們發現，動脈吲哚胺2,3—加雙氧酶1通過¹O₂的形成調節血壓。

我們觀察到，在過氧化氫存在的情形下，這種酶產生¹O₂，而這與l -色氨酸通過之前未被識別的氧化激活加雙氧酶活性，立體選擇性氧化為三環過氧化氫有關。色氨酸來源的過氧化氫在體內作為信號分子，誘導動脈鬆弛和降低血壓；這依賴於蛋白激酶G1αCys42。

我們的發現證明了¹O₂在哺乳動物中的病理生理作用，即通過形成一種氨基酸來源的過氧化氫，在炎症條件下調節血管張力和血壓。

Abstract

Singlet molecular oxygen (¹O₂) has well-established roles in photosynthetic plants, bacteria and fungi, but not in mammals. Here we show that arterial indoleamine 2,3-dioxygenase 1 regulates blood pressure via formation of¹O₂. We observed that in the presence of hydrogen peroxide, the enzyme generates¹O₂and that this is associated with the stereoselective oxidation of L-tryptophan to a tricyclic hydroperoxide via a previously unrecognized oxidative activation of the dioxygenase activity. The tryptophan-derived hydroperoxide acts in vivo as a signalling molecule, inducing arterial relaxation and decreasing blood pressure; this activity is dependent on Cys42 of protein kinase G1α. Our findings demonstrate a pathophysiological role for¹O₂in mammals through formation of an amino acid-derived hydroperoxide that regulates vascular tone and blood pressure under inflammatory conditions.

《自然》（20190228出版）一周論文導讀