To examine the role of T cell receptor (TCR) in gammadelta T cells in adaptive immunity, a macaque model was used to follow Vgamma2Vdelta2+ T cell responses to mycobacterial infections. These phosphoantigen-specific gammadelta T cells displayed major expansion during Mycobacterium bovis Bacille Calmette-Guérin (BCG) infection and a clear memory-type response after BCG reinfection. Primary and recall expansions of Vgamma2Vdelta2+ T cells were also seen during Mycobacterium tuberculosis infection of naive and BCG-vaccinated macaques, respectively. This capacity to rapidly expand coincided with a clearance of BCG bacteremia and immunity to fatal tuberculosis in BCG-vaccinated macaques. Thus, Vgamma2Vdelta2+ T cells may contribute to adaptive immunity to mycobacterial infections.

Transformers-based models, such as BERT, have been one of the most successful deep learning models for NLP. Unfortunately, one of their core limitations is the quadratic dependency (mainly in terms of memory) on the sequence length due to their full attention mechanism.To remedy this, we propose, BigBird, a sparse attention mechanism that reduces this quadratic dependency to linear. We show that BigBird is a universal approximator of sequence functions and is Turing complete, thereby preserving these properties of the quadratic, full attention model. Along the way, our theoretical analysis reveals some of the benefits of having O(1) global tokens (such as CLS), that attend to the entire sequence as part of the sparse attention mechanism. The proposed sparse attention can handle sequences of length up to 8x of what was previously possible using similar hardware. As a consequence of the capability to handle longer context, BigBird drastically improves performance on various NLP tasks such as question answering and summarization. We also propose novel applications to genomics data.

N 6 -methyladenosine (m 6 A) is a commonly present modification of mammalian mRNAs and plays key roles in various cellular processes. m 6 A modifiers catalyze this reversible modification. However, the underlying mechanisms by which these m 6 A modifiers are regulated remain elusive. Here we show that expression of m 6 A demethylase ALKBH5 is regulated by chromatin state alteration during leukemogenesis of human acute myeloid leukemia (AML), and ALKBH5 is required for maintaining leukemia stem cell (LSC) function but is dispensable for normal hematopoiesis. Mechanistically, KDM4C regulates ALKBH5 expression via increasing chromatin accessibility of ALKBH5 locus, by reducing H3K9me3 levels and promoting recruitment of MYB and Pol II. Moreover, ALKBH5 affects mRNA stability of receptor tyrosine kinase AXL in an m 6 Adependent way. Thus, our findings link chromatin state dynamics with expression regulation of m 6 A modifiers and uncover a selective and critical role of ALKBH5 in AML that might act as a therapeutic target of specific targeting LSCs.

Transformer models have advanced the state of the art in many Natural Language Processing (NLP) tasks.In this paper, we present a new Transformer architecture, Extended Transformer Construction (ETC), that addresses two key challenges of standard Transformer architectures, namely scaling input length and encoding structured inputs. To scale attention to longer inputs, we introduce a novel global-local attention mechanism between global tokens and regular input tokens. We also show that combining global-local attention with relative position encodings and a Contrastive Predictive Coding (CPC) pretraining objective allows ETC to encode structured inputs. We achieve state-of-the-art results on four natural language datasets requiring long and/or structured inputs.

The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle cryo-electron microscopy (cryo-EM) structure of the CR from Xenopus laevis NPC at average resolutions of 5.5-7.9 Å, with local resolutions reaching 4.5 Å. Improved resolutions allow identification and placement of secondary structural elements in the majority of the CR components. The two Y complexes in each CR subunit interact with each other and associate with those from flanking subunits, forming a circular scaffold. Within each CR subunit, the Nup358containing region wraps around the stems of both Y complexes, likely stabilizing the scaffold. Nup205 connects the short arms of the two Y complexes and associates with the stem of a neighboring Y complex. The Nup214-containing region uses an extended coiled-coil to link Nup85 of the two Y complexes and protrudes into the axial pore of the NPC. These previously uncharacterized structural features reveal insights into NPC assembly.

SignificanceLysyl oxidases (LOXs) catalyze oxidative deamination of peptidyl lysines on collagen and elastin, generating a highly reactive aldehyde group to initiate intermolecular cross-linking. In humans, this reaction plays fundamental roles in the formation and repair of extracellular matrix fiber networks and the development of connective tissues. Moreover, a relationship between LOX proteins and tissue fibrosis and cancer has been established. Since the identification of prototypic LOX, the atomic structure of LOX protein has remained to be elucidated. Here, we present the high-resolution structure of human lysyl oxidase-like 2 protein. The zinc-bound precursor-state structure provides an important framework for understanding the structure–function relationship of the LOX family and for drug discovery that aims to block LTQ generation of LOX proteins.

A unique direct printing method has been developed to additively pattern silver nanowires (AgNWs) with length of up to ~ 40 µm. Uniform and well-defined AgNW features have been printed on various substrates by optimizing a series of parameters including ink composition, printing speed, nozzle size, substrate temperature and hydrophobicity of the substrate surface. The capability of directly printing such long AgNWs is essential for

RNA-binding proteins (RBPs) are critical regulators of transcription and translation that are often dysregulated in cancer. Although RBPs are increasingly appreciated as being important for normal hematopoiesis and for hematological malignancies as oncogenes or tumor suppressors, essential RBPs for leukemia maintenance and survival remain elusive. Here we show that YBX1 is specifically required for maintaining myeloid leukemia cell survival in an m6A-dependent manner. We found that expression of YBX1 is significantly upregulated in myeloid leukemia cells, and deletion of YBX1 dramatically induces apoptosis, promotes differentiation, coupled with reduced proliferation and impaired leukemic capacity of primary human and mouse acute myeloid leukemia (AML) cells in vitro and in vivo. Loss of YBX1 does not obviously affect normal hematopoiesis. Mechanistically, YBX1 interacts with IGF2BPs and stabilizes m6A-tagged RNA. Moreover, YBX1 deficiency dysregulates the expression of apoptosis-related genes, and promotes mRNA decay of MYC and BCL2 in an m6A-dependent manner, which contributes to the defective survival due to YBX1 deletion. Thus, our findings uncover a selective and critical role of YBX1 in maintaining myeloid leukemia survival that might provide a rationale for the therapeutic targeting of YBX1 in myeloid leukemia.