Site-specific incorporation of citrulline into proteins in mammalian cells

Citrullination is a post-translational modification (PTM) of arginine that is crucial for several physiological processes, including gene regulation and neutrophil extracellular trap formation. Despite recent advances, studies of protein citrullination remain challenging due to the difficulty of accessing proteins homogeneously citrullinated at a specific site. Herein, we report a technology that enables the site-specific incorporation of citrulline (Cit) into proteins in mammalian cells. This approach exploits an engineered E. coli-derived leucyl tRNA synthetase-tRNA pair that incorporates a photocaged-citrulline (SM60) into proteins in response to a nonsense codon. Subsequently, SM60 is readily converted to Cit with light in vitro and in living cells. To demonstrate the utility of the method, we biochemically characterize the effect of incorporating Cit at two known autocitrullination sites in Protein Arginine Deiminase 4 (PAD4, R372 and R374) and show that the R372Cit and R374Cit mutants are 181- and 9-fold less active than the wild-type enzyme. This technology possesses the potential to decipher the biology of citrullination

Attack is Good Augmentation: Towards Skeleton-Contrastive Representation Learning

Contrastive learning, relying on effective positive and negative sample pairs, is beneficial to learn informative skeleton representations in unsupervised skeleton-based action recognition. To achieve these positive and negative pairs, existing weak/strong data augmentation methods have to randomly change the appearance of skeletons for indirectly pursuing semantic perturbations. However, such approaches have two limitations: 1) solely perturbing appearance cannot well capture the intrinsic semantic information of skeletons, and 2) randomly perturbation may change the original positive/negative pairs to soft positive/negative ones. To address the above dilemma, we start the first attempt to explore an attack-based augmentation scheme that additionally brings in direct semantic perturbation, for constructing hard positive pairs and further assisting in constructing hard negative pairs. In particular, we propose a novel Attack-Augmentation Mixing-Contrastive learning (A$^2$MC) to contrast hard positive features and hard negative features for learning more robust skeleton representations. In A$^2$MC, Attack-Augmentation (Att-Aug) is designed to collaboratively perform targeted and untargeted perturbations of skeletons via attack and augmentation respectively, for generating high-quality hard positive features. Meanwhile, Positive-Negative Mixer (PNM) is presented to mix hard positive features and negative features for generating hard negative features, which are adopted for updating the mixed memory banks. Extensive experiments on three public datasets demonstrate that A$^2$MC is competitive with the state-of-the-art methods

Predictive value of CpG island methylator phenotype for tumor recurrence in hepatitis B virus-associated hepatocellular carcinoma following liver transplantation

<p>Abstract</p> <p>Background</p> <p>CpG island methylator phenotype (CIMP), in which multiple genes concordantly methylated, has been demonstrated to be associated with progression, recurrence, as well as overall survival in some types of cancer.</p> <p>Methods</p> <p>We examined the promoter methylation status of seven genes including <it>P16, CDH1, GSTP1, DAPK, XAF1, SOCS1 </it>and <it>SYK </it>in 65 cases of HCC treated with LT by methylation-specific PCR. CIMP+ was defined as having three or more genes that are concordantly methylated. The relationship between CIMP status and clinicopathological parameters, as well as tumor recurrence was further analyzed.</p> <p>Results</p> <p>CIMP+ was more frequent in HCC with AFP > 400 ng/ml than those with AFP ≤ 400 ng/ml (<it>P </it>= 0.017). In addition, patients with CIMP+ were prone to have multiple tumor numbers than those with CIMP- (<it>P </it>= 0.007). Patients with CIMP+ tumors had significantly worse recurrence-free survival (RFS) than patients with CIMP-tumors by Kaplan-Meier estimates (<it>P </it>= 0.004). Multivariate analysis also revealed that CIMP status might be a novel independent prognostic factor of RFS for HCC patients treated with LT (HR: 3.581; 95% CI: 1.473-8.710, <it>P </it>= 0.005).</p> <p>Conclusion</p> <p>Our results suggested that CIMP could serve as a new prognostic biomarker to predict the risk of tumor recurrence in HCC after transplantation.</p

Double Opposing-Rhomboid Flaps for Closure of a Circular Facial Defect in a Special Position

Various techniques are used to repair circular defects in special positions on the face. Simple closure will yield unsatisfactory results because of skin tension. As an ideal method of reconstruction, various flaps are used to provide a versatile and safe alternative. The authors applied double opposing-rhomboid flaps, which provided for closure of a circular skin defect without alteration to the original shapes of the vital structures and resulted in an imperceptible scar. With careful designing, 21 patients with circular defects caused by skin tumor excisions to special facial positions have attained effective functional and aesthetic results using this method since 2004

Neoproterozoic to Paleozoic long-lived accretionary orogeny in the northern Tarim Craton

The Tarim Craton, located in the center of Asia, was involved in the assembly and breakup of the Rodinia supercontinent during the Neoproterozoic and the subduction-accretion of the Central Asian Orogenic Belt (CAOB) during the Paleozoic. However, its tectonic evolution during these events is controversial, and a link between the Neoproterozoic and Paleozoic tectonic processes is missing. Here we present zircon U-Pb ages, Hf isotopes, and whole-rock geochemical data for the extensive granitoids in the western Kuruktag area, northeastern Tarim Craton. Three distinct periods of granitoid magmatism are evident: circa 830–820 Ma, 660–630 Ma, and 420–400 Ma. The magma sources, melting conditions (pressure, temperature, and water availability), and tectonic settings of various granitoids from each period are determined. Based on our results and the geological, geochronological, geochemical, and isotopic data from adjacent areas, a long-lived accretionary orogenic model is proposed. This model involves an early phase (circa 950–780 Ma) of southward advancing accretion from the Tianshan to northern Tarim and a late phase (circa 780–600 Ma) of northward retreating accretion, followed by back-arc opening and subsequent bidirectional subduction (circa 460–400 Ma) of a composite back-arc basin (i.e., the South Tianshan Ocean). Our model highlights a long-lived accretionary history of the southwestern CAOB, which may have initiated as part of the circum-Rodinia subduction zone and was comparable with events occurring at the southern margin of the Siberian Craton, thus challenging the traditional southward migrating accretionary models for the CAOB