A two-amino-acid substitution in the transcription factor RORγt disrupts its function in T_H17 differentiation but not in thymocyte development

The transcription factor RORγt regulates differentiation of the T_H17 subset of helper T cells, thymic T cell development and lymph-node genesis. Although elimination of RORγt prevents T_H17 cell–mediated experimental autoimmune encephalomyelitis (EAE), it also disrupts thymocyte development, which could lead to lethal thymic lymphoma. Here we identified a two-amino-acid substitution in RORγt (RORγt^M) that 'preferentially' disrupted T_H17 differentiation but not thymocyte development. Mice expressing RORγt^M were resistant to EAE associated with defective T_H17 differentiation but maintained normal thymocyte development and normal lymph-node genesis, except for Peyer's patches. RORγt^M showed less ubiquitination at Lys69 that was selectively required for T_H17 differentiation but not T cell development. This study will inform the development of treatments that selectively target T_H17 cell–mediated autoimmunity but do not affect thymocyte development or induce lymphoma

Towards Understanding the Capability of Large Language Models on Code Clone Detection: A Survey

Code cloning, the duplication of code fragments, is common in software development. While some reuse aids productivity, excessive cloning hurts maintainability and introduces bugs. Hence, automatic code clone detection is vital. Meanwhile, large language models (LLMs) possess diverse code-related knowledge, making them versatile for various software engineering challenges. However, LLMs' performance in code clone detection is unclear and needs more study for accurate assessment. In this paper, we provide the first comprehensive evaluation of LLMs for clone detection, covering different clone types, languages, and prompts. We find advanced LLMs excel in detecting complex semantic clones, surpassing existing methods. Adding intermediate reasoning steps via chain-of-thought prompts noticeably enhances performance. Additionally, representing code as vector embeddings, especially with text encoders, effectively aids clone detection.Lastly, the ability of LLMs to detect code clones differs among various programming languages. Our study suggests that LLMs have potential for clone detection due to their language capabilities, offering insights for developing robust LLM-based methods to enhance software engineering.Comment: 13 pages, 3 figure

Carbon footprint and embodied nutrition evaluation of 388 recipes

Food consumption, which delivers fundamental energy and essential nutrients to human beings, is crucial for achieving a series of sustainable goals. Alongside rising population growth and living standards, there has been a significant increase in food cultivation demands, supply chain complexities, and waste management. Therefore, to protect human health and the environment, promoting sustainable food systems and the uptake of sustainable dietary habits are vital. Yet, information on the environmental and health impact of dietary choices remains inconsistent across multiple evaluation methods, which fail to deliver essential ideas to consumers. In this study, we formulate an integrated approach using Environmentally Extended Input-Output analysis, covering the food supply chain from production to the distribution phase, complemented with a hybrid Life Cycle Assessment for cooking and disposal processes, to quantify the carbon footprint of specific recipes. Our dataset also includes the distinct nutritional values of each recipe. This dataset not only informs the food industry and recipe platforms, enabling more sustainable choices, but also helps individuals balance nutritional value with environmental impact, leading to more informed and sustainable dietary decisions

The structural basis of rubisco phase separation in the pyrenoid

Approximately one-third of global CO2 fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO2-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein Essential Pyrenoid Component 1 (EPYC1) in the model alga Chlamydomonas reinhardtii. We find that EPYC1 consists of five evenly spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation and pyrenoid formation. Cryo-electron tomography supports a model in which EPYC1 and Rubisco form a codependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle

A two-amino-acid substitution in the transcription factor RORγt disrupts its function in T_H17 differentiation but not in thymocyte development

The transcription factor RORγt regulates differentiation of the T_H17 subset of helper T cells, thymic T cell development and lymph-node genesis. Although elimination of RORγt prevents T_H17 cell–mediated experimental autoimmune encephalomyelitis (EAE), it also disrupts thymocyte development, which could lead to lethal thymic lymphoma. Here we identified a two-amino-acid substitution in RORγt (RORγt^M) that 'preferentially' disrupted T_H17 differentiation but not thymocyte development. Mice expressing RORγt^M were resistant to EAE associated with defective T_H17 differentiation but maintained normal thymocyte development and normal lymph-node genesis, except for Peyer's patches. RORγt^M showed less ubiquitination at Lys69 that was selectively required for T_H17 differentiation but not T cell development. This study will inform the development of treatments that selectively target T_H17 cell–mediated autoimmunity but do not affect thymocyte development or induce lymphoma

The First Case of Ischemia-Free Kidney Transplantation in Humans

Background: Ischemia-reperfusion injury (IRI) has been considered an inevitable event in organ transplantation since the first successful kidney transplant was performed in 1954. To avoid IRI, we have established a novel procedure called ischemia-free organ transplantation. Here, we describe the first case of ischemia-free kidney transplantation (IFKT). Materials and Methods: The kidney graft was donated by a 19-year-old brain-dead donor. The recipient was a 47-year-old man with end-stage diabetic nephropathy. The graft was procured, preserved, and implanted without cessation of blood supply using normothermic machine perfusion. Results: The graft appearance, perfusion flow, and urine production suggested that the kidney was functioning well-during the whole procedure. The creatinine dropped rapidly to normal range within 3 days post-transplantation. The levels of serum renal injury markers were low post-transplantation. No rejection or vascular or infectious complications occurred. The patient had an uneventful recovery. Conclusion: This paper marks the first case of IFKT in humans. This innovation may offer a unique solution to optimizing transplant outcomes in kidney transplantation

Regulation of Heme Oxygenase-1 Expression and Function by Insulin through PI3-kinase/Akt-2 Pathway but not Nrf2 Activation.

金沢大学附属病院発行後1年より全文公開

miR-K12-7-5p Encoded by Kaposi's Sarcoma-Associated Herpesvirus Stabilizes the Latent State by Targeting Viral ORF50/RTA

Seventeen miRNAs encoded by Kaposi's sarcoma-associated herpesvirus (KSHV) have been identified and their functions have begun to be characterized. Among these miRNAs, we report here that miR-K12-7 directly targets the replication and transcription activator (RTA) encoded by open reading frame 50. We found that miR-K12-7 targeted the RTA 3′ untranslated region (RTA3′UTR) in a seed sequence-dependent manner. miR-K12-7-5p derived from miR-K12-7 mediates the inhibition of RTA expression, and the mutation of the seed match site totally abrogated the inhibitory effect of miR-K12-7 on RTA3′UTR. The inhibition of RTA expression by miR-K12-7 was further confirmed in the latently KSHV-infected 293/Bac36 cell line through transient transfection of miR-K12-7 expression plasmid or specific inhibitor of miR-K12-7-5p, respectively. The transient transfection of miR-K12-7 into 293/Bac36 cells reduced RTA expression and the expression of the downstream early genes regulated by RTA, and also the production of progeny virus was significantly reduced after treatment with chemical inducers. Our study revealed that another miRNA, miR-K12-7-5p, targets the viral immediate early gene RTA and that this miRNA contributes to the maintenance of viral latency