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2023 Vol. 53, No. 12

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Review
Orchestration of the dynamic molecular and cellular society in cancer by intratumoral bacteria
Rutian Zhong, Xingchen Yu, Fengrui Yang, Xuebiao Yao, Xing Liu
2023, 53(12): 1201. doi: 10.52396/JUSTC-2022-0186
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Abstract:
It has been a long-standing interest in the biomedical field to delineate pathogen‒host cell interactions. The latest advancements in single-cell analyses with multiomics approaches have begun to revolutionize our understanding of the impact of intratumoral bacteria on tumor development. Recent studies suggest that intratumoral bacteria modulate the communication between tumor cells and surrounding immune cells, which changes tumor progression and plasticity. Thus, a better understanding of the molecular mechanisms underlying intratumor bacteria-elicited pathogen‒host interactions will shed light on targeted interrogation in clinical oncology. This essay highlights recent progress in intratumor bacterial signaling and host cell plasticity control. In addition, we provide perspectives on how the molecular delineation of intratumor bacterial signaling and host cell plasticity control can help precision medicine and novel therapeutic development.
Chemistry
Highly efficient copper-catalyzed benzylic C–H alkoxylation with NFSI
Cheng Zhang, Pu-Sheng Wang
2023, 53(12): 1202. doi: 10.52396/JUSTC-2023-0080
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A sacrificial reductant-free copper-catalyzed benzylic C–H alkoxylation with N-Fluorobenzenesulfonimide (NFSI) was reported. Mechanistic studies suggested a novel pathway for the generation of active CuI species from Cu(OAc)2, NFSI and MeOH. A proper loading amount of copper catalyst was found to balance the reaction rates of benzylic C–H alkoxylation and overoxidation of benzyl ether to exhibit the best performance.
Tuning the photoluminescence of MoS2/TiO2 by molecular self-assembly films
Hechenyu Zha, Yue Xing, Miaomiao Xiang, Xiang Shao
2023, 53(12): 1206. doi: 10.52396/JUSTC-2023-0078
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Self-assembly films have demonstrated an efficient method to functionalize the surfaces of variously different materials. In this work, we preliminarily explored the modification effect of 10,12-pentacosadiynoic acid (PCDA) on the optical properties of monolayer molybdenum disulfide (MoS2) grown on a rutile titanium dioxide (r-TiO2) (110) single crystal surface. Atomic force microscopy (AFM) characterizations directly revealed that the PCDA molecules self-assemble into the same lamella structure as on pure MoS2, which can be further polymerized into conductive polydiacetylene (PDA) chains under ultraviolet light (UV) irradiation. Detailed photoluminescence (PL) measurements observed clearly increased luminescence of negative trions (A−) yet decreased total intensities for MoS2 upon adding the PCDA assembly, which is further enhanced after stimulating its polymerization. These results indicate that the PCDA assembly and its polymerization have different electron donability to MoS2, which hence provides a deepened understanding of the interfacial interactions within a multicomponent system. Our work also demonstrates the self-assembly of films as a versatile strategy to tune the electronic/optical properties of hybridized two-dimensional materials.
Molecular mechanism underlying ABC exporter gating: a computational study
Zi Wang, Jielou Liao
2023, 53(12): 1207. doi: 10.52396/JUSTC-2022-0134
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ATP-binding cassette (ABC) exporters are a class of molecular machines that transport substrates out of biological membranes by gating movements leading to transitions between outward-facing (OF) and inward-facing (IF) conformational states. Despite significant advances in structural and functional studies, the molecular mechanism underlying conformational gating in ABC exporters is not completely understood. A complete elucidation of the state transitions during the transport cycle is beyond the capability of the all-atom molecular dynamics (MD) method because of the limited time scale of MD. In the present work, a coarse-grained molecular dynamics (CG-MD) method with an improved sampling strategy is performed for the bacterial ABC exporter MsbA. The resultant potential of the mean force (PMF) along the center-of-mass (COM) distances, d1 and d2, between the two opposing subunits of the internal and external gates, respectively, are obtained, delicately showing the details of the $ {\rm{OF}}\to {\rm{IF}} $ transition occurring via an occluded (OC) state, in which the internal and external gates are both closed. The OC state has an important role in the unidirectionality of the transport function of ABC exporters. Our CG-MD simulations dynamically show that upon NBD dissociation, the opening of the internal gate occurs in a highly cooperative manner with the closure of the external gate. Based on our PMF calculations and CG-MD simulations in this paper, we proposed a mechanistic model that is significantly different from those recently published in the literature, shedding light on the molecular mechanism by which the ABC exporter executes conformational gating for substrate translocation.
Life Sciences
Structural knowledge error, rather than reward insensitivity, explains the reduced metacontrol in aging
Zhaoyu Zuo, Lizhuang Yang, Hai Li
2023, 53(12): 1203. doi: 10.52396/JUSTC-2023-0132
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Humans flexibly adjust their reliance on model-free (habitual) and model-based (goal-directed) strategies according to cost‒benefit trade-offs, the ability of which is known as metacontrol. Recent studies have suggested that older adults show reduced flexibility in metacontrol. However, whether the metacontrol deficit in aging is due to cognitive or motivational factors remains ambiguous. The present study investigated this issue using pupillometry recording and a sequential decision-making task with varied task structures and reward stakes. Our results revealed that older adults performed less model-based control and less flexibility when the reward stake level changed, consistent with previous studies. However, pupillometry analysis indicated that older adults showed comparable sensitivity to the reward stake. Older adults varied in task structure knowledge according to their oral reports, and the subgroup with good structural knowledge exerted a similar pattern to younger adults. Computational simulation verified that poor structure knowledge representation impaired metacontrol. These results suggest that the inflexible metacontrol in the elderly population might not be due to motivational factors but rather poor structure knowledge.
Machine-learning diet quality score and risk of cardiovascular disease
Can Yang, Qi Li, Yan Liu, Ling Zhang, Jian Gao, Xu Steven Xu, Min Yuan
2023, 53(12): 1204. doi: 10.52396/JUSTC-2023-0067
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Objectives: Various diet scores have been established to measure overall diet quality, especially for the prevention of cardiovascular disease (CVD). Diet scores constructed by utilizing modern machine learning techniques may contain independent information and can provide better dietary recommendations in combination with the existing diet scores. Methods: We proposed a novel machine-learning diet quality score (DQS) and examined the performance of DQS in combination with the Healthy Eating Index-2015 (HEI2015), Mediterranean Diet Score (MED), Alternative Healthy Eating Index-2010 (AHEI) and Dietary Approaches to Stop Hypertension score (DASH score). The data used in this study were from the 2011–2012 to 2017–2018 cycles of the US National Health and Nutrition Examination Survey (NHANES). Participants aged above 20 self-reported their food intake and information on relevant covariates. We used an elastic-net penalty regression model to select important food features and used a generalized linear regression model to estimate odds ratios (ORs) and 95% CIs after controlling for age, sex, and other relevant covariates. Results: A total of 16756 participants were included in the analysis. DQS was significantly associated with coronary artery disease (CAD) risk after adjusting for one of the other common diet scores. The ORs for DQS combined with the HEI2015, MED, AHEI, and DASH scores were all approximately 0.900, with p values smaller than 0.05. The OR for DQS in the full score model including all other scores was 0.905 (95% CI, 0.828–0.989, p=0.028). Only marginal associations were found between DQS and other CVDs after adjusting for other diet scores. Conclusions: Based on data from four continuous cycles of the NHANES, higher DQS was found to be consistently associated with a lower risk of CAD. The DQS captured unique predictive information independent of the existing diet scores and thus can be used as a complementary scoring system to further improve dietary recommendations for CAD patients.
Association study on bone metabolism in type 2 diabetes by using machine learning
Jiatong Hu, Mingqing Liu, Hongqi Li, Jiayin Yue, Wei Wang, Ji Liu
2023, 53(12): 1205. doi: 10.52396/JUSTC-2023-0089
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Abstract:
Type 2 diabetes mellitus is often accompanied by serious complications, including bone metabolic diseases, liver diseases, and kidney diseases, which are affected by the course of disease, sex, age and individual differences and cannot be a unified treatment paradigm. Therefore, for the in-depth analysis of clinical data, looking for the correlation of type 2 diabetes complication data has important guiding significance for the treatment of type 2 diabetes and its complications. In this paper, multiple linear regression models were established based on the clinical data of type 2 diabetes patients in Anhui Province. Our results suggest that the main factors affecting bone complications of type 2 diabetes include body shape indexes, creatinine, uric acid, triglycerides and blood pressure. Interestingly, the bone mineral density of lumbar vertebrae in patients with type 2 diabetes was increased, suggesting that there was a risk of lumbar hyperosteogeny.
Mathematics
A representation of Galois dual codes of algebraic geometry codes via Weil differentials
Jiaqi Li, Liming Ma
2023, 53(12): 1208. doi: 10.52396/JUSTC-2023-0019
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Galois dual codes are a generalization of Euclidean dual codes and Hermitian dual codes. We show that the $ h $-Galois dual code of an algebraic geometry code $ C_{ {\cal{L}},F}(D,G) $ from function field $ F/ \mathbb{F}_{p^e} $ can be represented as an algebraic geometry code $ C_{\varOmega,F'}(\phi_{h}(D),\phi_{h}(G)) $ from an associated function field $ F'/ \mathbb{F}_{p^e} $ with an isomorphism $\phi_{h}:F\rightarrow F'$ satisfying $ \phi_{h}(a) = a^{p^{e-h}} $ for all $ a\in \mathbb{F}_{p^e} $. As an application of this result, we construct a family of h-Galois linear complementary dual maximum distance separable codes (h-Galois LCD MDS codes).
2023-12 Abstract
2023, 53(12): 1-2.
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2023-12 Contents
2023, 53(12): 1-2.
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