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Excess body weight (EBW) increases the risk of colorectal cancer (CRC) and is linked to lower colonoscopy compliance. Here, we extensively analyzed 981 metagenome samples from multiple cohorts to pinpoint the specific microbial signatures and their potential capability distinguishing EBW patients with CRC. The gut microbiome displayed considerable variations between EBW and lean CRC. We identify 44 and 37 distinct multi-kingdom microbial species differentiating CRC and controls in EBW and lean populations, respectively. Unique bacterial-fungal associations are also observed between EBW-CRC and lean-CRC. Our analysis revealed specific microbial functions in EBW-CRC, including D-Arginine and D-ornithine metabolism, and lipopolysaccharide biosynthesis. The best-performing classifier for EBW-CRC, comprising 12 bacterial and three fungal species, achieved an AUROC of 0.90, which was robustly validated across three independent cohorts (AUROC = 0.96, 0.94, and 0.80). Pathogenic microbial species, Anaerobutyricum hallii, Clostridioides difficile and Fusobacterium nucleatum, are EBW-CRC specific signatures. This work unearths the specific multi-kingdom microbial signatures for EBW-CRC and lean CRC, which may contribute to precision diagnosis and treatment of CRC. Metagenomic analysis reveals distinctive multi-kingdom species, functional signatures and bacteria-fungi interactions pattern between excess body weight CRC and lean CRC in gut microbiome, which contribute to precision medicine of CRC. [ABSTRACT FROM AUTHOR]

Most tough hydrogels are reinforced by introducing energy dissipation mechanisms, but simultaneously realizing a high toughness and low hysteresis is challenging because the energy dissipation structure cannot recover rapidly. In this work, high mechanical performance highly entangled double network hydrogels without energy dissipation structure are fabricated, in which physical entanglements act as the primary effective crosslinking in the first network. This sliding entanglement structure allows the hydrogel network to form a highly uniform oriented structure during stretching, resulting in a high tensile strength of ~3 MPa, a fracture energy of 8340 J m−2 and a strain-stiffening capability of 47.5 in 90% water content. Moreover, almost 100% reversibility is obtained in this hydrogel via energy storage based on entropy loss. The highly entangled double network structure not only overcomes the typical trade-off between the high toughness and low hysteresis of hydrogels, but more importantly, it provides an insight into the application of entanglement structures in high-performance hydrogels. Tough hydrogels commonly utilise energy dissipation mechanisms, but this can lead to challenges in achieving low hysteresis. Here, the authors report a hydrogel with a highly entangled double network that allows reversibility following stretching. [ABSTRACT FROM AUTHOR]

Aims/hypothesis: Lifestyle interventions are the first-line treatment option for body weight and cardiometabolic health management. However, whether age groups or women and men respond differently to lifestyle interventions is under debate. We aimed to examine age- and sex-specific effects of a low-energy diet (LED) followed by a long-term lifestyle intervention on body weight, body composition and cardiometabolic health markers in adults with prediabetes (i.e. impaired fasting glucose and/or impaired glucose tolerance). Methods: This observational study used longitudinal data from 2223 overweight participants with prediabetes in the multicentre diabetes prevention study PREVIEW. The participants underwent a LED-induced rapid weight loss (WL) period followed by a 3 year lifestyle-based weight maintenance (WM) intervention. Changes in outcomes of interest in prespecified age (younger: 25–45 years; middle-aged: 46–54 years; older: 55–70 years) or sex (women and men) groups were compared. Results: In total, 783 younger, 319 middle-aged and 1121 older adults and 1503 women and 720 men were included in the analysis. In the available case and complete case analyses, multivariable-adjusted linear mixed models showed that younger and older adults had similar weight loss after the LED, whereas older adults had greater sustained weight loss after the WM intervention (adjusted difference for older vs younger adults −1.25% [95% CI −1.92, −0.58], p<0.001). After the WM intervention, older adults lost more fat-free mass and bone mass and had smaller improvements in 2 h plasma glucose (adjusted difference for older vs younger adults 0.65 mmol/l [95% CI 0.50, 0.80], p<0.001) and systolic blood pressure (adjusted difference for older vs younger adults 2.57 mmHg [95% CI 1.37, 3.77], p<0.001) than younger adults. Older adults had smaller decreases in fasting and 2 h glucose, HbA1c and systolic blood pressure after the WM intervention than middle-aged adults. In the complete case analysis, the above-mentioned differences between middle-aged and older adults disappeared, but the direction of the effect size did not change. After the WL period, compared with men, women had less weight loss (adjusted difference for women vs men 1.78% [95% CI 1.12, 2.43], p<0.001) with greater fat-free mass and bone mass loss and smaller improvements in HbA1c, LDL-cholesterol and diastolic blood pressure. After the WM intervention, women had greater fat-free mass and bone mass loss and smaller improvements in HbA1c and LDL-cholesterol, while they had greater improvements in fasting glucose, triacylglycerol (adjusted difference for women vs men −0.08 mmol/l [−0.11, −0.04], p<0.001) and HDL-cholesterol. Conclusions/interpretation: Older adults benefited less from a lifestyle intervention in relation to body composition and cardiometabolic health markers than younger adults, despite greater sustained weight loss. Women benefited less from a LED followed by a lifestyle intervention in relation to body weight and body composition than men. Future interventions targeting older adults or women should take prevention of fat-free mass and bone mass loss into consideration. Clinical trial registration number: ClinicalTrials.gov NCT01777893. [ABSTRACT FROM AUTHOR]

Associations between gut microbiota and colorectal cancer (CRC) have been widely investigated. However, the replicable markers for early-stage adenoma diagnosis across multiple populations remain elusive. Here, we perform an integrated analysis on 1056 public fecal samples, to identify adenoma-associated microbial markers for early detection of CRC. After adjusting for potential confounders, Random Forest classifiers are constructed with 11 markers to discriminate adenoma from control (area under the ROC curve (AUC) = 0.80), and 26 markers to discriminate adenoma from CRC (AUC = 0.89), respectively. Moreover, we validate the classifiers in two independent cohorts achieving AUCs of 0.78 and 0.84, respectively. Functional analysis reveals that the altered microbiome is characterized with increased ADP-l-glycero-beta-d-manno-heptose biosynthesis in adenoma and elevated menaquinone-10 biosynthesis in CRC. These findings are validated in a newly-collected cohort of 43 samples using quantitative real-time PCR. This work proves the validity of adenoma-specific markers across multi-populations, which would contribute to the early diagnosis and treatment of CRC. The gut microbiome plays an important role in colorectal carcinogenesis and predictive microbiome signatures have been proposed for colorectal cancer (CRC) diagnosis. Here the authors perform a meta-analysis of 16S rRNA-based profiles to identify microbial markers able to discriminate patients with adenoma from control and CRC, building a model that can be applied for the early detection of CRC. [ABSTRACT FROM AUTHOR]

Purpose: To compare the glycaemic response of whole grain oat kernels and pearled oats cooked under normal pressure or higher pressure and examine whether replacing half of the rice in a given meal with either of the two oat grains could make a difference in acute glycaemic responses. Methods: In a randomised crossover trial, ten healthy subjects consumed two groups of test meals: (1) oat grain-only, including whole grain oats cooked under normal pressure (WONP) and higher pressure (WOHP) as well as their pearled oat counterparts, PONP and POHP; and (2) mixed meals of aforementioned oat grains and cooked rice (OG + R), including WONP + R, WOHP + R, PONP + R and POHP + R. A postprandial blood glucose test, texture profile analysis and in vitro carbohydrate digestion assay were carried out for each test meal. Results: Compared with the rice reference, oat grain-only meals induced lower glucose levels at all time points, lower peak values and smaller glucose excursions at 120 min (P < 0.05), but OG + Rs did not have the abovementioned effects. The oat grain-only meals had glycaemic indexes (GIs) ranging from 51 to 58, while those of OG + Rs ranged from 59 to 70. WONP + R had a 21% lower iAUC0–60 and a 40% lower iAUC60–120 value than those of rice (P < 0.05). Oat-rice mixed meals had lower iAUC0–60 values compared with that of the rice control (P < 0.05), except for POHP + R. Excellent consistency between the hydrolysis index and the GI was observed (r = 0.969, P < 0.001) in oat grain-only meals. Conclusions: All oat grain-only meals could be included in the glycaemic management diet, regardless of the oat grain type or cooking treatment. In oat-rice mixed meals, whole grain oats and normal pressure cooking ensured a favourable glycaemic effect. [ABSTRACT FROM AUTHOR]

The development of new proton-pump inhibitors (PPIs) with less adverse effects by lowering the pKa values of nitrogen atoms in pyrimidine rings has been previously suggested by our group. In this work, we proposed that new PPIs should have the following features: (1) number of ring II = number of ring I + 1; (2) preferably five, six, or seven-membered heteroatomic ring for stability; and (3) 1 < pKa1 < 4. Six molecular scaffolds based on the aforementioned criteria were constructed, and R groups were extracted from compounds in extensive data sources. A virtual molecule dataset was established, and the pKa values of specific atoms on the molecules in the dataset were calculated to select the molecules with required pKa values. Drug-likeness screening was further conducted to obtain the candidates that significantly reduced the adverse effects of long-term PPI use. This study provided insights and tools for designing targeted molecules in silico that are suitable for practical applications. [ABSTRACT FROM AUTHOR]

The early history of life harbours many unresolved evolutionary questions, none more important than the genomic origin and cellular evolution of eukaryotes. An issue central to eukaryote origin concerns the position of eukaryotes in the tree of life and the relationship of the host lineage that acquired the mitochondrion some two billion years ago to lineages of modern-day archaea. Recent analyses indicate that the host lineage branches within the Archaea, prompting the search for novel archaeal lineages that can improve our understanding of the cellular evolution of eukaryotes. Here we give a brief review of the studies on Archaea, the tree of life and the cellular evolution of eukaryotes, which is followed by an overview of recent progress fueled by new genomic technologies and recent status of archaeal research in China. Future directions for the study of early evolution are considered. [ABSTRACT FROM AUTHOR]

Archaea are cosmopolitan in aerated soils around the world. While the dominance of Thaumarchaeota has been reported in most soils, the methanogens are recently found to be ubiquitous but with low abundances in the aerated soil globally. However, the seasonal changes of Archaea community in the aerated soils are still in the mist. In this study, we investigated the change of Archaea in the context of environmental variables over a period of 12 months in a subtropical soil on the Chongming Island, China. The results showed that Nitrososphaera spp. were the dominant archaeal population while the methanogens were in low proportions but highly diverse (including five genera: Methanobacterium, Methanocella, Methanosaeta, Methanosarcina, and Methanomassiliicoccus) in the aerated soil samples determined by high throughput sequencing. A total of 126 LSA correlations were found in the dataset including all the 72 archaeal OTUs and 8 environmental factors. A significance index defined as the pagerank score of each OTU divided by its relative abundance was used to evaluate the significance of each OTU. The results showed that five out of 17 methanogen OTUs were significantly positively correlated with temperature, suggesting those methanogens might increase with temperature rather than being dormant in the aerated soils. Given the metabolic response of methanogens to temperature under aerated soil conditions, their contribution to the global methane cycle warrants evaluation. [ABSTRACT FROM AUTHOR]

Motivation: Protein-binding sites prediction lays a foundation for functional annotation of protein and structure-based drug design. As the number of available protein structures increases, structural alignment based algorithm becomes the dominant approach for protein-binding sites prediction. However, the present algorithms underutilize the ever increasing numbers of three-dimensional protein-ligand complex structures (bound protein), and it could be improved on the process of alignment, selection of templates and clustering of template. Herein, we built so far the largest database of bound templates with stringent quality control. And on this basis, bSiteFinder as a protein-binding sites prediction server was developed. Results: By introducing Homology Indexing, Chain Length Indexing, Stability of Complex and Optimized Multiple-Templates Clustering into our algorithm, the efficiency of our server has been significantly improved. Further, the accuracy was approximately 2-10 % higher than that of other algorithms for the test with either bound dataset or unbound dataset. For 210 bound dataset, bSiteFinder achieved high accuracies up to 94.8 % (MCC 0.95). For another 48 bound/unbound dataset, bSiteFinder achieved high accuracies up to 93.8 % for bound proteins (MCC 0.95) and 85.4 % for unbound proteins (MCC 0.72). Our bSiteFinder server is freely available at , and the source code is provided at the methods page. Conclusion: An online bSiteFinder server is freely available at . Our work lays a foundation for functional annotation of protein and structure-based drug design. With ever increasing numbers of three-dimensional protein-ligand complex structures, our server should be more accurate and less time-consuming.[Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Antibody molecules interact with antigen proteins through the epitope area, where the epitope residues are found to be discontinuous or spatial or conformational rather than linear on the protein surface. There are various computational algorithms to predict the spatial epitopes, and each of them have an outstanding performance based on their individual testing dataset. In this work, an independent dataset was created through collection of the epitope residual sites which have been confirmed by experiments. Based on this dataset, 6 popular web-servers developed for B-cell structural epitope prediction, including SEPPA, CEP, DiscoTope, ElliPro, PEPOP and BEpro, were evaluated and compared according to sensitivity, the positive predictive value, the successful pick-up rate and the area under the curve of the receiver operator characteristic (AUC). The results showed that the general performance of spatial epitope prediction tools did obtain substantial advancement, and SEPPA gave the best performance among the 6 tools. However, the current prediction accuracy was still far from satisfaction. Moreover, our comparison elucidated that the performance of the web-servers was significantly affected by their training datasets and the algorithms adopted. In this sense, the results of our research may improve the design of B-cell epitope prediction tools and provide additional clues when the users utilize these tools in their related research. [ABSTRACT FROM AUTHOR]

Telomere maintenance is critical for chromosome stability. Here we report that periodic tryptophan protein 1 (PWP1) is involved in regulating telomere length homeostasis. Pwp1 appears to be essential for mouse development and embryonic stem cell (ESC) survival, as homozygous Pwp1-knockout mice and ESCs have never been obtained. Heterozygous Pwp1-knockout mice had shorter telomeres and decreased reproductive capacity. Pwp1 depletion induced rapid telomere shortening accompanied by reduced shelterin complex and increased DNA damage in telomeric regions. Mechanistically, PWP1 bound and stabilized the shelterin complex via its WD40 domains and regulated the overall level of H4K20me3. The rescue of telomere length in Pwp1-deficient cells by PWP1 overexpression depended on SUV4-20H2 co-expression and increased H4K20me3. Therefore, our study revealed a novel protein involved in telomere homeostasis in both mouse and human cells. This knowledge will improve our understanding of how chromatin structure and histone modifications are involved in maintaining telomere integrity. [ABSTRACT FROM AUTHOR]

Traditional Chinese Medicine (TCM) treatment has been commonly used to treat Chronic Hepatitis B (CHB) in Asian countries based on TCM syndrome diagnosis, also called 'ZHENG'. The syndrome is identified through the four-diagnostic methods, with certain degree of subjectivity and ambiguity from individual doctors. Normally those CHB patients also receive series of parameters from modern clinical examination, while they are routinely believed to be unrelated with the TCM syndrome diagnosis. In this study, we investigated whether these biomedical indexes in modern medicine could be beneficial to TCM syndrome diagnostics in an integrative way. Based on 634 patient samples from health controls and three subtypes of CHB syndromes, a two-view based hierarchical classification model was tested for TCM syndromes prediction based on totally 222 parameters integrated from both TCM practice and modern clinical tests. The results indicated that the performance of syndrome classification based on a proper integration of TCM and modern clinical indexes was significantly higher than those based on one view of parameters only. Furthermore, those indexes correlated with CHB syndrome diagnosis were successfully identified for CM indexes and biochemical indexes respectively, where potential associations between them were hinted to the MAPK signaling pathway. [ABSTRACT FROM AUTHOR]