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The purpose of this review is to provide medical researchers, especially those without a bioinformatics background, with an easy-to-understand summary of the concepts and technologies used in microbiome research. First, we define primary concepts such as microbiota, microbiome, and metagenome. Then, we discuss study design schemes, the methods of sample size calculation, and the methods for improving the reliability of research. We emphasize the importance of negative and positive controls in this section. Next, we discuss statistical analysis methods used in microbiome research, focusing on problems with multiple comparisons and ways to compare β-diversity between groups. Finally, we provide step-by-step pipelines for bioinformatics analysis. In summary, the meticulous study design is a key step to obtaining meaningful results, and appropriate statistical methods are important for accurate interpretation of microbiome data. The step-by-step pipelines provide researchers with insights into newly developed bioinformatics analysis methods.

Post-translational modification of proteins by N-phosphorylation of the basic amino acid residues plays important roles in biological processes. The high-energy P–N bond might have contributed to the evolution of prebiotic chemistry. N-phosphoryl amino acids（PAAs） can serve as interesting small molecular models for the study of P–N bonds in prebiotic chemical evolution. PAAs are capable of simultaneously producing several important biomolecules such as polypeptides and oligonucleotides under mild reaction conditions. In this review, we describe the chemistry of PAAs, discusse their likely prebiotic origins and their reactivity and how they relate to biological P–N bond species. We also depict a possible prebiotic scenario mediated by PAAs in which PAAs may have acted as one of the essential forces driving prebiotic biomolecules to the first protocell.

The design of functional materials with desired properties is essential in driving technological advances in areas such as energy storage, catalysis and carbon capture 1 , 2 – 3 . Generative models accelerate materials design by directly generating new materials given desired property constraints, but current methods have a low success rate in proposing stable crystals or can satisfy only a limited set of property constraints 4 , 5 , 6 , 7 , 8 , 9 , 10 – 11 . Here we present MatterGen, a model that generates stable, diverse inorganic materials across the periodic table and can further be fine-tuned to steer the generation towards a broad range of property constraints. Compared with previous generative models 4 , 12 , structures produced by MatterGen are more than twice as likely to be new and stable, and more than ten times closer to the local energy minimum. After fine-tuning, MatterGen successfully generates stable, new materials with desired chemistry, symmetry and mechanical, electronic and magnetic properties. As a proof of concept, we synthesize one of the generated structures and measure its property value to be within 20% of our target. We believe that the quality of generated materials and the breadth of abilities of MatterGen represent an important advancement towards creating a foundational generative model for materials design. MatterGen is a model that generates stable, diverse inorganic materials across the periodic table and can further be fine-tuned to steer the generation towards a broad range of property constraints.

Understanding and exploiting the redox properties of uranium is of great importance because uranium has a wide range of possible oxidation states and holds great potential for small molecule activation and catalysis. However, it remains challenging to stabilise both low and high-valent uranium ions in a preserved ligand environment. Herein we report the synthesis and characterisation of a series of uranium(II–VI) complexes supported by a tripodal tris(amido)arene ligand. In addition, one- or two-electron redox transformations could be achieved with these compounds. Moreover, combined experimental and theoretical studies unveiled that the ambiphilic uranium–arene interactions are the key to balance the stabilisation of low and high-valent uranium, with the anchoring arene acting as a δ acceptor or a π donor. Our results reinforce the design strategy to incorporate metal–arene interactions in stabilising multiple oxidation states, and open up new avenues to explore the redox chemistry of uranium. Understanding and exploiting the redox properties of uranium is of great importance but stabilizing both low and high valent uranium ions in a preserved ligand environment remains challenging. Here, the authors report the synthesis and characterisation of a series of uranium(II–VI) complexes supported by a tripodal tris(amido)arene ligand.

We combine the labeling of newly transcribed RNAs with 5-ethynyluridine with the characterization of bound proteins. This approach, named capture of the newly transcribed RNA interactome using click chemistry (RICK), systematically captures proteins bound to a wide range of RNAs, including nascent RNAs and traditionally neglected nonpolyadenylated RNAs. RICK has identified mitotic regulators amongst other novel RNA-binding proteins with preferential affinity for nonpolyadenylated RNAs, revealed a link between metabolic enzymes/factors and nascent RNAs, and expanded the known RNA-bound proteome of mouse embryonic stem cells. RICK will facilitate an in-depth interrogation of the total RNA-bound proteome in different cells and systems.

Expanded hexanucleotide repeats in the chromosome 9 open reading frame 72 (C9orf72) gene are the most common genetic cause of ALS and frontotemporal degeneration (FTD). Here, we identify nuclear RNA foci containing the hexanucleotide expansion (GGGGCC) in patient cells, including white blood cells, fibroblasts, glia, and multiple neuronal cell types (spinal motor, cortical, hippocampal, and cerebellar neurons). RNA foci are not present in sporadic ALS, familial ALS/FTD caused by other mutations (SOD1, TDP-43 , or tau), Parkinson disease, or nonneurological controls. Antisense oligonucleotides (ASOs) are identified that reduce GGGGCC-containing nuclear foci without altering overall C9orf72 RNA levels. By contrast, siRNAs fail to reduce nuclear RNA foci despite marked reduction in overall C9orf72 RNAs. Sustained ASO-mediated lowering of C9orf72 RNAs throughout the CNS of mice is demonstrated to be well tolerated, producing no behavioral or pathological features characteristic of ALS/FTD and only limited RNA expression alterations. Genome-wide RNA profiling identifies an RNA signature in fibroblasts from patients with C9orf72 expansion. ASOs targeting sense strand repeat-containing RNAs do not correct this signature, a failure that may be explained, at least in part, by discovery of abundant RNA foci with C9orf72 repeats transcribed in the antisense (GGCCCC) direction, which are not affected by sense strand-targeting ASOs. Taken together, these findings support a therapeutic approach by ASO administration to reduce hexanucleotide repeat-containing RNAs and raise the potential importance of targeting expanded RNAs transcribed in both directions.

Purpose Recent studies have determined that cartilage oligomeric matrix protein (COMP) plays a vital role in carcinogenesis. We sought to clarify the role of COMP in colon cancer. Methods We investigated gene expression data from The Cancer Genome Atlas (TCGA) dataset. Tissue microarrays (TMA) containing paired samples from 253 patients with colon cancer were subjected to immunostaining. COMP levels in serum of colon cancer patients and healthy donors were measured with ELISA. We established COMP-knockout cells using the CRISPR/Cas9 system and COMP-overexpressing cells using lentiviral vectors to detect the effects of COMP on colon cancer cells using Cell Counting Kit-8 (CCK8), colony formation, apoptosis detection kit, and tumorigenesis assays in nude mice. Results The analysis of TCGA dataset and the results of the TMA suggested that COMP expression levels were significantly higher in cancer tissues than in adjacent normal tissues. Moreover, high COMP expression was correlated with the poor outcome of colon cancer patients. COMP levels in the sera of preoperative patients with colon cancer were much higher than those in healthy donors and were significantly reduced after colectomy. Colon cancer cells without COMP were defective with respect to the ability to proliferate, colony formation, the ability to resist 5-Fluorouracil-induced apoptosis and the growth of xenograft tumors in mice. Contrasting results were observed in COMP overexpressed cells. COMP promoted colon cancer cell proliferation partially through the activation of PI3K/ Akt/ mTOR/ p70S6K pathway. Conclusions COMP may be a novel prognostic indicator and biomarker and also a potential therapeutic target for colon cancer.

The objective of the present meta-analysis was to evaluate the survival, recurrence rate, and complications in patients with stage I non-small cell lung cancer (NSCLC) who received video-assisted thoracoscopic surgery (VATS) or open lobectomy. A literature search was conducted on June 31, 2012 using combinations of the search terms video-assisted thoracic surgery, open thoracotomy, lobectomy, and non-small-cell lung cancer (NSCLC). Inclusion criteria were: 1) Compared video-assisted thoracic surgery (VATS) lobectomy with open lobectomy. 2) Stage I NSCLC. 2) No previous treatment for lung cancer. 4) Outcome data included 5-year survival rate, complication, and recurrence rate. Tests of heterogeneity, sensitivity, and publication bias were performed. A total of 23 studies (21 retrospective and 2 prospective) met the inclusion criteria. VATS was associated with a longer 5-year survival (odds ratio [OR] = 1.622, 95% confidence interval [CI] 1.272 to 2.069; P<0.001), higher local recurrence rate (OR = 2.152, 95% CI 1.349 to 3.434; P = 0.001), similar distant recurrence rate (OR = 0.91, 95% CI 0.33 to 2.48; P = 0.8560), and lower total complication rate (OR = 0.45, 95% CI 0.24 to 0.84; P = 0.013) compared to open lobectomy. VATS was also associated with lower rates arrhythmias, prolonged air leakage, and pneumonia but it did not show any statistical significance. Patients with stage I NSCLC undergoing VATS lobectomy had longer survival and fewer complications than those who received open lobectomy.

The RNA-binding protein FUS/TLS, mutation in which is causative of the fatal motor neuron disease amyotrophic lateral sclerosis (ALS), is demonstrated to directly bind to the U1-snRNP and SMN complexes. ALS-causative mutations in FUS/TLS are shown to abnormally enhance their interaction with SMN and dysregulate its function, including loss of Gems and altered levels of small nuclear RNAs. The same mutants are found to have reduced association with U1-snRNP. Correspondingly, global RNA analysis reveals a mutant-dependent loss of splicing activity, with ALS-linked mutants failing to reverse changes caused by loss of wild-type FUS/TLS. Furthermore, a common FUS/TLS mutant-associated RNA splicing signature is identified in ALS patient fibroblasts. Taken together, these studies establish potentially converging disease mechanisms in ALS and spinal muscular atrophy, with ALS-causative mutants acquiring properties representing both gain (dysregulation of SMN) and loss (reduced RNA processing mediated by U1-snRNP) of function. Dominant mutations in the RNA-binding protein FUS/TLS cause amyotrophic lateral sclerosis (ALS), an adult-onset motor neuron degenerative disease. Here, the authors show that ALS-causative FUS/TLS mutations directly bind the SMN and U1-snRNP complexes, producing both loss and gain of function effects on RNA processing.

CrFeNiTix (x = 0.2, 0.3, 0.4, 0.5, and 0.6 molar ratio) compositionally complex alloys were fabricated by vacuum arc melting to investigate the microstructure, hardness, and compressive properties. The results revealed that CrFeNiTix alloys consisted of the principal face-centered cubic (FCC) phase and body-centered cubic (BCC) solid solution, with an amount of (Ni, Ti)-rich hexagonal close-packed phase. CrFeNiTix alloys exhibited the typical dendrite. Ti0.2 and Ti0.3 alloys were composed of FCC and BCC solid solutions in the dendrite, as well as ε (Ni3Ti) and R (Ni2.67Ti1.33) phases in the inter-dendrite, simultaneously. For Ti0.4, Ti0.5, and Ti0.6 alloys, (Fe, Cr)-rich solid solution separated out and ε phase transformed into R phase gradually. Meanwhile, TEM analysis indicated that Ti0.4 alloy matrix consisted of the principal FCC phase containing (Ni, Ti)-rich intragranular nanoprecipitates. The hardness values of CrFeNiTix alloys were increased with the addition of Ti content and the high compressive strength of CrFeNiTix alloys was maintained, which was attributed to the solid solution strengthening and precipitation hardening.