Differential responses of rumen and fecal fermentation and microbiota of Liaoning cashmere goats after 2-hydroxy-4-(methylthio) butanoic acid isopropyl ester supplementation.

The 2-hydroxy-4-(methylthio) butanoic acid isopropyl ester (HMBi), a rumen protective methionine, has been extensively studied in dairy cows and beef cattle and has been shown to regulate gastrointestinal microbiota and improve production performance. However, knowledge of the application of HMBi on cashmere goats and the simultaneous study of rumen and hindgut microbiota is still limited. In this study, HMBi supplementation increased the concentration of total serum protein, the production of microbial protein in the rumen and feces, as well as butyrate production in the feces. The results of PCoA and PERMANOVA showed no significant difference between the rumen microbiota, but there was a dramatic difference between the fecal microbiota of the two groups of Cashmere goats after the HMBi supplementation. Specifically, in the rumen, HMBi significantly increased the relative abundance of some fiber-degrading bacteria (such as Fibrobacter) compared with the CON group. In the feces, as well as a similar effect as in the rumen (increasing the relative abundance of some fiber-degrading bacteria, such as Lachnospiraceae FCS020 group and ASV32), HMBi diets also increased the proliferation of butyrate-producing bacteria (including Oscillospiraceae UCG-005 and Christensenellaceae R-7 group). Overall, these results demonstrated that HMBi could regulate the rumen and fecal microbial composition of Liaoning cashmere goats and benefit the host.

Elevator block brake structural optimization design based on an approximate model.

An Aquila optimizer-back propagation (AO-BP) neural network was used to establish an approximate model of the relationship between the design variables and the optimization objective to improve elevator block brake capabilities and achieve a lightweight brake design. Subsequently, the constraint conditions and objective functions were determined. Moreover, the multi-objective genetic algorithm optimized the structural block brake design. Finally, the effectiveness of the optimization results was verified using simulation experiments. The results demonstrate that the maximum temperature of the optimized brake wheel during emergency braking was 222.09°C, which is 36.71°C lower than that of 258.8°C before optimization, with a change rate of 14.2%. The maximum equivalent stress after optimization was 246.89 MPa, 28.87 MPa lower than that of 275.66 MPa before optimization, with a change rate of 10.5%. In addition, the brake wheel mass was reduced from 58.85 kg to 52.40 kg, and the thermal fatigue life at the maximum equivalent stress increased from 64 times before optimization to 94 times after optimization.

Identification of the transcriptome signatures and immune-inflammatory responses in postmenopausal osteoporosis.

Postmenopausal osteoporosis is the most common type of osteoporosis in women. To date, little is known about their transcriptome signatures, although biomarkers from peripheral blood mononuclear cells are attractive for postmenopausal osteoporosis diagnoses. Here, we performed bulk RNA sequencing of 206 samples (124 postmenopausal osteoporosis and 82 normal samples) and described the clinical phenotypic characteristics of postmenopausal women. We then highlighted the gene set enrichment analyses between the extreme T-score group and the heathy control group, revealing that some immune-inflammatory responses were enhanced in postmenopausal osteoporosis, with representative pathways including the mitogen-activated protein kinase (NES = 1.6, FDR <0.11) pathway and B_CELL_RECEPTOR (NES = 1.69, FDR <0.15) pathway. Finally, we developed a combined risk prediction model based on lasso-logistic regression to predict postmenopausal osteoporosis, which combined eleven genes (PTGS2, CXCL16, NECAP1, RPS23, SSR3, CD74, IL4R, BTBD2, PIGS, LILRA2, MAP3K11) and three pieces of clinical information (age, procollagen I N-terminal propeptide, ß isomer of C-terminal telopeptide of type I) and provided the best prediction ability (AUC = 0.97). Taken together, this study filled a gap in the large-scale transcriptome signature profiles and revealed the close relationship between immune-inflammatory responses and postmenopausal osteoporosis, providing a unique perspective for understanding the occurrence and development of postmenopausal osteoporosis.

Plasma extrachromosomal circular DNA is a pathophysiological hallmark of short-term intensive insulin therapy for type 2 diabetes.

BACKGROUND: Extrachromosomal circular DNA (eccDNA) has emerged as a promising biomarker for disease diagnosis and prognosis prediction. However, its role in type 2 diabetes remains unexplored. OBJECTIVE: To investigate the characteristics and dynamics of circulating eccDNAs in newly diagnosed type 2 diabetes mellitus (T2DM) patients undergoing short-term intensive insulin therapy (SIIT), a highly effective treatment for inducing long-term glycemic remission. METHODS: We conducted Circle-Seq analysis on plasma samples from 35 T2DM patients at three time points: pre-SIIT, post-SIIT, and 1-year post-SIIT. Our analysis encompassed the characterization of eccDNA features, including GC content, eccDNA length distribution, genomic distribution, and the genes in eccDNAs. RESULTS: Following SIIT, we observed an increase in plasma eccDNA load, suggesting metabolic alterations during therapy. Notably, a correlation was identified between eccDNA profiles and glycemia in T2DM, both quantitatively and genetically. Our analysis also revealed the frequent presence of metabolism-related genes within T2DM plasma eccDNAs, some of which spanned gene exons and/or fractions. CONCLUSION: This study represents the first report of cell-free eccDNA in T2DM and underscores a compelling association between cell-free eccDNA and profound glycemic changes. These findings highlight the potential of eccDNAs as crucial players in the context of T2DM and glycemic control.

Non-invasive preoperative prediction of Edmondson-Steiner grade of hepatocellular carcinoma based on contrast-enhanced ultrasound using ensemble learning.

Purpose: This study aimed to explore the clinical value of non-invasive preoperative Edmondson-Steiner grade of hepatocellular carcinoma (HCC) using contrast-enhanced ultrasound (CEUS). Methods: 212 cases of HCCs were retrospectively included, including 83 cases of high-grade HCCs and 129 cases of low-grade HCCs. Three representative CEUS images were selected from the arterial phase, portal vein phase, and delayed phase and stored in a 3-dimensional array. ITK-SNAP was used to segment the tumor lesions manually. The Radiomics method was conducted to extract high-dimensional features on these contrast-enhanced ultrasound images. Then the independent sample T-test and the Least Absolute Shrinkage and Selection Operator (LASSO) were employed to reduce the feature dimensions. The optimized features were modeled by a classifier based on ensemble learning, and the Edmondson Steiner grading was predicted in an independent testing set using this model. Results: A total of 1338 features were extracted from the 3D images. After the dimension reduction, 10 features were finally selected to establish the model. In the independent testing set, the integrated model performed best, with an AUC of 0.931. Conclusion: This study proposed an Edmondson-Steiner grading method for HCC with CEUS. The method has good classification performance on independent testing sets, which can provide quantitative analysis support for clinical decision-making.

Controllable Synthesis and Charge Density Wave Phase Transitions of Two-Dimensional 1T-TaS2 Crystals.

1T-TaS2 has attracted much attention recently due to its abundant charge density wave phases. In this work, high-quality two-dimensional 1T-TaS2 crystals were successfully synthesized by a chemical vapor deposition method with controllable layer numbers, confirmed by the structural characterization. Based on the as-grown samples, their thickness-dependency nearly commensurate charge density wave/commensurate charge density wave phase transitions was revealed by the combination of the temperature-dependent resistance measurements and Raman spectra. The phase transition temperature increased with increasing thickness, but no apparent phase transition was found on the 2~3 nm thick crystals from temperature-dependent Raman spectra. The transition hysteresis loops due to temperature-dependent resistance changes of 1T-TaS2 can be used for memory devices and oscillators, making 1T-TaS2 a promising material for various electronic applications.

Genome-wide characterization of extrachromosomal circular DNA in gastric cancer and its potential role in carcinogenesis and cancer progression.

Extrachromosomal circular DNAs (eccDNAs) carrying random genomic segments are broadly found across different cancer types, but their molecular functions and impact in gastric cancer (GC) are rarely known. In this study, we aimed to investigate the potential role of eccDNA in GC. Using the Circle-seq strategy, we observed the eccDNA abundance in gastric cancer tissues (GCT) was aberrantly higher than that of normal adjacent tissues (NAT). The high abundance of eccDNAs carrying oncogene-segments in GCT may represent the DNA damage products of amplified oncogenes. Analysis of GCT over-represented eccDNA carrying enhancer (eccEnhancer) based on data from FANTOM5 project combined with TCGA database suggested the GC over-represented eccEnhancers may contribute to development of GC. GC over-represented eccDNAs carrying pre-miRNA (eccMIR) were enriched to multiple cancer-relevant signal pathways by KEGG analysis. We then synthesized the top six GC over-represented eccMIRs and found four of them enabled high expression of miRNAs and down-regulation of miRNA-target genes in MGC803 cells. Furthermore, we observed the inheritance of GC over-represented eccMIRs benefited host cell proliferation and promoted the aggressive features of host cells. Altogether, this study revealed the GC over-represented eccDNAs carrying functional genomic segments were related to the carcinogenesis of GC and presented the capability to facilitate cancer progression, suggesting the cancerous eccDNAs may serve as a dynamic reservoir for genome plasticity and rapid adaptive evolution of cancer. Therefore, blocking the pathways for eccDNAs generation may provide a novel therapeutic strategy for the treatment of gastric cancer.

The Temporal Dynamics of Stop Consonant Perception: Evidence from Context Effects.

Empirical evidence and theoretical models suggest that phonetic category perception involves two stages of auditory and phonetic processing. However, few studies examined the time course of these two processing stages. With brief stop consonant segments as context stimuli, this study examined the temporal dynamics of stop consonant perception by varying the inter-stimulus interval between context and target stimuli. The results suggest that phonetic category activation of stop consonants may appear before 100 ms of processing time. Furthermore, the activation of phonetic categories resulted in contrast context effects on identifying the target stop continuum; the auditory processing of stop consonants resulted in a different context effect from those caused by phonetic category activation. The findings provide further evidence for the two-stage model of speech perception and reveal the time course of auditory and phonetic processing.

Spatially Dependent Electronic Structures and Excitons in a Marginally Twisted Moiré Superlattice of Spiral WS2.

Twisted two-dimensional transition metal dichalcogenide (TMD) moiré superlattices provide an additional degree of freedom to engineer electronic and optical properties. Nevertheless, controllable synthesis of marginally twisted homo TMD moiré superlattices is still a challenge. Here, physical vapor deposition grown spiral WS2 nanosheets are demonstrated to be a marginally twisted moiré superlattice using scanning tunneling microscopy and spectroscopy. Periodic moiré superlattices are found on the third layer (3L) and 4L of the spiral WS2 nanosheet owing to the marginally twisted alignment between two neighboring layers, resulting in a highly localized flat band near the valence band maximum. Their bandgap depends on atomic stacking configurations, which gives a good interpretation for split moiré excitons using photoluminescence at 77 K. This work can benefit the development of twisted homo TMD moiré superlattices and could promote the profound research of twisted TMDs in the prospective field, such as strongly correlated physics and twistronics.

The single-cell expression profile of transposable elements and transcription factors in human early biparental and uniparental embryonic development.

Transposable elements (TEs) and transcription factors (TFs) are involved in the precise regulation of gene expression during the preimplantation stage. Activation of TEs is a key event for mammalian embryonic genome activation and preimplantation early embryonic development. TFs are involved in the regulation of drastic changes in gene expression patterns, but an inventory of the interplay between TEs and TFs during normal/abnormal human embryonic development is still lacking. Here we used single-cell RNA sequencing data generated from biparental and uniparental embryos to perform an integrative analysis of TE and TF expression. Our results showed that endogenous retroviruses (ERVs) are mainly expressed during the minor embryonic genome activation (EGA) process of early embryos, while Alu is gradually expressed in the middle and later stages. Some important ERVs (e.g., LTR5_Hs, MLT2A1) and Alu TEs are expressed at significantly lower levels in androgenic embryos. Integrative analysis revealed that the expression of the transcription factors CTCF and POU5F1 is correlated with the differential expression of ERV TEs. Comparative coexpression network analysis further showed distinct expression levels of important TFs (e.g., LEUTX and ZSCAN5A) in dizygotic embryos vs. parthenogenetic and androgenic embryos. This systematic investigation of TE and TF expression in human early embryonic development by single-cell RNA sequencing provides valuable insights into mammalian embryonic development.

Massively targeted evaluation of therapeutic CRISPR off-targets in cells.

Methods for sensitive and high-throughput evaluation of CRISPR RNA-guided nucleases (RGNs) off-targets (OTs) are essential for advancing RGN-based gene therapies. Here we report SURRO-seq for simultaneously evaluating thousands of therapeutic RGN OTs in cells. SURRO-seq captures RGN-induced indels in cells by pooled lentiviral OTs libraries and deep sequencing, an approach comparable and complementary to OTs detection by T7 endonuclease 1, GUIDE-seq, and CIRCLE-seq. Application of SURRO-seq to 8150 OTs from 110 therapeutic RGNs identifies significantly detectable indels in 783 OTs, of which 37 OTs are found in cancer genes and 23 OTs are further validated in five human cell lines by targeted amplicon sequencing. Finally, SURRO-seq reveals that thermodynamically stable wobble base pair (rG•dT) and free binding energy strongly affect RGN specificity. Our study emphasizes the necessity of thoroughly evaluating therapeutic RGN OTs to minimize inevitable off-target effects.

CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context.

A major challenge of CRISPR/Cas9-mediated genome engineering is that not all guide RNAs (gRNAs) cleave the DNA efficiently. Although the heterogeneity of gRNA activity is well recognized, the current understanding of how CRISPR/Cas9 activity is regulated remains incomplete. Here, we identify a sweet spot range of binding free energy change for optimal efficiency which largely explains why gRNAs display changes in efficiency at on- and off-target sites, including why gRNAs can cleave an off-target with higher efficiency than the on-target. Using an energy-based model, we show that local gRNA-DNA interactions resulting from Cas9 "sliding" on overlapping protospacer adjacent motifs (PAMs) profoundly impact gRNA activities. Combining the effects of local sliding for a given PAM context with global off-targets allows us to better identify highly specific, and thus efficient, gRNAs. We validate the effects of local sliding on gRNA efficiency using both public data and in-house data generated by measuring SpCas9 cleavage efficiency at 1024 sites designed to cover all possible combinations of 4-nt PAM and context sequences of 4 gRNAs. Our results provide insights into the mechanisms of Cas9-PAM compatibility and cleavage activation, underlining the importance of accounting for local sliding in gRNA design.

Characterization of Plasma Extrachromosomal Circular DNA in Gouty Arthritis.

Objective: Extrachromosomal circular DNA elements (eccDNAs) are known for their broad existence in cells and plasma, which may potentially play important roles in many biological processes. Our aim was to identify potentially functional or marked eccDNAs in gout patients. Methods: The Circle-Seq approach was applied for eccDNA detection from plasma in acute gout patients and healthy controls. Further analysis was performed on the distribution of genomic elements and eccDNA gene annotations in two groups. Results: We detected 57,216 and 109,683 eccDNAs from the acute gout and healthy control plasma, respectively. EccDNAs were mapped to the reference genome to identify diverse classes of genomic elements and there was no significant difference of eccDNAs on genomic element annotation between gout and control group. A total of 256 eccDNA-associated genes were detected as gout unique eccDNA genes, including COL1A1 and EPB42, which potentially contribute to hyperuricemia and gout, and a couple of genes involved in inflammation or immune response. Enrichment analysis showed that these eccDNA genes were highly correlated with defense response, stress response, and immune and inflammatory responses, including T cell receptor signaling pathway, Fc epsilon RI signaling pathway, and JAK-STAT signaling pathway. Conclusion: Our discovery reveals the novel potential biological roles of plasma eccDNAs in gouty arthritis.

Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs.

BACKGROUND: Extrachromosomal circular deoxyribonucleic acid (eccDNA) is evolving as a valuable biomarker, while little is known about its presence in urine. METHODS: Here, we report the discovery and analysis of urinary cell-free eccDNAs (ucf-eccDNAs) in healthy controls and patients with advanced chronic kidney disease (CKD) by Circle-Seq. RESULTS: Millions of unique ucf-eccDNAs were identified and comprehensively characterised. The ucf-eccDNAs are GC-rich. Most ucf-eccDNAs are less than 1000 bp and are enriched in four pronounced peaks at 207, 358, 553 and 732 bp. Analysis of the genomic distribution of ucf-eccDNAs shows that eccDNAs are found on all chromosomes but enriched on chromosomes 17, 19 and 20 with a high density of protein-coding genes, CpG islands, short interspersed transposable elements (SINEs) and simple repeat elements. Analysis of eccDNA junction sequences further suggests that microhomology and palindromic repeats might be involved in eccDNA formation. The ucf-eccDNAs in CKD patients are significantly higher than those in healthy controls. Moreover, eccDNA with miRNA genes is highly enriched in CKD ucf-eccDNA. CONCLUSIONS: This work discovers and provides the first deep characterisation of ucf-eccDNAs and suggests ucf-eccDNA as a valuable noninnvasive biomarker for urogenital disorder diagnosis and monitoring.

Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning.

The design of CRISPR gRNAs requires accurate on-target efficiency predictions, which demand high-quality gRNA activity data and efficient modeling. To advance, we here report on the generation of on-target gRNA activity data for 10,592 SpCas9 gRNAs. Integrating these with complementary published data, we train a deep learning model, CRISPRon, on 23,902 gRNAs. Compared to existing tools, CRISPRon exhibits significantly higher prediction performances on four test datasets not overlapping with training data used for the development of these tools. Furthermore, we present an interactive gRNA design webserver based on the CRISPRon standalone software, both available via https://rth.dk/resources/crispr/ . CRISPRon advances CRISPR applications by providing more accurate gRNA efficiency predictions than the existing tools.

Efficient correction of Duchenne muscular dystrophy mutations by SpCas9 and dual gRNAs.

CRISPR gene therapy is one promising approach for treatment of Duchenne muscular dystrophy (DMD), which is caused by a large spectrum of mutations in the dystrophin gene. To broaden CRISPR gene editing strategies for DMD treatment, we report the efficient restoration of dystrophin expression in induced myotubes by SpCas9 and dual guide RNAs (gRNAs). We first sequenced 32 deletion junctions generated by this editing method and revealed that non-homologous blunt-end joining represents the major indel type. Based on this predictive repair outcome, efficient in-frame deletion of a part of DMD exon 51 was achieved in HEK293T cells with plasmids expressing SpCas9 and dual gRNAs. More importantly, we further corrected a frameshift mutation in human DMD (exon45del) fibroblasts with SpCas9-dual gRNA ribonucleoproteins. The edited DMD fibroblasts were transdifferentiated into myotubes by lentiviral-mediated overexpression of a human MYOD transcription factor. Restoration of DMD expression at both the mRNA and protein levels was confirmed in the induced myotubes. With further development, the combination of SpCas9-dual gRNA-corrected DMD patient fibroblasts and transdifferentiation may provide a valuable therapeutic strategy for DMD.

Synthesis of Chiral Triarylmethanes Bearing All-Carbon Quaternary Stereocenters: Catalytic Asymmetric Oxidative Cross-Coupling of 2,2-Diarylacetonitriles and (Hetero)arenes.

A direct and enantioselective oxidative cross-coupling of racemic 2,2-diarylacetonitriles with electron-rich (hetero)arenes has been described, which allows for efficient construction of triarylmethanes bearing all-carbon quaternary stereocenters with excellent chemo- and enantioselectivity. The reaction has an excellent functional group tolerance, and exhibits a broad scope with respect to both 2,2-diarylacetonitrile and (hetero)arene components. The rich chemistry of the cyano group allows for facile synthesis of other valuable chiral triarylmethanes bearing all-carbon quaternary centers that are otherwise difficult to access.

Haplotyping by CRISPR-mediated DNA circularization (CRISPR-hapC) broadens allele-specific gene editing.

Allele-specific protospacer adjacent motif (asPAM)-positioning SNPs and CRISPRs are valuable resources for gene therapy of dominant disorders. However, one technical hurdle is to identify the haplotype comprising the disease-causing allele and the distal asPAM SNPs. Here, we describe a novel CRISPR-based method (CRISPR-hapC) for haplotyping. Based on the generation (with a pair of CRISPRs) of extrachromosomal circular DNA in cells, the CRISPR-hapC can map haplotypes from a few hundred bases to over 200 Mb. To streamline and demonstrate the applicability of the CRISPR-hapC and asPAM CRISPR for allele-specific gene editing, we reanalyzed the 1000 human pan-genome and generated a high frequency asPAM SNP and CRISPR database (www.crispratlas.com/knockout) for four CRISPR systems (SaCas9, SpCas9, xCas9 and Cas12a). Using the huntingtin (HTT) CAG expansion and transthyretin (TTR) exon 2 mutation as examples, we showed that the asPAM CRISPRs can specifically discriminate active and dead PAMs for all 23 loci tested. Combination of the CRISPR-hapC and asPAM CRISPRs further demonstrated the capability for achieving highly accurate and haplotype-specific deletion of the HTT CAG expansion allele and TTR exon 2 mutation in human cells. Taken together, our study provides a new approach and an important resource for genome research and allele-specific (haplotype-specific) gene therapy.

Cross-dehydrogenative coupling enables enantioselective access to CF3-substituted all-carbon quaternary stereocenters.

A cross-dehydrogenative coupling strategy for enantioselective access to acyclic CF3-substituted all-carbon quaternary stereocenters has been established. By using catalytic DDQ with MnO2 as an inexpensive terminal oxidant, asymmetric cross coupling of racemic δ-CF3-substituted phenols with indoles proceeded smoothly, providing CF3-bearing all-carbon quaternary stereocenters with excellent chemo- and enantioselectivities. The generality of the strategy is further demonstrated by efficient construction of all-carbon quaternary stereocenters bearing other polyfluoroalkyl and perfluoroalkyl groups such as CF2Cl, C2F5, and C3F7.