Basis of the H2AK119 specificity of the Polycomb repressive deubiquitinase.

Repression of gene expression by protein complexes of the Polycomb group is a fundamental mechanism that governs embryonic development and cell-type specification1-3. The Polycomb repressive deubiquitinase (PR-DUB) complex removes the ubiquitin moiety from monoubiquitinated histone H2A K119 (H2AK119ub1) on the nucleosome4, counteracting the ubiquitin E3 ligase activity of Polycomb repressive complex 1 (PRC1)5 to facilitate the correct silencing of genes by Polycomb proteins and safeguard active genes from inadvertent silencing by PRC1 (refs. 6-9). The intricate biological function of PR-DUB requires accurate targeting of H2AK119ub1, but PR-DUB can deubiquitinate monoubiquitinated free histones and peptide substrates indiscriminately; the basis for its exquisite nucleosome-dependent substrate specificity therefore remains unclear. Here we report the cryo-electron microscopy structure of human PR-DUB, composed of BAP1 and ASXL1, in complex with the chromatosome. We find that ASXL1 directs the binding of the positively charged C-terminal extension of BAP1 to nucleosomal DNA and histones H3-H4 near the dyad, an addition to its role in forming the ubiquitin-binding cleft. Furthermore, a conserved loop segment of the catalytic domain of BAP1 is situated near the H2A-H2B acidic patch. This distinct nucleosome-binding mode displaces the C-terminal tail of H2A from the nucleosome surface, and endows PR-DUB with the specificity for H2AK119ub1.

21.83% incident light can circumvent a 6.6 × 6.6 cm2 obstruction by introducing a layer of bubbles into the photovoltaic glass.

Obstruction is inevitable and will significantly impact the actual output performance of photovoltaic modules, even jeopardize their operational safety. We introduced a layer of bubbles into photovoltaic glass. These bubbles can alter the path of incident light, while the internal reflection at the glass/air interface enables the redirected light rays to have longer lateral propagation distance, circumventing the obstructions. The optimized photovoltaic glass with a bubble diameter of 1.8 mm and a surface density of 16 cm-2 enables the light intensity underneath a 6.6 × 6.6 cm2 obstruction to reach 21.83% of the incident light intensity. This enhancement permits a partial shading of the photovoltaic module, increasing its output power by ∼20.8% and decreasing the reverse bias voltage on the shaded cell by ∼1.4 V.

Stella safeguards the oocyte methylome by preventing de novo methylation mediated by DNMT1.

Postnatal growth of mammalian oocytes is accompanied by a progressive gain of DNA methylation, which is predominantly mediated by DNMT3A, a de novo DNA methyltransferase1,2. Unlike the genome of sperm and most somatic cells, the oocyte genome is hypomethylated in transcriptionally inert regions2-4. However, how such a unique feature of the oocyte methylome is determined and its contribution to the developmental competence of the early embryo remains largely unknown. Here we demonstrate the importance of Stella, a factor essential for female fertility5-7, in shaping the oocyte methylome in mice. Oocytes that lack Stella acquire excessive DNA methylation at the genome-wide level, including in the promoters of inactive genes. Such aberrant hypermethylation is partially inherited by two-cell-stage embryos and impairs zygotic genome activation. Mechanistically, the loss of Stella leads to ectopic nuclear accumulation of the DNA methylation regulator UHRF18,9, which results in the mislocalization of maintenance DNA methyltransferase DNMT1 in the nucleus. Genetic analysis confirmed the primary role of UHRF1 and DNMT1 in generating the aberrant DNA methylome in Stella-deficient oocytes. Stella therefore safeguards the unique oocyte epigenome by preventing aberrant de novo DNA methylation mediated by DNMT1 and UHRF1.

Recent advances in MOF-bio-interface: a review.

Metal-organic frameworks (MOFs), as a class of promising material with adjustable function and controllable structure, have been widely used in the food industry, chemical industry, biological medicine, and sensors. Biomacromolecules and living systems play a critical role in the world. However, the insufficiency in stability, recyclability, and efficiency, significantly impedes their further utilization in slightly harsh conditions. MOF-bio-interface engineering effectively address the above-mentioned shortages of biomacromolecules and living systems, and thereby attracting considerable attentions. Herein, we systematically review the achievements in the area of MOF-bio-interface. In particular, we summarize the interface between MOFs and proteins (enzymes and non-enzymatic proteins), polysaccharides, DNA, cells, microbes, and viruses. Meanwhile, we discuss the limitations of this approach and propose future research directions. We expect that this review could provide new insights and inspire new research efforts towards life science and material science.

Peptide supplementation relieves stress and enhances glycolytic flux in filamentous fungi during organic acid bioproduction.

Filamentous fungi occupy a uniquely favorable position in the bioproduction of organic acids. Intracellular stress is the main stimulator in filamentous fungi to produce and accumulate organic acids with high flux. However, stress can affect the physiological activities of filamentous fungi, thereby deteriorating their fermentation performance. Herein, we report that peptide supplementation during Rhizopus oryzae fermentation significantly improved fumaric acid production. Specifically, fumaric acid productivity was elevated by approximately 100%, fermentation duration was shortened from 72 to 36 h, while maintaining the final titer. Furthermore, transcriptome profile analysis and biochemical assays indicated that the overall capabilities of the stress defense systems (enzymatic and nonenzymatic) were significantly improved in R. oryzae. Consequently, glycolytic metabolism was distinctly enhanced, which eventually resulted in improved fumaric acid production and reduced fermentation duration. We expect our findings and efforts to provide essential insights into the optimization of the fermentation performance of filamentous fungi in industrial biotechnology and fermentation engineering.

Improving carrier separation at the TiO2/CsPbIBr2 interface by gradient Sn-doping.

Subhani et al. found that Sm-doping in CsPbIBr2 decreased its bandgap from 2.05 eV to 1.8 eV; thus, the efficiency of CsPbIBr2 solar cells was improved by ∼30%. However, Sm is a vital strategic resource with high costs. Metal Sn is much more abundant and cheaper than Sm; meanwhile, it has been proven that Sn can adjust the bandgap of CsPbIBr2 in a broader range, 2.05 eV to 1.64 eV. Therefore, Sn-doping in CsPbIBr2 may improve the efficiency of CsPbIBr2 solar cells, even to a greater extent. In this work, we established the TiO2/CsPbIBr2 interface model by gradient Sn-doping in CsPbIBr2 and investigated the impacts of such gradient doping on the carrier separation behaviors at the TiO2/CsPbIBr2 interface from the aspects of the cross-interface electric field, bandgap, and band matching, based on first-principles calculations. It is found that gradient Sn-doping can transfer more electrons from TiO2 to perovskites, thus creating an enhanced cross-interface electric field conducive to the separation of carriers at the TiO2/CsPbIBr2 interface. Affected by the existence of the interface, the bandgap of each perovskite layer gradually increases as it moves away from the interface; in addition, due to the gradient Sn-doping, the steps between the bandgaps of adjacent perovskite layers become smaller and more uniform, which is favorable for the separation of electrons. In summary, gradient Sn-doping can improve the carrier separation at the TiO2/CsPbIBr2 interface.

Recent advances in microbial production of L-malic acid.

Over the last few decades, increasing concerns regarding fossil fuel depletion and excessive CO2 emissions have led to extensive fundamental studies and industrial trials regarding microbial chemical production. As an additive or precursor, L-malic acid has been shown to exhibit distinctive properties in the food, pharmaceutical, and daily chemical industries. L-malic acid is currently mainly fabricated through a fumarate hydratase-based biocatalytic conversion route, wherein petroleum-derived fumaric acid serves as a substrate. In this review, for the first time, we comprehensively describe the methods of malic acid strain transformation, raw material utilization, malic acid separation, etc., especially recent progress and remaining challenges for industrial applications. First, we summarize the various pathways involved in L-malic acid biosynthesis using different microorganisms. We also discuss several strain engineering strategies for improving the titer, yield, and productivity of L-malic acid. We illustrate the currently available alternatives for reducing production costs and the existing strategies for optimizing the fermentation process. Finally, we summarize the present challenges and future perspectives regarding the development of microbial L-malic acid production. KEY POINTS: • A range of wild-type, mutant, laboratory-evolved, and metabolically engineered strains which could produce L-malic acid were comprehensively described. • Alternative raw materials for reducing production costs and the existing strategies for optimizing the fermentation were sufficiently summarized. • The present challenges and future perspectives regarding the development of microbial L-malic acid production were elaboratively discussed.

Stella protein facilitates DNA demethylation by disrupting the chromatin association of the RING finger-type E3 ubiquitin ligase UHRF1.

Stella is a maternal gene required for oogenesis and early embryogenesis. Stella overexpression in somatic cells causes global demethylation. As we have recently shown, Stella sequesters nuclear ubiquitin-like with PHD and RING finger domains 1 (UHRF1), a RING finger-type E3 ubiquitin ligase essential for DNA methylation mediated by DNA methyltransferase 1 and triggers global demethylation. Here, we report an overexpressed mutant Stella protein without nuclear export activity surprisingly retained its ability to cause global demethylation. By combining biochemical interaction assays, isothermal titration calorimetry, immunostaining, and live-cell imaging with fluorescence recovery after photobleaching, we found that Stella disrupts UHRF1's association with chromatin by directly binding to the plant homeodomain of UHRF1 and competing for the interaction between UHRF1 and the histone H3 tail. Consistently, overexpression of Stella mutants that do not directly interact with UHRF1 fails to cause genome-wide demethylation. In the presence of nuclear Stella, UHRF1 could not bind to chromatin and exhibited increased dynamics in the nucleus. Our results indicate that Stella employs a multilayered mechanism to achieve robust UHRF1 inhibition, which involves the dissociation from chromatin and cytoplasmic sequestration of UHRF1.

Patterned Amyloid Materials Integrating Robustness and Genetically Programmable Functionality.

The precise manipulation, localization, and assembly of biological and bioinspired molecules into organized structures have greatly promoted material science and bionanotechnology. Further technological innovation calls for new patternable soft materials with the long-sought qualities of environmental tolerance and functional flexibility. Here, we report a patterned amyloid material (PAM) platform for producing hierarchically ordered structures that integrate these material attributes. This platform, combining soft lithography with generic amyloid monomer inks (consisting of genetically engineered biofilm proteins dissolved in hexafluoroisopropanol), along with methanol-assisted curing, enables the spatially controlled deposition and in situ reassembly of amyloid monomers. The resulting patterned structures exhibit spectacular chemical and thermal stability and mechanical robustness under harsh conditions. The PAMs can be programmed for a vast array of multilevel functionalities, including anchoring nanoparticles, enabling diverse fluorescent protein arrays, and serving as self-supporting porous sheets for cellular growth. This PAM platform will not only drive innovation in biomanufacturing but also broaden the applications of patterned soft architectures in optics, electronics, biocatalysis, analytical regents, cell engineering, medicine, and other areas.

Small molecules capable of activating DNA methylation-repressed genes targeted by the p38 mitogen-activated protein kinase pathway.

Regulation of gene expression by epigenetic modifications such as DNA methylation is crucial for developmental and disease processes, including cell differentiation and cancer development. Genes repressed by DNA methylation can be derepressed by various compounds that target DNA methyltransferases, histone deacetylases, and other regulatory factors. However, some additional, unknown mechanisms that promote DNA methylation-mediated gene silencing may exist. Chemical agents that can counteract the effects of epigenetic repression that is not regulated by DNA methyltransferases or histone deacetylases therefore may be of research interest. Here, we report the results of a high-throughput screen using a 308,251-member chemical library to identify potent small molecules that derepress an EGFP reporter gene silenced by DNA methylation. Seven hit compounds were identified that did not directly target bulk DNA methylation or histone acetylation. Analyzing the effect of these compounds on endogenous gene expression, we discovered that three of these compounds (compounds LX-3, LX-4, and LX-5) selectively activate the p38 mitogen-activated protein kinase (MAPK) pathway and derepress a subset of endogenous genes repressed by DNA methylation. Selective agonists of the p38 pathway have been lacking, and our study now provides critical compounds for studying this pathway and p38 MAPK-targeted genes repressed by DNA methylation.

Oxidation of silicon nanowire can transport much more light into silicon substrate.

Silicon nanowire (SiNW) has been widely used for light-trapping in photovoltaics, optical sensors, and other optoelectronic devices. However, we found that 58.4% of the light trapped by a SiNW with a diameter of 60 nm and a length of 1 µm will be wasted: 64.5% of the trapped light will be absorbed within itself, and 90.5% of carriers excited by this part of light will recombine before being transported to the silicon substrate. In this work, it is shown that oxidation of SiNW can transport much more light into the silicon substrate. At first, our simulation results demonstrate that oxidation can dramatically reduce the percentage of absorbed light. In an oxidized SiNW (O-SiNW) with a total and silicon core diameter of 60 nm and 30 nm, respectively, the percentage is about 44.5%. Next, a low carrier recombination ratio, about 27.3%, can be obtained in O-SiNW due to the passivation effect of the oxide layer. As a result, oxidation of SiNW can reduce the proportion of wasted light from 58.4% to 12.1%. More importantly, oxidation almost doesn't sacrifice the light-trapping ability: experimental measurements demonstrate that the average reflectance of an O-SiNW array is only slightly higher than that of a SiNW array, 3.9% vs. 3.0%. Such O-SiNW is promising to be used for low-loss light-trapping in specially designed photovoltaic devices.

Specific distribution of the light captured by silver nanowire.

The silver nanowire (AgNW) has excellent light capture ability, showing great prospects in many fields. Based on discrete dipole approximation simulations, it is found that the captured light can be subdivided into three parts: the near-field light occupies ~27.3%, mainly confined around the nanowire with a distance <20nm; the far-field part occupies ~59.6%, showing a dramatic conical distribution; and ~13.1% is ohmically absorbed. These insights are helpful to estimate the limited performance of AgNW-based device utilizing each subdivision, and locate the functional zone. Besides, we found that the light capture efficiency of AgNW can be easily controlled as it increases linearly with nanowire length.

Light harvesting of silicon nanostructure for solar cells application.

Silicon nanostructures have light-harvesting effects for enhancing the performance of solar cells. Based on theoretical investigations on the optical properties of silicon nanowire (Si NW), the influencing laws of the size of Si NW on its light-harvesting effect are proposed. For the first time, we reveal that the resonant wavelength of Si NW predicted by the leaky mode theory does not correspond to the actual resonant wavelength calculated by the discrete dipole approximation method, but exactly coincides with the leftmost wavelength of the resonance peak. Then, the size dependency of the resonant intensity and width of Si NW is different from that of spherical nanoparticles, which can be deduced from the Mie theory. The size dependencies of resonant intensity and width are also applicative for silver/silicon composite nanowires. In addition, it is found that the harvested light by the Si and Ag/Si NW both show significant radial locality feature. The insight in this work is fundamental for the design and fabrication of efficient light -harvesting nanostructures for photovoltaic devices.

Effective light absorption and its enhancement factor for silicon nanowire-based solar cell.

Although nanowire (NW) antireflection coating can enhance light trapping capability, which is generally used in crystal silicon (CS) based solar cells, whether it can improve light absorption in the CS body depends on the NW geometrical shape and their geometrical parameters. In order to conveniently compare with the bare silicon, two enhancement factors E(T) and E(A) are defined and introduced to quantitatively evaluate the efficient light trapping capability of NW antireflective layer and the effective light absorption capability of CS body. Five different shapes (cylindrical, truncated conical, convex conical, conical, and concave conical) of silicon NW arrays arranged in a square are studied, and the theoretical results indicate that excellent light trapping does not mean more light can be absorbed in the CS body. The convex conical NW has the best light trapping, but the concave conical NW has the best effective light absorption. Furthermore, if the cross section of silicon NW is changed into a square, both light trapping and effective light absorption are enhanced, and the Eiffel Tower shaped NW arrays have optimal effective light absorption.

H3.3-H4 tetramer splitting events feature cell-type specific enhancers.

Previously, we reported that little canonical (H3.1-H4)(2) tetramers split to form "hybrid" tetramers consisted of old and new H3.1-H(4) dimers, but approximately 10% of (H3.3-H4)2 tetramers split during each cell cycle. In this report, we mapped the H3.3 nucleosome occupancy, the H3.3 nucleosome turnover rate and H3.3 nucleosome splitting events at the genome-wide level. Interestingly, H3.3 nucleosome turnover rate at the transcription starting sites (TSS) of genes with different expression levels display a bimodal distribution rather than a linear correlation towards the transcriptional activity, suggesting genes are either active with high H3.3 nucleosome turnover or inactive with low H3.3 nucleosome turnover. H3.3 nucleosome splitting events are enriched at active genes, which are in fact better markers for active transcription than H3.3 nucleosome occupancy itself. Although both H3.3 nucleosome turnover and splitting events are enriched at active genes, these events only display a moderate positive correlation, suggesting H3.3 nucleosome splitting events are not the mere consequence of H3.3 nucleosome turnover. Surprisingly, H3.3 nucleosomes with high splitting index are remarkably enriched at enhancers in a cell-type specific manner. We propose that the H3.3 nucleosomes at enhancers may be split by an active mechanism to regulate cell-type specific transcription.

DFT study on the atomic-scale nucleation path of graphene growth on the Cu(111) surface.

The nucleation path of graphene growth on the Cu(111) surface is investigated by importing carbon atoms step-by-step using density functional theory (DFT) calculations. An overall path of graphene nucleation has been proposed based on configuration and energy analysis. At the very first stage, linear chains will be formed and dominate the copper surface. Then, Y-type (furcate) carbon species will be shaped when new carbon atoms are absorbed aside the linear chains. Finally, ring-containing carbon species and graphene islands will be formed stepwise, with energetic preference. We find that the Y-type and ring-containing carbon species are not likely formed directly at the initial stage of graphene nucleation, but should be formed starting from linear chains. The nucleation limiting step is the formation of the Y-type species, which must pass an energy barrier of about 0.25 eV. These underlying observations are instructive to stimulate future experimental efforts on graphene synthesis.

The Diagnostic Accuracy Between Radiomics Model and Non-radiomics Model for Preoperative of Microvascular Invasion of Solitary Hepatocellular Carcinoma: A Systematic Review and Meta-analysis.

RATIONALE AND OBJECTIVES: Microvascular invasion (MVI) is a key prognostic factor for hepatocellular carcinoma (HCC). The predictive models for solitary HCC could potentially integrate more comprehensive tumor information. Owing to the diverse findings across studies, we aimed to compare radiomic and non-radiomic methods for preoperative MVI detection in solitary HCC. MATERIALS AND METHODS: Articles were reviewed from databases including PubMed, Embase, Web of Science, and the Cochrane Library until April 7, 2023. The pooled sensitivity, specificity, positive likelihood ratio (PLR), and negative likelihood ratio (NLR) were calculated using a random-effects model within a 95% confidence interval (CI). Diagnostic accuracy was assessed using summary receiver-operating characteristic curves and the area under the curve (AUC). Meta-regression and Z-tests identified heterogeneity and compared the predictive accuracy. Subgroup analyses were performed to compare the AUC of two methods according to study type, study design, tumor size, modeling methods, and imaging modality. RESULTS: The analysis incorporated 26 studies involving 3539 patients with solitary HCC. The radiomics models showed a pooled sensitivity and specificity of 0.79 (95%CI: 0.72-0.85) and 0.78 (95%CI: 0.73-0.82), with an AUC at 0.85 (95%CI: 0.82-0.88). Conversely, the non-radiomics models had sensitivity and specificity of 0.74 (95%CI: 0.65-0.81) and 0.88 (95%CI: 0.82-0.92) and an AUC of 0.88 (95%CI: 0.85-0.91). Subgroups with preoperative MRI, larger tumors, and functional imaging had higher accuracy than those using preoperative CT, smaller tumors, and conventional imaging. CONCLUSION: Non-radiomic methods outperformed radiomic methods, but high heterogeneity calls across studies for cautious interpretation.

Preoperative prediction power of radiomics and non-radiomics methods based on MRI for early recurrence in hepatocellular carcinoma: a systemic review and meta-analysis.

OBJECTIVE: To compare radiomics and non-radiomics in predicting early recurrence (ER) in patients with hepatocellular carcinoma (HCC) after curative surgery. METHODS: We systematically searched PubMed and Embase databases. Studies with clear reference criteria were selected. Data were extracted and assessed for quality using the quality in prognosis studies tool (QUIPS) by two independent authors. All included radiomics studies underwent radiomics quality score (RQS) assessment. We calculated sensitivity, specificity, positive likelihood ratio (PLR), and negative likelihood ratio (NLR) using random or fixed models with a 95%CI. Forest maps visualized the data, and summary receiver operating characteristic (sROC) curves with the area under the curve (AUC) were generated. Meta-regression and subgroup analyses explored sources of heterogeneity. We compared sensitivity, specificity, PLR, and NLR using the z-test and compared AUC values using the Delong test. RESULTS: Our meta-analysis included 10 studies comprising 1857 patients. For radiomics, the pooled sensitivity, specificity, AUC of sROC, PLR and NLR were 0.84(95%CI: 0.78-0.89), 0.80(95%CI: 0.75-0.85), 0.89(95%CI: 0.86-0.91), 4.28(95%CI: 3.48-5.27) and 0.20(95%CI: 0.14-0.27), respectively, but with significant heterogeneity (I2 = 60.78% for sensitivity, I2 = 55.79% for specificity) and potential publication bias (P = 0.04). The pooled sensitivity, specificity, AUC of sROC, PLR, NLR for non-radiomics were 0.75(95%CI:0.68-0.81), 0.78(95%CI:0.72-0.83), 0.83(95%CI: 0.80-0.86), 3.45(95%CI: 2.68-4.44) and 0.32(95%CI: 0.24-0.41), respectively. There was no significant heterogeneity in this group (I2 = 0% for sensitivity, I2 = 17.27% for specificity). Radiomics showed higher diagnostic accuracy (AUC: 0.89 vs. 0.83, P = 0.0456), higher sensitivity (0.84 vs. 0.75, P = 0.0385) and lower NLR (0.20 vs. 0.32, P = 0.0287). CONCLUSION: The radiomics from preoperative MRI effectively predicts ER of HCC and has higher diagnostic accuracy than non-radiomics. Due to potential publication bias and suboptimal RQS scores in radiomics, these results should be interpreted cautiously.

Turning waste into treasure: A new direction for low-cost production of lipid chemicals from Thraustochytrids.

Thraustochytrids are marine microorganisms known for their fast growth and ability to store lipids, making them useful for producing polyunsaturated fatty acids (PUFAs), biodiesel, squalene, and carotenoids. However, the high cost of production, mainly due to expensive fermentation components, limits their wider use. A significant challenge in this context is the need to balance production costs with the value of the end products. This review focuses on integrating the efficient utilization of waste with Thraustochytrids fermentation, including the economic substitution of carbon sources, nitrogen sources, and fermentation water. This approach aligns with the 3Rs principles (reduction, recycling, and reuse). Furthermore, it emphasizes the role of Thraustochytrids in converting waste into lipid chemicals and promoting sustainable circular production models. The aim of this review is to emphasize the value of Thraustochytrids in converting waste into treasure, providing precise cost reduction strategies for future commercial production.

Deoxynivalenol in food and feed: Recent advances in decontamination strategies.

Deoxynivalenol (DON) is a mycotoxin that contaminates animal feed and crops around the world. DON not only causes significant economic losses, but can also lead diarrhea, vomiting, and gastroenteritis in humans and farm animals. Thus, there is an urgent need to find efficient approaches for DON decontamination in feed and food. However, physical and chemical treatment of DON may affect the nutrients, safety, and palatability of food. By contrast, biological detoxification methods based on microbial strains or enzymes have the advantages of high specificity, efficiency, and no secondary pollution. In this review, we comprehensively summarize the recently developed strategies for DON detoxification and classify their mechanisms. In addition, we identify remaining challenges in DON biodegradation and suggest research directions to address them. In the future, an in-depth understanding of the specific mechanisms through which DON is detoxified will provide an efficient, safe, and economical means for the removal of toxins from food and feed.