Complete valorization of lignocellulose with one-step acidified monophasic phenoxyethanol fractionation.

Effective fractionation of lignocelluosic biomass and subsequent valorization of all three major components under mild conditions were achieved. Pretreatment with acidified monophasic phenoxyethanol (EPH) efficiently removed 92.6% lignin and 80% xylan from poplar at 110 ℃ in 60 min, yielding high-value EPH-xyloside, EPH-modified lignin (EPHL), and a solid residue nearly purely composed of carbohydrates. After removing the grafted acetyl groups using 1% NaOH at 50 ℃, the highest enzymatic digestibility reached 92.3%. EPHL could be recovered in high yield and purity with an uncondensed structure, while xylose was converted to EPH-xyloside, a potential precursor in biomedical industries. Additionally, the acidified monophasic EPH solvent could effectively fractionate biomass from species other than hardwood, achieving over 70% delignification from recalcitrant pinewood under the same mild conditions, demonstrating the high potential of monophasic EPH pretreatment.

Integrative genomic analyses of promoter G-quadruplexes reveal their selective constraint and association with gene activation.

G-quadruplexes (G4s) regulate DNA replication and gene transcription, and are enriched in promoters without fully appreciated functional relevance. Here we show high selection pressure on putative G4 (pG4) forming sequences in promoters through investigating genetic and genomic data. Analyses of 76,156 whole-genome sequences reveal that G-tracts and connecting loops in promoter pG4s display lower or higher allele frequencies, respectively, than pG4-flanking regions, and central guanines (Gs) in G-tracts show higher selection pressure than other Gs. Additionally, pG4-promoters produce over 72.4% of transcripts, and promoter G4-containing genes are expressed at relatively high levels. Most genes repressed by TMPyP4, a G4-ligand, regulate epigenetic processes, and promoter G4s are enriched with gene activation histone marks, chromatin remodeler and transcription factor binding sites. Consistently, cis-expression quantitative trait loci (cis-eQTLs) are enriched in promoter pG4s and their G-tracts. Overall, our study demonstrates selective constraint of promoter G4s and reinforces their stimulative role in gene expression.

Facilitation of axonal transcriptome analysis with quantitative microfluidic devices.

Microfluidic chambers are powerful tools for studying axonal mRNA localization and translation in neurons. In addition to specific manipulation and measurements of axons, microfluidic chambers are used for collecting axonal materials to perform axonal transcriptome analysis. However, traditional bipartite and tripartite chambers have limitations either in purity or quantity of collected axons. Here, we improved the design of traditional chambers. Moreover, we developed two new quantitative chambers, multi-compartmental quantitative bipartite chamber (MQBC) and long quantitative tripartite chamber (LQTC). Compared with the traditional chambers, MQBC and LQTC could dramatically increase the efficiency in collecting axonal RNA. Finally, we applied these chambers to do comparative axon transcriptome analysis of different types of neurons. Thus, our newly designed quantitative chambers significantly improve axon collection efficiency and facilitate axonal transcriptome analysis.

Applications of biomass-derived solvents in biomass pretreatment - Strategies, challenges, and prospects.

Biomass pretreatment is considered a key step in the 2nd generation biofuel production from lignocellulosic biomass. Research on conventional biomass pretreatment solvents has mainly been focused on carbohydrate conversion efficiency, while their hazardousness and/or carbon intensity were not comprehensively considered. Recent sustainability issues request further consideration for eco-friendly and sustainable alternatives like biomass-derived solvents. Carbohydrate and lignin-derived solvents have been proposed and investigated as green alternatives in many biomass processes. In this review, the applications of different types of biomass pretreatment solvents, including organic, ionic liquid, and deep eutectic solvents, are thoroughly discussed. The role of water as a co-solvent in these pretreatment processes is also reviewed. Finally, current research challenges and prospects of utilizing biomass-derived pretreatment solvents for pretreatment are discussed. Given bioethanol's market potential and increasing public awareness about environmental concerns, it will be a priority adopting sustainable and green biomass pretreatment solvents in biorefinery.

Review of chemical pretreatment of lignocellulosic biomass using low-liquid and low-chemical catalysts for effective bioconversion.

Chemical pretreatment of lignocellulosic biomass (LCB) is essential for effective biological conversion in subsequent steps to produce biofuels or biochemicals. For effective pretreatment, high lignin content and its recalcitrant nature of LCB are major factors influencing bioconversion, especially lignin is known to be effectively solubilized by alkaline, organic, and deep eutectic solvents, ionic liquids, while hemicellulose is effectively dissolved by various acid catalysts and organic solvents. Depending on the pretreatment method/catalyst used, different pretreatment process scheme should be applied with different amounts of catalyst and water inputs to achieve a satisfactory effect. In addition, the amount of processing water required in the following processes such as washing, catalyst recovery, and conditioning after pretreatment is critical factor for scale-up (commercialization). In this review, the amount of catalyst and/or water used, and the effect of pretreatment, properties of the products, and recovery of liquid are also discussed.

Utilization of guaiacol-based deep eutectic solvent for achieving a sustainable biorefinery.

This study proposed a renewable deep eutectic solvent (DES) pretreatment using lignin-derived guaiacol as the hydrogen bond donor. The DES showed excellent biomass fractionation efficiency after the incorporation of trace AlCl3 as the reinforcer, which removed 79.1 % lignin while preserving more than 90 % glucan. The pretreated bamboo exhibited 96.2 % glucan enzymatic hydrolysis yield at only 110 °C. The physicochemical properties of the pretreated solids were comprehensively investigated to explain how the DES fractionation overcame the biomass recalcitrance. The regenerated lignin from the DES pretreatment was also analyzed, which revealed that lignin ß-O-4 bond was significantly cleaved. This guaiacol-based DES could greatly contribute to establish a closed-loop biorefinery sequence with high lignin fractionation efficiency and great solvent recyclability.

Emerging Roles of LncRNAs in the EZH2-regulated Oncogenic Network.

Cancer is a life-threatening disease, but cancer therapies based on epigenetic mechanisms have made great progress. Enhancer of zeste homolog 2 (EZH2) is the key catalytic component of Polycomb repressive complex 2 (PRC2) that mediates the tri-methylation of lysine 27 on histone 3 (H3K27me3), a well-recognized marker of transcriptional repression. Mounting evidence indicates that EZH2 is elevated in various cancers and associates with poor prognosis. In addition, many studies revealed that EZH2 is also involved in transcriptional repression dependent or independent of PRC2. Meanwhile, long non-coding RNAs (lncRNAs) have been reported to regulate numerous and diverse signaling pathways in oncogenesis. In this review, we firstly discuss functional interactions between EZH2 and lncRNAs that determine PRC2-dependent and -independent roles of EZH2. Secondly, we summarize the lncRNAs regulating EZH2 expression at transcription, post-transcription and post-translation levels. Thirdly, we review several oncogenic pathways cooperatively regulated by lncRNAs and EZH2, including the Wnt/ß-catenin and p53 pathways. In conclusion, lncRNAs play a key role in the EZH2-regulated oncogenic network with many fertile directions to be explored.

Engineered Sorghum Bagasse Enables a Sustainable Biorefinery with p-Hydroxybenzoic Acid-Based Deep Eutectic Solvent.

Integrating multidisciplinary research in plant genetic engineering and renewable deep eutectic solvents (DESs) can facilitate a sustainable and economic biorefinery. Herein, we leveraged a plant genetic engineering approach to specifically incorporate C6 C1 monomers into the lignin structure. By expressing the bacterial ubiC gene in sorghum, p-hydroxybenzoic acid (PB)-rich lignin was incorporated into the plant cell wall while this monomer was completely absent in the lignin of the wild-type (WT) biomass. A DES was synthesized with choline chloride (ChCl) and PB and applied to the pretreatment of the PB-rich mutant biomass for a sustainable biorefinery. The release of fermentable sugars was significantly enhanced (∼190 % increase) compared to untreated biomass by the DES pretreatment. In particular, the glucose released from the pretreated mutant biomass was up to 12 % higher than that from the pretreated WT biomass. Lignin was effectively removed from the biomass with the preservation of more than half of the ß-Ο-4 linkages without condensed aromatic structures. Hydrogenolysis of the fractionated lignin was conducted to demonstrate the potential of phenolic compound production. In addition, a simple hydrothermal treatment could selectively extract PB from the same engineered lignin, showing a possible circular biorefinery. These results suggest that the combination of PB-based DES and engineered PB-rich biomass is a promising strategy to achieve a sustainable closed-loop biorefinery.

AKT1 is positively regulated by G-quadruplexes in its promoter and 3'-UTR.

AKT1 plays a key role in cell growth and survival, and its activation in cancers is mediated by different mechanisms. In this study, we investigated the potential of G-quadruplex (G4) formation by multiple consecutive G-tracts in the AKT1 promoter and its 3'-UTR. In circular dichroism analyses, synthetic oligonucleotides based on these G-tract regions showed molar ellipticity peaks at specific wavelengths of G4 structures. We verified G4 forming potential of these oligonucleotides using dimethyl sulfate footprinting, gel-shift and immunostaining assays. In reporter assays, mutations of the G-tracts in either the promoter or the 3'-UTR of AKT1 reduced expression mediated by these G-rich regions, suggesting positive regulation of AKT1 gene expression by these G4 structures. Furthermore, SP1 bound to its consensus sites regardless of the presence of G4 motifs in the AKT1 promoter, and both the G4 motifs and SP1 binding sites were needed to reach the strongest promoter strength.

The SNAIL1 promoter contains G-quadruplex structures regulating its gene expression and DNA replication.

SNAIL1 is a key regulator of epithelial-mesenchymal transition (EMT) and its expression is associated with tumor progression and poor clinical prognosis of cancer patients. Compared to the studies of SNAIL1 stability and its transcriptional regulation, very limited knowledge is available regarding effective approaches to directly target SNAIL1. In this study, we revealed the potential regulation of SNAIL1 gene expression by G-quadruplex structures in its promoter. We first revealed that the negative strand of the SNAIL1 promoter contained a multi-G-tract region with high potential of forming G-quadruplex structures. In circular dichroism studies, the oligonucleotide based on this region showed characteristic molar ellipticity at specific wavelengths of G-quadruplex structures. We also utilized native polyacrylamide gel electrophoresis, gel-shift assays, immunofluorescent staining, dimethyl sulfate footprinting and chromatin immunoprecipitation studies to verify the G-quadruplex structures formed by the oligonucleotide. In reporter assays, disruption of G-quadruplex potential increased SNAIL1 promoter-mediated transcription, suggesting that G-quadruplexes played a negative role in SNAIL1 expression. In a DNA synthesis study, we detected G-quadruplex-mediated retardation in the SNAIL1 promoter replication. Consistently, we discovered that the G-quadruplex region of the SNAIL1 promoter is highly enriched for mutations, implicating the clinical relevance of G-quadruplexes to the altered SNAIL1 expression in cancer cells.

Rhythmic light flicker rescues hippocampal low gamma and protects ischemic neurons by enhancing presynaptic plasticity.

The complex relationship between specific hippocampal oscillation frequency deficit and cognitive dysfunction in the ischemic brain is unclear. Here, using a mouse two-vessel occlusion (2VO) cerebral ischemia model, we show that visual stimulation with a 40 Hz light flicker drove hippocampal CA1 slow gamma and restored 2VO-induced reduction in CA1 slow gamma power and theta-low gamma phase-amplitude coupling, but not those of the high gamma. Low gamma frequency lights at 30 Hz, 40 Hz, and 50 Hz, but not 10 Hz, 80 Hz, and arrhythmic frequency light, were protective against degenerating CA1 neurons after 2VO, demonstrating the importance of slow gamma in cognitive functions after cerebral ischemia. Mechanistically, 40 Hz light flicker enhanced RGS12-regulated CA3-CA1 presynaptic N-type calcium channel-dependent short-term synaptic plasticity and associated postsynaptic long term potentiation (LTP) after 2VO. These results support a causal relationship between CA1 slow gamma and cognitive dysfunctions in the ischemic brain.

Surface plasmon resonance biosensor based on graphene and grating excitation.

A surface plasmon resonance biosensor based on a graphene-decorated grating excitation structure is proposed in this paper. The biosensor consists of a three-layer structure, including a graphene layer, a grating layer, and a high refractive index layer. The material of the grating layer is silica. The graphene is physically deposited on the grating ridges. An incident light with transverse magnetic polarization is used to excite surface plasmons in the mid-infrared spectral region, which is highly localized at both ends of the graphene layer. The property of the sensor is improved by the high refractive index dielectric layer, which enhances the absorption of incident light and increases the depth of the spectra. The finite-difference time-domain method is used to simulate the property of the sensor. The structure of the sensor could be optimized by changing the structural parameters and comparing the simulation results. The effective refractive index (RI) on the surface and the wavelength of the reflective resonance absorption peak will be changed when the surface of graphene adsorbs the surrounding analyte. The results show that the relationship between the analyte RI and the resonance wavelength is linear. The measurement range of analyte RI is 1-1.8, and the sensitivity is 2780 nm/RIU.

Deep Eutectic Solvent Pretreatment of Transgenic Biomass With Increased C6C1 Lignin Monomers.

The complex and heterogeneous polyphenolic structure of lignin confers recalcitrance to plant cell walls and challenges biomass processing for agroindustrial applications. Recently, significant efforts have been made to alter lignin composition to overcome its inherent intractability. In this work, to overcome technical difficulties related to biomass recalcitrance, we report an integrated strategy combining biomass genetic engineering with a pretreatment using a bio-derived deep eutectic solvent (DES). In particular, we employed biomass from an Arabidopsis line that expressed a bacterial hydroxycinnamoyl-CoA hydratase-lyase (HCHL) in lignifying tissues, which results in the accumulation of unusual C6C1 lignin monomers and a slight decrease in lignin molecular weight. The transgenic biomass was pretreated with renewable DES that can be synthesized from lignin-derived phenols. Biomass from the HCHL plant line containing C6C1 monomers showed increased pretreatment efficiency and released more fermentable sugars up to 34% compared to WT biomass. The enhanced biomass saccharification of the HCHL line is likely due to a reduction of lignin recalcitrance caused by the overproduction of C6C1 aromatics that act as degree of polymerization (DP) reducers and higher chemical reactivity of lignin structures with such C6C1 aromatics. Overall, our findings demonstrate that strategic plant genetic engineering, along with renewable DES pretreatment, could enable the development of sustainable biorefinery.

Lymphocyte-Activation Gene-3 Expression and Prognostic Value in Neoadjuvant-Treated Triple-Negative Breast Cancer.

PURPOSE: In this study, we aimed to evaluate lymphocyte-activation gene-3 (LAG-3) expression and its prognostic value in neoadjuvant-treated triple-negative breast cancer (TNBC). METHODS: LAG-3, programmed death-1 (PD-1), programmed death ligand-1 (PD-L1), and CD8+ tumor-infiltrating lymphocyte (TILs) levels were examined using immunohistochemistry in 148 preand 114 post-neoadjuvant chemotherapy (NACT) specimens of human TNBC tissue. Correlations between expression levels and clinicopathological features were analyzed. Prognostic values for combined detection in TNBC following NACT were evaluated. RESULTS: In pre-NACT specimens, LAG-3 expression showed a significant association with pathological complete response (pCR, p=0.038) and was correlated with PD-1 (p<0.001) and PD-L1 (p=0.008). In post-NACT specimens, high expression of LAG-3 showed significant effects on nodal status (p=0.023) and PD-1 (p<0.001). The expression of immune markers on TILs significantly increased following NACT. Multivariate analysis indicated that only nodal status (odds ratio [OR], 0.226; 95% confidence interval [CI], 0.079-0.644; p=0.005) and high quantities of CD8+TILs (OR, 3.186; 95% CI, 1.314-7.721; p=0.010) are independent predictors of pCR. Nodal status (hazard ratio [HR], 2.666; 95% CI, 1.271-5.594; p=0.010), CD8+TILs (HR, 0.313; 95% CI, 0.139-0.705; p=0.005), and the LAG-3-high/PD-L1-high group (HR, 2.829; 95% CI, 1.050-7.623; p=0.040) provided prognostic values for patients with TNBC following NACT. CONCLUSION: CD8+TILs were sensitive predictive markers in response to NACT. High expression of LAG-3 in residual tissues, especially in combination with PD-L1, was associated with poor prognosis.

Expression of Foxp3 and its prognostic significance in colorectal cancer.

The aim of this study was to explore the expression and clinical significance of Foxp3 in colorectal tumor cells. An immunohistochemistry assay was used to detect the expression of Foxp3 in 173 cases of colorectal cancer. The relationship between the clinicopathological factors and the prognosis of colorectal cancer was analyzed. The rate of positive Foxp3 expression in tumor cells was 89.7%. There were no significant differences between cases with and without expression of Foxp3 with regard to sex, age, primary cancer sites, and distal metastasis. The expression of Foxp3 was negatively correlated with lymph node metastasis and pathological tumor, node, metastasis (pTNM) stage in tumor cells ( P < 0.05), which reflects the depth of invasion. Foxp3 expression also had a positive correlation with the degree of differentiation ( P < 0.01). A high level of Foxp3 expression was observed more often in tumor cells compared to tumor-surrounding tissues ( P = 0.003). High expression of Foxp3 was also associated with longer overall and disease-free survival ( P ⩽ 0.001). Foxp3 expression in colorectal cancer cells correlates with many clinicopathological characteristics; moreover, high expression of Foxp3 may be a promising potential prognostic factor for patients with colorectal cancer.

Fatty acid synthase is a primary target of MiR-15a and MiR-16-1 in breast cancer.

Fatty acid synthase (FASN) is upregulated in breast cancer and correlates with poor prognosis. FASN contributes to mammary oncogenesis and serves as a bona fide target in cancer therapies. MicroRNAs inhibit gene expression through blocking mRNA translation or promoting mRNA degradation by targeting their 3'-UTRs. We identified four microRNAs in two microRNA clusters miR-15a-16-1 and miR-497-195 that share a common seed sequence to target the 3'-UTR of the FASN mRNA. In reporter assays, both of these microRNA clusters inhibited the expression of a reporter construct containing the FASN 3'-UTR. However, only ectopic miR-15a-16-1, but not miR-497-195, markedly reduced the levels of endogenous FASN in breast cancer cells. Both miR-15a and miR-16-1 contributes to inhibiting FASN expression and breast cancer cell proliferation. Consistently, a sponge construct consisting of eight repeats of the FASN 3'-UTR region targeted by these microRNAs could markedly increase endogenous FASN levels in mammary cells. When FASN expression was restored by ectopic expression in breast cancer cells, retarded cell proliferation caused by miR-15a-16-1 was partially rescued. In conclusion, we demonstrated that FASN expression is primarily downregulated by miR-15a and miR-16-1 in mammary cells and FASN is one of the major targets of these two tumor suppressive microRNAs.

Indications of clinical and genetic predictors for aromatase inhibitors related musculoskeletal adverse events in Chinese Han women with breast cancer.

BACKGROUND: Women with breast cancer treated with aromatase inhibitors (AIs) may experience musculoskeletal symptoms that lead to discontinuation of effective therapy. The purpose of the current study is to evaluate the clinical and genetic predictors for AIs-related musculoskeletal adverse events(MS-AEs). METHODOLOGY AND PRINCIPAL FINDINGS: We recruited 436 postmenopausal Chinese Han women receiving adjuvant AIs therapy for early-stage hormone-sensitive breast cancer. Patients completed a self-administered questionnaire assessing the presence of musculoskeletal symptoms that started or worsened after initiating AIs. 27 single nucleotide polymorphisms (SNP) of ESR1, ESR2 and PGR were analyzed by Sequenom MassARRAY assays and /or PCR-based TaqMan assays.Of the 436 enrolled women, 206 cases experienced musculoskeletal symptoms.Patients who received taxane chemotherapy were more than two times more likely than other patients to have AIs-related MS-AEs. Genetic assay had showed that only two ESR1 SNPs, rs2234693 and rs9340799 were associated with AIs-related MS-AEs.TT genotype and the T allele in rs2234693 was statistically significantly lower in AIs-Related MS-AEs group than controls (P = 0.001; P = 9.49E-7). The frequency of AA genotype and the A allele in rs9340799 was higher (P = 2.20E-5; P = 3.09E-4). CONCLUSIONS AND SIGNIFICANCE: Our results suggested that prior taxane-based chemotherapy was the clinical predictor, while rs2234693 and rs9340799 were the genetic predictors for AIs-related MS-AEs.