Annotation of 2,507 Saccharomyces cerevisiae genomes.

Saccharomyces cerevisiae (baker's yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry. Currently, a huge number of Saccharomyces cerevisiae genome sequences are available at the public domain. However, these genomes are distributed at different websites and a large number of them are released without annotation information. To provide one complete annotated genome data resource, we collected 2,507 Saccharomyces cerevisiae genome assemblies and re-annotated 2,506 assemblies using a custom annotation pipeline, producing a total of 15,407,164 protein-coding gene models. With a custom pipeline, all these gene sequences were clustered into families. A total of 1,506 single-copy genes were selected as marker genes, which were then used to evaluate the genome completeness and base qualities of all assemblies. Pangenomic analyses were performed based on a selected subset of 847 medium-high-quality genomes. Statistical comparisons revealed a number of gene families showing copy number variations among different organism sources. To the authors' knowledge, this study represents the largest genome annotation project of S. cerevisiae so far, providing rich genomic resources for the future studies of the model organism S. cerevisiae and its relatives.IMPORTANCESaccharomyces cerevisiae (baker's yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry. Though a huge number of Saccharomyces cerevisiae genome sequences are available at the public domain, these genomes are distributed at different websites and most are released without annotation, hindering the efficient reuse of these genome resources. Here, we collected 2,507 genomes for Saccharomyces cerevisiae, performed genome annotation, and evaluated the genome qualities. All the obtained data have been deposited at public repositories and are freely accessible to the community. This study represents the largest genome annotation project of S. cerevisiae so far, providing one complete annotated genome data set for S. cerevisiae, an important workhorse for fundamental biology, biotechnology, and industry.

Enhancing malting performance of harder barley varieties through ultrasound treatment.

Harder kernels of barley are regarded as one of the factors that restrict water and enzyme movement within the endosperm during malting. A comprehensive study of two domestic varieties was performed for evaluating malting quality. Both ß-glucan and total protein content of the Chinese domestic barley (Ganpi-6 and Kenpi-14) were significantly higher than Copeland. Grain hardness of the Chinese domestic barley was higher and water uptake ratio was lower compared with the Copeland. During germination, the expression levels of NCED1, NCED2 (major key regulatory enzymes for abscisic acid biosynthesis genes) were higher, whereas gibberelic acid (GA) synthesis genes (GA20ox1, GA2ox3, GA3ox2) were lower in the Ganpi-6, Kenpi-14 compared with Copeland. These two domestic barley varieties also showed significantly lower limit dextrinase and ß-glucanase activity compared with Copeland. Ultrasound treatment improved the malting quality of Ganpi-6 by enhancing water uptake and GA synthesis gene expression increased. Therefore, these findings provided insights into the future direction on the utilization of ultrasonication for the applications towards the improvement of the harder barley variety.

Bone metastasis in non-small-cell lung cancer: genomic characterization and exploration of potential targets.

Background: Bone metastasis (BM) seriously affects the quality of life and reduces the survival time of patients with non-small-cell lung cancer (NSCLC). The genomic characteristics and potential targets of BMs are yet to be fully explored. Objective: To explore the genetic characteristics and potential targets of BM in NSCLC. Design: In all, 83 patients with NSCLC were retrospectively selected in this study. Genomic characterization of BMs was explored with the analysis of NGS results from primary tumors and BMs in 6 patients, then combined with NGS results of lung tumors in 16 patients with initial recurrence in bone to analyze mutations potentially associated with BMs, and finally, the correlation was further validated in 61 postoperative patients. Methods: The next generation sequencing (NGS) was performed to identify genomic differences between pulmonary primary tumors and BM. Fluorescence in situ hybridization and immunohistochemistry were performed in postoperative tumor tissues from patients who had undergone radical surgery to validate the predictive role of molecular targets for BM. The correlation between cyclin-dependent kinase 4 (CDK4) and BM was evaluated by Pearson's chi-square test. The university of alabama at birminghan cancer data analysis portal (UALCAN) was carried out for the detection of CDK4 expression in lung cancer and the relationship between CDK4 and clinicopathological parameters. The relationship between prognosis and CDK4 expression was analyzed by the Kaplan-Meier plotter. Results: The rate of gene amplification was increased (24% versus 36%) while gene substitution/indel was decreased (64% versus 52%) in BMs. The BM-specific mutations were analyzed in 16 recurrent patients which revealed the highest incidence of CDK4 amplification (18.8%). According to the Kaplan-Meier plotter database, the NSCLC patients with high CDK4 gene expression showed poor overall survival (OS) and recurrence-free survival (RFS) (p < 0.05). The incidence of CDK4 amplification tended to be higher in recurrent patients compared to the patients without BM (18.8% versus 4.7%, p = 0.118). Conclusion: Compared to the primary tumors of NSCLC, the genome of BMs showed an increased proportion of amplification and a decreased proportion of gene substitution/indel. Furthermore, the CDK4 amplification ratio seemed to be elevated in NSCLC patients with BM which may be associated with poor OS and RFS.

Genomic characterization and potential targets of bone metastasis in non-small cell lung cancer NGS was performed on the matched primary tumors and bone metastases to explore the differences in the genomes of bone metastases, and it was found that gene amplification increased in bone metastases. Combined with the results of NGS in NSCLC patients with the first postoperative recurrence site in the bone, it was found that CDK4 amplification expression increased in bone metastases. Finally, the correlation between bone metastasis and CDK4 amplification was verified by expanding the sample.

Pulmonary salivary gland tumor-hyalinizing clear cell carcinoma: a literature review.

Primary pulmonary hyalinizing clear cell carcinoma (HCCC) is a very rare lung tumor that accounts for less than 0.09% of all primary lung tumors and has no specific epidemiology. The correct diagnosis requires imaging, laboratory, pathological, immunohistochemical, and molecular examination. The most typical feature of pulmonary HCCC is the clear cell component with clear stroma. In addition, the fusion gene EWSR1::ATF1 due to t(12;22)(q13;q12) is essential for the pathological diagnosis of pulmonary HCCC. The main treatment for pulmonary HCCC is surgery. This review focus on the pathological features, immunohistochemical examination, mutation analysis and treatment of pulmonary HCCC.

Codelivery of CuS and DOX into Deep Tumors with Size and Charge-Switchable PAMAM Dendrimers for Chemo-photothermal Therapy.

Accurate targeting of therapeutic agents to specific tumor tissues, especially via deep tumor penetration, has been an effective strategy in cancer treatments. Here, we described a flexible nanoplatform, pH-responsive zwitterionic acylsulfonamide betaine-functionalized fourth-generation PAMAM dendrimers (G4-AB), which presented multiple advantages for chemo-photothermal therapy, including template synthesis of ultrasmall copper sulfide (CuS) nanoparticles and further encapsulation of doxorubicin (DOX) (G4-AB-DOX/CuS), long-circulating performance by a relatively large size and zwitterionic surface in a physiological environment, combined size shrinkage, and charge conversions via pH-responsive behavior in an acidic tumor microenvironment (TME). Accordingly, high tumor penetration and positive cell uptake for CuS and DOX have been determined, which triggered an excellent combination treatment under near-infrared irradiation in comparison to the monochemotherapy system and irresponsive chemo-photothermal system. Our study represented great promise in constructing multifunctional carriers for the effective delivery of photothermal nanoparticles and drugs in chemo-photothermal therapy.

Beer-gut microbiome alliance: a discussion of beer-mediated immunomodulation via the gut microbiome.

As a long-established fermented beverage, beer is rich in many essential amino acids, vitamins, trace elements, and bioactive substances that are involved in the regulation of many human physiological functions. The polyphenols in the malt and hops of beer are also important active compounds that interact in both directions with the gut microbiome. This review summarizes the mechanisms by which polyphenols, fiber, and other beneficial components of beer are fermentatively broken down by the intestinal microbiome to initiate the mucosal immune barrier and thus participate in immune regulation. Beer degradation products have anti-inflammatory, anticoagulant, antioxidant, and glucolipid metabolism-modulating potential. We have categorized and summarized reported data on changes in disease indicators and in vivo gut microbiota abundance following alcoholic and non-alcoholic beer consumption. The positive effects of bioactive substances in beer in cancer prevention, reduction of cardiovascular events, and modulation of metabolic syndrome make it one of the candidates for microecological modulators.

Pickering emulsions stabilized by soybean protein isolate/chitosan hydrochloride complex and their applications in essential oil delivery.

In this work, fabrication of soybean protein isolate (SPI)/chitosan hydrochloride (CHC) composite particles stabilized O/W Pickering emulsions using soybean oil as an oil phase was optimized by examining the effects of pH, SPI/CHC mass ratio, SPI/CHC composite particle concentration and oil phase fraction on the stability of the emulsions. The results showed that under the conditions of SPI/CHC mass ratio 1:1, pH 4 and particle concentration 2 %, the SPI/CHC composite particles could stabilize the emulsions with oil phase fraction up to 80 %. At an oil phase fraction of 60 %, the emulsions had a minimum particle size. The microstructure, storage and oxidation stabilities and rheological properties of the emulsions were determined. Using this SPI/CHC composite particle-stabilized Pickering emulsion template, citrus essential oil (CEO) Pickering emulsion (CEOP) was prepared. CEOP was found to markedly inhibit two food-related microorganisms, Staphylococcus aureus and Escherichia coli. In addition, the CEOP emulsion dilution (containing 4500 µL CEO/L) not only improved the water solubility of CEO, but also effectively retarded the browning and bacterial growth of fresh-cut apple. The SPI/CHC-stabilized Pickering emulsion template constructed in this work provides a promising alternative for the delivery of antimicrobial essential oils in the food industry.

Glycopolymer-based multifunctional antibacterial hydrogel dressings for accelerating cutaneous wound healing.

Antimicrobial hydrogel dressings have received extensive attention for their wide and promising applications in preventing infections associated with wound healing. However, the development of versatile antibacterial hydrogels inevitably leads to complex structures, which restricts their applications. In this work, a multifunctional antibacterial hydrogel based on a reversible diolborate bond crosslinked network was prepared via the interactions between the zwitterionic glycopolymer poly[(2-methacryloyloxyethyl phosphorylcholine)-co-(N,N-dimethylacrylamide)-co-(2-lactobionamidoethyl methacrylamide)] (PMDL) and borax in conjunction with a simple mixing of Ag NPs within 10 s. The obtained PMDL-12%/borax/Ag NP hydrogel displays a rapid self-healing ability and excellent injectability, as well as good adhesiveness to biological tissues and surfaces of various materials. Moreover, the hydrogels exhibit efficient antibacterial activities against Escherichia coli and Staphylococcus aureus, which could prevent bacterial infections in wound care. The multifunctional hydrogel also shows good cytocompatibility and hemocompatibility. Importantly, in vivo wound healing evaluation of a mouse full-thickness skin defect model confirms that the hydrogel effectively accelerates cutaneous regeneration and wound healing by regulating inflammation and promoting collagen deposition. This multifunctional wound dressing hydrogel prepared using a facile strategy has promising application in biomedical areas.

Soybean protein isolate/chitosan complex-rutin microcapsules.

Rutin is a flavonoid polyphenol with excellent biological activity, but due to its instability and poor water solubility, the utilization rate is reduced in vivo. Preparation of rutin microcapsules from soybean protein isolate (SPI) and chitosan hydrochloride (CHC) by composite coacervation can improve this restriction. The optimal preparation conditions were as follows: the volume ratio of CHC/SPI 1:8, pH 6, and total concentration of CHC and SPI 2 %. The rutin encapsulation rate and loading capacity of the microcapsules were 90.34 % and 0.51 % under optimal conditions. The SPI-CHC-rutin (SCR) microcapsules had a gel mesh structure and good thermal stability, and the system was stable and homogeneous after 12 d storage. During in vitro digestion, the release rates of SCR microcapsules in simulated gastric and intestinal fluids were 16.97 % and 76.53 %, respectively, achieving a targeted release of rutin in intestinal fluids; and the digested products were found to exhibit superior antioxidant activity to that of free rutin digests, indicating a good protection of microencapsulation on the bioactivity of rutin. Overall, SCR microcapsules developed in this study effectively enhanced the bioavailability of rutin. The present work provides a promising delivery system for natural compounds with low bioavailability and stability.

Synthesis of pH-responsive polyzwitterions for activated cellular uptake and tumor accumulation of gold nanoparticles at tumorous acidity.

The response sensitivity of surface material plays an important role in adjustable nano-bio interactionin vivo. In this present, a zwitterionic polymer (polyzwitterion) containing quaternary ammonium cation and sulfonamide anion poly(4-((4-(3-(methacryloyloxy)propoxy)phenyl) sulfonamido)-N, N, N-trimethyl-4-oxobutan-1-aminium chloride) (PMPTSA) was synthesized by Reversible Addition-Fragmentation Chain Transfer Polymerization (RAFT) polymerization to explore the pH responsive behavior in tumors. The PMPTSA-coated gold nanoparticles (PMPTSA-@-Au NPs) showed zwitterionic nature such as antifouling ability, low cellular uptake and prolonged circulation time similar with common hydrophilic polymers, including polyethylene glycol (PEG), poly(carboxybetaine methacrylate) and poly(sulfobetaine methacrylate) functional gold nanoparticles in physiological environment (pH 7.4). A high sensitivity and reversible positive charge conversion of P(MPTSA)-@-Au NPs at tumor slight acidic microenvironment (∼pH 6.8) leaded to an enhanced cellular internalization than that at pH 7.4 and increased tumor accumulation compared with PEG, polycarboxybetaines and polymer sulphobetaine (PSB) functional gold nanoparticles. The highly pH responsive PMPTSA will provide the promising application in cancer nanomedicine.

Pulmonary Salivary Gland Tumor, Mucoepidermoid Carcinoma: A Literature Review.

Pulmonary mucoepidermoid carcinoma (PMEC) is the most common malignant salivary gland tumor in the lungs and accounts for 0.1-0.2% of all lung malignancies in adults. It has no specific epidemiological or clinical characteristics. Correct diagnosis requires the combined examinations of images, laboratories, pathology, and immunohistochemistry (IHC) as well as molecular characteristics. PMEC tumors are characterized by squamous, intermediate, and mucus-secreting cells. Currently, histological appearance, mitotic frequency, cellular atypia, and necrocytosis allow the classification of PMEC into low grade or high grade. Molecular changes are crucial to pathological diagnosis. The driver of PMEC seems to be the fusion protein MECT1-MAML2 that is generated from a genetic mutation in t (11; 19) (q21; p13), while other gene mutations are also reported. However, no treatment of PMEC exists so far; surgical excision is still the primary treatment, while the efficacies of chemotherapy or radiotherapy are undefined. Tyrosine kinase inhibitor (TKI) therapy and immunotherapy showed to have significant therapeutic effects but require more investigation and better understanding. This review focuses on the clinical characteristics, imaging and pathologic features, immunohistochemical examination, mutation analysis, differential diagnosis, prognosis, and treatment of PMEC.

Research on Broadband Matching Method for Capacitive Micromachined Ultrasonic Transducers Based on PDMS/TiO2 Particles.

The study of impedance matching between a transducer and its working medium is an important part of acoustic transducer design. The traditional quarter wavelength matching (Q-matching) scheme is not suitable for broadband capacitive micromachined ultrasonic transducers. To mitigate this issue, a 0-3 composite broadband matching layer based on polydimethylsiloxane (PDMS) substrate/TiO2 particles is designed to achieve electrical insulation and efficient acoustic energy transfer of underwater capacitive micromachined ultrasonic transducer (CMUT) devices. In this work, the coherent potential approximation model is used to analyze the properties of 0-3 composite materials. Samples are prepared for performance testing to determine the proportion of TiO2 particles that enable the 0-3 composite materials to have the same longitudinal acoustic impedance as water. The CMUT device is packaged by a spin coating and pouring process, and its performance tests are carried out. The experimental results show that the central frequency of the transducer remains at 1.74 MHz, the -6 dB fractional bandwidth increases from 97.3% to 100.3%, the 3 dB directional main beam width increases from 8.3° to 10.3°, the side lobes decrease significantly, and the device has good reception sensitivity. These values imply that the 0-3 composite material has good matching performance, and this matching scheme has the advantages of high efficiency and wide bandwidth. This broadband matching method endows CMUTs with great advantages in underwater detection systems, and it facilitates underwater ultrasonic imaging of CMUT.

Research on the Multi-Element Synthetic Aperture Focusing Technique in Breast Ultrasound Imaging, Based on the Ring Array.

As a widely clinical detection method, ultrasonography (US) has been applied to the diagnosis of breast cancer. In this paper, the multi-element synthetic aperture focusing (M-SAF) is applied to the ring array of breast ultrasonography (US) imaging, which addresses the problem of low imaging quality due to the single active element for each emission and the reception in the synthetic aperture focusing. In order to determine the optimal sub-aperture size, the formula is derived for calculating the internal sound pressure of the ring array with a 200 mm diameter, and the sound pressure distribution is analyzed. The ring array with 1024 elements (1024 ring array) is established in COMSOL Multiphysics 5.6, and the optimal sub-aperture size is 16 elements, according to the sound field beam simulation and the directivity research. Based on the existing experimental conditions, the ring array with 256 elements (256 ring array) is simulated and verified by experiments. The simulation has a spatial resolution evaluation in the k-Wave toolbox, and the experiment uses nylon rope and breast model imaging. The results show that if the sub-aperture size has four elements, the imaging quality is the highest. Specifically, the spatial resolution is the best, and the sound pressure amplitude and signal-to-noise ratio (SNR) are maintained at a high level in the reconstructed image. The optimal sub-aperture theory is verified by the two kinds of ring arrays, which also provide a theoretical basis for the application of the multi-element synthetic aperture focusing technology (M-SAF) in ring arrays.

Synergistic size and charge conversions of functionalized PAMAM dendrimers under the acidic tumor microenvironment.

Developing nanomedicine with highly adaptive behaviors has shown great effectiveness in cancer treatment. However, the multi-functional integration of nano-therapeutic systems inevitably leads to complexity in the structure and impairs the operational efficiency or performance. Herein, we describe a novel nano-therapeutic system, G4-AB, capable of simultaneous dual conversions of the size and charge while targeting the acidic tumor microenvironment. G4-AB, containing a hydrophobic inner cavity for doxorubicin (DOX) loading, was synthesized by modifying amine-terminated 4th-generation polyamidoamine (G4-PAMAM) dendrimers with acylsulfonamide betaine (AB). Due to the dipole-dipole interaction among the AB moieties, G4-AB self-assembles to form micellar clusters with a zwitterionic surface. Possessing an anti-fouling property and suitable size, G4-AB exhibits optimized blood circulation under physiological pH conditions. Moreover, the extracellular pH value of the tumor microenvironment (pH 6.5) can trigger the protonation of acylsulfonamide, resulting in the cationization of AB and dissociation of G4-AB into unimolecular micelles (∼12 nm) due to electrostatic repulsion. The synergistic dual conversions further ensure drug accumulation with enhanced tumor penetration and cell internalization. The in vitro and in vivo experiments demonstrate that the G4-AB-DOX nano-therapeutic system possesses better antitumor efficiency and lower toxicity than free DOX or PEGylated PAMAM.

Exploring the factors that affect the themostability of barley limit dextrinase - Inhibitor complex.

Barley Limit dextrinase (Hordeum vulgare HvLD) is the unique endogenous starch-debranching enzyme, determining the production of a high degree of fermentation. The activity of HvLD is regulated by an endogenous LD inhibitor protein (LDI). In beer production, free LD is easy to inactivate in mashing process under the condition of high temperature. The binding of LD with LDI protects it against heat inactivation. Exploring the factors affecting the themostability of HvLD-LDI complex is important for beer production. In this work, the themostability of HvLD-LDI complex at different NaCl concentrations and temperatures were explored by molecular dynamics simulation and binding free energy calculation. In NaCl solution, the complex exhibits higher conformational stability at 343 K and 363 K than those in pure water. Root mean square fluctuation (RMSF) analysis identified the thermal sensitive regions of HvLD and LDI. The binding free energy results suggest that the LD-LDI complex is more stable in NaCl solution than those in pure water at high temperature. The residues with high contribution to the complex were identified. The structural and dynamic details will help us to understand the driving forces that lead to the themostability of HvLD-LDI complex at different temperatures and different salt concentrations, which will facilitate the optimization conditions of beer production for maintaining the thermal stability and activity of HvLD.

Molecular brewing: The molecular structural effects of starch adjuncts on barley malt brewing performances.

In this study, the effects of starch adjuncts with different fine molecular structures obtained by size-exclusion chromatography on the mashing and fermentation efficiencies of barley malts were investigated. Following fermentation, violate compounds of freshly-fermented beer samples were determined by headspace-solid-phase microextraction coupled with gas chromatography-mass spectrometry analysis (HS-SMPE-GC-MS). High performance liquid chromatography results showed that depending on their molecular structures, starch adjuncts addition significantly increased wort maltose and maltotriose content, whereas reducing the glucose content and thus both the ratios of glucose and maltotriose to that of the maltose. The whole fermentation by dry beer yeast was finished within the first 48 h and reached to equilibrium for the rest 72 h, represented by the stable soluble protein content. Results also showed that the addition of starch adjuncts resulted into increased alcohol content, which was mainly attributed to the altered glucose/maltose ratio. The HS-SPME-GC-MS results showed that whether or not with starch adjuncts addition, the composition of violate compounds were not significantly influenced, their content, on the contrary, were altered, represented by different peak heights. This study provides important information concerning the molecular effects of starch adjuncts on brewing performances of barley malts, and also provides a new pathway for choosing suitable types of adjuncts for making beer with better quality.

Corrigendum: Understanding Thermostability Factors of Barley Limit Dextrinase by Molecular Dynamics Simulations.

[This corrects the article DOI: 10.3389/fmolb.2020.00051.].

Understanding Thermostability Factors of Barley Limit Dextrinase by Molecular Dynamics Simulations.

Limit dextrinase (LD) is the only endogenous starch-debranching enzyme in barley (Hordeum vulgare, Hv), which is the key factor affecting the production of a high degree of fermentation. Free LD will lose its activity in the mashing process at high temperature in beer production. However, there remains a lack of understanding on the factor affecting the themostability of HvLD at the atomic level. In this work, the molecular dynamics simulations were carried out for HvLD to explore the key factors affecting the thermal stability of LD. The higher value of root mean square deviation (RMSD), radius of gyration (R g), and surface accessibility (SASA) suggests the instability of HvLD at high temperatures. Intra-protein hydrogen bonds and hydrogen bonds between protein and water decrease at high temperature. Long-lived hydrogen bonds, salt bridges, and hydrophobic contacts are lost at high temperature. The salt bridge interaction analysis suggests that these salt bridges are important for the thermostability of HvLD, including E568-R875, D317-R378, D803-R884, D457-R214, D468-R395, D456-R452, D399-R471, and D541-R542. Root mean square fluctuation (RMSF) analysis identified the thermal-sensitive regions of HvLD, which will facilitate enzyme engineering of HvLD for enhanced themostability.

The activated DNA double-strand break repair pathway in cumulus cells from aging patients may be used as a convincing predictor of poor outcomes after in vitro fertilization-embryo transfer treatment.

Women with advanced maternal age exhibit low anti-Müllerian hormone (AMH) levels and an altered follicular environment, which is associated with poor oocyte quality and embryonic developmental potential. However, the underlying mechanism is poorly understood. The present study aimed to assesswhether aging patients exhibit an activated DNA double-strandbreak (DSB) repair pathway in cumulus cells and thus, an association with poor outcomes after in vitro fertilization-embryo transfer (IVF-ET) treatment. Cumulus cells from young (≤29 y) and aging (≥37 y) human female patients were collected after oocyte retrieval. Our results indicated that aging patients showed a higher rate of γ-H2AX-positive cells than in young patients (24.33±4.55 vs.12.40±2.31, P<0.05). We also found that the mRNA expression levels of BRCA1, ATM, MRE11 and RAD51 were significantly elevated in aging cumulus cells. Accordingly, significantly increased protein levels of phospho-H2AX, BRCA1, ATM, MRE11 and RAD51 could be observed in aging cumulus cells. Moreover, aging cumulus cells showed a more frequent occurrence of early apoptosis than young cumulus cells. This study found that increases in DSBs and the activation of the repair pathway are potential indicators that may be used to predictoutcomes after IVF-ET treatment.

Effect of Hydraulic Retention Time on Anaerobic Digestion of Wheat Straw in the Semicontinuous Continuous Stirred-Tank Reactors.

Three semicontinuous continuous stirred-tank reactors (CSTR) operating at mesophilic conditions (35°C) were used to investigate the effect of hydraulic retention time (HRT) on anaerobic digestion of wheat straw. The results showed that the average biogas production with HRT of 20, 40, and 60 days was 46.8, 79.9, and 89.1 mL/g total solid as well as 55.2, 94.3, and 105.2 mL/g volatile solids, respectively. The methane content with HRT of 20 days, from 14.2% to 28.5%, was the lowest among the three reactors. The pH values with HRT of 40 and 60 days were in the acceptable range compared to that with HRT of 20 days. The propionate was dominant in the reactor with HRT of 20 days, inhibiting the activities of methanogens and causing the lower methane content in biogas. The degradation of cellulose, hemicellulose, and crystalline cellulose based on XRD was also strongly influenced by HRTs.