824 resultados para HOT-SPOTS
Resumo:
The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold space is available to a repertoire of diverse sequences. The key question is what factors lead to the formation of a fold from diverse sequences. Here, with the NAD(P)-binding Rossmann fold domains as a case study and using the concepts of network theory, we have unveiled the consensus structural features that drive the formation of this fold. We have proposed a graph theoretic formalism to capture the structural details in terms of the conserved atomic interactions in global milieu, and hence extract the essential topological features from diverse sequences. A unified mathematical representation of the different structures together with a judicious concoction of several network parameters enabled us to probe into the structural features driving the adoption of the NAD(P)-binding Rossmann fold. The atomic interactions at key positions seem to be better conserved in proteins, as compared to the residues participating in these interactions. We propose a ``spatial motif'' and several ``fold specific hot spots'' that form the signature structural blueprints of the NAD(P)-binding Rossmann fold domain. Excellent agreement of our data with previous experimental and theoretical studies validates the robustness and validity of the approach. Additionally, comparison of our results with statistical coupling analysis (SCA) provides further support. The methodology proposed here is general and can be applied to similar problems of interest.
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Heat fluxes around short, three-dimensional protuberances on sharp and blunt cones in hypersonic flow were experimentally measured using platinum thin-film sensors deposited on macor inserts. A parametric study of different protrusion geometries and flow conditions were conducted. Excessive heating was observed at locations near the protrusion where increased vorticity is expected, with the hottest spot being presented at the foot of the protuberance immediately upstream of it. If left unchecked, these hot spots could prove detrimental to hypersonic flight vehicles. Z-type schlieren technique was used to visualize the flow features qualitatively. New correlations to predict the heat flux at the hot spot have been proposed. (C) 2014 Elsevier Inc. All rights reserved.
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We have constructed plasmids to be used for in vitro signature-tagged mutagenesis (STM) of Campylobacter jejuni and used these to generate STM libraries in three different strains. Statistical analysis of the transposon insertion sites in the C. jejuni NCTC 11168 chromosome and the plasmids of strain 81-176 indicated that their distribution was not uniform. Visual inspection of the distribution suggested that deviation from uniformity was not due to preferential integration of the transposon into a limited number of hot spots but rather that there was a bias towards insertions around the origin. We screened pools of mutants from the STM libraries for their ability to colonize the ceca of 2-week-old chickens harboring a standardized gut flora. We observed high-frequency random loss of colonization proficient mutants. When cohoused birds were individually inoculated with different tagged mutants, random loss of colonization-proficient mutants was similarly observed, as was extensive bird-to-bird transmission of mutants. This indicates that the nature of campylobacter colonization in chickens is complex and dynamic, and we hypothesize that bottlenecks in the colonization process and between-bird transmission account for these observations.
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A mantle plume is understood as a hot, narrow, upwelling flow in the earth's mantle and accompanied by an efficient transfer of mass and energy from deep to upper layer of the earth. The cylindrical plume in earth's mantle plays an important role in explaining the origin of the surface hot spots and linear island chains. From the basic hydrodynamical equations, the detailed mechanical and thermal structure of a cylindrical plume of Newtouian fluids with temperature and pressure-dependent viscosity are given in the present paper. For two sets of rheological parameters the radial profiles of upward velocity, temperature and viscosity in the plume and radiuses of the plume at various depths have been calculated.
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Features of homologous relationship of proteins can provide us a general picture of protein universe, assist protein design and analysis, and further our comprehension of the evolution of organisms. Here we carried Out a Study of the evolution Of protein molecules by investigating homologous relationships among residue segments. The motive was to identify detailed topological features of homologous relationships for short residue segments in the whole protein universe. Based on the data of a large number of non-redundant Proteins, the universe of non-membrane polypeptide was analyzed by considering both residue mutations and structural conservation. By connecting homologous segments with edges, we obtained a homologous relationship network of the whole universe of short residue segments, which we named the graph of polypeptide relationships (GPR). Since the network is extremely complicated for topological transitions, to obtain an in-depth understanding, only subgraphs composed of vital nodes of the GPR were analyzed. Such analysis of vital subgraphs of the GPR revealed a donut-shaped fingerprint. Utilization of this topological feature revealed the switch sites (where the beginning of exposure Of previously hidden "hot spots" of fibril-forming happens, in consequence a further opportunity for protein aggregation is Provided; 188-202) of the conformational conversion of the normal alpha-helix-rich prion protein PrPC to the beta-sheet-rich PrPSc that is thought to be responsible for a group of fatal neurodegenerative diseases, transmissible spongiform encephalopathies. Efforts in analyzing other proteins related to various conformational diseases are also introduced. (C) 2009 Elsevier Ltd. All rights reserved.
Resumo:
Marine mammals, such as dolphins, can serve as key indicator species in coastal areas by reflecting the effects of natural and anthropogenic stressors. As such they are often considered sentinels of environmental and ecosystem health (Bossart 2006; Wells et al. 2004; Fair and Becker 2000). The bottlenose dolphin is an apex predator and a key component of many estuarine environments in the southeastern United States (Woodward-Clyde Consultants 1994; SCDNR 2005). Health assessments of dolphins are especially critical in areas where populations are depleted, show signs of epidemic disease and/or high mortality and/or where habitat is being altered or impacted by human activities. Recent assessments of environmental conditions in the Indian River Lagoon, Florida (IRL) and the estuarine waters surrounding Charleston, South Carolina (CHS) highlight the need for studies of the health of local bottlenose dolphins. While the condition of southeastern estuaries was rated as fair in the National Coastal Condition Report (U.S. EPA 2001), it was noted that the IRL was characterized by poorer than expected benthic communities, significant sediment toxicity and increased nutrient concentrations. Similarly, portions of the CHS estuary have sediment concentrations of aliphatic aromatic hydrocarbons, select inorganic metals, and some persistent pesticides far in excess of reported bioeffect levels (Hyland et al. 1998). Long-term trends in water quality monitoring and recent scientific research suggest that waste load assimilation, non-point source runoff impacts, contaminated sediments, and toxic pollutants are key issues in the CHS estuary system. Several ‘hot spots’ with high levels of heavy metals and organic compounds have been identified (Van Dolah et al. 2004). High concentrations of anthropogenic trace metals, polychlorinated biphenyls (PCB’s) and pesticides have been found in the sediments of Charleston Harbor, as well as the Ashley and Cooper Rivers (Long et al. 1998). Two superfund sites are located within the CHS estuary and the key contaminants of concern associated with these sites are: polycyclic aromatic hydrocarbons (PAH), lead, chromium, copper, arsenic, zinc and dioxin. Concerns related to the overall health of IRL dolphins and dermatologic disease observed in many dolphins in the area (Bossart et al. 2003) initiated an investigation of potential factors which may have impacted dolphin health. From May-August 2001, 35 bottlenose dolphins died in the IRL during an unusual mortality event (MMC 2003). Many of these dolphins were diagnosed with a variety of skin lesions including proliferative ulcerative dermatitis due to protozoa and fungi, dolphin pox and a vesicular dermatopathy of unknown etiology (Bossart et al. 2003). Multiple species from fish to dolphins in the IRL system have exhibited skin lesions of various known and unknown etiologies (Kane et al. 2000; Bossart et al. 2003; Reif et al. 2006). On-going photo-identification (photo-ID) studies have documented skin diseases in IRL dolphins (Mazzoil et al. 2005). In addition, up to 70% of green sea turtles in the IRL exhibit fibropapillomas, with the highest rates of occurrence being seen in turtles from the southern IRL (Hirama 2001).
Resumo:
In May 2001, the National Marine Fisheries Service (NMFS) opened two areas in the northwestern Atlantic Ocean that had been previously closed to the U.S. sea scallop (Placopecten magellanicus) dredge fishery. Upon reopening these areas, termed the “Hudson Canyon Controlled Access Area” and the “Virginia Beach Controlled Access Area,” NMFS observers found that marine turtles were being caught incidentally in scallop dredges. This study uses the generalized linear model and the generalized additive model fitting techniques to identify environmental factors and gear characteristics that influence bycatch rates, and to predict total bycatch in these two areas during May-December 2001 and 2002 by incorporating environmental factors into the models. Significant factors affecting sea turtle bycatch were season, time-of-day, sea surface temperature, and depth zone. In estimating total bycatch, rates were stratified according to a combination of all these factors except time-of-day which was not available in fishing logbooks. Highest bycatch rates occurred during the summer season, in temperatures greater than 19°C, and in water depths from 49 to 57 m. Total estimated bycatch of sea turtles during May–December in 2001 and 2002 in both areas combined was 169 animals (CV=55.3), of which 164 (97%) animals were caught in the Hudson Canyon area. From these findings, it may be possible to predict hot spots for sea turtle bycatch in future years in the controlled access areas.
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During the reporting period, NaFIRRI realigned its projects under ARTP II extension to focus on: 1. Determination of appropriate technologies and methods for harvesting and conservation of fish species in the Albert and Kyoga Systems 2. Impact of policies and technologies on livelihoods 3. Generation of knowledge for the management of aquatic invasive weeds and their hot spots in Lakes Albert and Kyoga 5. Determination of environmental factors influencing productivity for fisheries in Lakes Albert and Kyoga Systems 6. MSI - Nile perch project 7. Adaptation and Facilitating Dissemination of Appropriate technologies for harvesting Commercial Species 8. Identification of fish species suitable for culture and marketing, and promotion of their commercial culture in the Eastern AEZ.
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In this study, a detailed analysis of both previously published and new data was performed to determine whether complete, or almost complete, mtDNA sequences can resolve the long-debated issue of which Asian mtDNAs were founder sequences for the Native American mtDNA pool. Unfortunately, we now know that coding region data and their analysis are not without problems. To obtain and report reasonably correct sequences does not seem to be a trivial task, and to discriminate between Asian-and Native American mtDNA ancestries may be more complex than previously believed. It is essential to take into account the effects of mutational hot spots in both the control and coding regions, so that the number of apparent Native American mtDNA founder sequences is not erroneously inflated. As we report here, a careful analysis of all available data indicates that there is very little evidence that more than five founder mtDNA sequences entered Beringia before the Last Glacial Maximum and left their traces in the current Native American mtDNA pool.
Resumo:
Relationships between nutrient concentrations and water hyacinth biomass and composition have been studied in the shallow inshore bays of lakes Victoria, Kyoga and Albert. Additional information was obtained from Victoria Nile, Albert Nile and Kagera River. In this section, seasonal changes in nutrients and oxygen concentrations are used to explain changes in water hyacinth composition, biomass and distribution in Lake Victoria. Lake Victoria is of particular interest because it experienced strong hyacinth infestations in 1995, a sink in 1998 and resurgence in 2001. The lake has also been extensively sampled and provides time series data in nutrient, oxygen, mixing and thermal stratification which provide an opportunity to relate water hyacinth distribution and biomass to environmental factors. The possible origins and impacts of nutrient loads into Lake Victoria are also discussed in relation to water hyacinth proliferation and distribution especially in relation to known 'hot-spots'.
Resumo:
Mitochondrial DNA (mtDNA) of six breeds of native domestic pigs from Yunnan province, southwest China, and two wild boars obtained from Sichuan, China, and Vietnam was analyzed using 20 restriction endonucleases that recognize six nucleotides. Restriction maps were made by double-digestion methods and polymorphic sites were located on the map. According to their mtDNA restriction types, all the breeds were classified into six groups. Genetic distances among groups were calculated to define their phylogenetic relationships. The relationship between the Sichuan wild boar and domestic pigs is close, while the Vietnamese wild boar is relatively far from them, so the domestic pigs in southwest China are likely to have originated from a wild pig which distributed in west China. We compare our results with previous reports in literature and discuss the relationship among Chinese pigs, Japanese pigs, and European pigs. The mtDNA cleavage pattern of the Mingguang pig digested by EcoRV was identical to that of Duroc; mutations at the EcoRI site, detected in the mtDNA of two Dahe pigs, are the same as in the Vietnamese wild boar, suggesting that mutational hot spots exist in the mtDNA of pigs.
Resumo:
We present radio images of NRAO 530 on scales ranging from pc to kpc. The observations include the EVN at 5 GHz, the VLBA at 1.6, 8.6 and 15 GHz, the MERLIN at 1.6 and 5 GHz, and the VLA at 5, 8.4, 15, 22, and 43 GHz. The VLBI images show a core-jet structure with an oscillating trajectory on a scale of about 30 mas north of the strongest compact component (core). Superluminal motions are detected in five of the jet components with apparent velocities in the range of 13.6 to 25.2c. A new component is detected at 15 GHz with the VLBA observations, which appears to be associated with the outburst in 2002. Significant polarized emission is detected around the core with the VLBA observations at 15 GHz. Rapid variations of the polarization intensity and angle are found between the epochs in 2002 and 2004. On the kpc-scale, a distant component (labelled as WL) located 11 aresec west (PA=-86 degrees) of the core is detected beyond the core-jet structure which extended to several hundreds of mas in the north-west direction (-50 degrees). A significant emission between the core-jet structure and the WL is revealed. A clump of diffuse emission (labelled EL, 12 arcsec long) at PA 70 degrees to the core, is also detected in the VLA observations, suggesting the presence of double lobes in the source. The core component shows a flat spectrum, while the distant components WL and EL have steep spectra. The steep spectra of the distant components and the detection of the arched emission suggest that the distant components are lobes or hot-spots powered by the core of NRAO 530. The morphologies from pc- to kpc-scales and the bending of jets are investigated. The observed radio morphology from pc to kcp appears to favor the model in which precession or wobbling of the nuclear disk drives the helical motion of the radio plasma and produces the S-shaped structure on kpc scale.
Resumo:
In this paper, the codes of Pattern Informatics (PI) method put forward by Rundle et al. have been worked out according to their algorithm published, and the retrospective forecast of PI method to North China (28.0 degrees-42.0 degrees N, 108.0 degrees-125.0 degrees E) and to Southwest China (22.0 degrees-28.3 degrees N, 98.0 degrees-106.0 degrees E) has been tested. The results show that the hit rates in different regions show a great difference. In Southwest China, 32 earthquakes with M(L)5.0 or larger have occurred during the predicted time period 2000-2007, and 26 out of the 32 earthquakes occurred in or near the hot spots. In North China, the total number of M(L)5.0 or larger was 12 during the predicted time period 2000-2007, and only 3 out of the 12 earthquakes occurred in or near the hot spots. From our results, we hold that if the PI method could be applied to all kinds of regions, the parameters associated with time points and time windows should be chosen carefully to obtain the higher hit rate. We also found that the aftershocks in a strong earthquake sequence affect the PI results obviously. Copyright (c) 2009 John Wiley & Sons, Ltd.
Resumo:
In this paper, the codes of Pattern Informatics (PI) method put forward by Rundle et al. have been worked out according to their algorithm published, and the retrospective forecast of PI method to North China (28.0 degrees-42.0 degrees N, 108.0 degrees-125.0 degrees E) and to Southwest China (22.0 degrees-28.3 degrees N, 98.0 degrees-106.0 degrees E) has been tested. The results show that the hit rates in different regions show a great difference. In Southwest China, 32 earthquakes with M(L)5.0 or larger have occurred during the predicted time period 2000-2007, and 26 out of the 32 earthquakes occurred in or near the hot spots. In North China, the total number of M(L)5.0 or larger was 12 during the predicted time period 2000-2007, and only 3 out of the 12 earthquakes occurred in or near the hot spots. From our results, we hold that if the PI method could be applied to all kinds of regions, the parameters associated with time points and time windows should be chosen carefully to obtain the higher hit rate. We also found that the aftershocks in a strong earthquake sequence affect the PI results obviously. Copyright (c) 2009 John Wiley & Sons, Ltd.
Resumo:
木质纤维素原料种类多、分布广、数量巨大,通过燃料乙醇生产技术、厌氧沼气发酵技术将其转化成乙醇、沼气等二次能源,一定程度上可以缓解化石能源的不断消耗所带来的能源危机,也解决了农林废弃物引起的环境污染问题。其中以木质纤维素原料生产燃料乙醇,还可以避免以淀粉类和糖类原料生产燃料乙醇时带来的“与人争粮”等一系列问题。因此具有重要的经济效益、环境效益和社会效益。 然而,木质纤维素原料结构致密,木质素包裹在纤维素、半纤维素外围,导致其很难被降解利用,必须进行适当的预处理,去除木质素,打破原有的致密结构,利于原料的后续利用。因此,预处理成为木质纤维素原料能源化利用的关键。而目前预处理环节的费用过于昂贵,于是寻找一种高效、低成本的预处理方法是当今研究的热点。 本论文采用组合白腐真菌对木质纤维素原料进行生物预处理研究,与其他物理化学法相比,该法有着专一性较强、反应温和、不造成环境污染、成本低等优势。白腐真菌主要通过分泌木质素降解酶对木质素进行降解,从而破坏原料的致密结构,提高后续利用效率。所以木质素降解酶酶活的高低是影响原料预处理效果的一个关键因素。于是本论文首先通过将白腐真菌进行组合的方式提高木质素降解酶(漆酶,Lac)酶活;接着对组合菌的菌株相互作用机理进行研究,阐明组合菌Lac 酶活提高的原因,为菌株组合提高Lac 酶活这种方法的应用提供理论依据,同时也为后续组合白腐真菌预处理木质纤维素原料提供指导;进一步采用固态发酵和木质素降解酶两种方式对木质纤维素原料进行预处理研究,最大化去除木质素成分,破坏原料的致密结构;最终对预处理后原料的酶解糖化进行初步研究,为原料后续的能源化应用奠定基础。具体研究结果如下: (1) 以实验室保存的三株主要分泌Lac 的白腐真菌为出发菌株,筛选得到一组Lac 酶活明显提高的组合菌55+m-6,其中菌株55 为Trametes trogii sp.,m-6 为Trametes versicolor sp.,组合后Lac 酶活较单菌株分别提高24.13倍和4.07 倍。组合菌的最适产酶条件为pH 6.5、C/N 16:1、Tween 80 添加量为0.01%,在该条件下组合菌的Lac 酶活峰值比未优化时提高4.11倍。 (2) 对组合菌55+m-6 菌株间相互作用机理进行研究,发现菌株之间不存在抑制作用;平板培养时,菌丝交界处Lac 酶活最高并分泌棕色色素;液体培养时,菌株m-6 对组合后Lac 酶活的提高起着更为重要的作用:菌株m-6的菌块、过滤灭菌胞外物以及高温灭菌胞外物均能明显刺激菌株55 的Lac产生;菌株55、m-6 进行组合后,同工酶种类未发生增减,但有三种Lac同工酶浓度有所提高;对菌株胞外物进行薄层层析和质谱分析,结果表明组合前后菌株胞外物中各物质在浓度上存在较大的变化。推测组合菌Lac酶活的明显提高,主要是由于菌株m-6 胞外物中的一些物质能刺激菌株55 分泌大量Lac 进行代谢,且这些刺激物质并非菌株m-6 特有,菌株55自身也可以代谢生成,但是适当的浓度才能刺激Lac 的大量分泌。 (3) 将组合菌55+m-6 用于固态发酵预处理木质纤维素原料,发现其对玉米秆的降解程度最大,在粉碎度40 目、含水率65%的最优处理条件下,处理至第15d,秸秆失重率为41.24%,其中木质素、纤维素、半纤维素均有降解,且Lac 和纤维素酶(CMC)酶活以及还原糖量均达到峰值。 (4) 对玉米秆进行木质素降解酶预处理,发现Lac/1-羟基苯并三唑(HBT)系统对玉米秆木质素的降解效果最好,在最优处理条件时,即HBT 用量0.2%、处理时间1d、Lac 用量50U/g,木质素降解率可达12.60%。预处理后玉米秆的致密结构被破坏,比表面积增大,利于后续酶与纤维素、半纤维素成分的结合。 (5) 对预处理后的玉米秆进行酶解糖化,其中组合菌固态发酵预处理后玉米秆的糖化率比对照高4.33 倍;Lac/HBT 系统预处理后玉米秆的糖化率比对照高2.99%,糖化液中主要含有木糖、葡萄糖两种单糖。 There are many kinds and large quantities of lignocellulosic biomass widely distributed on the earth. They can be converted into secondary energy such as fuel ethanol, biogas, et al., which can relieve the energy crisis caused by consumption of fossil energy resources and solve the problem of environmental pollution caused by agriculture and forestry waste. Meanwhile, the production of fuel ethanol from lignocellulosic biomass can ensure food supply to human kind instead of starch- and sugar-containing raw materials. So the energy conversion of lignocellulosic biomass contributes considerable economic, environment and social benefits. However, lignocellulosic biomass has the compact structure, in which lignin surrounds cellulose and hemicellulose, so it must be pretreated before energy usage and pretreatment is one of the most critical steps in the energy conversion of lignocellulosic biomass. At present, the cost of pretreatment is too expensive, so looking for an efficient and low-cost pre-treatment method is one of recent research hot spots. In this research, combined white rot fungi pretreatment method was used, which had some advantages in low cost, high specificity, mild reacting conditions and friendly environmental effects compared with the other physical and chemical methods. White rot fungi secrete lignin degrading enzymes to degrade the content of lignin and damage the contact structure of lignocellulosic biomass, so the activity of the lignin degrading enzymes is the key factor to the degradation effect of raw materials. Firstly, the combined fungi with high laccase activity were screened; secondly, the interaction mechanism between strains was studied, and the cause of higher laccase activity after strains combination was also preliminary clarified; under the guidance of the mechanism, lignocellulosic biomass was pretreated by the combined fungi; lastly, the enzymatic hydrolysis of pretreated lignocellulosic biomass was also preliminary studied; all of the researches could lay the foundation for the energy application of lignocellulosic biomass. The specific research results were as follows: (1) The combined fungi 55+m-6 with significant higher laccase activity were screened from the three white rot fungi stored in our lab which mainly secreted laccase. Strain 55 and strain m-6 were Trametes trogii sp. and Trametes versicolor sp., respectively. The laccase activity of combined fungi was 24.13 and 4.07-fold than strain 55 and strain m-6, respectively. The optimized condition for laccase production of the combined fungi in liquid medium was pH 6.5, C/N 16:1 and Tween 80 0.01%. In this optimized condition, the laccase activity of combined fungi was 4.11-fold higher comparing with which in non-optimized medium. (2) The interaction mechanism between strain 55 and strain m-6 was further studied, and no inhibition effect was observed. Brown pigment was secreted on the junction of the two strains on the plate, where the highest laccase activity was detected. Strain m-6 was much important to boost laccase activity of combined fungi in liquid medium, and strain 55 was stimulated by fungal plug, filter sterilized extracellular substances and high temperature sterilized extracellular substances of strain m-6 to produce laccase. The types of laccase isozymes did not change after combining strain 55 and strain m-6, but the concentrations of three types increased. Mass Spectrometry and TLC analysis of extracellular substances of each strain showed that concentration of some substances considerably changed after strains were combined. It was supposed that the cause of higher laccase activity of combined fungi was mainly due to some extracellular substances of strain m-6 with the appropriate concentration which stimulated laccase secretion of strain 55 and generated not only by strain m-6 but also by strain 55. (3) Combined fungi 55+m-6 were used to lignocellulosic biomass pretreatment with the type of solid-state fermentation. The highest degree of degradation of corn straw was obtained, including the rate of weight loss was 41.24% and the lignin, cellulose and hemicellulose were degraded partially under the optimized condition of 40 mesh, 65% water content on 15th day. Laccase, CMCase activities and content of reducing sugar reached the maximum value on that day. (4) Lignin degrading enzymes from combined fungi 55+m-6 were used for corn straw pretreatment. The most remarkable degradation of lignin in corn straw with Lac/1-hydroxybenzotriazole (HBT) system was observed, and the 12.60% lignin degradation was obtained under the optimized condition of 0.2% HBT, 50 U/g laccase for 1 d. After pretreated by Lac/HBT, the tight structure of corn straw was demolished and specific surface area increased, which had advantages for accessible of enzyme to cellulose and hemicellulose. (5) The corn straws pretreated by combined fungi 55+m-6 with the type of solid-state fermentation and Lac/HBT were used for enzymatic hydrolysis, and the saccharification rates of each pretreatment type were 4.33 times and 2.99% higher than CK, respectively. The enzymatic hydrolysis liquid of corn straw pretreated by Lac/HBT mainly contained xylose and glucose.