Machine learning and bioinformatics to identify biomarkers in response to Burkholderia pseudomallei infection in mice

Objective:In the realm of Class I pathogens,Burkholderia pseudomallei(BP)stands out for its propensity to induce severe pathogenicity.Investigating the intricate interactions between BP and host cells is imperative for comprehending the dynamics of BP infection and discerning biomarkers indicative of the host cell response process.Methods:mRNA extraction from BP-infected mouse macrophages constituted the initial step of our study.Employing gene expression arrays,the extracted RNA underwent conversion into digital signals.The percentile shift method facilitated data processing,with the identification of genes manifesting significant differences accomplished through the application of the t-test.Subsequently,a comprehensive analysis involving Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway was conducted on the differentially expressed genes(DEGs).Leveraging the ESTIMATE algorithm,gene signatures were utilized to compute risk scores for gene expression data.Support vector machine analysis and gene enrichment scores were instrumental in establishing correlations between biomarkers and macrophages,followed by an evaluation of the predictive power of the identified biomarkers.Results:The functional and pathway associations of the DEGs predominantly centered around G protein-coupled receptors.A noteworthy positive correlation emerged between the blue module,consisting of 416 genes,and the StromaScore.FZD4,identified through support vector machine analysis among intersecting genes,indicated a robust interaction with macrophages,suggesting its potential as a robust biomarker.FZD4 exhibited commendable predictive efficacy,with BP infection inducing its expression in both macrophages and mouse lung tissue.Western blotting in macrophages confirmed a significant upregulation of FZD4 expression from 0.5 to 24 h post-infection.In mouse lung tissue,FZD4 manifested higher expression in the cytoplasm of pulmonary epithelial cells in BP-infected lungs than in the control group.Conclusion:Thesefindings underscore the upregulation of FZD4 expression by BP in both macrophages and lung tissue,pointing to its prospective role as a biomarker in the pathogenesis of BP infection.

Biofilm analyses and exoproduct release by clinical and environmental isolates of Burkholderia pseudomallei from Brazil

Objective:To characterize biofilm production by clinical(n=21)and environmental(n=11)isolates of Burkholderia pseudomallei and evaluate the production of proteases,hemolysins and siderophores.Methods:Initially,the 32 strains were evaluated for biofilm production in Müller-Hinton broth-1%glucose(MH-1%glucose)and BHI broth-1%glucose,using the crystal violet staining technique.Subsequently,growing(48 h)and mature(72 h)biofilms were evaluated by confocal microscopy.Finally,the production of proteases,hemolysins and siderophores by planktonic aggregates,growing biofilms and mature biofilms was evaluated.Results:All isolates produced biofilms,but clinical isolates had significantly higher biomass in both MH-1%glucose(P<0.001)and BHI-glucose 1%(P=0.005).The structural analyses by confocal microscopy showed thick biofilms,composed of multiple layers of cells,homogeneously arranged,with mature biofilms of clinical isolates presenting higher biomass(P=0.019)and thickness of the entire area(P=0.029),and lower roughness coefficient(P=0.007)than those of environmental isolates.Protease production by growing biofilms was significantly greater than that of planktonic(P<0.001)and mature biofilms(P<0.001).Hemolysin release by planktonic aggregates was higher than that of biofilms(P<0.001).Regarding siderophores,mature biofilms presented higher production than growing biofilms(P<0.001)and planktonic aggregates(P<0.001).Conclusions:Clinical isolates have higher production of biofilms than their environmental counterparts;protease and siderophores seem important for growth and maintenance of Burkholderia pseu­domallei biofilms.

T6SS-5 and the cGAS-STING pathway in Burkholderia pseudomallei infection and immunity

Burkholderia pseudomallei is a causative agent of melioidosis that can infect humans and animals in endemic countries,specifically in Southeast Asia and tropical Australia.A fundamental component for the pathogenesis of Burkholderia pseudomallei is the capability of the bacterium to enter,survive,replicate,and cause disease in a host cell by inducing the host cell fusion.Cell fusion results in multinucleated-giant cell formation,thus enabling the dissemination of Burkholderia pseudomallei intracellularly.cGAS reacts to Burkholderia pseudomallei infection by activating the cGAS-STING pathway and subsequently limiting host's aberrant cell division and cellular replication by inducing autophagic cell death.In this review,we discuss the host-pathogen interactions between the typeⅥsecretion system 5(T6SS-5)of Burkholderia pseudomallei and human cGAS pathway in melioidosis infections.Since T6SS-5 is a main virulent factor in Burkholderia pseudomallei and the c GAS pathway is vital for host immune response,elucidating their functions is important for better understanding the pathogenesis of Burkholderia pseudomallei.

Fatal hemophagocytic lymphohistiocytosis-induced multiorgan dysfunction secondary to Burkholderia pseudomallei sepsis: A case report

BACKGROUND Burkholderia pseudomallei(B.pseudomallei)is a short,straight,medium-sized Gramnegative bacterium that mostly exists alone,without a capsule or spores,has more than three flagella at one end,and actively moves.B.pseudomallei confers high morbidity and mortality,with frequent granulocytopenia in B.pseudomallei sepsisrelated deaths.However,mortality may be related to hemophagocytic lymphohistiocytosis(HLH)secondary to B.pseudomallei infection.CASE SUMMARY A 12-year-old female was referred from a local hospital to the pediatric intensive care unit with suspected septic shock and fever,cough,dyspnea,and malaise.After admission,supportive symptomatic treatments including fluid resuscitation,anti-infective therapy,mechanical ventilation,and a vasoactive drug maintenance cycle were carefully initiated.The patient became unconscious,her blood pressure could not be maintained even under the exposure of vasoactive drugs,and she experienced cardiorespiratory arrest.The patient died due to ineffective high-quality in-hospital cardiopulmonary resuscitation.A subsequent bone marrow smear examination revealed extensive phagocytosis,and the blood culture was positive for B.pseudomallei.Family history revealed a sibling death from B.pseudomallei sepsis 5 years earlier.CONCLUSION The higher mortality rate in patients with B.pseudomallei sepsis may be related to secondary HLH after infection,wherein multiorgan dysfunction syndrome may be directly related to infection or immune damage caused by secondary HLH.Patients with B.pseudomallei can be asymptomatic and can become an infective source.

Pathogenesis and drug resistance mechanism of Burkholderia pseudomallei

Burkholderia pseudomallei is the pathogen that causes melioidosis.Melioidosis has a long duration of chronic infection,atypical clinical manifestations at acute onset,and is prone to life-threatening complications and poor prognosis.Understanding the pathogenesis and drug resistance mechanism of Burkholderia pseudomallei will effectively help the diagnosis and treatment of the disease and improve the prognosis.This review focuses on the extracellular movement of Burkholderia pseudomallei in host cells,the way of infecting host cells,virulence factors,and drug resistance mechanisms(efflux pumps,changes in target sites,etc.).This study provides a possible direction for the early diagnosis,treatment and control of melioidosis caused by this bacterium.

Construction and biological characterization of Burkholderia pseudomallei sRNA gene deletion strain

Objective:Construction of Burkholderia pseudomallei(B.pseudomallei)sRNA knockout strains and observation of their biological function.Methods:Design 9sF/9sR,9xF/9xR and R1/F1 primers,which were used to amplify the homologous arm fragment upstream and downstream of the sRNA gene,through enzyme cutting,ligation,and transformation,the sRNA gene was knocked out from the B.pseudomallei by homologous recombination method.Results:The sRNA mutant was successfully constructed.In comparison with wild strain HNBP001,the growth rate,motility and biofilm formation ofΔsRNA decreased,but the antibiotic sensitivity has no differences.Conclusion:The sRNA knockout strain of B.pseudomallei was successfully constructed,laying a foundation for further research on its mechanism of regulating B.pseudomallei.

功能化离子液体修饰的SBA-15固定化Burkholderia cepacia脂肪酶

采用含不同碳链长度咪唑环的烷基功能化离子液体修饰介孔材料SBA-15,并通过X-射线衍射、元素分析、N2吸附-脱附、红外光谱和扫描电镜等方法研究了离子液体修饰对SBA-15结构的影响.以三乙酸甘油酯的水解为探针反应,考察了甲基、丁基、辛基等不同链长烷基取代咪唑类离子液体修饰的SBA-15固定化Burkholderia cepacia脂肪酶(BCL)的酶活、最适反应条件及稳定性等酶学性质.结果表明,离子液体修饰后材料保持了原有的介孔结构,其固定化酶对温度及低pH的敏感度降低,比活力及稳定性均显著提高.其中甲基功能化离子液体修饰的SBA-15固定化酶的比活力最高,是原粉SBA-15固定化酶的2.4倍;辛基功能化离子液体修饰的SBA-15固定化酶的热稳定性、储存稳定性、重复使用性及有机溶剂耐受性最佳.

Burkholderia Cepacia脂肪酶在氨基功能化离子液体修饰的SBA-15上的共价固定

合成了氨基以及氨基功能化离子液体修饰的介孔材料SBA-15(NH2-SBA和NH2-IL-SBA),并以戊二醛为活化剂对NH2-IL-SBA进行活化处理(CA-NH2-IL-SBA),通过元素分析、N2吸附-脱附、X射线衍射、红外光谱等方法研究了修饰及活化对SBA-15结构的影响.将所得新型固定化载体用于Burkholderia cepacia脂肪酶(BCL)的吸附固定、共价交联固定及聚集包被固定.以三乙酸甘油酯的水解为模型反应,考察了固定化BCL的酶活、最适反应条件、稳定性等酶学性质.结果表明,离子液体修饰后的载体保持了原有的孔道结构,与氨基修饰以及原粉SBA-15吸附固定的BCL(BCL-NH2-SBA和BCL-SBA-15)相比,其固定化酶的比活力和稳定性都得到了明显提高,对温度及低pH的敏感性降低.其中聚集包被固定的BCL在获得了相对较高酶负载量的同时显示了最好的稳定性,其热稳定性和重复使用性分别为BCL-SBA-15的4倍和2倍.

洋葱伯克霍尔德菌(Burkholderia cepacia)CF-66发酵生产新型抗菌物质CF66I培养基的优化

利用基于统计学的实验设计RSM(Responsesurfacemethodology)优化了BurkholderiacepaciaCF-66产新型抗菌活性物质CF66I的发酵培养基组成。首先,用部分重复因子实验对培养基组分NH4Cl,MgSO4·7H2O,柠檬酸钠及酵母粉浓度对菌株产CF66I的影响进行评价,找出主要影响因子为柠檬酸钠和酵母粉。两者均为正影响,其他组分对CF66I活性的影响不显著。其次用最陡爬坡路径逼近最大响应区域。最后用中心组合设计及响应面分析确定主要影响因子的最佳浓度。菌株在优化培养基中培养较初始培养基CF66I活性提高了约两倍。

Burkholderia cepacia X4降解油脂特性研究

从长期受油污染的土壤中分离筛选得到的Burkholderia cepaciaX4菌株能高效降解油脂。该菌株降解油脂的最适温度和pH分别为30℃和7.0,菌株降解油脂时适宜的氮源为硫酸铵,适宜碳氮比为4∶1。共基质碳源的添加有利于生物量的迅速增加和油脂降解率的提高,添加适量的葡萄糖能使油脂降解率提高8%～10%。50mg/L Ca2＋对菌株生长和油脂降解更有利。在橄榄油浓度高达20g/L条件下最大油脂降解率仍可达83%。在油脂浓度≤2500mg/L时,该菌对油脂的降解符合抑制动力学Monod方程。

Burkholderia cepacia S31细菌高产位置非特异性脂肪酶的发酵条件优化

从油脂污染的土壤中分离获得了1株高效产脂肪酶的细菌S31,经鉴定为Burkholderia cepacia(洋葱伯克霍尔德菌)。B.cepacia S31所产脂肪酶具有活性高、耐高温、耐有机溶剂和位置非特异性水解甘油三酯等优良特性。为了进一步提高S31菌株的产酶量,对该菌产酶的发酵条件进行优化。通过单因子试验筛选出最佳碳源为麸皮,最佳氮源为蛋白胨,最佳诱导物为Tween-80。通过对培养基各组分及外部培养条件因素的正交试验,确定S31菌产脂肪酶的摇瓶发酵最优条件为:以20 g.L-1麸皮、10 g.L-1蛋白胨、40 g.L-1Tween-80、0.5 g.L-1MgSO4和2 g.L-1K2HPO4为培养基(pH 7.0),250 mL三角瓶装40 mL培养基,3%接种量,30℃、180 r.min-1培养66 h可获得最理想的酶产量,达283.6 U.mL-1,比优化前提高2.73倍。

Burkholderia Vietnamiensis对水中结晶紫的降解

从福州某印染厂活性污泥中分离筛选出1株对结晶紫染料有强脱色能力的菌株,根据其形态学特征和生理生化鉴定以及16S rRNA基因序列分析,鉴定为Burkholderia Vietnamiensis C09V。在振荡培养条件下对该菌株的脱色降解特性进行了研究,结果表明,菌株C09V的最佳碳源为葡萄糖;最佳氮源为KNO3;最适脱色初始pH为5.0;最佳菌投加体积分数为5%;最适脱色温度为35℃;在最适脱色条件下脱色36 h,该菌株对30 mg.L-1结晶紫脱色率可达到96.5%。

The Factors Shaping Synonymous Codon Usage in the Genome of Burkholderia mallei

Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as ＇optimal codons＇ might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders.

Burkholderia cepecia JS-02酶法制备对羟基-D-苯甘氨酸的研究

对BurkholderiacepeciaJS 02"一菌双酶法"制备对羟基 D 苯甘氨酸过程的调控进行了研究,探讨了反应液pH值对于酶反应各个进程的影响,实施了调节反应液pH恒定为7 2的调控策略,使得D 海因酶与D N 氨甲酰基氨基酸水解酶同时具有较高的活力,并且较未调控前更有利于L 对羟基苯海因的消旋及DL 对羟基苯海因的溶解,底物转化率与产品收率分别由未调控时的92%与85%提高至99 5%与94%,反应时间由40h缩短至30h,生产速率由0 462g/(L·h)提高至0 681g/(L·h)

Burkholderia属luxIR同源群体感应系统的研究进展

介绍了群体感应系统和Burkholderia属概况,阐述了Burkhkolderia菌属中的群体感应系统,并展望了其应用前景。

Burkholderia cepecia.njut1中的海因酶的纯化及性质

经过硫酸铵分级沉淀、热处理、HiPrepTM Phenyl FF (high sub)疏水层析、DEAE Fastflow离子交换层析以及Sephadex G-200凝胶过滤,从Burkholderia cepecia.njut1中得到了海因酶,收率8.98%,纯化倍数为69.Burkholderia cepecia njut1海因酶是同源四聚体,亚基分子量52ku,等电点是5.09,具有严格的光学选择性,是D-型海因酶,并具有较广泛的底物适应性,对苄基海因和对羟苯海因有较高的亲和力.Burkholderia cepecia. njut1海因酶的最适催化的pH值为9.0. 酶在pH 6.5～10.0下稳定. 60℃时酶活力较高,但在此温度下酶的热稳定性较差.Burkholderia cepecia. njut1海因酶是金属依赖性酶,金属螯合剂EDTA对海因酶有抑制作用.二价金属离子对酶有较大的影响.

草莓采后灰霉病生防菌Burkholderia contaminans培养基优化分析

旨在研究洋葱伯克霍尔德菌Burkholderia contaminans在摇瓶条件下的生物量最大培养基配方。试验采用多因素二次通用旋转组合设计的方法,通过对不同碳源、氮源和无机盐种类和浓度对B.contaminans生长的影响,确定拮抗菌浓度最大的培养基配方。筛选出的最佳培养基配方为:麦芽浸粉2.11%、酵母提取物1.90%、磷酸二氢钾0.05%,硫酸锰0.05%。在该培养条件下,伯克氏菌Burkholderia contaminans B-1生物量达到最大值,且经过进一步验证,其优化效果较好。拮抗菌株B.contaminans培养条件的优化分析为该菌高产发酵工艺的建立奠定了基础,促进了该菌株在果蔬采后生物防治的应用与产业化开发。

洋葱伯克氏菌Burkholderia contaminans抗菌蛋白分离纯化及生物学特性分析

洋葱伯克氏菌(Burkholderia contaminans)从杏果实表面分离,实验证明其对果蔬采后多种病原真菌具有较强的抑制作用。为了进一步揭示其抑菌机理,通过菌体裂解、硫酸铵分级盐析、纤维素DE-52阴离子交换柱层析及Sephadex G-100凝胶过滤柱层析,得到一种具有抗菌活性的蛋白。经十二烷基硫酸钠-聚丙烯酰胺凝胶电泳(sodium dodecyl sulfate-polyacrylamide gel electrophoresis,SDS-PAGE)检测结果表明,该蛋白呈单一条带,其分子质量约为17.6kDa。粗提蛋白溶液具有一定热稳定性,在不同pH值条件下稳定,对有机试剂、紫外照射、蛋白酶不敏感。50mg/mL的Tween-80处理粗提液,活性比对照增加了12.5%,对还原剂SDS和二硫苏糖醇敏感。

H_2O_2供氧条件下Burkholderia cepacia好氧降解三氯乙烯和苯酚的共代谢机理

氯代有机溶剂与酚类化合物复合污染地下水的现象较为普遍,但地下水环境中溶解氧缺乏,好氧微生物降解作用难以发挥。本文驯化好氧微生物Burkholderia cepacia耐受高浓度H2O2,并利用H2O2作为供氧源降解地下水环境中的三氯乙烯(TCE)和苯酚。结果表明,对于Burkholderia cepacia的生长过程,H2O2的最佳投加量为4mmol/L,加入H2O2后,会短暂抑制TCE降解,但最终大幅提高了TCE的降解率,达到79.80%。动力学分析表明,在H2O2供氧条件下,共代谢苯酚与TCE的比降解速率可以由Monod模型和Haldane模型分别进行描述,且显著相关。研究结果为好氧微生物控制地下水环境中的TCE和苯酚复合污染提供了科学依据。

一株Burkholderia细菌的抗植物病源真菌及生物学特性的研究

目的研究分离的一株Burkholderia细菌对病原真菌的拮抗功能及其生物学特性。方法通过纸片法和菌块法分别对Burkholderia菌体及培养上清液作了抑菌活性测定,并对其碳、氮源利用,最适温度、pH等生长条件也进行了测定。同时,还测定了Siderophores和氢氰酸等的生成。结果发现细菌对小麦赤霉、烟草赤星、马铃薯干腐、西瓜枯萎,及棉花、番茄、酥梨病害的霉菌有明显的和不同程度的抑制作用。同时还发现该菌产生少量Siderophores。结论Burkholderia细菌可用于多种植物霉菌病害的生物防治。