探讨中国生物医学文献数据库改版升级“一框六键”检索技巧与应用

目的：探讨中国生物医学文献数据库（CBM）改版升级＂一框六键＂检索技巧与应用。方法：通过介绍新版CBM数据库系统与旧版CBM数据库的检索功能进行比较,并对新版CBM数据库总结为＂一框六键＂,即＂一框＂为检索入口框;＂六键＂为基本检索键、主题词检索键、分类检索键、期刊检索键、作者检索键及检索历史键。逐一对各检索功能进行操作使用说明及例举。结果：利用文献数字对象唯一标识符（XML）技术,实现CBM数据库题录数据与维普全文数据库的链接。结论：突出了新版CBM数据库系统新增检索功能—新增字段、全文链接及检索结果分析,提供更加完善、强大的检索功能,更新频率快,标引更规范,使检索更加丰富、准确及人性化,且会受到越来越多用户关注与使用。     

A family of starch-active polysaccharide monooxygenases

The recently discovered fungal and bacterial polysaccharide monooxygenases (PMOs) are capable of oxidatively cleaving chitin, cellulose, and hemicelluloses that contain β(1→4) linkages between glucose or substituted glucose units. They are also known collectively as lytic PMOs, or LPMOs, and individually as AA9 (formerly GH61), AA10 (formerly CBM33), and AA11 enzymes. PMOs share several conserved features, including a monocopper center coordinated by a bidentate N-terminal histidine residue and another histidine ligand. A bioinformatic analysis using these conserved features suggested several potential new PMO families in the fungus Neurospora crassa that are likely to be active on novel substrates. Herein, we report on NCU08746 that contains a C-terminal starch-binding domain and an N-terminal domain of previously unknown function. Biochemical studies showed that NCU08746 requires copper, oxygen, and a source of electrons to oxidize the C1 position of glycosidic bonds in starch substrates, but not in cellulose or chitin. Starch contains α(1→4) and α(1→6) linkages and exhibits higher order structures compared with chitin and cellulose. Cellobiose dehydrogenase, the biological redox partner of cellulose-active PMOs, can serve as the electron donor for NCU08746. NCU08746 contains one copper atom per protein molecule, which is likely coordinated by two histidine ligands as shown by X-ray absorption spectroscopy and sequence analysis. Results indicate that NCU08746 and homologs are starch-active PMOs, supporting the existence of a PMO superfamily with a much broader range of substrates. Starch-active PMOs provide an expanded perspective on studies of starch metabolism and may have potential in the food and starch-based biofuel industries.Polysaccharide monooxygenases (PMOs) are enzymes secreted by a variety of fungal and bacterial species (1–5). They have recently been found to oxidatively degrade chitin (6–8) and cellulose (8–14). PMOs have been shown to oxidize either the C1 or C4 atom of the β(1→4) glycosidic bond on the surface of chitin (6, 7) or cellulose (10–12, 14), resulting in the cleavage of this bond and the creation of new chain ends that can be subsequently processed by hydrolytic chitinases and cellulases. Several fungal PMOs were shown to significantly enhance the degradation of cellulose by hydrolytic cellulases (9), indicating that these enzymes can be used in the conversion of plant biomass into biofuels and other renewable chemicals.There are three families of PMOs characterized thus far: fungal PMOs that oxidize cellulose (9–12) (also known as GH61 and AA9); bacterial PMOs that are active either on chitin (6, 8) or cellulose (8, 13) (also known as CBM33 and AA10); and fungal PMOs that oxidize chitin (AA11) (7). Sequence homology between these three families is very low. Nevertheless, the available structures of PMOs from all three families reveal a conserved fold, including an antiparallel β-sandwich core and a highly conserved monocopper active site on a flat protein surface (Fig. 1A) (2, 6, 7, 9, 10, 15–17). Two histidine residues in a motif termed the histidine brace coordinate the copper center. The N-terminal histidine ligand binds in a bidentate mode, and its imidazole ring is methylated at the N_ε position in fungal PMOs (Fig. 1A).Open in a separate windowFig. 1.(A) Representative overall and active site structures of fungal PMOs (PDB ID code 2YET) (10). (B) Structure of cellulose (18, 19). Chitin also contains β(1→4) linkages and has similar crystalline higher order structure to cellulose. (C) Model structure of amylopectin (23–25). Hydrogen bonds are shown with green dashed lines.Considering the conserved structural features, it is not surprising that the currently known PMOs act on substrates with similar structures. Cellulose and chitin contain long linear chains of β(1→4) linked glucose units and N-acetylglucosamine units, respectively (Fig. 1B). The polymer chains form extensive hydrogen bonding networks, which result in insoluble and very stable crystalline structures (18–21). PMOs are thought to bind to the substrate with their flat active site surface, which orients the copper center for selective oxidation at the C1 or C4 position (6, 16, 22). Some bacterial chitin-binding proteins are cellulose-active PMOs (8, 13, 14), further suggesting that the set of PMO substrates is restricted to β(1→4) linked polymers of glucose and glucose derivatives.Here, we report on the identification of new families of PMOs that contain several key features of previously characterized PMOs, but act on substrates different from cellulose or chitin. A member of one of these novel families of PMOs, NCU08746, was shown to oxidatively cleave amylose, amylopectin, and starch. We designate the NCU08746 family as starch-active PMOs. Both amylose and amylopectin contain linear chains of α(1→4) linked glucose, whereas the latter also contains α(1→6) glycosidic linkages at branch points in the otherwise α(1→4) linked polymer. Unlike cellulose and chitin, amylose and amylopectin do not form microcrystals; instead, they exist in disordered, single helical, and double helical forms (23–27) (see Fig. 1C for example). Starch exists partially in nanocrystalline form, but lacks the flat molecular surfaces as those found in chitin and cellulose. The discovery of starch-active PMOs shows that this oxidative mechanism of glycosidic bond cleavage is more widespread than initially expected.     

中美两数据库中有关PICC并发症及异常情况的文献分析

目的探讨国内外护理工作中对PICC并发症及其异常情况的研究状况。方法对中国生物医学文献数据库（CBM数据库）及美国PubMed数据库1999年1月-2007年12月有关PICC并发症及异常情况的文章进行检索分析。结果在数量上，CBM数据库中，统计符合纳入标准的文献有207篇，收录的文献逐年增加，由1999年的5篇增至2007年38篇；在PubMed数据库共检索到符合纳入标准文献37篇。在文献质量上,2个数据库中大多数文献都集中在C、D级，CBM数据库中，高质量的系统评价文献0篇，D级文献128篇，占61．8％，其中主要是一些描述性研究和没有对照的病例观察；PubMed数据库中，有3篇系统评价，D级文献13篇，占35．1％，其中9篇是个案分析。在文献内容方面，两数据库发表的有关PICC并发症及异常情况的文献在用途方面的差别无统计学意义（x ^2=10．25，P〉0．05）；PICC并发症有静脉炎，穿刺部位的渗血、血肿和感染，导管相关性感染等；异常情况有导管头端异位、导管漂移或脱出、导管破裂或断裂、导管堵塞等。结论对PICC并发症及异常情况的研究在世界范围内得到关注且发展迅速，国内发展也很快，但某些领域如恶性胸腔积液、顽旧性肝硬化腹水应用PICC治疗，以及一些罕见并发症，如臂动静脉瘘管、神经损伤、心律失常、呼吸窘迫、液体渗漏肝实质引起腹痛和呼吸困难等需要国内护理同行们进一步研究。     

A bioassay for Lafora disease and laforin glucan phosphatase activity

Objectives

Lafora disease is a rare yet invariably fatal form of progressive neurodegenerative epilepsy resulting from mutations in the phosphatase laforin. Several therapeutic options for Lafora disease patients are currently being explored, and these therapies would benefit from a biochemical means of assessing functional laforin activity following treatment. To date, only clinical outcomes such as decreases in seizure frequency and severity have been used to indicate success of epilepsy treatment. However, these qualitative measures exhibit variability and must be assessed over long periods of time. In this work, we detail a simple and sensitive bioassay that can be used for the detection of functional endogenous laforin from human and mouse tissue.

Design and methods

We generated antibodies capable of detecting and immunoprecipitating endogenous laforin. Following laforin immunoprecipitation, laforin activity was assessed via phosphatase assays using para-nitrophenylphosphate (pNPP) and a malachite green-based assay specific for glucan phosphatase activity.

Results

We found that antibody binding to laforin does not impede laforin activity. Furthermore, the malachite green-based glucan phosphatase assay used in conjunction with a rabbit polyclonal laforin antibody was capable of detecting endogenous laforin activity from human and mouse tissues. Importantly, this assay discriminated between laforin activity and other phosphatases.

Conclusions

The bioassay that we have developed utilizing laforin antibodies and an assay specific for glucan phosphatase activity could prove valuable in the rapid detection of functional laforin in patients to which novel Lafora disease therapies have been administered.     

2001-2011年我国乳腺癌药物治疗的文献计量分析

目的 从文献计量学角度了解国内2001-2011年乳腺癌药物治疗的研究情况.方法 以中国生物医学文献数据库为数据源,利用文献计量学方法,对国内公开发表的乳腺癌药物治疗研究文献进行分析.结果 2001-2011年我国乳腺癌药物治疗文献2 466篇,年均224篇,其中2006年篇数最多为335篇,2011年篇数最少为182篇.有2篇以上文献的药物68种,20种主要治疗乳腺癌的药物中以紫杉醇、顺铂、长春瑞滨和卡培他滨等4种药物治疗的文献最多达929篇.结论 2001-2011年我国乳腺癌药物治疗文献量基本平稳,乳腺癌药物治疗的热点为紫杉醇、顺铂等.     

CBM数据库作者机构非规范著录数据自动检测研究

对CBM数据库中作者机构非规范著录情况进行分析、归纳总结,依据已有的作者机构著录标准,开发非规范著录数据自动检测程序。结果表明该程序在显著提高工作效率的同时,保证较高的检测准确性,有助于提高CBM机构数据的标准化水平。     

基于著者共现的CBM机构名称规范研究

以中国生物医学文献数据库收录的期刊论文为数据源，从发文著者这个重要关联因素着手，开展基于共现分析的著者机构名称规范机制研究，提出基于著者共现的同一机构发现算法，经评测该算法推荐结果准确率达85%，具有较好的可参考性。     

PMAP-23-LK-CBM3融合蛋白的原核表达、纯化与鉴定

目的构建抗菌肽-23与3型碳水化合物结合分子（CBM3）融合蛋白的原核表达载体并进行诱导表达、纯化和鉴定。方法PCR扩增PMAP-23-LK-CBM3融合蛋白,产物经酶切、纯化、回收后与经同样双酶切并回收后的pET21a原核表达载体相连接,连接产物转化感受态DH5α菌,经菌落PCR筛选出阳性菌落并提取质粒进行初步酶切鉴定后进一步行双向测序鉴定,插入序列完全正确者命名为pET21a-PMAP-23-LK-CBM3重组载体,并将其转化感受态大肠埃希菌BL21（DE3）,加入IPTG诱导PMAP-23-LK-CBM3融合蛋白表达后提取菌体蛋白行亲和层析纯化,并对纯化产物进行SDS-PAGE鉴定和Western Blot鉴定。结果成功构建了pET21a-PMAP-23-LK-CBM3融合重组质粒,成功诱导、纯化并鉴定出PMAP-23-LK-CBM3融合蛋白,分子量与理论值相符。结论成功表达并纯化、鉴定出了PMAP-23-LK-CBM3融合蛋白,为进一步将其应用于抗菌机制和药理实验的研究奠定了基础。     

Approach bias modification in alcohol dependence: Do clinical effects replicate and for whom does it work best?

BackgroundAlcoholism is a progressive neurocognitive developmental disorder. Recent evidence shows that computerized training interventions (Cognitive Bias Modification, CBM) can reverse some of these maladaptively changed neurocognitive processes. A first clinical study of a CBM, called alcohol-avoidance training, found that trained alcoholic patients showed less relapse at one-year follow-up than control patients. The present study tested the replication of this result, and questions about mediation and moderation.Methods509 alcohol-dependent patients received treatment as usual (primarily Cognitive Behavior Therapy) inpatient treatment. Before and after treatment, the implicit approach bias was measured with the Alcohol Approach-Avoidance Task. Half of the patients were randomly assigned to CBM, the other half received treatment as usual only. Background variables, psychopathology and executive control were tested as possible moderating variables of CBM. One year after treatment, follow-up data about relapse were collected.ResultsThe group receiving CBM developed alcohol-avoidance behavior and reported significantly lower relapse rates at one-year follow-up. Change in alcohol-approach bias mediated this effect. Moderation analyses demonstrated that older patients and patients with a strong approach-bias at pretest profited most from CBM.ConclusionsCBM is a promising treatment add-on in alcohol addiction and may counter some of the maladaptive neurocognitive effects of long-term alcoholism.     

Case report: Fever- pneumonia- lymphadenectasis- osteolytic- subcutaneous nodule: Disseminated chromoblastomycosis caused by phialophora

Chromoblastomycosis (CBM) is a chronic cutaneous and subcutaneous fungal infection caused by certain dematiaceous fungi (usually Fonsecaea, Phialophora, or Cladophialophora). Histologically, CBM is characterized by the presence of medlar bodies. However, the diagnosis is difficult because of the rarity of these pathognomonic presentations and the wide variety of presentations. Treatment of these infections is challenging as it lacks standardization. Herein, we report a case of chromoblastomycosis caused by Phialophora, in a 42-year-old immunocompetent male agriculturist from the humid and subtropical region of southern China. He had a 3-month history of pneumonia with intermittent fever, coughing, and expectoration. The infection subsequently spread to the bone and lymph nodes forming deep lesions and eventually resulting in osteolysis and lymphadenectasis. These subcutaneous nodules were observed after 9 months. Antifungal treatment was administered for 20 months leading to clinical improvement before the patient was lost to follow-up. This case is unique because such deep lesions are rare in immunocompetent individuals and because the initial onset was associated with pneumonia.