Microbial biosensors: a review

A microbial biosensor is an analytical device which integrates microorganism(s) with a physical transducer to generate a measurable signal proportional to the concentration of analytes. In recent years, a large number of microbial biosensors have been developed for environmental, food, and biomedical applications. Starting with the discussion of various sensing techniques commonly used in microbial biosensing, this review article concentrates on the summarization of the recent progress in the fabrication and application of microbial biosensors based on amperometry, potentiometry, conductometry, voltammetry, microbial fuel cell, fluorescence, bioluminescence, and colorimetry, respectively. Prospective strategies for the design of future microbial biosensors will also be discussed.     

Long non‐coding RNA highly up‐regulated in liver cancer promotes epithelial‐to‐mesenchymal transition process in oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is an oral and maxillofacial malignancy that exhibits high incidence worldwide. In diverse human cancers, the long non‐coding RNA (lncRNA) highly up‐regulated in liver cancer (HULC) is aberrantly expressed, but how HULC affects OSCC development and progression has remained mostly unknown. We report that HULC was abnormally up‐regulated in oral cancer tissues and OSCC cell lines, and that suppression of HULC expression in OSCC cells not only inhibited the proliferation, drug tolerance, migration and invasion of the cancer cells, but also increased their apoptosis rate. Notably, in a mouse xenograft model, HULC depletion reduced tumorigenicity and inhibited the epithelial‐to‐mesenchymal transition process. Collectively, our findings reveal a crucial role of the lncRNA HULC in regulating oral cancer carcinogenesis and tumour progression, and thus suggest that HULC could serve as a novel therapeutic target for OSCC.     

Winter spatial distribution of fish larvae assemblages relative to the hydrography of the waters surrounding Taiwan

The aim of this study was to investigate the species composition and distribution of fish larvae in relation to hydrographic conditions in the waters surrounding Taiwan Island (TI) in February 2003. In total, 242 kinds of fish larvae belonging to 127 genera and 75 families were recognized. Among these, 109 taxa were identified to the family or genus level, others to the species level. The 12 predominant types, which constituted 71% of the total fish larvae, were Engraulis japonica, Scomber sp., Diaphus spp., Benthosema pterotum, Carangoides ferdau, Embolichthys mitsukurii, Maurolicus sp., unidentified Myctophidae, Gonostoma gracile, Trichiurus lepturus, unidentified Gobiidae, and Myctophum asperum. The distribution of fish larvae showed a clear association with water masses around TI, with higher abundances and lower species richness northwest of TI where the China Coastal Current prevails, and lower abundances and higher species diversity east of TI where the Kuroshio Current dominates. Cluster analysis distinguished three station groups and four species groups, and the distribution patterns of fish larvae also corresponded to hydrographic conditions. The total abundances of fish larvae and eight of the 12 predominant taxa showed significant and positive correlations with zooplankton abundance, which suggests that food source might be a key factor determining the abundance and distribution of fish larvae during the winter.     

乏情和发情初产母猪下丘脑–垂体–卵巢轴中lincRNAs表达谱比较分析

初产母猪断奶后能否正常发情对养猪生产影响重大,也是初产母猪被淘汰的主要原因。本研究以乏情和发情初产母猪为研究对象,首次利用RNA-seq技术对其下丘脑-垂体-卵巢轴中的基因间长链非编码RNAs(long intergenic noncoding RNAs,lincRNAs)进行筛选比较,得到lincRNAs的表达图谱,并对其特征和功能进行了初步分析。结果显示,在乏情和发情初产母猪下丘脑–垂体–卵巢轴中鉴定得到3519个lincRNAs,以发情组为对照共有17个lincRNAs存在差异表达,其中12个表达上调,5个表达下调(FC≥2,P<0.05)。选择4个差异表达的lincRNAs经qRT-PCR验证,其表达水平与测序结果基本一致。对这17个差异表达的lincRNAs进行GO分析、KEGG通路分析及lincRNA-mRNA共表达网络分析,发现这些lincRNAs主要与猪卵母细胞减数分裂成熟、卵巢细胞分化及颗粒细胞凋亡等生殖活动相关。本研究结果丰富了猪lincRNAs数据资源,为进一步深入研究初产母猪的生殖机能提供了理论依据。     

13C标记代谢流分析中天然稳定性同位素修正矩阵构建方法及应用

稳定性同位素¹³C标记实验是分析细胞代谢流的一种重要手段,主要通过质谱检测胞内代谢物中¹³C标记的同位素分布,并作为胞内代谢流计算时的约束条件,进而通过代谢流分析算法得到相应代谢网络中的通量分布。然而在自然界中,并非只有C元素存在天然稳定性同位素¹³C,其他元素如O元素也有其天然稳定性同位素¹⁷O、¹⁸O等,这使得质谱方法所测得的同位素分布中会夹杂除¹³C标记之外的其他元素的同位素信息,特别是分子中含有较多其他元素的分子,这将导致很大的实验误差,因此需要在进行代谢流计算前进行质谱数据的矫正。本研究提出了一种基于Python语言的天然同位素修正矩阵的构建方法,用于修正同位素分布测量值中由于天然同位素分布引起的测定误差。文中提出的基本修正矩阵幂方法用于构建各元素修正矩阵,结构简单、易于编码实现,可直接应用于¹³C代谢流分析软件数据前处理。将该修正方法应用于¹³C标记的黑曲霉（Aspergillus niger）胞内代谢流分析,结果表明本研究提出的方法准确有效,为准确获取微生物胞内代谢流分析提供了可靠的数据修正方法。     

Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis

The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.     

精胺和Mg~（2＋）对tRNA~（Ile）圆二向色谱的影响

由于精胺（ｓｐｅｒｍｉｎｅ）能特异地刺激哺乳动物ｔＲＮＡ~（Ｉｌｅ）的氨基酰化,本文用纯化的牛肝ｔＲＮＡ~（Ｉｌｅ）观察了精胺和Ｍｇ（２＋）对ｔＲＮＡ~（Ｉｌｅ）ＣＤ光谱的影响。结果显示：Ｍｇ（２＋）可使牛肝ｔＲＮＡ~（Ｉｌｅ）ＣＤ光谱峰向短波方向偏移２ｎｍ,波峰为２６３ｎｍ,峰值被增大约１０％,ΔθＭｇ（２＋）＝２．３×１０３ｄｅｇ·ｃｍ２／ｄｍｏｌ;而精胺使牛肝ｔＲＮＡ~（Ｉｌｅ）ＣＤ光谱峰减少４０％,Δθｓｐｅｒｍｉｎｅ＝１×１０（－４）ｄｅｇ·ｃｍ２／ｄｍｏｌ;精胺和Ｍｇ（２＋）对肝ｔＲＮＡ~（Ｉｌｅ）－ＩｌｅＲＳ复合物或ＩｌｅＲＳ的ＣＤ光谱基本无影响。表明Ｍｇ（２＋）和精胺可影响牛肝ｔＲＮＡ~（Ｉｌｅ）的构象。实验同时以酵母ｔＲＮＡ（Ｐｈｅ）和Ｅ·ｃｏｌｉｔＲＮＡ~（Ｉｌｅ）作为对照。     

阿维链霉菌Streptomyces avermitilis碱性脂肪酶LpsA2的表达和酶学性质分析

【目的】本研究将推测的阿维链霉菌(Streptomyces avermitilis)脂肪酶基因lpsA2在大肠杆菌(Escherichia coli)中进行异源表达及系统的酶学性质分析。【方法】提取阿维链霉菌基因组,设计特异性引物,PCR扩增脂肪酶基因lpsA2,使其在大肠杆菌中异源表达,利用6个组氨酸标签纯化脂肪酶LpsA2,并进行酶学性质分析;对LpsA2进行序列比对和进化分析。【结果】氨基酸序列比对显示LpsA2具有脂肪酶典型的由Ser、His和Asp构成的活性部位,即Ser130-Asp221-His25,其中Ser位于保守的五肽结构(Gly128-His129-Ser130-Gln131-Gly132)中;分子系统学分析显示,LpsA2是脂肪酶第一家族亚家族成员(Subfamily I.7);实验测得纯化的重组脂肪酶LpsA2的最适反应pH为8.0,最适反应温度为50℃;最适底物为对硝基苯酚豆蔻酸酯;在10℃-50℃范围内该酶的激活自由能为6.3 kcal/mol;1 mmol/L Co2+、Hg2+、Zn2+可使酶活性提高至250%以上;15%的二甲基甲酰胺和二甲基亚砜使酶活分别提高至110.7%和138%;0.1%和1%的Span-20可使酶活性分别提高至352.7%和189.7%。【结论】本研究对推测的来源于S.avermitilis的脂肪酶基因lpsA2进行了异源表达和酶学功能鉴定,不仅为脂肪酶的研究积累了更多数据,也为具有优良性能的脂肪酶生物工程菌的筛选奠定了基础,更为其在食品加工、药物合成等工业生产中的应用提供了依据。     

Accumulation of lipid production in Chlorella minutissima by triacylglycerol biosynthesis-related genes cloned from Saccharomyces cerevisiae and Yarrowia lipolytica

Discovery of an alternative fuel is now an urgent matter because of the impending issue of oil depletion. Lipids synthesized in algal cells called triacylglycerols (TAGs) are thought to be of the most value as a potential biofuel source because they can use transesterification to manufacture biodiesel. Biodiesel is deemed as a good solution to overcoming the problem of oil depletion since it is capable of providing good performance similar to that of petroleum. Expression of several genomic sequences, including glycerol-3-phosphate dehydrogenase, glycerol-3-phosphate acyltransferase, lysophosphatidic acid acyltransferase, phosphatidic acid phosphatase, diacylglycerol acyltransferase, and phospholipid:diacylglycerol acyltransferase, can be useful for manipulating metabolic pathways for biofuel production. In this study, we found this approach indeed increased the storage lipid content of C. minutissima UTEX 2219 up to 2-fold over that of wild type. Thus, we conclude this approach can be used with the biodiesel production platform of C. minutissima UTEX 2219 for high lipid production that will, in turn, enhance productivity.