FTIR spectro-imaging of collagens for characterization and grading of gliomas

Collagens are a family of at least 30 protein types organized as networks. They constitute the main support material of cells under the form of extracellular matrix as well as for membranes in vessels, organs, and tissue compartments. Collagen network abnormalities are at the origin of many diseases, including myopathies and fibroses. The characterization of collagens remains an analytical challenge due to the insolubility of these molecules and the difficulty encountered in isolating given types without altering their structure or in maintaining network organization, which is critical to diagnosing related pathologies. We have proposed using a vibrational spectroscopy based imaging technique, namely Fourier-transform infrared (FTIR) imaging, for a spatially-resolved analysis of secondary structure of different collagen types in complex samples, and more specifically for characterizing gliomas. With newly developed spectral data treatments and chemometrics using secondary structure parameters of collagen proteins, FTIR imaging is now able to distinguish between several types. On this basis, gliomas have been investigated as specific collagen-rich tissues developing in a non-collagenous environment, providing high specificity to this FTIR imaging utilization. Here, we review the recent advances in this imaging approach for understanding glioma development, with FTIR imaging now being proposed as a molecular histopathology tool for clinicians.     

根癌农杆菌介导的VHb异源表达及其对里氏木霉的影响

里氏木霉是生产纤维素酶的重要菌株,在其浸没式发酵过程中,氧传递是重要影响因素。为了减轻溶氧的限制,本研究借助根癌农杆菌将透明颤菌血红蛋白基因vgb引入里氏木霉。qPCR结果表明,pki及gpd启动子均可以有效启动vgb在里氏木霉中的表达。进一步实验结果表明,在摇瓶培养中,供氧充足情况下野生菌和转化株的生长无明显差异,但是在静止培养条件下,氧气供应受限,转化菌株的干重是野生菌的17.8~25.5倍。     

Expression, purification, and characterization of recombinant NOD1 (NLRC1): A NLR family member

NOD1 (NLRC1) is a member of the NLR family of innate immunity proteins, which are important cellular sensors of various pathogens. Deregulated NOD1 signaling is involved in various autoimmune, inflammatory, and allergic diseases, making it a potential target for drug discovery. However, to date, the successful high-yield purification NOD1 protein has not been reported. Here we describe the large-scale expression of recombinant NOD1 protein in non-adherent mammalian cells. One-step immunoaffinity purification was carried out, yielding highly pure protein with excellent yields. Gel-sieve chromatography studies showed that the purified NOD1 protein eluted almost exclusively as a monomer. Addition of the NOD1 ligand (γ-Tri-DAP) stimulated NOD1 protein oligomerization. Using purified NOD1 protein for nucleotide binding studies by the Fluorescence Polarization Assay (FPA) method, we determined that NOD1 binds preferentially to ATP over ADP and AMP or dATP. We also documented that purified NOD1 protein binds directly to purified pro-apoptotic protein Bid, thus extending recent data that have identified Bid as an enhancer of NOD1 signaling. This expression and purification strategy will enable a wide variety of biochemical studies of mechanisms of NOD1 regulation, as well as laying a foundation for future attempts at drug discovery.     

Triple helix DNA oligomer melting measured by fluorescence polarization anisotropy

A synthetic DNA triple helix sequence was formed by annealing a pyrimidinic 21 mer single strand sequence onto the complementary purinic sequence centred on a 27 mer duplex DNA. Melting of the third strand was monitored by UV spectrophotometry in the temperature range 10-90 degrees C. The T(m) of the triplex, 37 degrees C, was well separated from the onset of duplex melting. When the same triple helix was formed on the duplex bearing one nick in the center of the pyrimidinic sequence the T(m) of the triplex was shifted to approximately 32 degrees C and overlapped the melting of the duplex. We have used fluorescence polarization anisotropy (FPA) measurements of ethidium bromide (EB) intercalated in duplex and triplex samples to determine the hydrodynamic parameters in the temperature range 10-40 degrees C. The fluorescence lifetime of EB in the samples of double and triple stranded DNA is the same (21.3 +/- 0.5 ns) at 20 degrees C, indicating that the geometries of the intercalation sites are similar. The values for the hydration radii of the duplex, normal triplex, and nicked triplex samples were 10.7 +/- 0.2, 12.2 +/- 0.2, and 12.0 +/- 0.2 A. FPA measurements on normal triplex DNA as a function of temperature gave a melting profile very similar to that derived by UV absorption spectroscopy. For the triplex carrying a nick, the melting curve obtained using FPA showed a clear shift compared with that obtained for the normal triplex sample. The torsional rigidity of the triplex forms was found to be higher than that of the duplex form.     

Experimental ATR device for real-time FTIR imaging of living cells using brilliant synchrotron radiation sources

In this contribution we present the design of an original Attenuated Total Reflection (ATR)-based device designed for an IR microscope coupled to a FPA detector and optimized for in-vivo cell imaging. The optical element has been designed to perform real time experiments of cell biochemical processes. The device includes a manually removable Ge-crystal that guarantees an ease manipulation during the cell culture and a large flat surface to support the cell growth and the required change of the culture wells. This layout will allow performing sequential ATR IR imaging with the crystal immersed in the culture wells, minimizing contributions due to water vapors in the optical system. Using existing brilliant synchrotron radiation sources this ATR device may collect images at the surface of the Ge crystal at a sub-cellular spatial resolution with a penetration depth of the evanescent wave inside the sample of ~ 500 nm within few seconds. A brief summary of the cellular components that should be detected with such optical device is also presented.     

Structural basis of γH2AX recognition by human PTIP BRCT5-BRCT6 domains in the DNA damage response pathway

Human Pax2 transactivation domain-interacting protein (hPTIP), containing six BRCT domains, is an essential protein required for the IR induced DDR process with an unclear role. Here we report that the tandem BRCT5–BRCT6 domain of hPTIP recognizes the γH2AX tail, and this interaction depends on the phosphorylation of H2AX Ser139 and binding with the carboxyl ending peptide to the aminoacyl ending peptide. The 2.15 Å crystal structure of hPTIP BRCT5/6–γH2AX complex and mutation analysis provide molecular evidence for direct interactions between PTIP and γH2AX. This interaction proffers a new clue to identify the role of PTIP in DDR pathways.

Structured summary of protein interactions

PTIP and gamma H2AXbind by fluorescence polarization spectroscopy (View Interaction: 1, 2, 3, 4, 5, 6).PTIP and gamma H2AXbind by X-ray crystallography (View interaction).     

Improvement of corn stover bioconversion efficiency by using plant glycoside hydrolase

Plant cell wall is the most abundant substrate for bioethanol production, and plants also represent a key resource for glycoside hydrolase (GH). To exploit efficient way for bioethanol production with lower cellulase loading, the potential of plant GH for lignocellulose bioconversion was evaluated. The GH activity for cell wall proteins (CWPs) was detected from fresh corn stover (FCS), and the synergism of which with Trichoderma reesei cellulase was also observed. The properties for the GH of FCS make it a promising enzyme additive for lignocellulose biodegradation. To make use of the plant GH, novel technology for hydrolysis and ethanol fermentation was developed with corn stover as substrate. Taking steam-exploded corn stover as substrate for hydrolysis and ethanol fermentation, compared with T. reesei cellulase loaded alone, the final glucose and ethanol accumulation increased by 60% and 63% respectively with GH of FCS as an addition.     

青海高原降解纤维素微生物的调查、分离、鉴定

从青海高原林区分离筛选 3 0 0余株分解纤维素的细菌及 3 1株降解纤维素的真菌。测定纤维素分解菌含量土样为 2 6× 1 0 5 g。对纤维素酶水解圈较大的 1 1株真菌 ,根据其滤纸酶活筛选出一株分离自互助北山森林的高产纤维素酶的真菌No 0 1 43菌株 ,根据其形态学及培养特征鉴定为康氏木霉 (TrichodermakoningiiQudem) ,该菌湿固体发酵物含滤纸酶活力(FPA)为 1 5u g。该菌无毒副作用 ,可用于饲料业     

降解棉秸秆耐热菌株的鉴定及降解条件优化

【目的】鉴定从新疆棉花秸秆高温堆肥中分离出的两株耐热真菌Z1、Z2的属种,并通过优化影响菌株产生纤维素酶的因素来提高菌株对秸秆的降解率。【方法】经形态学和菌株的ITS区克隆与序列分析确定属种,以液体摇瓶发酵产滤纸酶活性(FPA)变化为衡量指标,对Z1、Z2以及二者混合菌(MS)的纤维素酶产生条件进行优化。【结果】菌株Z1为曲霉属烟曲霉(Aspergillus fumigatus Fresen),Z2为蚀丝霉属(Myceliophthora Cost.)。确定Z1以棉秸秆为碳源、以NaNO3为氮源、起始pH 9.5、接种量11%、50°C摇床培养10 d,对棉秸秆降解率为10.19%;Z2以麦秸秆为碳源、以NaNO3为氮源、起始pH 5.5、接种量9%、50°C摇床培养10 d,对麦秆降解率为27.50%;MS以棉花秸秆为碳源、以蛋白胨为氮源、起始pH 5.5、接种量11%、50°C摇床培养10 d,对棉秸秆的降解率为53.45%。【结论】实验表明,MS(Z1、Z2混合)对秸秆的降解效果优于单株菌,降解率达到一半以上,本研究中的两株耐热真菌在降解棉花秸秆、小麦秸秆等农作物废弃秸秆中具有较高的应用价值。