Use of carbonate extraction in analyzing moderately hydrophobic transmembrane proteins in the mitochondrial inner membrane

Resistance to sodium carbonate extraction is regarded as a canonical way to distinguish integral membrane proteins (MPs) from other membrane‐associated proteins. However, it has been observed that carbonate extraction releases some mitochondrial integral MPs. Here, by analyzing both artificially designed and native mitochondrial inner MPs containing transmembrane domains (TMDs) of different hydrophobicities, we show that carbonate treatment can release moderately hydrophobic TMDs from the mitochondrial inner membrane. These results suggest that resistance and sensitivity to carbonate extraction may be interpreted with caution when analyzing the nature of mitochondrial inner MPs.     

红背山麻杆叶的化学成分研究(Ⅳ)—多酚类化合物

红背山麻杆(Alchornea trewioides )为山麻杆属植物,作为传统的中药被用来减轻疾病和身体不适,但它的药效物质基础尚未完全清楚。为了全面掌握红背山麻杆药效物质基础,采用80％丙酮对其新鲜叶进行提取,并利用 MCI gel CHP 20P、Sephadex LH-20等色谱柱进行分离共得到9个化合物。这些化合物的结构经氢谱与碳谱比较分析鉴定为鞣花酸(1)、3-O-甲基没食子酸(2)、decarboxyellagic acid(3)、1-O-没食子酰基-β-D-葡萄糖(4)、1,6-二-O-没食子酰基-β-D-葡萄糖(5)、柯里拉京(6)、叶下珠鞣质 D(7)、furosonin(8)、老鹳草素(9)。其中化合物2~9均为首次从该属植物中分离得到。     

杨树胞外蛋白的提取分离及2-D电泳体系的建立

该研究以美洲黑杨杂种优良无性系NL895杨(Populus deltoides×Populus euramericana cv.)组培苗叶片和茎段为研究对象,对NL895杨叶片细胞壁蛋白(cell wall proteins,CWPs)和茎段质外体蛋白(apoplastic proteins,APPs)的提取、分离和双向电泳等技术进行了系统研究。结果表明:10g以上叶片、超声波破碎10min、CaCl2法提取的细胞壁蛋白效果较好,经G-6-PDH酶活性检测,提取的细胞壁蛋白胞质污染率较低;真空渗透法提取的茎段质外体蛋白胞质污染率较前者高,但在允许范围之内。TCA/丙酮沉淀法纯化提取的细胞壁蛋白、pH 4~7的24cm胶条、上样量为500μg的双向电泳体系,其蛋白电泳图谱中的斑点多而清晰,斑点数达550多个,是叶片细胞壁蛋白电泳分析较适合的体系;pH 3~10胶条对茎段质外体蛋白的电泳分离效果较好。该研究初步建立了杨树胞外蛋白的提取、分离及2-DE电泳体系,为木本植物胞外蛋白的研究奠定了基础。     

Optimized microRNA purification from TRIzol-treated plasma

Background

MicroRNAs (miRNAs) represent new and potentially informative diagnostic targets for disease detection and prognosis. However, little work exists documenting the effect of TRIzol, a common viral inactivation and nucleic acid extraction reagent, on miRNA purification. Here, we developed an optimized protocol for miRNA extraction from plasma samples by evaluating five different RNA extraction kits, TRIzol phase separation, purification additives, and initial plasma sample volume. This method was then used for downstream profiling of plasma miRNAs found in archived samples from one nonhuman primate (NHP) experimentally challenged with Ebola virus by the aerosol route.

Results

Comparison of real-time RT-PCR results for spiked-in and endogenous miRNA sequences determined extraction efficiencies from five different RNA purification kits. These experiments showed that 50 μL plasma processed using the QIAGEN miRNeasy Mini Kit with 5 μg of glycogen as a co-precipitant yielded the highest recovery of endogenous miRNAs. Using this optimized protocol, miRNAs from archived plasma samples of one rhesus macaque challenged with aerosolized Ebola virus was profiled using a targeted real-time PCR array. A total of 519 of the 752 unique miRNAs assayed were present in the plasma samples at day 0 and day 7 (time of death) post-exposure. Statistical analyses revealed 25 sequences significantly up- or down-regulated between day 0 and day 7 post infection, validating the utility of the extraction method for plasma miRNA profiling.

Conclusions

This study contributes to the knowledgebase of circulating miRNA extraction methods and expands on the potential applications of cell-free miRNA profiling for diagnostics and pathogenesis studies. Specifically, we optimized an extraction protocol for miRNAs from TRIzol-inactivated plasma samples that can be used for highly pathogenic viruses.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1299-5) contains supplementary material, which is available to authorized users.     

REDHORSE-REcombination and Double crossover detection in Haploid Organisms using next-geneRation SEquencing data

Background

Next-generation sequencing technology provides a means to study genetic exchange at a higher resolution than was possible using earlier technologies. However, this improvement presents challenges as the alignments of next generation sequence data to a reference genome cannot be directly used as input to existing detection algorithms, which instead typically use multiple sequence alignments as input. We therefore designed a software suite called REDHORSE that uses genomic alignments, extracts genetic markers, and generates multiple sequence alignments that can be used as input to existing recombination detection algorithms. In addition, REDHORSE implements a custom recombination detection algorithm that makes use of sequence information and genomic positions to accurately detect crossovers. REDHORSE is a portable and platform independent suite that provides efficient analysis of genetic crosses based on Next-generation sequencing data.

Results

We demonstrated the utility of REDHORSE using simulated data and real Next-generation sequencing data. The simulated dataset mimicked recombination between two known haploid parental strains and allowed comparison of detected break points against known true break points to assess performance of recombination detection algorithms. A newly generated NGS dataset from a genetic cross of Toxoplasma gondii allowed us to demonstrate our pipeline. REDHORSE successfully extracted the relevant genetic markers and was able to transform the read alignments from NGS to the genome to generate multiple sequence alignments. Recombination detection algorithm in REDHORSE was able to detect conventional crossovers and double crossovers typically associated with gene conversions whilst filtering out artifacts that might have been introduced during sequencing or alignment. REDHORSE outperformed other commonly used recombination detection algorithms in finding conventional crossovers. In addition, REDHORSE was the only algorithm that was able to detect double crossovers.

Conclusion

REDHORSE is an efficient analytical pipeline that serves as a bridge between genomic alignments and existing recombination detection algorithms. Moreover, REDHORSE is equipped with a recombination detection algorithm specifically designed for Next-generation sequencing data. REDHORSE is portable, platform independent Java based utility that provides efficient analysis of genetic crosses based on Next-generation sequencing data. REDHORSE is available at http://redhorse.sourceforge.net/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1309-7) contains supplementary material, which is available to authorized users.     

Selector Screening for Enantioseparation of dl‐α‐Methyl Phenylglycine Amide by Liquid–Liquid Extraction

Enantioseparation through liquid extraction technology is an emerging field, e.g., enantioseparations of amino acids (and derivatives thereof), amino alcohols, amines, and carboxylic acids have been reported. Often, when a new selector is developed, the versatility of substrate scope is investigated. From an industrial point of view, the problem is typically approached the other way around, and for a target racemate, a selector needs to be found in order to accomplish the desired enantioseparation. This study presents such a screening approach for the separation of the enantiomers of dl ‐α‐methyl phenylglycine amide (dl ‐α‐MPGA), a model amide racemate with high industrial relevance. Chiral selectors that were reported for other classes of racemates were investigated, i.e., several macrocyclic selectors and Pd‐BINAP complexes. It appeared very challenging to obtain both high extraction yields and good enantioselectivity for most selectors, but Pd‐BINAP‐based selectors performed well, with enantioselectivities up to 7.4 with an extraction yield of the desired enantiomer of 95.8%. These high enantioselectivities were obtained using dichloromethane as solvent. Using less volatile chlorobenzene or 1‐chloropentane, reasonable selectivities of up to 1.7 were measured, making these the best alternative solvents for dichloromethane. Chirality 27:123–130, 2015. © 2014 Wiley Periodicals, Inc.     

高光谱技术——生态学领域研究的新方法

高光谱技术是一种新的地物探测技术,该技术以其敏锐的地物光谱特征探测能力为精准识别地物属性提供了强有力的手段,在生态系统过程与属性研究中具有广阔的应用前景。该文以可见光-近红外光谱分析技术为例概述了高光谱技术的原理、特点与优势,以及高光谱技术分析的流程;总结并归纳了其在土壤、植物生理、农产品品质检测、凋落物分解方面的研究应用,指出高光谱技术与遥感成像技术结合在生态监测研究中的优势;归纳了高光谱技术应用中面临的问题,并希望高光谱技术在生态学领域研究中得到更广泛的应用。     

Extraction of natural red colorants from the fermented broth of Penicillium purpurogenum using aqueous two‐phase polymer systems

Safety concerns related to the increasing and widespread application of synthetic coloring agents have increased the demand for natural colorants. Fungi have been employed in the production of novel and safer colorants. In order to obtain the colorants from fermented broth, suitable extraction systems must be developed. Aqueous two‐phase polymer systems (ATPPS) offer a favorable chemical environment and provide a promising alternative for extracting and solubilizing these molecules. The aim of this study was to investigate the partitioning of red colorants from the fermented broth of Penicillium purpurogenum using an ATPPS composed of poly(ethylene glycol) (PEG) and sodium polyacrylate (NaPA). Red colorants partitioned preferentially to the top (PEG‐rich phase). In systems composed of PEG 6,000 g/mol/NaPA 8,000 g/mol, optimum colorant partition coefficient (K_C) was obtained in the presence of NaCl 0.1 M (K_C = 10.30) while the PEG 10,000 g/mol/NaPA 8,000 g/mol system in the presence of Na₂SO₄ 0.5 M showed the highest K_C (14.78). For both polymers, the mass balance (%MB) and yield in the PEG phase (%η_TOP) were close to 100 and 79%, respectively. The protein selectivity in all conditions evaluated ranged from 2.0–3.0, which shows a suitable separation of the red colorants and proteins present in the fermented broth. The results suggest that the partitioning of the red colorants is dependent on both the PEG molecular size and salt type. Furthermore, the results obtained support the potential application of ATPPS as the first step of a purification process to recover colorants from fermented broth of microorganisms. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1295–1304, 2015     

Application of an aqueous two‐phase micellar system to extract bromelain from pineapple (Ananas comosus) peel waste and analysis of bromelain stability in cosmetic formulations

Bromelain is a set of proteolytic enzymes found in pineapple (Ananas comosus) tissues such as stem, fruit and leaves. Because of its proteolytic activity, bromelain has potential applications in the cosmetic, pharmaceutical, and food industries. The present study focused on the recovery of bromelain from pineapple peel by liquid–liquid extraction in aqueous two‐phase micellar systems (ATPMS), using Triton X‐114 (TX‐114) and McIlvaine buffer, in the absence and presence of electrolytes CaCl₂ and KI; the cloud points of the generated extraction systems were studied by plotting binodal curves. Based on the cloud points, three temperatures were selected for extraction: 30, 33, and 36°C for systems in the absence of salts; 40, 43, and 46°C in the presence of KI; 24, 27, and 30°C in the presence of CaCl₂. Total protein and enzymatic activities were analyzed to monitor bromelain. Employing the ATPMS chosen for extraction (0.5 M KI with 3% TX‐114, at pH 6.0, at 40°C), the bromelain extract stability was assessed after incorporation into three cosmetic bases: an anhydrous gel, a cream, and a cream‐gel formulation. The cream‐gel formulation presented as the most appropriate base to convey bromelain, and its optimal storage conditions were found to be 4.0 ± 0.5°C. The selected ATPMS enabled the extraction of a biomolecule with high added value from waste lined‐up in a cosmetic formulation, allowing for exploration of further cosmetic potential. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:937–945, 2015     

Production of lignosulfonate in NSSC‐based biorefinery

The spent liquor (SL) of a neutral sulfite semichemical (NSSC) pulping process contains a considerable amount of lignocelluloses and is treated in wastewater systems. The lignocelluloses, however, can be used for producing value‐added products if they are isolated from the SL. In this article, solvent treatment (mixing acetone, ethanol, or isopropyl with SL) was used as a method for isolating lignosulfonate from SL. The maximum lignosulfonate removal was obtained via mixing isopropyl alcohol with SL at the weight ratio of 20/80, room temperature, and 5.7 pH. The results also showed that the molecular weight and anionic charge density of the precipitates were in the range of 5,000–70,000 g/mol and 0.2–1.8 meq/g, respectively. Based on these results, a process was proposed for isolating lignosulfonate from SL and converting the NSSC process to an NSSC‐based biorefinery. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1508–1514, 2015