Electrophoresis of DNA in oriented agarose gels

Oriented agarose gels were prepared by applying an electric field to molten agarose while it was solidifying. Immediately afterwards, DNA samples were applied to the gel and electrophoresed in a constant unidirectional electric field. Regardless of whether the orienting field was applied parallel or perpendicular to the eventual direction of electrophoresis, the mobilities of linear and supercoiled DNA molecules were either faster (80% of the time) or slower (20% of the time) than observed in control, unoriented gels run simultaneously. The difference in mobility in the oriented gel (whether faster or slower) usually increased with increasing DNA molecular weight and increasing voltage applied to orient the agarose matrix. In perpendicularly oriented gels linear DNA fragments traveled in lanes skewed toward the side of the gel; supercoiled DNA molecules traveled in straight lanes. If the orienting voltage was applied parallel to the direction of electrophoresis, both linear and supercoiled DNA molecules migrated in straight lanes. These effects were observed in gels cast from different types of agarose, using various agarose concentrations and two different running buffers, and were observed both with and without ethidium bromide incorporated in the gel. Similar results were observed if the agarose was allowed to solidify first, and the orienting electric field was then applied to the gel for several hours before the DNA samples were added and electrophoresed. The results suggest that the agarose matrix can be oriented by electric fields applied to the gel before and probably during electrophoresis, and that orientation of the matrix affects the mobility and direction of migration of DNA molecules. The skewed lanes observed in the perpendicularly oriented gels suggest that pores or channels can be created in the matrix by application of an electric field. The oriented matrix becomes randomized with time, because DNA fragments in oriented and unoriented gels migrated in straight lanes with identical velocities 24 hours later.     

新疆一号冰川土壤细菌多样性的研究

应用变性梯度凝胶电泳（DGGE）技术分离PCR扩增的16SrDNA来研究土壤微生物的多样性。直接从新疆一号冰川不同海拔高度的土壤样品中提取总DNA。用两套细菌通用引物分别扩增16SrDNA的V3和V6／V9高变区的特异性片段,PCR产物进行DGGE分析。PCR—DGGE图谱表明,PCR产物经DGGE检测到的条带清晰且分离效果好。结果表明,PCR—DGGE是一种快速研究微生物群落结构的有效方法。     

New DGGE strategies for the analyses of methanotrophic microbial communities using different combinations of existing 16S rRNA-based primers

Methane-oxidising microbial communities are studied intensively because of their importance for global methane cycling. A suite of molecular microbial techniques has been applied to the study of these communities. Denaturing gradient gel electrophoresis (DGGE) is a diversity screening tool combining high sample throughput with phylogenetic information of high resolution. The existing 16S rRNA-based DGGE assays available for methane-oxidising bacteria suffer from low-specificity, low phylogentic information due to the length of the amplified fragments and/or from lack of resolving power. In the present study we developed new combinations of existing primers and applied these on methane-oxidising microbial communities in a freshwater wetland marsh. The designed strategies comprised nested as well as direct amplification of environmental DNA. Successful application of direct amplification using combinations of universal and specific primers circumvents the nested designs currently used. All developed assays resulted in identical community profiles in wetland soil cores with Methylobacter sp. and Methylocystis sp.-related sequences. Changes in the occurrence of Methylobacter-related sequences with depth in the soil profile may be related to the decrease in methane-oxidizing activity.     

Comparative microbial diversity in the gastrointestinal tracts of food animal species

Molecular tools based on small subunit (SSU) rDNA gene sequencesoffer a powerful and rapid tool for the analysis of complexmicrobial communities found in the gastrointestinal tracts (GIT)of food animal species. Extensive comparative sequence analysisof SSU rRNA molecules representing a wide diversity of organismsshows that different regions of the molecule vary in sequenceconservation. Oligonucleotides complementing regions of universallyconversed SSU rRNA sequences are used as universal probes, whilethose complementing more variable regions of sequence are usefulas selective probes targeting species, genus, or phylogeneticgroups. Different approaches derive different information andthis is highly dependent on the type of target nucleic acidemployed and the conceptual and technical basis used for nucleicacid probe design. Generally these approaches can be dividedinto DNA-based methods employing empirically characterized probesand rRNA-based methods based on comparative sequence analysisfor design and interpretation of "rational" probes. Polymerasechain reaction (PCR) based techniques can also be applied tothe analysis of microbial communities in the GIT. Direct cloningof SSU rDNA genes amplified from these complex communities canbe used to determine the extent of diversity in these GIT communities.Denaturing gradient gel electrophoresis (DGGE) is another powerfultool for profiling microbial diversity of microbial communitiesin GI tracts. Sequence analysis of the excised DGGE ampliconscan then be used to presumptively identify predominant bacterialspecies. Examples of how these molecular approaches are beingused to study the microbial diversity of communities from steersfed different diets, swine fed probiotics, and Atlantic salmonfed aquaculture diets are presented.     

Application of fluorescence-based semi-automated AFLP analysis in barley and wheat

Genetic mapping and the selection of closely linked molecular markers for important agronomic traits require efficient, large-scale genotyping methods. A semi-automated multifluorophore technique was applied for genotyping AFLP marker loci in barley and wheat. In comparison to conventional ³³P-based AFLP analysis the technique showed a higher resolution of amplicons, thus increasing the number of distinguishable fragments. Automated sizing of the same fragment in different lanes or different gels showed high conformity, allowing subsequent unambigous allele-typing. Simultaneous electrophoresis of different AFLP samples in one lane (multimixing), as well as simultaneous amplification of AFLP fragments with different primer combinations in one reaction (multiplexing), displayed consistent results with respect to fragment number, polymorphic peaks and correct size-calling. The accuracy of semi-automated co-dominant analysis for hemizygous AFLP markers in an F₂ population was too low, proposing the use of dominant allele-typing defaults. Nevertheless, the efficiency of genetic mapping, especially of complex plant genomes, will be accelerated by combining the presented genotyping procedures. Received: 10 April 1999 / Accepted: 11 May 1999     

Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments

Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.     

Terminal restriction fragment length polymorphism analysis for human fecal microbiota and its application for analysis of complex bifidobacterial communities

Terminal restriction fragment length polymorphism (T-RFLP) analysis was used to characterize and compare human fecal microbiota among individuals. T-RFLP patterns of fecal 16S ribosomal DNA (rDNA) PCR products from three adults revealed host-specific bacterial communities and were in good agreement with those reported in our previous study. In addition, we applied T-RFLP analysis for the analysis of complex bifidobacterial communities in human fecal samples. The developed method based on Bifidobacterium genus-specific PCR and T-RFLP could identify more than one bifidobacterial species. T-RFLP patterns of Bifidobacterium genus-specific PCR products from the fecal samples were host-specific as well as those of fecal 16S rDNA PCR products. These results were confirmed by PCR-denaturing gradient gel electrophoresis (DGGE) with primers specific for the genus Bifidobacterium and Bifidobacterium species- and group-specific PCR. Our study demonstrates that T-RFLP analysis is useful for assessment of the diversity of the human fecal microbiota and rapid comparison of the community structure among individuals, and that the applied method is useful for rapid and sensitive analysis of bifidobacterial community.     

Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns

Technical developments in molecular biology have found extensive applications in the field of microbial ecology. Among these techniques, fingerprinting methods such as denaturing gel electrophoresis (DGE, including the three options: DGGE, TGGE and TTGE) has been applied to environmental samples over this last decade. Microbial ecologists took advantage of this technique, originally developed for the detection of single mutations, for the analysis of whole bacterial communities. However, until recently, the results of these high quality fingerprinting patterns were restricted to a visual interpretation, neglecting the analytical potential of the method in terms of statistical significance and ecological interpretation. A brief recall is presented here about the principles and limitations of DGE fingerprinting analysis, with an emphasis on the need of standardization of the whole analytical process. The main content focuses on statistical strategies for analysing the gel patterns, from single band examination to the analysis of whole fingerprinting profiles. Applying statistical method make the DGE fingerprinting technique a promising tool. Numerous samples can be analysed simultaneously, permitting the monitoring of microbial communities or simply bacterial groups for which occurrence and relative frequency are affected by any environmental parameter. As previously applied in the fields of plant and animal ecology, the use of statistics provides a significant advantage for the non-ambiguous interpretation of the spatial and temporal functioning of microbial communities.     

Improved method for making nondenaturing composite gradient gels for the electrophoretic separation of lipoproteins

Nondenaturing gradient gel electrophoresis continues to be used widely for resolution and characterization of lipoprotein subclasses. Methods for making such gels in the laboratory have been published, but occasionally samples do not display uniform mobilities for all lanes in a laboratory-made gel. To help overcome this limitation, we recommend a modification     

Characterization of spelt (Triticum spelta L.) forms by gel-electrophoretic analyses of seed storage proteins. II. The glutenins

 Seed proteins of 28 spelt cultivars (Triticum spelta L.), 16 cross combinations between spelt forms or between spelt and English winter wheat cultivars, and ten winter wheat varieties (Triticum aestivum L.) were analysed by SDS (sodium dodecyl sulphate)-PAGE (polyacrylamide-gel electrophoresis). Different wheat types were chosen for distinct purposes: five popular German wheat cultivars were used for a comparison of wheat and spelt protein band patterns, two of them are old varieties (‘Kanzler’ and ‘Jubilar’) and one is a modern wheat standard (‘Orestis’); five English winter wheat varieties with short straw were used for the crosses with spelt cultivars to improve seed yield and especially the lodging resistance of spelt. The objectives of these studies were the adaptation of existing SDS-PAGE methods, which have been successfully applied in other crops, for the analysis of seed proteins in spelt, and the characterization and differentiation of spelt varieties from corresponding cross combinations with other spelt forms or with winter wheat cultivars using gel-electrophoretic methods (SDS-PAGE). Considerable differences in protein band patterns were found between spelt and winter wheat varieties, especially in three distinct lanes of the electropherogrammes where the molecular weights range from 40 to 49 , 53 to 62 and 74 to 115 kDa. Spelt cross combinations, and especially crosses between spelt and winter wheat cultivars, were easily distinguishable particularly after a preceding extraction in chlorethanol. Received: 4 December 1996 1 / Accepted: 6 December 1996     

Persistence of free-living protozoan communities across rearing cycles in commercial poultry houses

The introduction and survival of zoonotic bacterial pathogens in poultry farming have been linked to bacterial association with free-living protozoa. To date, however, no information is available on the persistence of protozoan communities in these environments across consecutive rearing cycles and how it is affected by farm- and habitat-specific characteristics and management strategies. We therefore investigated the spatial and temporal dynamics of free-living protozoa in three habitats (pipeline, water, and miscellaneous samples) in three commercial poultry houses across three rearing cycles by using the molecular fingerprinting technique denaturing gradient gel electrophoresis (DGGE). Our study provides strong evidence for the long-term (ca. 6-month) persistence of protozoa in broiler houses across consecutive rearing cycles. Various free-living protozoa (flagellates, ciliates, and amoebae), including known vectors of bacterial pathogens, were observed during the down periods in between rearing cycles. In addition, multivariate analysis and variation partitioning showed that the protozoan community structure in the broiler houses showed almost no change across rearing cycles and remained highly habitat and farm specific. Unlike in natural environments, protozoan communities inside broiler houses are therefore not seasonal. Our results imply that currently used biosecurity measures (cleaning and disinfection) applied during the down periods are not effective against many protozoans and therefore cannot prevent potential cross-contamination of bacterial pathogens via free-living protozoa between rearing cycles.     

Optimization of the scratch assay for in vitro skeletal muscle wound healing analysis

To isolate mitochondrial complexes, we have combined elements from the classic Laemmli protocol and blue native polyacrylamide gel electrophoresis (BN–PAGE) methods to develop a straightforward modified native electrophoresis protocol. This modified protocol presented good resolution for native electrophoresis of inner mitochondrial membrane proteins, where bands were easily visualized with no leftover stain or gel lanes overlap. Enzymatic tests revealed that complexes I and V remain active in the gel. This protocol, designed to overcome specific limitations of the standard protocols, provides a potential methodology to study membrane proteins in their functional form.     

Microplate-array diagonal-gel electrophoresis (MADGE) and melt-MADGE: tools for molecular-genetic epidemiology

Microplate-array diagonal-gel electrophoresis (MADGE) was invented for molecular-genetic epidemiological studies. It combines direct compatibility with microplates, convenient polyacrylamide-gel electrophoresis and economy of time and reagents at minimal capital cost, and enables one user to run up to several-thousand gel lanes per day for the direct assay of single-base variations. Melt-MADGE adds temporal-thermal-ramp apparatus to achieve similar throughput for de novo mutation scanning.     

徐州权台煤矿井下700 m水平微生物群落分布特征

煤矿井下与表生环境具有明显差异,研究其微生物群落分布及多样性对深入探讨井下水-岩-气-生作用机制具有重要意义.本研究在徐州权台煤矿井下700 m水平采集了8个沉积物样本,对样品进行了理化指标测试和Miseq高通量测序.结果表明,煤矿井下具有丰富的微生物多样性,8个样本共检测到35个细菌门类,其中变形菌门(Proteob...     

Fluorographic detection of tritiated glycopeptides and oligosaccharides separated on polyacrylamide gels: analysis of glycans from Dictyostelium discoideum glycoproteins

Previous workers have shown that oligosaccharides and glycopeptides can be separated by electrophoresis in buffers containing borate ions. However, normal fluorography of tritium-labeled structures cannot be performed because the glycans are soluble and can diffuse during equilibration with scintillants. This problem has been circumvented by equilibration of the gel with 2,5-diphenyloxazole (PPO) prior to electrophoresis. The presence of PPO in the gel during electrophoresis does not alter mobility of the glycopeptides and oligosaccharides. After electrophoresis, the gel is simply dried and fluorography performed. This allows sensitive and precise comparisons of labeled samples in parallel lanes of a slab gel and, since mobilities are highly reproducible, between different gels. The procedure is preparative in that after fluorography the gel bands can be quantitatively eluted for further study, without any apparent modification by the procedure. In this report, the procedure is illustrated by fractionation of both neutral and anionic glycopeptides produced by the cellular slime mold Dictyostelium discoideum.     

DGGE技术在环境微生物多样性研究中的应用

微生物是污水净化的主要作用者之一.采用变性梯度凝胶电泳(denaturing gradient gel electrophresis,DGGE)方法培育和鉴定土壤微生物具有可靠性强、重复性好、方便快捷等优点,已被广泛应用于环境科学和污染防治研究领域.综述了基于PCR-DGGE技术的基本原理、关键环节及其在微生物多样性研究中的应用,同时就其自身存在的不足进行了评价并提出了解决方案.     

Microbial community fingerprinting by differential display-denaturing gradient gel electrophoresis

Complex microbial communities exhibit a large diversity, hampering differentiation by DNA fingerprinting. Herein, differential display-denaturing gradient gel electrophoresis is proposed. By adding a nucleotide to the 3' ends of PCR primers, 16 primer pairs and fingerprints were generated per community. Complexity reduction in each partial fingerprint facilitates sample comparison.     

DGGE/TGGE a method for identifying genes from natural ecosystems.

Five years after the introduction of denaturing gradient gel electrophoresis(DGGE) and temperature gradient gel electrophoresis (TGGE) in environmental microbiology these techniques are now routinely used in many microbiological laboratories worldwide as molecular tools to compare the diversity of microbial communities and to monitor population dynamics. Recent advances in these techniques have demonstrated their importance in microbial ecology.     

Absence of oxytocin-neurophysin messenger RNA in the day-18 bovine conceptus

Total cellular RNA was isolated from conceptus tissue obtained from 22 superovulated cows 18 days after artificial insemination. Total RNA was also isolated from luteal tissue from 3 cyclic cows 7 and 8 days after oestrus. Luteal and conceptus RNA were simultaneously subjected to formaldehyde-agarose gel electrophoresis and transferred to nitrocellulose by bidirectional diffusion blotting. Northern blots were probed using cDNAs specific for bovine oxytocin and bovine beta-actin gene sequences. Hybridization of the oxytocin cDNA to RNA was consistently observed on autoradiographs as a 0.6 kilobase (kb) band in lanes containing corpus luteum RNA, but was not detected in lanes containing conceptus RNA. The presence of conceptus RNA on the blots was confirmed by hybridization of the actin cDNA to conceptus RNA, which resulted in a 2.0 kb band on autoradiographs. These results suggest that oxytocin is not synthesized by the bovine conceptus on Day 18 of gestation.