Clone libraries

Niu SQ, Fukushima J, Jiang Y, Ishikawa Y, Ueda T, Matsumoto S (2006) Analysis of bacterial community structure in the natural circulation system wastewater bioreactor by using a 16S rRNA gene clone library. Microbiol Immunol 50 937-950... 

The field of DNA microarray has evolved Ifom the key insight of Ed Southern (13), who showed that it is possible to attach nucleic acid to solid support. The resulting Southern blot can be viewed has the first DNA array (14). It was only a small step to improve the technique to filter-based screening of clone libraries, which introduced a one-to-one correspondence between the clone and the hybridization signal (15) in a fixed position in this way the clone could be uniquely identified and information about it accumulated. 

Completion of second-generation DNA clone libraries representing each human chromosome by LLNL and LBNL. 

Cottrell, M. T., and D. L. Kirchman. 2000a. Community composition of marine bacterio-plankton determined by 16S rDNA clone libraries and fluorescence in situ hybridization. Applied and Environmental Microbiology 66 5116-5122. 

Covert and Moran (2002) Marine Whole, HMW, and LMW DOM Bacterial respiration 16S rDNA clone libraries and T-RFLP No 6 weeks LMW DOM 4-1 Ox more bioavailable HMW DOM community dominated by a- and p-Proteobacteria LMW DOM community dominated by y- and 8-Proteobacteria... 

Second, it is important to consider whether a clone library will be representative of a particular repeated sequence. Besides the genetic factors, above, unusual patterns of restriction sites in some repeated sequences may influence their relative abundance in a library. This would be more likely for a tandemly repeated sequence or a very long repeated sequence than for short, interspersed repeated DNA sequences. Traditional A or plasmid libraries would be sufficient for most studies, but in certain situations it might be necessary to resort to DNA libraries of randomly frag-... 

In conclusion, these results further open the door to the creation of numerous minisatellite probes to survey for VNTR loci. Such probes can be used not only for restriction fragment length polymorphism (RFLP) analyses of the many biological applications outlined in the introduction, but they can also be employed to screen cloned libraries with the ultimate goal of determining the sequences flanking VNTR loci. The latter information provides perhaps the most accurate and rapid means of utilizing the variation at such loci via the PCR analysis of alternate alleles. 

A disadvantage of these systems is probably the lower efficiency and convenience of cloning libraries of DNA molecules. This difficulty has been alleviated by using a Cre-loxP recombination strategy the fusion gene is cloned in a small plasmid and then efficiently recombined in vivo into the phage [25],... 

Dworkin, M.B., David, I.B. (1980). Use of a cloned library for the study of abundant poly (A)+ RNA during Xenopus laevis development. Dev. Biol. 76 449-64. 

Clone libraries may give some indication of the relative abundance of target organisms. In this case, it would be instructive to know the percentage of a total bacterial 16S rRNA clones that were identified as AOB or NOB- like sequences. AOB sequences are easily retrieved when targeted directly with AOB-specific primers, but are very rare in total 16S rRNA libraries. 

Based partly on anecdotal evidence from culture work, observations in waste water treatment systems with very high particulate loads, the tendency of nitrifiers to grow in aggregates in bioreactor biofilms, and the prevalence of small particles in natural waters, it has been suggested that nitrification occurs mainly on particles and is mediated by particle-attached bacteria (Hagopian and Riley, 1998). Nitrifier sequences were found both associated with particles and in the bulk seawater phase in the northwestern Mediterranean Sea. In the clone library of 16S rRNA sequences, Nitrosomonas-like sequences were preferentially associated with particles and Nitrosospira-]ike sequences dominated in clones from the planktonic phase (PhiUips et al, 1999). This may indicate niche preference by the different groups on the basis of attachment to particles, substrate concentration or other physical/... 

Our understanding of the biochemistry of nitrification is based largely on insights from cultivated strains. Molecular data obtained from clone libraries indicate that the most important AOB in the ocean are not represented in the culture collection. The same is probably true for NOB, but much less molecular information is available for these organisms. At this stage, the most... 

EST Profiling. An EST is a short, single sequence run collecting data over about 200-400 bases from a clone selected from a cCNA library. Typically, cDNA clone libraries... 

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