Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3’s functionality. In this article, we describe Primer3’s current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement—a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.

https://faircloth-lab.org/assets/pdf/untergasser-et-al-2012-nucleic-acids-research.pdf

Primer3—new capabilities and interfaces

A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.

/pdf/the-human-microbiome-project-1armeyuv2c.pdf

The human microbiome project.

The development of novel materials is a fundamental focal point of chemical research; and this interest is mandated by advancements in all areas of industry and technology. A good example of the synergism between scientific discovery and technological development is the electronics industry, where discoveries of new semiconducting materials resulted in the evolution from vacuum tubes to diodes and transistors, and eventually to miniature chips. The progression of this technology led to the development * To whom correspondence should be addressed. B.L.C.: (504) 2801385 (phone); (504) 280-3185 (fax); bcushing@uno.edu (e-mail). C.J.O.: (504)280-6846(phone);(504)280-3185(fax);coconnor@uno.edu (e-mail). 3893 Chem. Rev. 2004, 104, 3893−3946

http://depa.fquim.unam.mx/amyd//archivero/FidelmarLechugaSanabria_4940.pdf

Recent advances in the liquid-phase syntheses of inorganic nanoparticles.

Microbial diversity and function in soil: from genes to ecosystems

▪ Abstract Agricultural soils suppressive to soilborne plant pathogens occur worldwide, and for several of these soils the biological basis of suppressiveness has been described. Two classical types of suppressiveness are known. General suppression owes its activity to the total microbial biomass in soil and is not transferable between soils. Specific suppression owes its activity to the effects of individual or select groups of microorganisms and is transferable. The microbial basis of specific suppression to four diseases, Fusarium wilts, potato scab, apple replant disease, and take-all, is discussed. One of the best-described examples occurs in take-all decline soils. In Washington State, take-all decline results from the buildup of fluorescent Pseudomonas spp. that produce the antifungal metabolite 2,4-diacetylphloroglucinol. Producers of this metabolite may have a broader role in disease-suppressive soils worldwide. By coupling molecular technologies with traditional approaches used in plant patholog...

Microbial populations responsible for specific soil suppressiveness to plant pathogens.

To determine the potential of DNA array technology for assessing functional gene diversity and distribution, a prototype microarray was constructed with genes involved in nitrogen cycling: nitrite reductase (nirS and nirK) genes, ammonia mono-oxygenase (amoA) genes, and methane mono-oxygenase (pmoA) genes from pure cultures and those cloned from marine sediments. In experiments using glass slide microarrays, genes possessing less than 80 to 85% sequence identity were differentiated under hybridization conditions of high stringency (65°C). The detection limit for nirS genes was approximately 1 ng of pure genomic DNA and 25 ng of soil community DNA using our optimized protocol. A linear quantitative relationship (r2 = 0.89 to 0.94) was observed between signal intensity and target DNA concentration over a range of 1 to 100 ng for genomic DNA (or genomic DNA equivalent) from both pure cultures and mixed communities. However, the quantitative capacity of microarrays for measuring the relative abundance of targeted genes in complex environmental samples is less clear due to divergent target sequences. Sequence divergence and probe length affected hybridization signal intensity within a certain range of sequence identity and size, respectively. This prototype functional gene array did reveal differences in the apparent distribution of nir and amoA and pmoA gene families in sediment and soil samples. Our results indicate that glass-based microarray hybridization has potential as a tool for revealing functional gene composition in natural microbial communities; however, more work is needed to improve sensitivity and quantitation and to understand the associated issue of specificity.

/pdf/development-and-evaluation-of-functional-gene-arrays-for-5dis598ssw.pdf

Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment

Five bacterial strains were isolated from anaerobic enrichment cultures that had originated from inoculations with samples collected from the deep subsurface environments of the millions-of-years-old, geologically and hydrologically isolated Piceance Basin in Colorado. Small-subunit rRNA gene-based analyses indicated that all of these bacteria were closely related to Thermoanaerobacter ethanolicus, with similarities of 99.4 to 99.5%. Three isolates (X513, X514, and X561) from the five bacterial strains were used to examine physiological characteristics. These thermophilic bacteria were able to use acetate, glucose, hydrogen, lactate, pyruvate, succinate, and xylose as electron donors while reducing Fe(III), cobalt(III), chromium(VI), manganese(IV), and uranium(VI) at 60°C. One of the isolates (X514) was also able to utilize hydrogen as an electron donor for Fe(III) reduction. These bacteria exhibited diverse mineral precipitation capabilities, including the formation of magnetite (Fe3O4), siderite (FeCO3), rhodochrosite (MnCO3), and uraninite (UO2). The gas composition of the incubation headspace and the ionic composition of the incubation medium exerted profound influences on the types of minerals formed. The susceptibility of the thermophilic Fe(III)-reducing cultures to metabolic inhibitors specific for ferric reductase, hydrogenase, and electron transport indicated that iron reduction by these bacteria is an enzymatic process.

http://envismadrasuniv.org/Microbes%20and%20Radionuclide%20Pollution/pdf/Isolation%20and%20Characterization%20of%20Metal.pdf

Isolation and Characterization of Metal-Reducing Thermoanaerobacter Strains from Deep Subsurface Environments of the Piceance Basin, Colorado

Changes in mRNA and protein expression profiles of Shewanella oneidenesis MR-1 during switch from aerobic to fumarate-, Fe(III)-, or nitrate-reducing conditions were examined using DNA microarrays and two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). In response to changes in growth conditions, 121 of the 691 arrayed genes displayed at least a two-fold difference in transcript abundance as determined by microarray analysis. Genes involved in aerobic respiration encoding cytochrome c and d oxidases and TCA cycle enzymes were repressed under anaerobic conditions. Genes induced during anaerobic respiration included those involved in cofactor biosynthesis and assembly (moaACE, ccmHF, nosD, cysG), substrate transport (cysUP, cysTWA, dcuB), and anaerobic energy metabolism (dmsAB, psrC, pshA, hyaABC, hydA). Transcription of genes encoding a periplasmic nitrate reductase (napBHGA), cytochrome c552, and prismane was elevated 8- to 56-fold in response to the presence of nitrate, while cymA, ifcA, and f...

Gene and Protein Expression Profiles of Shewanella oneidensis during Anaerobic Growth with Different Electron Acceptors

Motivation: DNA microarray is a powerful high-throughput tool for studying gene function and regulatory networks. Due to the problem of potential cross hybridization, using full-length genes for microarray construction is not appropriate in some situations. A bioinformatic tool, PRIMEGENS, has recently been developed for the automatic design of PCR primers using DNA fragments that are specific to individual open reading frames (ORFs). Result: PRIMEGENS first carries out a BLAST search for each target ORF against all other ORFs of the genome to quickly identify possible homologous sequences. Then it performs optimal sequence alignment between the target ORF and each of its homologous ORFs using dynamic programming. PRIMEGENS uses the sequence alignments to select gene- specific fragments, and then feeds the fragments to the Primer3 program to design primer pairs for PCR amplification. PRIMEGENS can be run from the command line on Unix/Linux platforms as a stand-alone package or it can be used from a Web interface. The program runs efficiently, and it takes a few seconds per sequence on a typical workstation. PCR primers specific to individual ORFs from Shewanella oneidensis MR-1 and Deinococcus radiodurans R1 have been designed. The PCR amplification results indicate that this method is very efficient and reliable for designing specific probes for microarray analysis. Availability: The software is available at http://compbio.

Guangshan Li

Papers

Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment

Isolation and Characterization of Metal-Reducing Thermoanaerobacter Strains from Deep Subsurface Environments of the Piceance Basin, Colorado

Gene and Protein Expression Profiles of Shewanella oneidensis during Anaerobic Growth with Different Electron Acceptors

PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.