Molecular Techniques (2015-2016). Lesson 7

Powerpoint slides for Lesson 7.

Molecular Techniques (2015-2016). Lesson 8

Powerpoint slides for Lesson 8.

Molecular Techniques (2015-2016). Lesson 9

Powerpoint slides for Lesson 9.

Molecular Techniques (2015-2016). Lesson 10

Powerpoint slides for Lesson 10.

Molecular Techniques (2015-2016). Protocol for the Genetics Laboratory practices

Protocol for the Genetics Laboratory practices.

Molecular Techniques (2015-2016). Slides for the Genetics Laboratory practices introduction

Slides for the Genetics Laboratory practices introduction.

Molecular Techniques (2015-2016). Exercises to be discussed and solved during the laboratory practices

Exercises to be discussed and solved during the laboratory practices.

Molecular Techniques (2015-2016). Problems to be solved by the students

Problems to be solved by the students.

Recolonization of mortars by endolithic organisms on the walls of San Roque church in Campeche (Mexico): A case of tertiary bioreceptivity

San Roque church (Campeche, Mexico) was built at the end of the 17th century with a micritic limestone and lime mortar in baroque style. In 2005 the church exhibited heavy biodeterioration associated with the development of extensive dark green phototrophic-based biofilms. Several cyanobacteria belonging to the order Chroococcales and lichenized fungi (Toninia nordlandica, Lobaria quercizans, Lecanora subcarnea, Cystocoleus ebeneus) were predominant in the dark biofilm samples, as revealed by DNA-based molecular techniques. In 2009, a cleaning and restoration intervention was adopted; however, after few months, microbial recolonization started to be noticeable on the painted church walls, representing an early phototrophic-based recolonization. According to molecular analysis, scanning electron microscopy observations and digital image analysis of cross sections, new phototrophic-based colonization, composed of cyanobacteria and bryophytes, developed mainly beneath the restored mortars. The intrinsic properties of the mortars, the tropical climate of Campeche and the absence of a biocide treatment in the restoration protocol influenced the recolonization of the church façades and enhanced the overall rate of deterioration in a short-term period.

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.

Novel silica membrane material for molecular sieve applications

Development of new silica membranes properties, e.g., molecular sieving properties, has been increasingly gaining importance in the last few years. A novel unsupported silica membrane, referred to as hydrophobic metal-doped silica, was developed by cobalt-doping within the organic templated silica matrix. The novel material was prepared by the acid-catalyzed hydrolysis and condensation process of tetraethylorthosilicate (TEOS) and methyltriethoxysilane (MTES), which is the precursor for methyl ligand covalently bounded to the silica matrix. The synthesis and surface properties of the novel unsupported silica membrane as well as the unsupported blank silica and modified silica membranes were revealed by surface and microstructural techniques, such as water contact angle measurement, FTIR, X-ray, Solid-state 29Si MAS NMR, TGA and N2 and CO2 adsorption measurements. The results showed that the thermal stability of the organic templated silica matrix was enhanced by cobalt-doping process. A hydrophobic microporous silica membrane material with high thermal stability up to ∼560 °C in oxidizing atmosphere and a narrow pore size distribution centered at 1.1 nm was obtained. Therefore, a novel precursor material for molecular sieve silica membranes applications has been achieved and developed.

X-Ray Imaging of SAPO-34 Molecular Sieves at the Nanoscale: Influence of Steaming on the Methanol-to-Hydrocarbons Reaction

The effect of a severe steaming treatment on the physicochemical properties and catalytic performance of H-SAPO-34 molecular sieves during the methanol-to-hydrocarbons (MTH) reaction has been investigated with a combination of scanning transmission X-ray microscopy (STXM), catalytic testing, and bulk characterization techniques, including ammonia temperature programmed desorption and 27Al and 29Si magic angle spinning nuclear magnetic resonance. For this purpose, two samples, namely a calcined and a steamed H-SAPO-34 catalyst powder, have been compared. It has been found that calcined H-SAPO-34 displays a high selectivity towards light olefins, yet shows a poor stability as compared to a zeolite H-ZSM-5 catalyst. Moreover, in situ STXM at the carbon K-edge during the MTH reaction allows construction of nanoscale chemical maps of the hydrocarbon species formed within the H-SAPO-34 aggregates as a function of reaction time and steam post-treatment. It was found that there is an initial preferential formation of coke precursor species within the core of the H-SAPO-34 aggregates. For longer times on stream the formation of the coke precursor species is extended to the outer regions, progressively filling the entire H-SAPO-34 catalyst particle. In contrast, the hydrothermally treated H-SAPO-34 showed similar reaction selectivity, but decreased activity and catalyst stability with respect to its calcined counterpart. These variations in MTH performance are related to a faster and more homogeneous formation of coke precursor species filling up the entire steamed H-SAPO-34 catalyst particle. Finally, the chemical imaging capabilities of the STXM method at the Al and Si K-edge are illustrated by visualizing the silicon islands at the nanoscale before and after steaming H-SAPO-34.