As MAD as can be

Endophytic bacteria in the rice plant

Endophytic bacteria are defined as bacteria detected inside surface-sterilized plants or extracted from inside plants and having no visibly harmful effects on the plants. Various kinds of endophytic bacteria, such as Pantoea, Methylobacterium, Azospirillum, Herbaspirillum, Burkholderia and Rhizobium etc., have been found inside rice plants. This minireview summarizes and discusses recent studies of endophytic bacteria residing in rice plants, focusing on flora, origin, movement, and interaction with plants/other microbes and referring to endophytes in other plants. The findings concerning bacterial flora obtained by cultural and non-cultural methods are also compared and discussed. Some attempts to apply endophytes to the rice plant and the resultant effects are introduced. The future perspective to deepen the study of endophytes in terms of both application and basic science is considered.

Effect of the herbicide glyphosate on the culturable fraction of glyphosate-tolerant maize rhizobacterial communities using two different growth media

A comparison was drawn between the effect of glyphosate (Roundup Plus), a post-emergence applied herbicide, and Harness GTZ, a pre-emergence applied herbicide, on the culturable fraction of the rhizobacterial communities of genetically modified NK603 glyphosate-tolerant maize. Two different non-selective rich media were used to grow fast-growing culturable bacteria, BHI and NB, as a more accurate estimation of the soil fast-growing culturable bacterial population would be obtained from the results of cultivating in more than one medium. The potential effect was monitored by direct amplification, cloning and sequencing of bacterial DNA encoding 16S rRNA, and high-throughput DNA pyrosequencing of the bacterial DNA coding for the 16S rRNA hypervariable V6 region from bacterial communities grown in the two different media. The estimated relative composition of the culturable maize rhizobacterial population varied considerably in accordance with the growth medium used. Both herbicides do, in fact, affect the maize rhizobacterial communities, glyphosate being, to a great extent, the less aggressive herbicide, regardless of the cultivation medium used. The pyrosequencing analysis of the fast-growing bacterial populations from the different soils represents a useful and invaluable tool to estimate the bacterial biodiversity of the culturable rhizobacteria of agricultural soils.

The 'fingerprint' that X-rays can leave on structures

BACKGROUND

Exposure of biomacromolecules to ionising radiation results in damage that is initiated by free radicals and progresses through a variety of mechanisms. A widely used technique to study the three-dimensional structures of biomacromolecules is crystallography, which makes use of ionising X-rays. It is crucial to know to what extent structures determined using this technique might be biased by the inherent radiation damage.

RESULTS

The consequences of radiation damage have been investigated for three dissimilar proteins. Similar results were obtained for each protein, atomic B factors increase, unit-cell volumes increase, protein molecules undergo slight rotations and translations, disulphide bonds break and decarboxylation of acidic residues occurs. All of these effects introduce non-isomorphism. The absorbed dose in these experiments can be reached during routine data collection at undulator beamlines of third generation synchrotron sources.

CONCLUSIONS

X-rays can leave a 'fingerprint' on structures, even at cryogenic temperatures. Serious non-isomorphism can be introduced, thus hampering multiple isomorphous replacement (MIR) and multiwavelength anomalous dispersion (MAD) phasing methods. Specific structural changes can occur before the traditional measures of radiation damage have signalled it. Care must be taken when assigning structural significance to features that might easily be radiation-damage-induced changes. It is proposed that the electron-affinic disulphide bond traps electrons that migrate over the backbone of the protein, and that the sidechains of glutamic acid and aspartic acid donate electrons to nearby electron holes and become decarboxylated successively. The different disulphide bonds in each protein show a clear order of susceptibility, which might well relate to their intrinsic stability.

New trends in macromolecular X-ray crystallography

Advances in experimental and computational techniques have reaffirmed the role of protein X-ray crystallography as one of the primary providers of structural information both to enhance our fundamental understanding of biological systems and also to assist the design and optimization of important therapeutics. Today, the most important challenge facing macromolecular X-ray crystallography is the need to grow suitable crystals of a given protein. Once this has been accomplished, most often the question is not whether the structure will be solved but rather how fast this will be done. A dramatic example of this is the crystal structure of cytochrome c oxidase. The search for crystallization conditions took about 15 years and then the structure was solved in about one year.

Synchrotron radiation applications to macromolecular crystallography

Progress has been rapid in the development and application of four different types of macromolecular crystallographic experiment at synchrotron hard X-ray sources: multiwavelength anomalous diffraction; studies of crystals with very large unit cell dimensions; structure determination at atomic or near-atomic resolution; and time-resolved studies. The results illustrate the interplay between the advanced technical capabilities available at new beamlines and more challenging scientific issues.