Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia coli 70S ribosome with a global resolution of 2.0 A. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.

/pdf/structures-of-the-bacterial-ribosome-at-3-5-a-resolution-4pbqytwxq1.pdf

Structures of the bacterial ribosome at 3.5 Å resolution

https://www.researchgate.net/profile/Rupam_Kapoor/publication/26881549_Arbuscular_mycorrhizal_fungi_in_alleviation_of_salt_stress_A_review/links/0c960523fd2cc5ec7f000000.pdf

Arbuscular mycorrhizal fungi in alleviation of salt stress: a review.

Excessive salt accumulation in soils is a major ecological and agronomical problem, in particular in arid and semi-arid areas. Excessive soil salinity affects the establishment, development, and growth of plants, resulting in important losses in productivity. Plants have evolved biochemical and molecular mechanisms that may act in a concerted manner and constitute the integrated physiological response to soil salinity. These include the synthesis and accumulation of compatible solutes to avoid cell dehydration and maintain root water uptake, the regulation of ion homeostasis to control ion uptake by roots, compartmentation and transport into shoots, the fine regulation of water uptake and distribution to plant tissues by the action of aquaporins, the reduction of oxidative damage through improved antioxidant capacity and the maintenance of photosynthesis at values adequate for plant growth. Arbuscular mycorrhizal (AM) symbiosis can help the host plants to cope with the detrimental effects of high soil salinity. There is evidence that AM symbiosis affects and regulates several of the above mentioned mechanisms, but the molecular bases of such effects are almost completely unknown. This review summarizes current knowledge about the effects of AM symbiosis on these physiological mechanisms, emphasizing new perspectives and challenges in physiological and molecular studies on salt-stress alleviation by AM symbiosis.

Regulation by arbuscular mycorrhizae of the integrated physiological response to salinity in plants: new challenges in physiological and molecular studies

Quantitative and simultaneous detection of four foodborne bacterial pathogens with a multi-channel SPR sensor.

During the elongation cycle of protein biosynthesis, the specific amino acid coded for by the mRNA is delivered by a complex that is comprised of the cognate aminoacyl-tRNA, elongation factor Tu and GTP. As this ternary complex binds to the ribosome, the anticodon end of the tRNA reaches the decoding center in the 30S subunit. Here we present the cryo- electron microscopy (EM) study of an Escherichia coli 70S ribosome-bound ternary complex stalled with an antibiotic, kirromycin. In the cryo-EM map the anticodon arm of the tRNA presents a new conformation that appears to facilitate the initial codon–anticodon interaction. Furthermore, the elbow region of the tRNA is seen to contact the GTPase-associated center on the 50S subunit of the ribosome, suggesting an active role of the tRNA in the transmission of the signal prompting the GTP hydrolysis upon codon recognition.

https://www.embopress.org/doi/pdf/10.1093/emboj/cdf326

Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process

Bioinformatics--the application of computational and analytical methods to biological problems--is a rapidly evolving scientific discipline. Genome sequencing projects are producing vast amounts of biological data for many different organisms, and, increasingly, storing these data in public databases. Such biological databases are growing exponentially, along with the biological literature. It's impossible for even the most zealous researcher to stay on top of necessary information in the field without the aid of computer-based tools. Bioinformatics is all about building these tools. Developing Bioinformatics Computer Skills is for scientists and students who are learning computational approaches to biology for the first time, as well as for experienced biology researchers who are just starting to use computers to handle their data. The book covers the Unix file system, building tools and databases for bioinformatics, computational approaches to biological problems, an introduction to Perl for bioinformatics, data mining, and data visualization. Written in a clear, engaging style, Developing Bioinformatics Computer Skills will help biologists develop a structured approach to biological data as well as the tools they'll need to analyze the data.

/pdf/developing-bioinformatics-computer-skills-m1byzzf9i2.pdf

Developing bioinformatics computer skills

Continuum electrostatic methods applied to pH-dependent properties of antibody-antigen association.

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Developing bioinformatics computer skills

Continuum electrostatic methods applied to pH-dependent properties of antibody-antigen association.