Nominal genera and species of Diptera misidentified as to family by A.Z. Lehrer (Diptera: Muscidae, Tachinidae)

Nominal genera and species misidentified to family by A.Z. Lehrer are revised and annotated, with habitus photographs given for all holotypes. New synonyms in the Muscidae: Dobrogiella Lehrer & Oprişan, 2013 = Pyrellia Robineau-Desvoidy, 1830, syn. nov., Dobrogiella phallogreciana Lehrer & Oprişan, 2013 = Pyrellia vivida Robineau-Desvoidy, 1830, syn. nov. New synonyms and new combinations in the Tachinidae: Benigramma Lehrer, 2013 = Thelairosoma Villeneuve, 1916, syn. nov., B. bellanda Lehrer, 2013 = Thelairosoma bellanda (Lehrer, 2013), comb. nov.; Eweka Lehrer, 2012 = Pales Robineau-Desvoidy, 1830, syn. nov., Eweka cordicerci Lehrer, 2012 = Ctenophorocera [now Pales] pauciseta Mesnil, 1950, syn. nov.; Mawuphalla Lehrer, 2013 = Ceracia Rondani, 1865, syn. nov., Mawuphalla antennomyia Lehrer, 2013 = Myothyria [now Ceracia] africana Mesnil, 1959, syn. nov.; Paraphalloides Lehrer, 2013 = Pales Robineau-Desvoidy, 1830, syn. nov., Paraphalloides epiphallops Lehrer, 2013 = Pales epiphallops (Lehrer, 2013), comb. nov.; Spinuphalla Lehrer, 2013 = Drino Robineau-Desvoidy, 1863, syn. nov., Spinuphalla juxtina Lehrer, 2013 = Drino (Palexorista Townsend, 1921) juxtina (Lehrer, 2013), comb. nov.

Gas hydrate dissociation off Svalbard induced by isostatic rebound rather than global warming

Methane seepage from the upper continental slopes of Western Svalbard has previously been attributed to gas hydrate dissociation induced by anthropogenic warming of ambient bottom waters. Here we show that sediment cores drilled off Prins Karls Foreland contain freshwater from dissociating hydrates. However, our modeling indicates that the observed pore water freshening began around 8 ka BP when the rate of isostatic uplift outpaced eustatic sea-level rise. The resultant local shallowing and lowering of hydrostatic pressure forced gas hydrate dissociation and dissolved chloride depletions consistent with our geochemical analysis. Hence, we propose that hydrate dissociation was triggered by postglacial isostatic rebound rather than anthropogenic warming. Furthermore, we show that methane fluxes from dissociating hydrates were considerably smaller than present methane seepage rates implying that gas hydrates were not a major source of methane to the oceans, but rather acted as a dynamic seal, regulating methane release from deep geological reservoirs.

Methane seepage from continental slopes has been attributed to gas hydrate dissociation induced by anthropogenic bottom water warming. Here, the authors show that hydrates dissociated before the Anthropocene when the isostatic rebound induced by deglaciation of the Arctic ice sheet outpaced eustatic sea-level rise.

Widespread methane seepage along the continental margin off Svalbard - from Bjørnøya to Kongsfjorden

Numerous articles have recently reported on gas seepage offshore Svalbard, because the gas emission from these Arctic sediments was thought to result from gas hydrate dissociation, possibly triggered by anthropogenic ocean warming. We report on findings of a much broader seepage area, extending from 74° to 79°, where more than a thousand gas discharge sites were imaged as acoustic flares. The gas discharge occurs in water depths at and shallower than the upper edge of the gas hydrate stability zone and generates a dissolved methane plume that is hundreds of kilometer in length. Data collected in the summer of 2015 revealed that 0.02-7.7% of the dissolved methane was aerobically oxidized by microbes and a minor fraction (0.07%) was transferred to the atmosphere during periods of low wind speeds. Most flares were detected in the vicinity of the Hornsund Fracture Zone, leading us to postulate that the gas ascends along this fracture zone. The methane discharges on bathymetric highs characterized by sonic hard grounds, whereas glaciomarine and Holocene sediments in the troughs apparently limit seepage. The large scale seepage reported here is not caused by anthropogenic warming.

Morphology successfully separates third instar larvae of Muscina

Three representatives of the muscid genus Muscina Robineau-Desvoidy (Diptera: Musicidae), Muscina levida (Harris), Muscina prolapsa (Harris) and Muscina stabulans (Fallén), are well known for their medical, veterinary and forensic importance. However, data in the literature provide contradictory information for the identification of third instar larvae of these species. This hinders easy species differentiation because it requires the rearing of material to adult stages in order to facilitate reliable identification. Third instar larvae of these three Muscina species were studied in detail using light and scanning electron microscopy to provide thorough redescriptions of their morphology. Existing information concerning third instar morphology, with particular reference to its value for taxonomy and identification, is revised and discussed. Emden's spiracular distance factor (SDF) is considered here as inappropriate for identification purposes in third instar larvae of Muscina spp. because its values are not constant ratios but increase during larval maturation and overlap in the examined species. These species were, instead, discriminated here by differences in the spinulation patterns of their abdominal segments.

Morphology and identification of first instars of European and Mediterranean blowflies of forensic importance. Part III: Calliphorinae

First instars of Calliphora vomitoria (Linnaeus) and Cynomya mortuorum (Linnaeus) (both: Diptera: Calliphoridae) are thoroughly documented with scanning electron microscopy images, light microscopy photographs and line drawings. Substantial new data are provided for the following morphological structures: pseudocephalon; antennal complex; maxillary palpus; facial mask; cephaloskeleton; thoracic and abdominal spinulation; spiracular field, and posterior spiracles. Earlier descriptions are summarized and major discrepancies with the current study are discussed. An identification key to first-instar larvae of the five European species of Calliphorinae of forensic importance is presented. However, it remains impossible to distinguish the first instars of Ca. vicina and Cy. mortuorum based on external morphology with the current level of knowledge.

Morphology of the first instar larva of obligatory traumatic myiasis agents (Diptera: Calliphoridae, Sarcophagidae)

There are only three fly species that are obligate agents of traumatic myiasis of humans and livestock: a single species of flesh fly, Wohlfahrtia magnifica (Sarcophagidae), and two species of blow flies, Chrysomya bezziana and Cochliomyia hominivorax (Calliphoridae). The morphology of their first instar larvae is thoroughly and consistently documented here with light microscopy photographs and scanning electron microscopy micrographs. The following morphological structures are documented: pseudocephalon, antennal complex, maxillary palpus, oral ridges, thoracic and abdominal spinulation, spiracular field, posterior spiracles and cephaloskeleton. New diagnostic features drawn from the cephaloskeleton and the spinulation of abdominal segments, including the anal pad, are discovered and extensively described. Earlier descriptions in the literature are revisited, and major discrepancies between these and the results of the current study are discussed. The present results allow clarification, correction and, especially, complementation of information provided by earlier authors. The relatively distant taxonomic position of all three species is evidence that obligatory myiasis has arisen independently, and the extensively similar morphology in the first instar larvae of Chrysomya bezziana, Cochliomyia hominivorax and W. magnifica in comparison to necrophagous species, especially the enhancement of the anterior part of the cephaloskeleton and the segmental spinulation, is therefore best interpreted as homoplasic adaptations to a life strategy as obligate vertebrate parasites. An identification key for first instar larvae of all obligatory traumatic myiasis agents of mammals is provided.

Morphology and identification of first instars of the European and Mediterranean blowflies of forensic importance. Part II. Luciliinae

First instars of Lucilia ampullacea Villeneuve, Lucilia caesar Linnaeus, Lucilia cuprina Weidemann, Lucilia richardsi Collin, Lucilia sericata Meigen and Lucilia silvarum Meigen (Diptera: Calliphoridae) are thoroughly documented with scanning electron microscopy images, light microscopy photographs and line drawings. The following morphological structures are documented: pseudocephalon, antennal complex, maxillary palpus, facial mask, cephaloskeleton, thoracic and abdominal spinulation, spiracular field, and posterior spiracles. New diagnostic features of the cephaloskeleton are presented and the spinulation of the abdominal segments is described. Earlier descriptions are summarized and major discrepancies with the current study are discussed. The present results allow for the clarification, correction and, especially, complementing existing information provided by numerous authors. The first instar larva of L. richardsi is described for the first time and an identification key to the first instars of European species of Lucilia Robineau-Desvoidy of forensic importance is presented.

Larval morphology of the lesser housefly, Fannia canicularis

The morphology of all larval instars of Fannia canicularis (Linnaeus) (Diptera: Fanniidae) is documented using a combination of light and scanning electron microscopy. The following structures are documented for all instars: antennal complex; maxillary palpus; facial mask; cephaloskeleton; ventral organ; anterior spiracle; Keilin's organ; posterior spiracle; fleshy processes, and anal pad. Structures reported for the first time for all instars include: two pairs of lateral prominences on the prothoracic segment; additional ventrolateral prominences on the second thoracic segment, and a papilla at the base of the posterior spiracle. Other structures reported for the first time are anterior spiracles in the first instar and a serrated tip on the mouthhook in the second instar. A trichoid sensillum on the posterior spiracular plate, representing a sensory organ otherwise unknown in the Calyptratae, is described in the second and third instars. Results are discussed and compared with existing knowledge on dipteran larval morphology.

A new dipteran forensic indicator in buried bodies

The first breeding records of miltogrammine fleshflies in buried vertebrate carrion are presented. First instars of Eumacronychia persolla Reinhard (Nearctic) (Diptera: Sarcophagidae) and Phylloteles pictipennis Loew (Palaearctic) (Diptera: Sarcophagidae) are able to penetrate dry, loose soil and reach deeply buried animal remains, an ability which distinguishes is unique to necrophagous Calyptratae. Their broad geographical distribution, fast location and colonization of carrion, complete development on buried food resources and easy identification make these species useful forensic indicators in buried bodies in dry habitats.

Morphology of the first instar of Calliphora vicina, Phormia regina and Lucilia illustris (Diptera, Calliphoridae)

Scanning electron microscopy documentation of first instar Calliphora vicina Robineau-Desvoidy, Phormia regina (Meigen) and Lucilia illustris (Meigen) (Diptera: Calliphoridae) is presented for the first time, and the following morphological structures are documented: pseudocephalon; antenna; maxillary palpus; facial mask; labial lobe; thoracic and abdominal spinulation; spiracular field; posterior spiracles, and anal pad. Light microscopy documentation and illustrations are provided for the cephaloskeleton in lateral and ventral views. New diagnostic features are revealed in the configuration of the facial mask, cephaloskeleton and posterior spiracles. The first instar morphology of C. vicina, Ph. regina and L. illustris is discussed in the light of existing knowledge about early instars of blowflies.

Carbon pools and isotopic trends in a hypersaline cyanobacterial mat

The fine-scale depth distribution of major carbon pools and their stable carbon isotopic signatures (delta(13)C) were determined in a cyanobacterial mat (Salin-de-Giraud, Camargue, France) to study early diagenetic alterations and the carbon preservation potential in hypersaline mat ecosystems. Particular emphasis was placed on the geochemical role of extracellular polymeric substances (EPS). Total carbon (C(tot)), organic carbon (C(org)), total nitrogen (N(tot)), total hydrolysable amino acids (THAA), carbohydrates, cyanobacteria-derived hydrocarbons (8-methylhexadecane, n-heptadec-5-ene, n-heptadecane) and EPS showed highest concentrations in the top millimetre of the mat and decreased with depth. The hydrocarbons attributed to cyanobacteria showed the strongest decrease in concentration with depth. This correlated well with the depth profiles of oxygenic photosynthesis and oxygen, which were detected in the top 0.6 and 1.05 mm, respectively, at a high down-welling irradiance (1441 micromol photons m(-2) s(-1)). At depths beneath the surface layer, the C(org) was composed mainly of amino acids and carbohydrates. A resistance towards microbial degradation could have resulted from interactions with diverse functional groups present in biopolymers (EPS) and with minerals deposited in the mat. A (13)C enrichment with depth for the total carbon pool (C(tot)) was observed, with delta(13)C values ranging from -16.3 per thousand at the surface to -11.3 per thousand at 9-10 mm depth. Total lipids depicted a delta(13)C value of -17.2 per thousand in the top millimetre and then became depleted in (13)C with depth (-21.7 to -23.3 per thousand). The delta(13)C value of EPS varied only slightly with depth (-16.1 to -17.3 per thousand) and closely followed the delta(13)C value of C(org) at depths beneath 4 mm. The EPS represents an organic carbon pool of preservation potential during early stages of diagenesis in recent cyanobacterial mats as a result of a variety of possible interactions. Their analyses might improve our understanding of fossilized microbial remains from mat ecosystems.

Loss-of-function mutations in the Nav1.7 gene underlie congenital indifference to pain in multiple human populations

Congenital indifference to pain (CIP) is a rare condition in which patients have severely impaired pain perception, but are otherwise essentially normal. We identified and collected DNA from individuals from nine families of seven different nationalities in which the affected individuals meet the diagnostic criteria for CIP. Using homozygosity mapping and haplotype sharing methods, we narrowed the CIP locus to chromosome 2q24-q31, a region known to contain a cluster of voltage-gated sodium channel genes. From these prioritized candidate sodium channels, we identified 10 mutations in the SCN9A gene encoding the sodium channel protein Nav1.7. The mutations completely co-segregated with the disease phenotype, and nine of these SCN9A mutations resulted in truncation and loss-of-function of the Nav1.7 channel. These genetic data further support the evidence that Nav1.7 plays an essential role in mediating pain in humans, and that SCN9A mutations identified in multiple different populations underlie CIP.

A second paradigm for gene activation in bacteria

Control of gene expression is key to development and adaptation. Using purified transcription components from bacteria, we employ structural and functional studies in an integrative manner to elaborate a detailed description of an obligatory step, the accessing of the DNA template, in gene expression. Our work focuses on a specialized molecular machinery that utilizes ATP hydrolysis to initiate DNA opening and permits a description of how the events triggered by ATP hydrolysis within a transcriptional activator can lead to DNA opening and transcription. The bacterial EBPs (enhancer binding proteins) that belong to the AAA(+) (ATPases associated with various cellular activities) protein family remodel the RNAP (RNA polymerase) holoenzyme containing the sigma(54) factor and convert the initial, transcriptionally silent promoter complex into a transcriptionally proficient open complex using transactions that reflect the use of ATP hydrolysis to establish different functional states of the EBP. A molecular switch within the model EBP we study [called PspF (phage shock protein F)] is evident, and functions to control the exposure of a solvent-accessible flexible loop that engages directly with the initial RNAP promoter complex. The sigma(54) factor then controls the conformational changes in the RNAP required to form the open promoter complex.

Hypoderma sinense: solving a century-old enigma

Among the species of Hypoderma (Diptera: Oestridae) that have been described and named over the last three centuries, Hypoderma sinense Pleske has been the subject of several scientific discussions. Hypoderma sinense was described by T. Pleske in 1926 on the basis of only three females collected by the Russian explorer P. K. Kozlov nearly 25 years earlier during a scientific expedition to China (1900-1901). This species was examined by the foremost oestrid authorities and synonomized with H. lineatum. Recently a unique, unidentified species of Hypoderma was observed to infect cattle and yaks in China. Molecular and morphological observations confirmed the unique nature of the third-stage larvae. This data initiated a debate within the scientific community regarding the proper name of this species, in particular with reference to previous taxonomical discussion on the validity of H. sinense. The present work provides a historical overview of the Russian scientific expeditions that collected the specimens and of the explorers and the entomologists who contributed to the description of H. sinense. The morphological examination of the original type material of H. sinense and the comparison with females of H. lineatum indicated that the H. sinense lectotype, deposited at the Zoological Institute of the Russian Academy of Sciences, St Petersburg, was within the range of variation of H. lineatum. Comparisons of the cox1 (688 bp) sequence obtained from the leg of a paralectotype of H. sinense with those of H. bovis (Linneaus), H. lineatum (De Villers) and of a sixth valid species of Hypoderma identified as "H. sinense" available in GenBank revealed differences of 9.7%, 7.2% and 0.3%, respectively. On the basis of these results, we concluded that the nominal species H. sinense should be treated as valid.

DNA-based identification and molecular systematics of forensically important Sarcophagidae (Diptera)

Sarcophagid flies have many characteristics that make them ideal forensic indicators. However, their utility is severely limited because it is difficult or impossible to determine the species of a sarcophagid larva, and in many instances an adult specimen, based on anatomy. We developed a database of mitochondrial DNA sequence data that makes it possible to identify all sarcophagid species likely to be found feeding on a human corpse at an urban location in Canada or the USA. Analyses were based on a 783 base pair region of the gene for cytochrome oxidase subunit one (COI). The species analyzed, including some of no forensic importance that were included for purposes of phylogenetic comparisons, were members of the genera Sarcophaga, Peckia, Blaesoxipha, Rovinia, Wohlfahrtia, Brachicoma (all Sarcophagidae), and Musca (Muscidae).

Direct localization by cryo-electron microscopy of secondary structural elements in Escherichia coli 23 S rRNA which differ from the corresponding regions in Haloarcula marismortui

Insertions were introduced by a two-step mutagenesis procedure into each of five double-helical regions of Escherichia coli 23 S rRNA, so as to extend the helix concerned by 17 bp. The helices chosen were at sites within the 23 S molecule (h9, h25, h45, h63 and h98) where significant length variations between different species are known to occur. At each of these positions, with the exception of h45, there are also significant differences between the 23 S rRNAs of E. coli and Haloarcula marismortui. Plasmids carrying the insertions were introduced into an E. coli strain lacking all seven rrn operons. In four of the five cases the cells were viable and 50 S subunits could be isolated; only the insertion in h63 was lethal. The modified subunits were examined by cryo-electron microscopy (cryo-EM), with a view to locating extra electron density corresponding to the insertion elements. The results were compared both with the recently determined atomic structure of H. marismortui 23 S rRNA in the 50 S subunit, and with previous 23 S rRNA modelling studies based on cryo-EM reconstructions of E. coli ribosomes. The insertion element in h45 was located by cryo-EM at a position corresponding precisely to that of the equivalent helix in H. marismortui. The insertion in h98 (which is entirely absent in H. marismortui) was similarly located at a position corresponding precisely to that predicted from the E. coli modelling studies. In the region of h9, the difference between the E. coli and H. marismortui secondary structures is ambiguous, and the extra electron density corresponding to the insertion was seen at a location intermediate between the position of the nearest helix in the atomic structure and that in the modelled structure. In the case of h25 (which is about 50 nucleotides longer in H. marismortui), no clear extra cryo-EM density corresponding to the insertion could be observed.

Single-particle electron cryo-microscopy: towards atomic resolution

1. Introduction 308

2. Electron microscopy 311

2.1 Specimen preparation 311

2.2 The electron microscope 311

2.3 Acceleration voltage, defocus, and the electron gun 312

2.4 Magnification and data collection 313

3. Digitisation and CTF correction 317

3.1 The patchwork densitometer 318

3.2 Particle selection 320

3.3 Position dependent CTF correction 321

3.4 Precision of CTF determination 321

4. Single particles and angular reconstitution 323

4.1 Preliminary filtering and centring of data 323

4.2 Alignments using correlation functions 324

4.3 Choice of first reference images 324

4.4 Multi-reference alignment of data 325

4.5 MSA eigenvector/eigenvalue data compression 328

4.6 MSA classification 330

4.7 Euler angle determination (‘angular reconstitution’) 332

4.8 Sinograms and sinogram correlation functions 332

4.9 Exploiting symmetry 335

4.10 Three-dimensional reconstruction 337

4.11 Euler angles using anchor sets 339

4.12 Iterative refinements 339

5. Computational hardware/software aspects 341

5.1 The (IMAGIC) image processing workstation 342

5.2 Operating systems and GUIs 342

5.3 Computational logistics 344

5.4 Shared memory machines 344

5.5 Farming on loosely coupled computers 346

5.6 Implementation using MPI protocol 347

5.7 Software is what it's all about 347

6. Interpretation of results 348

6.1 Assessing resolution: the Fourier Shell Correlation 348

6.2 Influence of filtering 351

6.3 Rendering 351

6.4 Searching for known sub-structures 352

6.5 Interpretation 353

7. Examples 353

7.1 Icosahedral symmetry: TBSV at 5·9 Å resolution 354

7.2 The D6 symmetrical worm hemoglobin at 13 Å resolution 356

7.3 Functional states of the 70S E. coli ribosome 357

7.4 The 50S E. coli ribosomal subunit at 7·5 Å resolution 359

8. Perspectives 361

9. Acknowledgements 364

10. References 364

In the past few years, electron microscopy (EM) has established itself as an important – still upcoming – technique for studying the structures of large biological macromolecules. EM is a very direct method of structure determination that complements the well-established techniques of X-ray crystallography and NMR spectroscopy. Electron micrographs record images of the object and not just their diffraction patterns and thus the classical ‘phase’ problem of X-ray crystallography does not exist in EM. Modern microscopes may reach resolution levels better than ∼ 1·5 Å, which is more than sufficient to elucidate the polypeptide backbone in proteins directly. X-ray structures at such resolution levels are considered ‘excellent’. The fundamental problem in biological EM is not so much the instrumental resolution of the microscopes, but rather the radiation sensitivity of the biological material one wants to investigate. Information about the specimen is collected in the photographic emulsion with the arrival of individual electrons that have (elastically) interacted with the specimen. However, many electrons will damage the specimen by non-elastic interactions. By the time enough electrons have passed through the object to produce a single good signal-to-noise (SNR) image, the biological sample will have been reduced to ashes. In contrast, stable inorganic specimens in material science often show interpretable details down to the highest possible instrumental resolution.

Boyer's model of scholarly nursing applied to professional development

Scholarship in nursing often is difficult to define and identify, but it is an important element in nursing. Scholars are needed in every practice setting to question the status quo and pursue fresh approaches to issues. This article examines Boyer's revised model of scholarship, which uses paradigms of discovery, integration, application, and teaching. Knowledge dissemination is emphasized as an important component for sharing information with fellow nurses and the public. Boyer's model of nursing scholarship provides institutions and OR nurse managers with a scholarly method for evaluating employee efforts. Strategies offered include professional development plans and employee portfolios. These applications encourage scholarly activities.

Intact aminoacyl-tRNA is required to trigger GTP hydrolysis by elongation factor Tu on the ribosome

GTP hydrolysis by elongation factor Tu (EF-Tu) on the ribosome is induced by codon recognition. The mechanism by which a signal is transmitted from the site of codon-anticodon interaction in the decoding center of the 30S ribosomal subunit to the site of EF-Tu binding on the 50S subunit is not known. Here we examine the role of the tRNA in this process. We have used two RNA fragments, one which contains the anticodon and D hairpin domains (ACD oligomer) derived from tRNA(Phe) and the second which comprises the acceptor stem and T hairpin domains derived from tRNA(Ala) (AST oligomer) that aminoacylates with alanine and forms a ternary complex with EF-Tu. GTP. While the ACD oligomer and the ternary complex containing the Ala-AST oligomer interact with the 30S and 50S A site, respectively, no rapid GTP hydrolysis was observed when both were bound simultaneously. The presence of paromomycin, an aminoglycoside antibiotic that binds to the decoding site and stabilizes codon-anticodon interaction in unfavorable coding situations, did not increase the rate of GTP hydrolysis. These results suggest that codon recognition as such is not sufficient for GTPase activation and that an intact tRNA molecule is required for transmitting the signal created by codon recognition to EF-Tu.

Conformational switch in the decoding region of 16S rRNA during aminoacyl-tRNA selection on the ribosome

Binding of aminoglycoside antibiotics to 16S ribosomal RNA induces a particular structure of the decoding center and increases the misincorporation of near-cognate amino acids. By kinetic analysis we show that this is due to stabilization of the near-cognate codon recognition complex and the acceleration of two rearrangements that limit the rate of amino acid incorporation. The same rearrangement steps are accelerated in the cognate coding situation. We suggest that cognate codon recognition, or near-cognate codon recognition augmented by aminoglycoside binding, promote the transition of 16S rRNA from a 'binding' to a 'productive' conformation that determines the fidelity of decoding.

The Escherichia coli large ribosomal subunit at 7.5 A resolution

BACKGROUND

In recent years, the three-dimensional structure of the ribosome has been visualised in different functional states by single-particle cryo-electron microscopy (cryo-EM) at 13-25 A resolution. Even more recently, X-ray crystallography has achieved resolution levels better than 10 A for the ribosomal structures of thermophilic and halophilic organisms. We present here the 7.5 A solution structure of the 50S large subunit of the Escherichia coli ribosome, as determined by cryo-EM and angular reconstitution.

RESULTS

The reconstruction reveals a host of new details including the long alpha helix connecting the N- and C-terminal domains of the L9 protein, which is found wrapped like a collar around the base of the L1 stalk. A second L7/L12 dimer is now visible below the classical L7/L12 'stalk', thus revealing the position of the entire L8 complex. Extensive conformational changes occur in the 50S subunit upon 30S binding; for example, the L9 protein moves by some 50 A. Various rRNA stem-loops are found to be involved in subunit binding: helix h38, located in the A-site finger; h69, on the rim of the peptidyl transferase centre cleft; and h34, in the principal interface protrusion.

CONCLUSIONS

Single-particle cryo-EM is rapidly evolving towards the resolution levels required for the direct atomic interpretation of the structure of the ribosome. Structural details such as the minor and major grooves in rRNA double helices and alpha helices of the ribosomal proteins can already be visualised directly in cryo-EM reconstructions of ribosomes frozen in different functional states.

Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome

The fidelity of aminoacyl-tRNA (aa-tRNA) selection by the bacterial ribosome is determined by initial selection before and proofreading after GTP hydrolysis by elongation factor Tu. Here we report the rate constants of A-site binding of a near-cognate aa-tRNA. The comparison with the data for cognate aa-tRNA reveals an additional, important contribution to aa-tRNA discrimination of conformational coupling by induced fit. It is found that two rearrangement steps that limit the chemical reactions of A-site binding, i.e. GTPase activation (preceding GTP hydrolysis) and A-site accommodation (preceding peptide bond formation), are substantially faster for cognate than for near-cognate aa-tRNA. This suggests an induced-fit mechanism of aa-tRNA discrimination on the ribosome that operates in both initial selection and proofreading. It is proposed that the cognate codon-anticodon interaction, more efficiently than the near-cognate one, induces a particular conformation of the decoding center of 16S rRNA, which in turn promotes GTPase activation and A-site accommodation of aa-tRNA, thereby accelerating the chemical steps. As kinetically favored incorporation of the correct substrate has also been suggested for DNA and RNA polymerases, the present findings indicate that induced fit may contribute to the fidelity of template-programed systems in general.

A systems approach to resolving OR conflict

Effective communication and courteous interaction with other hospital departments are essential for a smooth-running OR. To function effectively in a perioperative setting, OR personnel need patience, knowledge, and skill in problem-solving techniques. When health care employees are not taught these techniques and protocols are not in place to manage conflict, friction develops and productivity suffers. In this article, conflict situations between two hospital departments and on OR are presented to characterize successful conflict resolution methods using a systems approach. The results include reduction of surgical procedure delays, efficient ordering of supplies, and improved interpersonal relations.

Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome

The kinetic mechanism of elongation factor Tu (EF-Tu)-dependent binding of Phe-tRNAPhe to the A site of poly(U)-programmed Escherichia coli ribosomes has been established by pre-steady-state kinetic experiments. Six steps were distinguished kinetically, and their elemental rate constants were determined either by global fitting, or directly by dissociation experiments. Initial binding to the ribosome of the ternary complex EF-Tu.GTP.Phe-tRNAPhe is rapid (k1 = 110 and 60/micromM/s at 10 and 5 mM Mg2+, 20 degreesC) and readily reversible (k-1 = 25 and 30/s). Subsequent codon recognition (k2 = 100 and 80/s) stabilizes the complex in an Mg2+-dependent manner (k-2 = 0.2 and 2/s). It induces the GTPase conformation of EF-Tu (k3 = 500 and 55/s), instantaneously followed by GTP hydrolysis. Subsequent steps are independent of Mg2+. The EF-Tu conformation switches from the GTP- to the GDP-bound form (k4 = 60/s), and Phe-tRNAPhe is released from EF-Tu.GDP. The accommodation of Phe-tRNAPhe in the A site (k5 = 8/s) takes place independently of EF-Tu and is followed instantaneously by peptide bond formation. The slowest step is dissociation of EF-Tu.GDP from the ribosome (k6 = 4/s). A characteristic feature of the mechanism is the existence of two conformational rearrangements which limit the rates of the subsequent chemical steps of A-site binding.

Legal and ethical considerations of informed consent

The law of informed consent remains ineffective at resolving patient comprehension issues primarily because differing interpretations exist regarding who is responsible for the duty to inform. Court cases continue to set precedents for practicing physicians and other health care providers; however, other measures can be applied for effectual patient advocacy. Health care personnel should rewrite typical consent forms in simpler terms, use larger print, and create duplicate copies. If patients are given copies of the permits they sign, the can reread the forms at home when they are more comfortable. For true autonomy to exist in informed consent for surgical procedures, consent forms should contain patients' primary languages whenever possible, or an adequate interpreter should be made available. Surgeons, nurses, and other health care providers must become aware of their responsibilities related to informed consent for treatment. It is necessary for health care personnel to develop and use effective communication techniques and remember that although some patients are more visually attuned to new information, other patients may benefit more from listening or reading. The cases in this article show that a patient's autonomy is part of the informed consent process and the duty to inform the patient lies with the person performing the procedure. A more important issue, however, involves the patient's comprehension of the information given, because without it, the patient cannot achieve true autonomy in making decisions. Ensuring that all elements of informed consent are met to obtain informed consent will result in fewer malpractice claims, greater patient satisfaction, and an improved professional image. Nevertheless, nurses should make themselves aware of the state laws in which they practice, including their nurse practice acts. They then should advocate for patient rights by encompassing all elements of informed consent.

The G222D mutation in elongation factor Tu inhibits the codon-induced conformational changes leading to GTPase activation on the ribosome

Elongation factor Tu (EF-Tu) from Escherichia coli carrying the mutation G222D is unable to hydrolyze GTP on the ribosome and to sustain polypeptide synthesis at near physiological Mg2+ concentration, although the interactions with guanine nucleotides and aminoacyl-tRNA are not changed significantly. GTPase and polypeptide synthesis activities are restored by increasing the Mg2+ concentration. Here we report a pre-steady-state kinetic study of the binding of the ternary complexes of wild-type and mutant EF-Tu with Phe-tRNA(Phe) and GTP to the A site of poly(U)-programed ribosomes. The kinetic parameters of initial binding to the ribosome and subsequent codon-anticodon interaction are similar for mutant and wild-type EF-Tu, independent of the Mg2+ concentration, suggesting that the initial interaction with the ribosome is not affected by the mutation. Codon recognition following initial binding is also not affected by the mutation. The main effect of the G222D mutation is the inhibition, at low Mg2+ concentration, of codon-induced structural transitions of the tRNA and, in particular, their transmission to EF-Tu that precedes GTP hydrolysis and the subsequent steps of A-site binding. Increasing the Mg2+ concentration to 10 mM restores the complete reaction sequence of A-site binding at close to wild-type rates. The inhibition of the structural transitions is probably due to the interference of the negative charge introduced by the mutation with negative charges either of the 3' terminus of the tRNA, bound in the vicinity of the mutated amino acid in domain 2 of EF-Tu, or of the ribosome. Increasing the Mg2+ concentration appears to overcome the inhibition by screening the negative charges.

Initial binding of the elongation factor Tu.GTP.aminoacyl-tRNA complex preceding codon recognition on the ribosome

The first step in the sequence of interactions between the ribosome and the complex of elongation factor Tu (EF-Tu), GTP, and aminoacyl-tRNA, which eventually leads to A site-bound aminoacyl-tRNA, is the codon-independent formation of an initial complex. We have characterized the initial binding and the resulting complex by time-resolved (stopped-flow) and steady-state fluorescence measurements using several fluorescent tRNA derivatives. The complex is labile, with rate constants of 6 x 10(7) M-1 s-1 and 24 s-1 (20 degrees C, 10 mM Mg2+) for binding and dissociation, respectively. Both thermodynamic and activation parameters of initial binding were determined, and five Mg2+ ions were estimated to participate in the interaction. While a cognate ternary complex proceeds form initial binding through codon recognition to rapid GTP hydrolysis, the rate constant of GTP hydrolysis in the non-cognate complex is 4 orders of magnitude lower, despite the rapid formation of the initial complex in both cases. Hence, the ribosome-induced GTP hydrolysis by EF-Tu is strongly affected by the presence of the tRNA. This suggests that codon-anticodon recognition, which takes place after the formation of the initial binding complex, provides a specific signal that triggers fast GTP hydrolysis by EF-Tu on the ribosome.

Elongation factor Tu, a GTPase triggered by codon recognition on the ribosome: mechanism and GTP consumption

The mechanism of elongation factor Tu (EF-Tu) catalyzed aminoacyl-tRNA (aa-tRNA) binding to the A site of the ribosome was studied. Two types of complexes of EF-Tu with GTP and aa-tRNA, EF-Tu.GTP-aa-tRNA (ternary) and (EF-Tu.GTP)2.aa-tRNA (quinternary), can be formed in vitro depending on the conditions. On interaction with the ribosomal A site, generally only one molecule of GTP is hydrolysed per aa-tRNA bound and peptide bond formed. The second GTP molecule from the quinternary complex is hydrolyzed only during translation of an oligo(U) tract in the presence of EF-G. The first step in the interaction between the ribosome and the ternary complex is the codon-independent formation of an initial complex. In the absence of codon recognition, the aa-tRNA-EF-Tu complex does not enter further steps of A site binding and remains in the initial binding state. Despite the rapid formation of the initial complex, the rate constant of GTP hydrolysis in the noncognate complex is four orders of magnitude lower compared with the cognate complex. This, together with the results of time-resolved fluorescence measurements, suggests that codon recognition by the ternary complex on the ribosome initiates a series of structural rearrangements that result in a conformational change of EF-Tu, presumably involving the effector region, which, in turn, triggers GTP hydrolysis and the subsequent steps of A site binding.

A method to impregnate wet soil samples, producing high-quality thin sections

[120.031]Mineral soils with different moisture content and texture were impregnated successfully by the method described. The water present in the soil sample is replaced by acetone and the acetone-saturated sample is impregnated by FitzPatrick's method (1970) (using acetone as thinner of the polyester resin Synolith 544). Shrinkage is minimal and the thin sections are of high quality. It should be possible to correlate thin section data obtained by this method with physical data obtained from undisturbed material. Micromorphologically, a better understanding of the plasmic fabrics should be possible. (Abstract retrieved from CAB Abstracts by CABI’s permission)