Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme

The structure of E. coli core RNA polymerase (RNAP) has been determined to approximately 23 A resolution by three-dimensional reconstruction from electron micrographs of flattened helical crystals. The structure reveals extensive conformational changes when compared with the previously determined E. coli RNAP holoenzyme structure, but resembles the yeast RNAPII structure. While each of these structures contains a thumb-like projection surrounding a channel 25 A in diameter, the E. coli RNAP holoenzyme thumb defines a deep but open groove on the molecule, whereas the thumb of E. coli core and yeast RNAPII form part of a ring that surrounds the channel. This may define promoter-binding and elongation conformations of RNAP, as E. coli holoenzyme recognizes promoter sites on double-stranded DNA, while both E. coli core and yeast RNAPII are elongating forms of the polymerase and are incapable of promoter recognition.

GreA protein: a transcription elongation factor from Escherichia coli

A protein identified as the 158-amino acid product of the greA gene was isolated from Escherichia coli. When added to a halted ternary transcription complex, the GreA protein induced cleavage and removal of the 3' proximal dinucleotide from the nascent RNA. The new 3' terminus generated by the cleavage could be extended into longer transcripts. GreA-mediated cleavage of a transcript appears to permit a ternary complex to resume transcription from a state of indefinite elongation arrest induced by a specific DNA site. The GreA protein tended to interact with RNA polymerase during purification and recycled between RNA polymerase molecules in the course of the in vitro cleavage reaction. Similar biochemical activities have been reported in eukaryotic RNA polymerases, indicating that transcript cleavage and restart of elongation may be a general transcriptional mechanism.

Crystal structure of the GreA transcript cleavage factor from Escherichia coli

Transcription elongation factors stimulate the activity of DNA-dependent RNA polymerases by increasing the overall elongation rate and the completion of RNA chains. One group of such factors, which includes Escherichia coli GreA, GreB and eukaryotic SII (TFIIS), acts by inducing hydrolytic cleavage of the transcript within the RNA polymerase, followed by release of the 3'-terminal fragment. Here we report the crystal structure of GreA at 2.2 A resolution. The structure contains an amino-terminal domain consisting of an antiparallel alpha-helical coiled-coil dimer which extends into solution, reminiscent of the coiled coil in seryl-tRNA synthetases. A site near the tip of the coiled-coil 'finger' plays a direct role in the transcript cleavage reaction by contacting the 3'-end of the transcript. The structure exhibits an unusual asymmetric charge distribution which indicates the manner in which GreA interacts with the RNA polymerase elongation complex.

Histidine-tagged RNA polymerase: dissection of the transcription cycle using immobilized enzyme

A stretch of six histidine residues (His6) has been genetically fused to the C terminus of the beta' polypeptide of Escherichia coli RNA polymerase. The His6-tagged beta' subunit assembles into RNA polymerase molecules which perform all vital in vivo functions and behave qualitatively normally in vitro. The His6 tag permits rapid purification of the enzyme directly from crude cell extracts or from an in vitro reconstitution reaction by adsorption to Ni(2+)-chelating agarose resin, followed by elution with imidazole. The enzyme bound to the matrix remains transcriptionally active. The immobilized enzyme can withstand repeated buffer changes without substantial activity loss and permits controlled stepwise 'walking' of the transcriptional complex along the DNA template, and isolation of defined intermediates in the transcription cycle. The immobilized RNA polymerase provides a powerful experimental system for structural and functional analysis of RNA polymerase and its interaction with regulatory factors.

Synthesis of a new element with atomic number Z = 117

The discovery of a new chemical element with atomic number Z=117 is reported. The isotopes (293)117 and (294)117 were produced in fusion reactions between (48)Ca and (249)Bk. Decay chains involving 11 new nuclei were identified by means of the Dubna gas-filled recoil separator. The measured decay properties show a strong rise of stability for heavier isotopes with Z > or = 111, validating the concept of the long sought island of enhanced stability for superheavy nuclei.

Reaching the theoretical resonance quality factor limit in coaxial plasmonic nanoresonators fabricated by helium ion lithography

Optical antenna structures have revolutionized the field of nano-optics by confining light to deep subwavelength dimensions for spectroscopy and sensing. In this work, we fabricated coaxial optical antennae with sub-10-nanometer critical dimensions using helium ion lithography (HIL). Wavelength dependent transmission measurements were used to determine the wavelength-dependent optical response. The quality factor of 11 achieved with our HIL fabricated structures matched the theoretically predicted quality factor for the idealized flawless gold resonators calculated by finite-difference time-domain (FDTD). For comparison, coaxial antennae with 30 nm critical dimensions were fabricated using both HIL and the more common Ga focus ion beam lithography (Ga-FIB). The quality factor of the Ga-FIB resonators was 60% of the ideal HIL results for the same design geometry due to limitations in the Ga-FIB fabrication process.

Topology of the RNA polymerase active center probed by chimeric rifampicin-nucleotide compounds

Spatial organization of the binding sites for the priming substrate, the template DNA, and the transcription inhibitor rifampicin (Rif) in Escherichia coli RNA polymerase (EC 2.7.7.6) was probed with chimeric compounds in which Rif is covalently attached to a ribonucleotide. The compounds bind to RNA polymerase in bifunctional manner and serve as substrates for RNA chain extension, yielding chains up to 8 nucleotides in length, with Rif linked to their 5' termini. These products act as potent inhibitors of normal transcription. Using the linker between the two ligands as ruler, we determined the distance between the sites for Rif and the priming nucleotide to be approximately 15 A. A reactive side group placed in the linker next to Rif crosslinks to the template strand of DNA at the -2 or -3 position of the promoter. Thus, bound Rif is juxtaposed to DNA immediately upstream of the start site, suggesting that Rif plugs the channel leading RNA out of the active center.

Sound lateralization and interaural discrimination. Effects of brainstem infarcts and multiple sclerosis lesions

Subjects with brainstem lesions due to either an infarct or multiple sclerosis (MS) underwent two types of binaural testing (lateralization testing and interaural discrimination) for three types of sounds (clicks and high and low frequency narrow-band noise) with two kinds of interaural differences (level and time). Two major types of abnormalities were revealed in the lateralization performances: perception of all stimuli, regardless of interaural differences (time and/or level) in the center of the head (center-oriented), or lateralization of all stimuli to one side or the other of the head (side-oriented). Similar patterns of abnormal lateralization (center-oriented and side-oriented) occurred for MS and stroke patients. A subject's pattern of abnormal lateralization testing was the same regardless of the type of stimulus or type of interaural disparity. Lateralization testing was a more sensitive test than interaural discrimination testing for both types of subjects. Magnetic resonance image (MRI) scanning in three orthogonal planes of the brainstem was used to detect lesions. A semi-automated algorithm superimposed the auditory pathway onto each MRI section. Whenever a lesion overlapped the auditory pathway, some binaural performance was abnormal and vice versa. Given a lateralization test abnormality, whether the pattern was center-oriented or side-oriented was mainly determined by lesion site. Center-oriented performance was principally associated with caudal pontine lesions and side-oriented performance with lesions rostral to the superior olivary complex. For lesions restricted to the lateral lemniscus and/or inferior colliculus, whether unilateral or bilateral, just noticeable differences (JNDs) were nearly always abnormal, but for caudal pontine lesions JNDs could be normal or abnormal. MS subjects were more sensitive to interaural time delays than interaural level differences particularly for caudal pontine lesions, while stroke patients showed no differential sensitivity to the two kinds of interaural differences. These results suggest that neural processing of binaural stimuli is multilevel and begins with independent interaural time and level analyzers in the caudal pons.

Plasmon resonance tuning in metallic nanocavities

Nanocavities fabricated in a metallic surface have important and technologically useful properties of complete light absorption and strong field enhancement. Here, we demonstrate how a nanometerthick alumina deposition inside such a cavity can be used to gain an exquisite control over the resonance wavelength. This process allows achieving a precise control over the spectral response and is completely reversible allowing many tuning attempts to be made on a single structure until the optimum performance is achieved.

How common is add-on use and how do patients decide whether to use them? A national survey of IVF patients

STUDY QUESTION

What is the prevalence and pattern of IVF add-on use in Australia?

SUMMARY ANSWER

Among women having IVF in the last 3 years, 82% had used one or more IVF add-on, most commonly acupuncture, preimplantation genetic testing for aneuploidy and Chinese herbal medicine.

WHAT IS KNOWN ALREADY

IVF add-ons are procedures, techniques or medicines which may be considered nonessential to IVF, but usually used in attempts to improve the probability of conception and live birth. The use of IVF add-ons is believed to be widespread; however, there is little information about the prevalence and patterns of use in different settings.

STUDY DESIGN, SIZE, DURATION

An online survey was distributed via social media to women in Australia who had undergone IVF since 2017. Women were excluded if they were gestational surrogates, used a surrogate, or underwent ovarian stimulation for oocyte donation or elective oocyte cryopreservation only. The survey was open from 21 June to 14 July 2020.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Survey questions included demographics, IVF and medical history, and use of IVF add-ons including details of the type of add-on, costs and information sources used. Participants were also asked about the relative importance of evidence regarding safety and effectiveness, factors considered in decision-making and decision regret.

MAIN RESULTS AND THE ROLE OF CHANCE

A total of 1590 eligible responses were analysed. Overall, 82% of women had used one or more add-ons and these usually incurred an additional cost (72%). Around half (54%) had learned about add-ons from their fertility specialist, and most reported that the decision to use add-ons was equally shared with the specialist. Women placed a high level of importance on scientific evidence for safety and efficacy, and half (49%) assumed that add-ons were known to be safe. Most women experienced some regret at the decision to use IVF add-ons (66%), and this was more severe among women whose IVF was unsuccessful (83%) and who believed that the specialist had a larger contribution to the decision to use add-ons (75%).

LIMITATIONS, REASONS FOR CAUTION

This retrospective survey relied on patient recall. Some aspects were particularly prone to bias such as contributions to decision-making. This approach to capturing IVF add-on use may yield different results to data collected directly from IVF clinics or from fertility specialists.

WIDER IMPLICATIONS OF THE FINDINGS

There is a very high prevalence of IVF add-on use in Australia which may be generalisable to other settings with similar models of IVF provision. Although women placed high importance on scientific evidence to support add-ons, most add-ons do not have robust evidence of safety and effectiveness. This suggests that IVF patients are not adequately informed about the risks and benefits of IVF add-ons, or are not aware of the paucity of evidence to support their use.

STUDY FUNDING/COMPETING INTEREST(S)

This research was supported by a McKenzie Postdoctoral Fellowship Grant (University of Melbourne), a Department of Obstetrics and Gynaecology Innovation Grant (University of Melbourne) and an NHMRC Investigator Grant (APP1195189). A.P. declares that he provides fertility services at Melbourne IVF (part of Virtus Health). J.W. reports grants from Wellcome Trust, during the conduct of the study, and that publishing benefits his career. The remaining authors report no conflict of interest.

TRIAL REGISTRATION NUMBER

N/A.

Insights into Escherichia coli RNA polymerase structure from a combination of x-ray and electron crystallography

Our goal is to understand the mechanism of transcription and its regulation. Determining structures of RNA polymerase and transcription complexes is an essential step. Because of their large size and complexity, determination of these structures will require a combination of electron microscopy, biophysical methods, and biochemical methods to identify functionally and structurally relevant subassemblies and domains and x-ray crystallography to determine high-resolution structures of RNA polymerase components and accessory factors. We recently solved the 2.5-A crystal structure of the Escherichia coli RNA polymerase alpha subunit N-terminal domain, which is the first high-resolution structure of a core component required for RNA polymerase assembly and basal transcription. This structure, combined with a new 19-A resolution structure determined by cryo-electron microscopy of helical crystals of E. coli core RNAP embedded in vitreous ice, leads to a model for the organization of the RNAP subunits.

Effects of localized pontine lesions on auditory brain-stem evoked potentials and binaural processing in humans

OBJECTIVES AND METHODS

Four sets of measurements were obtained from 11 patients (44-80 years old) with small, localized pontine lesions due to vascular disease: (1) Monaural auditory brain-stem evoked potentials (ABEPs; peaks I to VI); (2) Binaural ABEPs processed for their binaural interaction components (BICs) in the latency range of peaks IV to VI; (3) magnetic resonance imaging (MRI) of the brain-stem; and (4) psychoacoustics of interaural time disparity measures of binaural localization. ABEPs and BICs were analyzed for peak latencies and interpeak latency differences. Three-channel Lissajous' trajectories (3-CLTs) were derived for ABEPs and BICs and the latencies and orientations of the equivalent dipoles of ABEP and BICs were inferred from them.

RESULTS

Intercomponent latency measures of monaurally evoked ABEPs were abnormal in only 3 of the 11 patients. Consistent correlations between sites of lesion and neurophysiological abnormality were obtained in 9 of the 11 patients using 3-CLT measures of BICs. Six of the 11 patients had absence of one or more BIC components. Seven of the 11 had BICs orientation abnormality and 3 had latency abnormalities. Trapezoid body (TB) lesions (6 patients) were associated with an absent (two patients with ventral-caudal lesions) or abnormal (one patient with ventral-rostral lesions) dipole orientation of the first component (at the time of ABEPs IV), and sparing of this component with midline ventral TB lesions (two patients). A deviant orientation of the second BICs component (at the time of ABEPs V) was observed with ventral TB lesions. Psychoacoustic lateralization in these patients was biased toward the center. Rostral lateral lemniscus (LL) lesions (3 patients) were associated with absent (one patient) or abnormal (two patients) orientation of the third BICs component (at the time of ABEPs VI); and a side-biased lateralization with behavioral testing.

CONCLUSIONS

These results indicate that: (1) the BICs component occurring at the time of ABEPs peak IV is dependent on ventral-caudal TB integrity; (2) the ventral TB contributes to the BICs component at the time of ABEPs peak V; and (3) the rostral LL is a contributing generator of the BICs component occurring at the time of ABEP peak VI.

Low diversity of t haplotypes in the eastern form of the house mouse, Mus musculus L

In previous studies, 13 different recessive embryonic lethal genes have been associated with t haplotypes in the wild mice of the species Mus domesticus. In this communication we have analyzed five populations of Mus musculus for the presence and identity of t haplotypes. The populations occupy geographically distant regions in the Soviet Union: Altai Mountains, western and eastern Siberia, Azerbaijan and Turkmenistan. No t haplotypes were found in mice from eastern Siberia. In the remaining four populations, t haplotypes occurred with frequencies ranging from 0.07 to 0.21. All the t haplotypes extracted from these populations and analyzed by the genetic complementation test were shown to carry the same lethal gene tcl-w73. In one population (that of western Siberia), another lethal gene (tcl-w5) was found to be present on the same chromosome as tcl-w73. This situation is in striking contrast to that found in the populations of the western form of the house mouse, M. domesticus. In the latter species, tcl-w73 has not been found at all and the different populations are characterized by the presence of several different lethal genes. The low diversity of t haplotypes in M. musculus is consistent with lower genetic variability of other traits and indicates a different origin and speciation mode compared to M. domesticus. Serological typing for H-2 antigenic determinants suggests that most, if not all, of the newly described t haplotypes might have arisen by recombination of tw73 from M. musculus with t haplotypes from M. domesticus either in the hybrid zone between the two species or in regions where the two species mixed accidentally.

Plasmon-enhanced photocathode for high brightness and high repetition rate x-ray sources

In this Letter, we report on the efficient generation of electrons from metals using multiphoton photoemission by use of nanostructured plasmonic surfaces to trap, localize, and enhance optical fields. The plasmonic surface increases absorption over normal metals by more than an order of magnitude, and due to the localization of fields, this results in over 6 orders of magnitude increase in effective nonlinear quantum yield. We demonstrate that the achieved quantum yield is high enough for use in rf photoinjectors operating as electron sources for MHz repetition rate x-ray free electron lasers.

Visualization of the binding site for the transcript cleavage factor GreB on Escherichia coli RNA polymerase

The structure of Escherichia coli core RNA polymerase (RNAP) complexed with the transcript cleavage factor GreB was determined from electron micrographs of negatively stained, flattened helical crystals. A binding assay was developed to establish that GreB was incorporated into the RNA polymerase crystals with high occupancy through interactions between the globular C-terminal domain and the RNA polymerase. Comparison of the core RNAP:GreB structure with the previously determined structure of core RNAP located the GreB binding site on one face of the RNA polymerase, next to but not in the 25 A-diameter channel of RNA polymerase.

Detailed analysis of auditory brainstem responses in patients with noise-induced tinnitus

The role of the auditory brainstem in tinnitus is questionable. This study aimed comprehensively to assess auditory brainstem responses (ABRs) in patients suffering from noise-induced tinnitus (NIT). ABRs were recorded from 13 chronic NIT patients (21 ears) and 11 (21 ears) age and hearing matched control subjects without tinnitus. ABRs were recorded with scalp electrodes placed ipsilateral and contralateral to the stimulated ear, and in three orthonormal differential configurations. The ABRs were analyzed as a function of time, frequency and voltage space. A significantly enhanced ipsilaterally recorded, time domain wave III amplitude was observed for the tinnitus patients. This finding was not confirmed by any of the other ABR measures, which were indistinguishable between subject groups. Although this may be a spurious result, it nonetheless may point to an alteration in the functioning of the putative wave III auditory brainstem generator, which deserves further study.

Evidence for spatio-topic organization of binaural processing in the human brainstem

Three-channel Lissajous' trajectories (3-CLT) of the binaural interaction (BI) in auditory brainstem evoked potentials (ABEP) were derived from 13 normally and symmetrically hearing adults by subtracting the response to binaural clicks from the algebraic sum of monaural responses. ABEPs were recorded from four channels, three of them orthonormal to each other, in response to alternating polarity clicks, presented at a rate of 11/s with interaural time differences (ITD) of 0.2, 0.4 and 1.0 ms and an intensity of 65 dB nHL, or isochronic to both ears with interaural intensity differences (IIDs) of 5, 10 and 15 dB (65 dB nHL +/- 2.5, 5.0 and 7.5 dB, respectively). All 3-CLTs included 6 planar segments (labeled BdI, BdII, BdIII, BeI, BeII and Bf). Amplitudes of 3-CLT BI components were not significantly affected by increasing ITDs and IIDs, but latencies of all components increased significantly. The most remarkable finding was a significant change in apex orientations of BeI and BeII of the BI 3-CLT across stimulus conditions. The changes in BeI and BeII apex orientations, across stimulus conditions, may reflect differences in the anatomical representation of activity evoked by differently lateralized sounds. We suggest that this may indicate spatio-topic organization in the human brainstem.

Evidence for separate processing in the human brainstem of interaural intensity and temporal disparities for sound lateralization

Sound lateralization can be induced by interaural intensity disparities (IIDs) or by interaural temporal disparities (ITDs). The purpose of this study was to indicate whether IIDs and ITDs are processed by the same central units that detect interaural disparity in timing of afferent activity. If sound lateralization to intensity and time cues was determined by the same afferent latency disparity detectors in the brainstem, lateralization would be the same, regardless of whether latency disparity was induced by IIDs or ITDs. Moreover, the disparity detectors, and thus their dipole equivalents, would be the same for equal lateralizations, whether induced by IIDs or ITDs. Auditory brainstem evoked potentials (ABEPs) were recorded in response to monaural and binaural clicks, with a variety of IIDs and ITDs. Peak II (proximal auditory nerve activity), peak III (input to the superior olivary complex), and binaural interaction components (BICs) BeI and BeII (binaurally activated upper pons) were identified and their latencies measured. The psychophysical lateralization of the clicks (in cm from vertex) was also measured in response to the same binaural stimuli. The correlations between interaural afferent latency disparities (difference in corresponding peak latencies originating in each ear) and psychophysical click lateralization were calculated. Similarly, the correlations with click lateralization of the BICs equivalent dipole latency as well as orientation change (relative to symmetrical clicks) were determined. A strong correlation with lateralization was found for peaks II and III latency disparities, with steeper slopes for IIDs than for ITDs. Moreover, binaural activity across the same lateralizations differed between IIDs and ITDs. These results, therefore, indicate that interaural time and intensity cues are processed by separate systems in the brainstem, both at the afferent convergence level and after interaural disparities are determined.

Three-channel Lissajous' trajectory of the binaural interaction components in human auditory brain-stem evoked potentials

The 3-channel Lissajous' trajectory (3-CLT) of the binaural interaction components (BI) in auditory brain-stem evoked potentials (ABEPs) was derived from 17 normally hearing adults by subtracting the response to binaural clicks (B) from the algebraic sum of monaural responses (L + R). ABEPs were recorded in response to 65 dB nHL, alternating polarity clicks, presented at a rate of 11/sec. A normative set of BI 3-CLT measures was calculated and compared with the corresponding measures of simultaneously recorded, single-channel vertex-left mastoid and vertex-neck derivations of BI and of ABEP L + R and B. 3-CLT measures included: apex latency, amplitude and orientation, as well as planar segment duration and orientation. The results showed 3 apices and associated planar segments ("BdII," "Be" and "Bf") in the 3-CLT of BI which corresponded in latency to the vertex-mastoid and vertex-neck peaks IIIn, V and VI of ABEP L + R and B. These apices corresponded in latency and orientation to apices of the 3-CLT of ABEP L + R and ABEP B. This correspondence suggests generators of the BI components between the trapezoid body and the inferior colliculus output. Durations of BI planar segments were approximately 1.0 msec. Apex amplitudes of BI 3-CLT were larger than the respective peak amplitudes of the vertex-mastoid and vertex-neck recorded BI, while their intersubject variabilities were comparable.

Production and decay of the heaviest nuclei (293,294)117 and (294)118

Two years after the discovery of element 117, we undertook a second campaign using the (249)Bk+(48)Ca reaction for further investigations of the production and decay properties of the isotopes of element 117 on a larger number of events. The experiments were started in the end of April 2012 and are still under way. This Letter presents the results obtained in 1200 hours of an experimental run with the beam dose of (48)Ca of about 1.5×10(19) particles. The (249)Bk target was irradiated at two energies of (48)Ca that correspond to the maximum probability of the reaction channels with evaporation of three and four neutrons from the excited (297)117. In this experiment, two decay chains of (294)117 (3n) and five decay chains of (293)117 (4n) were detected. In the course of the long-term work, (249)Cf-the product of decay of (249)Bk (330 d)-is being accumulated in the target. Consequently, in the present experiment, we also detected a single decay of the known isotope (294)118 that was produced during 2002-2005 in the reaction (249)Cf((48)Ca,3n)(294)118. The obtained results are compared with the data from previous experiments. The experiments are carried out in the Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, using the heavy-ion cyclotron U400.

Three-channel Lissajous' trajectory of human middle latency auditory evoked potentials

OBJECTIVE

We provide the normative values for middle latency auditory evoked potentials (MLAEPs) measures (three-channel Lissajous' trajectories or 3-CLT) in response to clicks and tone pips, which are the stimuli most widely used in MLAEP clinical testing. The relationship of 3-CLT measures to the more widely used latency and amplitude characteristics of the single-channel MLAEP of the same subjects was also evaluated. We further relate the 3-CLT findings to the question of MLAEP generators.

DESIGN

3-CLT of MLAEPs were derived from 12 humans (24 ears) in response to 65 dB nHL, rarefaction clicks as well as tone pips (1000 Hz), presented at a rate of 3.3/sec. A normative set of 3-CLT measures was calculated and compared with the corresponding measures of simultaneously recorded, single-channel vertex-left mastoid and vertex-neck derivation of MLAEP.

RESULTS

Apex latencies of 3-CLT were comparable to peak latencies of the vertex-neck record, both in absolute values and in intersubject variability. Durations of planar segments were approximately 5.0 msec. Size and shape measures of planar segments were variable across subjects, making their clinical use, in their present form, questionable.

CONCLUSIONS

The results showed two apices and associated planar segments (i1 and i2) in the 3-CLT of MLAEP which corresponded to the vertex-neck component Pa. These results and earlier studies that indicated a dual set of generators for Pa are compatible with a primary auditory cortex generator for i1 and ascending subcortical generators for i2.