Expanding the flexibility of base editing for high-throughput genetic screens in bacteria

Genome-wide screens have become powerful tools for elucidating genotype-to-phenotype relationships in bacteria. Of the varying techniques to achieve knockout and knockdown, CRISPR base editors are emerging as promising options. However, the limited number of available, efficient target sites hampers their use for high-throughput screening. Here, we make multiple advances to enable flexible base editing as part of high-throughput genetic screening in bacteria. We first co-opt the Streptococcus canis Cas9 that exhibits more flexible protospacer-adjacent motif recognition than the traditional Streptococcus pyogenes Cas9. We then expand beyond introducing premature stop codons by mutating start codons. Next, we derive guide design rules by applying machine learning to an essentiality screen conducted in Escherichia coli. Finally, we rescue poorly edited sites by combining base editing with Cas9-induced cleavage of unedited cells, thereby enriching for intended edits. The efficiency of this dual system was validated through a conditional essentiality screen based on growth in minimal media. Overall, expanding the scope of genome-wide knockout screens with base editors could further facilitate the investigation of new gene functions and interactions in bacteria.

Bothersome Hot Flashes Following Neoadjuvant Androgen Deprivation Therapy and Stereotactic Body Radiotherapy for Localized Prostate Cancer

PURPOSE/OBJECTIVE(S)

Androgen deprivation therapy (ADT) may improve cancer control in unfavorable localized prostate cancer treated with stereotactic body radiotherapy (SBRT). ADT is known to cause hormonally related symptoms that resolve with testosterone recovery. Hot flashes are particularly burdensome. This study sought to evaluate the timeline of hot flashes following short-course ADT and SBRT as well as its relationship with testosterone recovery.

MATERIALS/METHODS

Institutional IRB approval was obtained for this retrospective review of prospectively collected data (IRB#: 2009-510). ADT was initiated three months prior to the start of SBRT. Hot flashes were self-reported via question 13a a healthcare software prior to ADT initiation, the first day of robotic SBRT, and at each follow-up (1, 3, 6, 9, 12, 18, 24 and 36 months). The responses were grouped into three relevant categories (no problem, very small-small problem and moderate-big problem). Scores were transformed to a 0-100 scale with higher scores reflecting less bother. Testosterone levels were measured at each follow-up.

RESULTS

From 2007 to 2010, 122 localized prostate cancer patients (9 low-, 64 intermediate-, and 49 high-risk according to the D'Amico classification) at a median age of 72 years (range 54.5-88.3) were treated with short course ADT (3-6 months) and SBRT (35-36.25 Gy) at Georgetown University Hospital. Thirty-two percent were black and 27% were obese. 77% of patient received three months of ADT. At baseline, 2% of men experienced hot flashes that were a "moderate to big problem" and that proportion peaked at the start of SBRT (45%) before returning to baseline 9 months post-SBRT with a cumulative incidence of 52.4%. The median baseline healthcare software hot flash score of 94 declined to 50 at the start of SBRT but this returned to baseline by six months post SBRT. These changes were both statistically and clinically significant (MID = 9.5083). Testosterone recovery (> 230 ng/dL) occurred in approximately 70% of patients by 12 months post SBRT. Resolution of hot flashes correlated with testosterone recovery.

CONCLUSION

Bothersome hot flashes occur in greater than 50% of men treated with neoadjuvant ADT. Resolution of hot flashes occurs in the majority of patients within one year after treatment. Reassurance of the temporary nature of hot flashes may assist in reducing patient anxiety. Measuring testosterone levels at follow-up visits may allow for anticipatory counseling that may limit the associated bother.

Bothersome Gynecomastia Following Neoadjuvant GnRH Agonists and Stereotactic Body Radiotherapy for Localized Prostate Cancer

PURPOSE/OBJECTIVE(S)

Androgen deprivation therapy (ADT) is increasingly utilized in combination with stereotactic body radiotherapy (SBRT) for unfavorable prostate cancer. ADT such as gonadotropin releasing hormone (GnRH) agonists are known to cause hormonal-related side effects such as gynecomastia. The incidence of bothersome breast tenderness and/or enlargement following short course GnRH agonists and SBRT is unknown. This study sought to evaluate the timeline of gynecomastia as well as its relationship with testosterone recovery.

MATERIALS/METHODS

Gynecomastia was self-reported via question 13b of a healthcare software prior to ADT initiation, the first day of robotic SBRT, and at each follow-up (1, 3, 6, 9, 12, 18, 24 and 36 months). The responses were grouped into three relevant categories (no problem, very small-small problem, and moderate-big problem). Scores were transformed to a 0-100 scale with higher scores reflecting less bother. Testosterone levels were measured at each follow-up.

RESULTS

From 2007 to 2010, 122 localized prostate cancer patients (9 low-, 64 intermediate-, and 49 high-risk according to the D'Amico classification) at a median age of 72 years (range 54.5-88.3) were treated with short course ADT (3-6 months) and SBRT (35-36.25 Gy) at Georgetown University Hospital. Of the participants, 48% percent were non-white and 48% were overweight. 77% of patients received three months of ADT. At baseline, 2% of men experienced gynecomastia that was a "moderate to big problem" and that proportion peaked at 3 and 12 months post-SBRT (7%) before returning to less than baseline (0%) 24 months post-SBRT with a cumulative incidence of 14.75%. The median baseline healthcare software hot flash score of 98 declined to 90 at 3 months post-SBRT but this returned to baseline by 24 months post SBRT. These changes were both statistically and clinically significant (MID = 6.5). Testosterone recovery (> 230 ng/dL) occurred in approximately 70% of patients by 12 months post SBRT. The development and resolution of gynecomastia fluctuated at various timepoints and did not directly correlate with testosterone recovery.

CONCLUSION

Bothersome gynecomastia occurs in less than 15% of men treated with neoadjuvant ADT. Resolution of gynecomastia occurs in most patients within two years after treatment. Reassurance of the temporary nature of gynecomastia may assist in reducing patient anxiety. Institutional IRB (IRB#: 2009-510) approval was obtained for retrospective review of prospectively collected data.

Marginless 5-Fraction Robotic Radiosurgery for Unfavorable Nonfunctioning Pituitary Macroadenoma: 5-year Outcomes from a Single Institution Protocol

PURPOSE/OBJECTIVE(S)

Nonfunctioning macroadenoma is a commonly diagnosed pituitary tumor. Resection is the favored treatment, with radiosurgery often utilized for residual or progressing disease. Long-term outcomes are established for single-session radiosurgery, but mature outcomes are lacking for multisession radiosurgery. We report our institution's 5-year efficacy and safety results for unfavorable nonfunctioning pituitary macroadenoma patients treated with marginless 5-fraction robotic radiosurgery.

MATERIALS/METHODS

Between 2010-2020, patients who completed marginless 5-fraction radiosurgery for the treatment of unfavorable nonfunctioning pituitary macroadenomas were included. A tumor was considered unfavorable if the gross tumor volume (GTV) was larger than 5 cc or if it closely approached a critical structure (optic apparatus, brainstem or pituitary gland). Local control was calculated using the Kaplan-Meier Method.

RESULTS

Twenty predominately female patients (60%), age from 21-77 (median: 53 years) were included in this study. All underwent primary resection. Indications for radiosurgery included unresectable recurrence (85%) and residual disease progression (70%). Median tumor volume was 3.4 cm3 (range: 0.3-20.8 cm3) and 40% of the tumors were suprasellar. A mean dose of 28.8 Gy (range: 25 Gy-30 Gy), was delivered to a median isodose line of 80% (range: 75%-89%). The median optic chiasm maximum point dose was 21.8 Gy (range: 12.0-25.9 Gy). Toxicity was minimal with 12 patients (40%) developing acute short-lived headaches and 1 patient (5%) developing a brief ipsilateral 6th nerve palsy. There was no radiation induced optic or pituitary dysfunction identified in this cohort. At a median follow up of 5 years local control was 95%. There was 1 in-field failure pathologically confirmed following surgery for pituitary tumor hemorrhage and 2 radiographically confirmed out-of-field failures in patients with large tumors (>20 cc).

CONCLUSION

The treatment of unfavorable nonfunctioning pituitary macroadenoma with marginless 5-fraction robotic radiosurgery provides excellent local control to date, with minimal toxicity. However, tumors with GTV's greater than 20 cc may require conventionally fractionated treatment with a margin to optimize local control.

Low Incidence of Late Lymphopenia Following Stereotactic Body Radiotherapy for Localized Prostate Cancer

PURPOSE/OBJECTIVE(S)

Stereotactic body radiotherapy (SBRT) is increasing in use for the treatment of localized prostate cancer. The utilization of highly conformal photon therapy such as SBRT may increase the whole-body integral dose. Lymphocytes are very radiation sensitive. This dose increase could lead to unintended consequences such as lymphopenia. Prior studies have shown that lymphopenia following radiation therapy may negatively impact long-term outcomes. This study sought to evaluate the incidence and timeline of chronic lymphopenia following prostate SBRT.

MATERIALS/METHODS

Institutional IRB (IRB#: 2012-1175) approval was obtained. The absolute lymphocyte count was measured 1-2 hours prior to robotic SBRT (35-36.25 Gy in 5 fractions) and at each follow-up (3, 6, 12, 18 and 24 months). Lymphopenia was graded using the CTCAEv.4: Grade 1 (1.0-0.8 k/μl), Grade 2 (0.8-0.5 k/μl), Grade 3 (0.5-0.2 k/μl) and Grade 4 (<0.2 k/μl). Late lymphopenia was defined as lymphopenia occurring 3 or more months post-SBRT.

RESULTS

From 2019 to 2022, 198 localized prostate cancer patients (23 low-, 148 intermediate-, and 27 high-risk according to the D'Amico classification) at a median age of 73.5 years were treated with SBRT (35-36.25 Gy) at Georgetown University Hospital on a prospective clinical trial. Baseline lymphopenia was uncommon: Grade 1 (3.5%), Grade 2 (1.5%) and Grade 3 (0%). The baseline ALC of 1.9 k/μl decreased to 1.5 k/μl at 3 months post-SBRT and then remained stable for the remainder of the two-year follow-up. Overall, 14.6% of men experienced lymphopenia in the two years following SBRT: Grade 1 (7.6%), Grade 2 (6.6%) and Grade 3 (0.5%). No patient experienced Grade 4 lymphopenia.

CONCLUSION

Prostate SBRT leads to a low rate of late lymphopenia with the vast majority of toxicities being low grade. The peak incidence occurred at 3 months post-SBRT. Resolution of lymphopenia occurs in most patients within two years after SBRT. Future studies should explore the possible impact on quality of life and cancer control outcomes.

A target expression threshold dictates invader defense and prevents autoimmunity by CRISPR-Cas13

CRISPR-Cas systems must enact robust immunity against foreign genetic material without inducing cytotoxic autoimmunity. For type VI systems that use Cas13 nucleases and recognize RNA targets, immune activation requires extensive CRISPR RNA (crRNA) guide-target complementarity and a target-flanking motif. Here, we report a third requirement shaping the immune response: the expression of the target transcript exceeding a threshold. We found that endogenous non-essential transcripts targeted by crRNAs rarely elicited autoimmunity. Instead, autoimmune induction required over-expressing the targeted transcripts above a threshold. A genome-wide screen confirmed target expression levels as a global determinant of cytotoxic autoimmunity and revealed that this threshold shifts with each guide-target pair. This threshold further ensured defense against a lytic bacteriophage yet allowed the tolerance of a targeted beneficial gene expressed from an invading plasmid. These findings establish target expression levels as an additional criterion for immune defense by RNA-targeting CRISPR-Cas systems, preventing autoimmunity and distinguishing pathogenic and benign invaders.

Four-year Prostate-specific Antigen Response Rate as a Predictive Measure in Intermediate-risk Prostate Cancer Treated With Ablative Therapies: The SPRAT Analysis

AIMS

There is a lack of early predictive measures of outcome for patients with intermediate-risk prostate cancer (PCa) treated with stereotactic body radiotherapy (SBRT). The aim of the present study was to explore 4-year prostate-specific antigen response rate (4yPSARR) as an early predictive measure.

MATERIALS AND METHODS

Individual patient data from six institutions for patients with intermediate-risk PCa treated with SBRT between 2006 and 2016 with a 4-year (42-54 months) PSA available were analysed. Cumulative incidences of biochemical failure and metastasis were calculated using Nelson-Aalen estimates and overall survival was calculated using the Kaplan-Meier method. Biochemical failure-free survival was analysed according to 4yPSARR, with groups dichotomised based on PSA <0.4 ng/ml or ≥0.4 ng/ml and compared using the Log-rank test. A multivariable competing risk analysis was carried out to predict for biochemical failure and the development of metastases.

RESULTS

Six hundred and thirty-seven patients were included, including 424 (67%) with favourable and 213 (33%) with unfavourable intermediate-risk disease. The median follow-up was 6.2 years (interquartile range 4.9-7.9). The cumulative incidence of biochemical failure and metastasis was 7 and 0.6%, respectively; overall survival at 6 years was 97%. The cumulative incidence of biochemical failure at 6 years if 4yPSARR <0.4 ng/ml was 1.7% compared with 27% if 4yPSARR ≥0.4 ng/ml (P < 0.0001). On multivariable competing risk analysis, 4yPSARR was a statistically significant predictor of biochemical failure-free survival (subdistribution hazard ratio 15.3, 95% confidence interval 7.5-31.3, P < 0.001) and metastasis-free survival (subdistribution hazard ratio 31.2, 95% confidence interval 3.1-311.6, P = 0.003).

CONCLUSION

4yPSARR is an encouraging early predictor of outcome in patients with intermediate-risk PCa treated with SBRT. Validation in prospective trials is warranted.

In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii

Saccharomyces boulardii is a probiotic yeast that exhibits rapid growth at 37 °C, is easy to transform, and can produce therapeutic proteins in the gut. To establish its ability to produce small molecules encoded by multigene pathways, we measured the amount and variance in protein expression enabled by promoters, terminators, selective markers, and copy number control elements. We next demonstrated efficient (>95%) CRISPR-mediated genome editing in this strain, allowing us to probe engineered gene expression across different genomic sites. We leveraged these strategies to assemble pathways enabling a wide range of vitamin precursor (β-carotene) and drug (violacein) titers. We found that S. boulardii colonizes germ-free mice stably for over 30 days and competes for niche space with commensal microbes, exhibiting short (1-2 day) gut residence times in conventional and antibiotic-treated mice. Using these tools, we enabled β-carotene synthesis (194 μg total) in the germ-free mouse gut over 14 days, estimating that the total mass of additional β-carotene recovered in feces was 56-fold higher than the β-carotene present in the initial probiotic dose. This work quantifies heterologous small molecule production titers by S. boulardii living in the mammalian gut and provides a set of tools for modulating these titers.

Sequence-independent RNA sensing and DNA targeting by a split domain CRISPR-Cas12a gRNA switch

CRISPR technologies increasingly require spatiotemporal and dosage control of nuclease activity. One promising strategy involves linking nuclease activity to a cell's transcriptional state by engineering guide RNAs (gRNAs) to function only after complexing with a ‘trigger’ RNA. However, standard gRNA switch designs do not allow independent selection of trigger and guide sequences, limiting gRNA switch application. Here, we demonstrate the modular design of Cas12a gRNA switches that decouples selection of these sequences. The 5′ end of the Cas12a gRNA is fused to two distinct and non-overlapping domains: one base pairs with the gRNA repeat, blocking formation of a hairpin required for Cas12a recognition; the other hybridizes to the RNA trigger, stimulating refolding of the gRNA repeat and subsequent gRNA-dependent Cas12a activity. Using a cell-free transcription-translation system and Escherichia coli, we show that designed gRNA switches can respond to different triggers and target different DNA sequences. Modulating the length and composition of the sensory domain altered gRNA switch performance. Finally, gRNA switches could be designed to sense endogenous RNAs expressed only under specific growth conditions, rendering Cas12a targeting activity dependent on cellular metabolism and stress. Our design framework thus further enables tethering of CRISPR activities to cellular states.

Ocean acidification effects on fish hearing

Humans are rapidly changing the marine environment through a multitude of effects, including increased greenhouse gas emissions resulting in warmer and acidified oceans. Elevated CO₂ conditions can cause sensory deficits and altered behaviours in marine organisms, either directly by affecting end organ sensitivity or due to likely alterations in brain chemistry. Previous studies show that auditory-associated behaviours of larval and juvenile fishes can be affected by elevated CO₂ (1000 µatm). Here, using auditory evoked potentials (AEP) and micro-computer tomography (microCT) we show that raising juvenile snapper, Chrysophyrs auratus, under predicted future CO₂ conditions resulted in significant changes to their hearing ability. Specifically, snapper raised under elevated CO₂ conditions had a significant decrease in low frequency (less than 200 Hz) hearing sensitivity. MicroCT demonstrated that these elevated CO₂ snapper had sacculus otolith's that were significantly larger and had fluctuating asymmetry, which likely explains the difference in hearing sensitivity. We suggest that elevated CO₂ conditions have a dual effect on hearing, directly effecting the sensitivity of the hearing end organs and altering previously described hearing induced behaviours. This is the first time that predicted future CO₂ conditions have been empirically linked through modification of auditory anatomy to changes in fish hearing ability. Given the widespread and well-documented impact of elevated CO₂ on fish auditory anatomy, predictions of how fish life-history functions dependent on hearing may respond to climate change may need to be reassessed.

Your Base Editor Might Be Flirting with Single (Stranded) DNA: Faithful On-Target CRISPR Base Editing without Promiscuous Deamination

Jin et al. (2020) engineered new variants of CRISPR base editors that make precise genomic edits in rice protoplasts while minimizing untargeted mutagenesis.

Observation of strong nonlinear interactions in parametric down-conversion of X-rays into ultraviolet radiation

Nonlinear interactions between X-rays and long wavelength radiation can be used as a powerful atomic-scale probe for light-matter interactions and for properties of valence electrons. However, reported X-ray nonlinear effects were small and their observations required tremendous efforts. Here we report the observation of strong nonlinearities in parametric down-conversion (PDC) of X-rays to long wavelength radiation in gallium arsenide and lithium niobate crystals, with efficiencies about 4 orders of magnitude stronger than the efficiencies measured in any material studied before. Furthermore, we show that the efficiency in the ferroelectric phase of strontium barium niobite is two orders of magnitude stronger than in its paraelectric phase. This observation suggests that the lack of inversion symmetry is the origin for the strong observed nonlinearity. Additionally, we demonstrate the ability to use the effect for the investigation of the spectral response of non-centrosymmetric materials at wavelengths ranging from infrared to soft X-rays.

Here, the authors report parametric down-conversion of X-rays into long wavelength radiation in gallium arsenide and lithium niobate crystals, with efficiencies about 4 orders of magnitude stronger than the efficiencies measured in any material studied previously. They explore the lack of inversion symmetry as a possible physical mechanism.

Selective probing of magnetic order on Tb and Ir sites in stuffed Tb2Ir2O7 using resonant x-ray scattering

We study the magnetic structure of the 'stuffed' (Tb-rich) pyrochlore iridate Tb_2+x Ir_2-x O_7-y (x ∼ 0.18), using resonant elastic x-ray scattering (REXS). In order to disentangle contributions from Tb and Ir magnetic sublattices, experiments were performed at the Ir L ₃ and Tb M ₅ edges, which provide selective sensitivity to Ir 5d and Tb 4f  magnetic moments, respectively. At the Ir L ₃ edge, we found the onset of long-range [Formula: see text] magnetic order below [Formula: see text] K, consistent with the expected signal of all-in all-out (AIAO) magnetic order. Using a single-ion model to calculate REXS cross-sections, we estimate an ordered magnetic moment of [Formula: see text] at 5 K. At the Tb M ₅ edge, long-range [Formula: see text] magnetic order appeared below  ∼[Formula: see text] K, also consistent with an AIAO magnetic structure on the Tb site. Additional insight into the magnetism of the Tb sublattice is gleaned from measurements at the M ₅ edge in applied magnetic fields up to 6 T, which is found to completely suppress the Tb AIAO magnetic order. In zero applied field, the observed gradual onset of the Tb sublattice magnetisation with temperature suggests that it is induced by the magnetic order on the Ir site. The persistence of AIAO magnetic order, despite the greatly reduced ordering temperature and moment size compared to stoichiometric Tb₂Ir₂O₇, for which [Formula: see text] K and [Formula: see text], indicates that stuffing could be a viable means of tuning the strength of electronic correlations, thereby potentially offering a new strategy to achieve topologically non-trivial band crossings in pyrochlore iridates.

An enhanced assay to characterize anti-CRISPR proteins using a cell-free transcription-translation system

The characterization of CRISPR-Cas immune systems in bacteria was quickly followed by the discovery of anti-CRISPR proteins (Acrs) in bacteriophages. These proteins block different steps of CRISPR-based immunity and, as some inhibit Cas nucleases, can offer tight control over CRISPR technologies. While Acrs have been identified against a few CRISPR-Cas systems, likely many more await discovery and application. Here, we report a rapid and scalable method for characterizing putative Acrs against Cas nucleases using an E. coli-derived cell-free transcription-translation system. Using known Acrs against type II Cas9 nucleases as models, we demonstrate how the method can be used to measure the inhibitory activity of individual Acrs in under two days. We also show how the method can overcome non-specific inhibition of gene expression observed for some Acrs. In total, the method should accelerate the interrogation and application of Acrs as CRISPR-Cas inhibitors.

Critical fluctuations in the spin-orbit Mott insulator Sr3Ir2O7

X-ray magnetic critical scattering measurements and specific heat measurements were performed on the perovskite iridate [Formula: see text]. We find that the magnetic interactions close to the Néel temperature [Formula: see text] are three-dimensional. This contrasts with previous studies which suggest two-dimensional behaviour like Sr₂IrO₄. Violation of the Harris criterion ([Formula: see text]) means that weak disorder becomes relevant. This leads a rounding of the antiferromagnetic phase transition at [Formula: see text], and modifies the critical exponents relative to the clean system. Specifically, we determine that the critical behaviour of [Formula: see text] is representative of the diluted 3D Ising universality class.

An educational module to explore CRISPR technologies with a cell-free transcription-translation system

Within the last 6 years, CRISPR-Cas systems have transitioned from adaptive defense systems in bacteria and archaea to revolutionary genome-editing tools. The resulting CRISPR technologies have driven innovations for treating genetic diseases and eradicating human pests while raising societal questions about gene editing in human germline cells as well as crop plants. Bringing CRISPR into the classroom therefore offers a means to expose students to cutting edge technologies and to promote discussions about ethical questions at the intersection of science and society. However, working with these technologies in a classroom setting has been difficult because typical experiments rely on cellular systems such as bacteria or mammalian cells. We recently reported the use of an E. coli cell-free transcription-translation (TXTL) system that simplifies the demonstration and testing of CRISPR technologies with shorter experiments and limited equipment. Here, we describe three educational modules intended to expose undergraduate students to CRISPR technologies using TXTL. The three sequential modules comprise (i) designing the RNAs that guide DNA targeting, (ii) measuring DNA cleavage activity in TXTL and (iii) testing how mutations to the targeting sequence or RNA backbone impact DNA binding and cleavage. The modules include detailed protocols, questions for group discussions or individual evaluation, and lecture slides to introduce CRISPR and TXTL. We expect these modules to allow students to experience the power and promise of CRISPR technologies in the classroom and to engage with their instructor and peers about the opportunities and potential risks for society.

Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System

CRISPR-Cas systems offer versatile technologies for genome engineering, yet their implementation has been outpaced by ongoing discoveries of new Cas nucleases and anti-CRISPR proteins. Here, we present the use of E. coli cell-free transcription-translation (TXTL) systems to vastly improve the speed and scalability of CRISPR characterization and validation. TXTL can express active CRISPR machinery from added plasmids and linear DNA, and TXTL can output quantitative dynamics of DNA cleavage and gene repression-all without protein purification or live cells. We used TXTL to measure the dynamics of DNA cleavage and gene repression for single- and multi-effector CRISPR nucleases, predict gene repression strength in E. coli, determine the specificities of 24 diverse anti-CRISPR proteins, and develop a fast and scalable screen for protospacer-adjacent motifs that was successfully applied to five uncharacterized Cpf1 nucleases. These examples underscore how TXTL can facilitate the characterization and application of CRISPR technologies across their many uses.

Parametric Down-Conversion of X Rays into the Optical Regime

We report the observation of parametrically down-converted x-ray signal photons at photon energies that correspond to idler photons at optical wavelengths. The count-rate dependence on the angles of the input beam and of the detector and on the slit sizes agrees with theory within the experimental uncertainties. The nonlinear susceptibility, which we calculated from the measured efficiencies, is comparable to the nonlinear susceptibility evaluated from the measurements of x-ray and optical wave mixing. The results of the present Letter advance the development of a spectroscopy method for probing valence-electron charges and the microscopic optical response of crystals with atomic-scale resolution.

Band Filling Control of the Dzyaloshinskii-Moriya Interaction in Weakly Ferromagnetic Insulators

We observe and explain theoretically a dramatic evolution of the Dzyaloshinskii-Moriya interaction (DMI) in the series of isostructural weak ferromagnets, MnCO_{3}, FeBO_{3}, CoCO_{3}, and NiCO_{3}. The sign of the interaction is encoded in the phase of the x-ray magnetic diffraction amplitude, observed through interference with resonant quadrupole scattering. We find very good quantitative agreement with first-principles electronic structure calculations, reproducing both sign and magnitude through the series, and propose a simplified "toy model" to explain the change in sign with 3d shell filling. The model gives insight into the evolution of the DMI in Mott and charge transfer insulators.

Short DNA containing χ sites enhances DNA stability and gene expression in E. coli cell-free transcription-translation systems

Escherichia coli cell-free transcription-translation (TXTL) systems offer versatile platforms for advanced biomanufacturing and for prototyping synthetic biological parts and devices. Production and testing could be accelerated with the use of linear DNA, which can be rapidly and cheaply synthesized. However, linear DNA is efficiently degraded in TXTL preparations from E. coli. Here, we show that double-stranded DNA encoding χ sites-eight base-pair sequences preferentially bound by the RecBCD recombination machinery-stabilizes linear DNA and greatly enhances the TXTL-based expression and activity of a fluorescent reporter gene, simple regulatory cascades, and T7 bacteriophage particles. The χ-site DNA and the DNA-binding λ protein Gam yielded similar enhancements, and DNA with as few as four χ sites was sufficient to ensure robust gene expression in TXTL. Given the affordability and scalability of producing the short χ-site DNA, this generalized strategy is expected to advance the broad use of TXTL systems across its many applications. Biotechnol. Bioeng. 2017;114: 2137-2141. © 2017 Wiley Periodicals, Inc.

Multiple Supersonic Phase Fronts Launched at a Complex-Oxide Heterointerface

Selective optical excitation of a substrate lattice can drive phase changes across heterointerfaces. This phenomenon is a nonequilibrium analogue of static strain control in heterostructures and may lead to new applications in optically controlled phase change devices. Here, we make use of time-resolved nonresonant and resonant x-ray diffraction to clarify the underlying physics and to separate different microscopic degrees of freedom in space and time. We measure the dynamics of the lattice and that of the charge disproportionation in NdNiO_{3}, when an insulator-metal transition is driven by coherent lattice distortions in the LaAlO_{3} substrate. We find that charge redistribution propagates at supersonic speeds from the interface into the NdNiO_{3} film, followed by a sonic lattice wave. When combined with measurements of magnetic disordering and of the metal-insulator transition, these results establish a hierarchy of events for ultrafast control at complex-oxide heterointerfaces.

On the possibility of using X-ray Compton scattering to study magnetoelectrical properties of crystals

The possibility of using X-ray Compton scattering to reveal antisymmetric components of the electron momentum density, as a fingerprint of magnetoelectric sample properties, is investigated experimentally and theoretically by studying the polar ferromagnet GaFeO₃.

This paper discusses the possibility of using Compton scattering – an inelastic X-ray scattering process that yields a projection of the electron momentum density – to probe magnetoelectrical properties. It is shown that an antisymmetric component of the momentum density is a unique fingerprint of such time- and parity-odd physics. It is argued that polar ferromagnets are ideal candidates to demonstrate this phenomenon and the first experimental results are shown, on a single-domain crystal of GaFeO₃. The measured antisymmetric Compton profile is very small (≃ 10⁻⁵ of the symmetric part) and of the same order of magnitude as the statistical errors. Relativistic first-principles simulations of the antisymmetric Compton profile are presented and it is shown that, while the effect is indeed predicted by theory, and scales with the size of the valence spin–orbit interaction, its magnitude is significantly overestimated. The paper outlines some important constraints on the properties of the antisymmetric Compton profile arising from the underlying crystallographic symmetry of the sample.

Diffuse multiple scattering

A new form of diffraction lines similar to Rutherford, Kikuchi and Kossel lines has been identified. They can be used to eliminate the need for sample/source matching in Lonsdale’s triple convergent line method in lattice-parameter determination.

A new form of diffraction lines has been identified, similar to Rutherford, Kikuchi and Kossel lines. This paper highlights some of the properties of these lines and shows how they can be used to eliminate the need for sample/source matching in Lonsdale’s triple convergent line method in lattice-parameter determination.

Effects of dispersion and absorption in resonant Bragg diffraction of x-rays

Resonant diffraction of x-rays by crystals with anisotropic optical properties is investigated theoretically, to assess how the intensity of a Bragg spot is influenced by effects related to dispersion (birefringence) and absorption (dichroism). Starting from an exact but opaque expression, simple analytic results are found to expose how intensity depends on dispersion and absorption in the primary and secondary beams and, also, the azimuthal angle (rotation of the crystal about the Bragg wavevector). If not the full story for a given application, our results are more than adequate to explore consequences of dispersion and absorption in the intensity of a Bragg spot. Results are evaluated for antiferromagnetic copper oxide, and low quartz. For CuO, one of our results reproduces all salient features of a previously published simulation of the azimuthal-angle dependence of a magnetic Bragg peak. It is transparent in our analytic result that dispersion and absorption effects alone cannot reproduce published experimental data. Available data for the azimuthal-angle dependence of space-group forbidden reflections (0,0, l), with l ≠ 3n, of low quartz depart from symmetry imposed by the triad axis of rotation symmetry. The observed asymmetry can be induced by dispersion and absorption even though absorption coefficients are constant, independent of the azimuthal angle, in this class of reflections.

Hybrid diamond-silicon angular-dispersive x-ray monochromator with 0.25-meV energy bandwidth and high spectral efficiency

We report on the design, implementation, and performance of an x-ray monochromator with ultra-high energy resolution (ΔE/E ≃ 2.7 × 10(-8)) and high spectral efficiency using x rays with photon energies E ≃ 9.13 keV. The operating principle of the monochromator is based on the phenomenon of angular dispersion in Bragg back-diffraction. The optical scheme of the monochromator is a modification of a scheme reported earlier [Shvyd'ko et al., Phys. Rev. A 84, 053823 (2011)], where a collimator/wavelength selector Si crystal was replaced with a 100-μm-thick type IIa diamond crystal. This modification provides a very-small-energy bandwidth ΔE ≃ 0.25 meV, a 3-fold increase in the aperture of the accepted beam, a reduction in the cumulative angular dispersion rate of x rays emanating from the monochromator for better focusing on a sample, a sufficient angular acceptance matching the angular divergence of an undulator source (≈ 10 μrad), and an improved throughput due to low x-ray absorption in the thin diamond crystal. The measured spectral efficiency of the monochromator was ≈ 65% with an aperture of 0.3 × 1 mm(2). The performance parameters of the monochromator are suitable for inelastic x-ray spectroscopy with an absolute energy resolution ΔE < 1 meV.

Locking of iridium magnetic moments to the correlated rotation of oxygen octahedra in Sr₂IrO₄ revealed by x-ray resonant scattering

Sr2IrO4 is a prototype of the class of Mott insulators in the strong spin-orbit interaction (SOI) limit described by a Jeff = 1/2 ground state. In Sr2IrO4, the strong SOI is predicted to manifest itself in the locking of the canting of the magnetic moments to the correlated rotation by 11.8(1)° of the oxygen octahedra that characterizes its distorted layered perovskite structure. Using x-ray resonant scattering at the Ir L3 edge we have measured accurately the intensities of Bragg peaks arising from different components of the magnetic structure. From a careful comparison of integrated intensities of peaks due to basal-plane antiferromagnetism, with those due to b-axis ferromagnetism, we deduce a canting of the magnetic moments of 12.2(8)°. We thus confirm that in Sr2IrO4 the magnetic moments rigidly follow the rotation of the oxygen octahedra, indicating that, even in the presence of significant non-cubic structural distortions, it is a close realization of the Jeff = 1/2 state.

Robustness of basal-plane antiferromagnetic order and the J(eff)=1/2 state in single-layer iridate spin-orbit Mott insulators

The magnetic structure and electronic ground state of the layered perovskite Ba(2)IrO(4) have been investigated using x-ray resonant magnetic scattering. Our results are compared with those for Sr(2)IrO(4), for which we provide supplementary data on its magnetic structure. We find that the dominant, long-range antiferromagnetic order is remarkably similar in the two compounds and that the electronic ground state in Ba(2)IrO(4), deduced from an investigation of the x-ray resonant magnetic scattering L(3)/L(2) intensity ratio, is consistent with a J(eff)=1/2 description. The robustness of these two key electronic properties to the considerable structural differences between the Ba and Sr analogues is discussed in terms of the enhanced role of the spin-orbit interaction in 5d transition metal oxides.

On the magnetic structure of Sr3Ir2O7: an x-ray resonant scattering study

This report presents azimuthal dependent and polarization dependent x-ray resonant magnetic scattering at the Ir L(3) edge for the bilayered iridate compound Sr(3)Ir(2)O(7). The two magnetic wave vectors, k1 = (1/2, 1/2, 0) and k2 = (1/2, -1/2, 0), result in domains of two symmetry-related G-type antiferromagnetic structures, denoted A and B, respectively. These domains are approximately 0.02 mm(2) and are independent of the thermal history. An understanding of this key aspect of the magnetism is necessary for an overall picture of the magnetic behaviour in this compound. The azimuthal and polarization dependence of the magnetic reflections, relating to both magnetic wavevectors, show that the Ir magnetic moments in the bilayer compound are oriented along the c axis. This contrasts with single layer Sr(2)IrO(4) where the moments are confined to the ab plane.

Ab initio calculations of the forbidden Bragg reflections energy spectra in wurtzites versus temperature

Thermal-motion induced (TMI) scattering is caused by the influence of atomic displacements on electronic states in crystals and strongly depends on temperature. It corresponds to dipole-dipole resonant x-ray scattering, but is usually accompanied by dipole-quadrupole scattering. The phenomenological theory supposes the dipole-quadrupole term to be temperature independent (TI). As a result, the transformation of the energy spectra with temperature observed experimentally in ZnO and GaN corresponds to the interference between the TMI and TI terms. In the present paper the direct confirmation of this theoretical prediction is given. Ab initio molecular dynamics was used to simulate the sets of atomic sites at various temperatures followed by quantum mechanical calculation of resonant Bragg reflection energy spectra. The results of simulation are in excellent coincidence with experimental energy spectra of forbidden reflections and confirm the earlier phenomenological conjecture about the interference between the TI dipole-quadrupole and TMI dipole-dipole contributions to the resonant atomic factor.

Risk factors associated with cataracts and lens luxations in captive pinnipeds in the United States and the Bahamas

OBJECTIVE

To determine risk factors for lens luxation and cataracts in captive pinnipeds in the United States and the Bahamas.

DESIGN

Cross-sectional study.

ANIMALS

111 pinnipeds (99 California sea lions [Zalophus californianus], 10 harbor seals [Phoca vitulina], and 2 walruses [Odobenus rosmarus]) from 9 facilities.

PROCEDURES

Eyes of each pinniped were examined by a veterinary ophthalmologist for the presence of cataracts or lens luxations and photographed. Information detailing husbandry practices, history, and facilities was collected with a questionnaire, and descriptive statistical analyses were performed for continuous and categorical variables. Odds ratios and associated 95% confidence intervals were estimated from the final model.

RESULTS

Risk factors for lens luxation, cataracts, or both included age >or= 15 years, history of fighting, history of ocular disease, and insufficient access to shade.

CONCLUSIONS AND CLINICAL RELEVANCE

Diseases of the lens commonly affect captive pinnipeds. Access to UV-protective shade, early identification and medical management of ocular diseases, and prevention of fighting can limit the frequency or severity of lens-related disease in this population. An extended life span may result from captivity, but this also allows development of pathological changes associated with aging, including cataracts.

Numerical simulation of the forbidden Bragg reflection spectra observed in ZnO

Thermal motion induced (TMI) scattering is a unique probe of changes in electronic states with atomic displacements in crystals. We show that it provides a novel approach to extract atomic correlation functions. Using numerical calculations, we are able to reproduce the temperature-dependent energy spectrum of the 115 'forbidden' Bragg reflection in ZnO. Our previous experimental studies showed that the intensity growth of such reflections over a wide range of temperatures is accompanied by a dramatic change in the resonant spectral lineshape. This is the result of the interplay between the temperature-independent (TI) and temperature-dependent TMI contributions. Here, we confirm that the TI part of the resonant structure factor can be associated with the dipole-quadrupole contribution to the structure factor and show that the temperature-dependent part arises from the zinc and oxygen vibrations, which provide additional temperature-dependent dipole-dipole tensor components to the structure factor. By fitting the experimental data at various temperatures we have determined the temperature dependences of autocorrelation <u(x)(2)(Zn)> and correlation <u(x)(O)u(x)(Zn)> functions.

The influence of interfacial roughness on the coherence of structure and magnetic coupling across barriers in Fe/MgO multilayers

Single-crystal Fe/MgO multilayers are model systems in which to study magnetic tunnel junctions. We find that the interfacial roughness leads to the loss of coherence of the crystal structure. For thick MgO layers ferromagnetic (FM) ordering is found using polarized neutron reflectivity (PNR). For thin MgO layers magnetization measurements reveal the presence of antiferromagnetic (AF) interactions, but no long-range AF order is found using PNR. After cycling in a hysteresis loop, FM correlations are found at the coercive point, and this will limit the maximum tunnelling magnetoresistance.

Determination of the absolute chirality of tellurium using resonant diffraction with circularly polarized x-rays

Many proteins, sugars and pharmaceuticals crystallize into two forms that are mirror images of each other (enantiomers) like our right and left hands. Tellurium is one enantiomer having a space group pair, P3(1)21 (right-handed screw) and P3(2)21 (left-handed screw). X-ray diffraction with dispersion correction terms has been playing an important role in determining the handedness of enantiomers for a long time. However, this approach is not applicable for an elemental crystal such as tellurium or selenium. We have demonstrated that positive and negative circularly polarized x-rays at the resonant energy of tellurium can be used to absolutely distinguish right from left tellurium. This method is applicable to chiral motifs that occur in biomolecules, liquid crystals, ferroelectrics and antiferroelectrics, multiferroics, etc.

Interplay of inequivalent atomic positions in resonant x-ray diffraction of Fe(3)BO(6)

'Forbidden' Bragg reflections of iron orthoborate Fe(3)BO(6) were studied theoretically and experimentally in the vicinity of the iron K edge. Their energy spectra are explained as resulting from the interference of x-rays scattered from two inequivalent crystallographic sites occupied by iron ions. This particular structure property gives rise to complex azimuthal dependences of the reflection intensities in the pre-edge region as they result from the interplay of site specific dipole-quadrupole and quadrupole-quadrupole resonant scattering. Also evidenced is an anisotropic character of the absorption spectrum. Self-absorption correction to the diffraction data, as well as possible contributions of thermal vibrations and magnetic order, are discussed. Particular care is given to extracting clean spectra from the data, and it is demonstrated that excellent results can be obtained even from measurements that appear corrupted by several effects such as poor crystal quality and multiple scattering.

Hysteresis effect in FePd magnetic stripes studied by coherent soft X-ray resonant magnetic scattering

An FePd thin film sample, showing magnetic stripe domains as imaged by magnetic force microscopy, has been measured by soft X-ray resonant magnetic scattering in reflection geometry. Illumination with coherent radiation, produced by inserting a 20 microm pinhole in front of the sample, leads to a magnetic speckle pattern in the scattered intensity that gives access to the domain morphology. Application of an in-plane magnetic field for a few seconds gives a strong change in the observed intensity fluctuations, which indicates a large degree of variation between the two patterns taken before and after field exposure. From the speckle pattern we calculate a degree of coherence of beta = 0.5 for the incident beam.

Soft X-ray resonant magnetic scattering from a Ni layer with modulated magnetic anisotropy

Soft X-ray resonant magnetic scattering studies on a magnetically modulated, but nominally chemically homogenous, 5 nm Ni layer in a Cu/Ni/Cu/Co/NiO/GaAs(110) system are reported. It was possible to estimate the main chemical structure of the sample on the basis of the results from specular reflectivity and rocking scans, probing the scattering vector components in the perpendicular and in-plane direction to the Ni wires, respectively. The magnetic scattering using polarized X-rays demonstrates the magnetic modulation of the Ni layer.

Observation of divergent-beam X-ray diffraction from a crystal of diamond using synchrotron radiation

In 1947 Kathleen Lonsdale conducted a series of experiments on X-ray diffraction using a divergent beam external to a crystal sample. Unlike the Kossel technique, where divergent X-rays are excited by the presence of fluorescing atoms within the crystal, the use of an external divergent source made it possible to study non-fluorescing crystals. The resulting photographs not only illustrated the complexity of X-ray diffraction from crystals in a truly beautiful way, but also demonstrated unprecedented experimental precision. This long-forgotten work is repeated here using a synchrotron radiation source and, once again, considerable merit is found in Lonsdale's technique. The results of this experiment suggest that, through the use of modern 'third-generation' synchrotron sources, divergent-beam diffraction could soon enjoy a renaissance for high-precision lattice-parameter determination and the study of crystal perfection.

Direct observation of orbital ordering in La0.5Sr1.5MnO4 using soft x-ray diffraction

We report the first direct resonant soft x-ray scattering observations of orbital ordering. We have studied the low temperature phase of La0.5Sr1.5MnO4, a compound that displays charge and orbital ordering. Previous claims of orbital ordering in such materials have relied on observations at the manganese K edge. These claims have been questioned in several theoretical studies. Instead we have employed resonant soft x-ray scattering at the manganese L(III) and L(II) edges which probes the orbital ordering directly. Energy scans at constant wave vector are compared to theoretical predictions and suggest that at all temperatures there are two separate contributions to the scattering: direct orbital ordering and strong cooperative Jahn-Teller distortions of the Mn3+ ions.

X-ray birefringence and dichroism obtained from magnetic materials

In the past decade, synchrotron radiation has triggered a surge in studies of the polarization dependence of X-ray beams passing through non-isotropic materials. A vast range of experimental results concerning polarization-dependent absorption (dichroism) and dispersion (birefringence, for example) are available from materials which are either magnetic or exhibit preferred directions due to the local atomic environment. This article aims to bring together the diversity of modern experiments in this field with established methods of optical calculus, in a way that highlights the simplicity of the underlying physics. A useful framework is formed when observable quantities, in the X-ray case, are related to atomic variables of the sample material. Atomic descriptions of absorption spectra with various levels of complexity are considered, and some well documented sum-rules are encountered. The framework is the most general allowed within the electric dipole approximation. By way of illustration, dichroic X-ray absorption by two materials with highly anisotropic properties and magnetic ions with different valence shells are considered; namely, a 3d-transition ion in ferrous niobate, and a lanthanide ion in dysprosium borocarbide. Both materials display interesting magnetic properties that are challenging to interpret at an atomic level of detail, and it is shown how absorption experiments can contribute to resolving some issues.

Fluorescent in situ hybridizaton evaluation of p53 gene deletions at a tumor interface of lingual carcinoma

OBJECTIVE/HYPOTHESIS

To evaluate the ability of fluorescent in situ hybridization (FISH) to detect malignant cells missed by standard histological assessment at an interface between malignant and normal tissue in lingual squamous cell carcinoma (SCC) and to correlate findings of FISH assessment with patients' clinical stages.

STUDY DESIGN

Retrospective assessment of archival tissue from 31 patients with lingual SCC treated at University of Wisconsin Hospital and Clinics in Madison.

METHODS

An assay combining standard histological and FISH techniques was used to assess a tumor interface tissue section and allow identification of each tumor's ploidy characteristics and p53 gene deletions and the presence or absence of malignant cells within tissue viewed as "normal" on histological review.

RESULTS

Forty-five percent of tumors (14 of 31) demonstrated ploidy changes and 84% (26 of 31) showed p53 deletions. Of these 26 tumors with p53 deletions, 14 were found to have "microfoci" with p53 deletions within tissue that appeared normal on histological examination. These microfoci were found in 75% of late-stage tumors and in only 35% of early-stage tumors.

CONCLUSIONS

FISH allowed identification of malignant cells in tissue viewed as normal on standard histological assessment, and this finding occurred more frequently in late-stage tumors.

LKB1, a novel serine/threonine protein kinase and potential tumour suppressor, is phosphorylated by cAMP-dependent protein kinase (PKA) and prenylated in vivo

Peutz-Jeghers syndrome (PJS) is an autosomal dominant disease characterized by melanocytic macules, hamartomatous polyps and an increased risk for numerous cancers. The human LKB1 (hLKB1) gene encodes a serine/threonine protein kinase that is deficient in the majority of patients with PJS. The murine LKB1 (mLKB1) cDNA was isolated, sequenced and shown to produce a 2.4-kb transcript encoding a 436 amino acid protein with 90% identity with hLKB1. RNA blot and RNase-protection analysis revealed that mLKB1 mRNA is expressed in all tissues and cell lines examined. The widespread expression of LKB1 transcripts is consistent with the elevated risk of multiple cancer types in PJS patients. The predicted LKB1 protein sequence terminates with a conserved prenylation motif (Cys(433)-Lys-Gln-Gln(436)) directly downstream from a consensus cAMP-dependent protein kinase (PKA) phosphorylation site (Arg(428)-Arg-Leu-Ser(431)). The expression of enhanced green fluorescent protein (EGFP)-mLKB1 chimaeras demonstrated that LKB1 possesses a functional prenylation motif that is capable of targeting EGFP to cellular membranes. Mutation of Cys(433) to an alanine residue, but not phosphorylation by PKA, blocked membrane localization. These findings suggest that PKA does phosphorylate LKB1, although this phosphorylation does not alter the cellular localization of LKB1.

Cyclic AMP- and cyclic GMP-dependent protein kinases differ in their regulation of cyclic AMP response element-dependent gene transcription

The ability of cGMP-dependent protein kinases (cGKs) to activate cAMP response element (CRE)-dependent gene transcription was compared with that of cAMP-dependent protein kinases (cAKs). Although both the type Ibeta cGMP-dependent protein kinase (cGKIbeta) and the type II cAMP-dependent protein kinase (cAKII) phosphorylated the cytoplasmic substrate VASP (vasodilator- and A kinase-stimulated phosphoprotein) to a similar extent, cyclic nucleotide regulation of CRE-dependent transcription was at least 10-fold higher in cAKII-transfected cells than in cGKIbeta-transfected cells. Overexpression of each kinase in mammalian cells resulted in a cytoplasmic localization of the unactivated enzyme. As reported previously, the catalytic (C) subunit of cAKII translocated to the nucleus following activation by 8-bromo-cyclic AMP. However, cGKIbeta did not translocate to the nucleus upon activation by 8-bromo-cyclic GMP. Replacement of an autophosphorylated serine (Ser79) of cGKIbeta with an aspartic acid resulted in a mutant kinase with constitutive kinase activity in vitro and in vivo. The cGKIbetaS79D mutant localized to the cytoplasm and was only a weak activator of CRE-dependent gene transcription. However, an amino-terminal deletion mutant of cGKIbeta was found in the nucleus as well as the cytoplasm and was a strong activator of CRE-dependent gene transcription. These data suggest that the inability of cGKs to translocate to the nucleus is responsible for the differential ability of cAKs and cGKs to activate CRE-dependent gene transcription and that nuclear redistribution of cGKs is not required for NO/cGMP regulation of gene transcription.

Phosphorylation-dependent inhibition of protein phosphatase-1 by G-substrate. A Purkinje cell substrate of the cyclic GMP-dependent protein kinase

G-substrate, a specific substrate of the cGMP-dependent protein kinase, has previously been localized to the Purkinje cells of the cerebellum. We report here the isolation from mouse brain of a cDNA encoding G-substrate. This cDNA was used to localize G-substrate mRNA expression, as well as to produce recombinant protein for the characterization of G-substrate phosphatase inhibitory activity. Brain and eye were the only tissues in which a G-substrate transcript was detected. Within the brain, G-substrate transcripts were restricted almost entirely to the Purkinje cells of the cerebellum, although transcripts were also detected at low levels in the paraventricular region of the hypothalamus and the pons/medulla. Like the native protein, the recombinant protein was preferentially phosphorylated by cGMP-dependent protein kinase (Km = 0.2 microM) over cAMP-dependent protein kinase (Km = 2.0 microM). Phospho-G-substrate inhibited the catalytic subunit of native protein phosphatase-1 with an IC50 of 131 +/- 27 nM. Dephospho-G-substrate was not found to be inhibitory. Both dephospho- and phospho-G-substrate were weak inhibitors of native protein phosphatase-2A1, which dephosphorylated G-substrate 20 times faster than the catalytic subunit of protein phosphatase-1. G-substrate potentiated the action of cAMP-dependent protein kinase on a cAMP-regulated luciferase reporter construct, consistent with an inhibition of cellular phosphatases in vivo. These results provide the first demonstration that G-substrate inhibits protein phosphatase-1 and suggest a novel mechanism by which cGMP-dependent protein kinase I can regulate the activity of the type 1 protein phosphatases.

Station 16.3: a high-resolution single-crystal diffraction facility at the SRS, Daresbury

SRS station 16.3 is now a fully scheduled user facility for high-resolution and high-energy single-crystal X-ray diffraction. It is based on a large three-axis diffractometer, designed and constructed at Daresbury for a wide range of physics and materials science applications. Served by wiggler 16 (a 6 T superconducting wavelength-shifter), the station has access to a broad spectrum of photon energies, extending to over 50 keV, and is designed for simple polarization-state tuning by motorized height adjustment of all optical components. This paper outlines the key design features and some of the science projects carried out during the first year of operation.

Stretched polymers for X-ray linear and circular polarization

X-ray linear dichroism at the iodine K-edge of Polaroid H-sheet is explored with a view to using stretched polymers for X-ray linear-polarization analysis. The potential use of such materials as phase plates for generating elliptically polarized beams is also considered.

The effects of the atypical antipsychotics clozapine, remoxipride and risperidone on the contractile characteristics of rat skeletal muscle in vitro

The therapeutic use of the atypical antipsychotics clozapine, remoxipride and risperidone has been reported to be associated with a reduced occurrence of the extrapyramidal side-effects seen during therapy with classical (or typical) antipsychotics such as trifluoperazine and haloperidol. The aim of this study was to determine the effects of the atypical antipsychotics clozapine, remoxipride and risperidone on rat skeletal muscle in vitro. Remoxipride and risperidone did not produce contracture in muscle. Clozapine induced a small muscle contracture at high concentrations. Pre-treatment of muscle with trifluoperazine or haloperidol in vitro caused the muscle to display contracture responses to halothane, and haloperidol also potentiated a contracture response to caffeine. Pre-treatment of muscle with remoxipride and risperidone did not induce contracture in response to halothane and did not potentiate caffeine contracture. Clozapine pre-treatment caused muscle fibre bundles to display a small halothane-induced contracture and caused significant potentiation of caffeine-induced contracture.

Characterization of PKIgamma, a novel isoform of the protein kinase inhibitor of cAMP-dependent protein kinase

Attempts to understand the physiological roles of the protein kinase inhibitor (PKI) proteins have been hampered by a lack of knowledge concerning the molecular heterogeneity of the PKI family. The PKIgamma cDNA sequence determined here predicted an open reading frame of 75 amino acids, showing 35% identity to PKIalpha and 30% identity to PKIbeta1. Residues important for the high affinity of PKIalpha and PKIbeta1 as well as nuclear export of the catalytic (C) subunit of cAMP-dependent protein kinase were found to be conserved in PKIgamma. Northern blot analysis showed that a 1.3-kilobase PKIgamma message is widely expressed, with highest levels in heart, skeletal muscle, and testis. RNase protection analysis revealed that in most tissues examined PKIgamma is expressed at levels equal to or higher than the other known PKI isoforms and that in several mouse-derived cell lines, PKIgamma is the predominant PKI message. Partial purification of PKI activities from mouse heart by DEAE ion exchange chromatography resolved two major inhibitory peaks, and isoform-specific polyclonal antibodies raised against recombinant PKIalpha and PKIgamma identified these inhibitory activities to be PKIalpha and PKIgamma. A comparison of inhibitory potencies of PKIalpha and PKIgamma expressed in Escherichia coli revealed that PKIgamma was a potent competitive inhibitor of Calpha phosphotransferase activity in vitro (Ki = 0.44 nM) but is 6-fold less potent than PKIalpha (Ki = 0.073 nM). Like PKIalpha, PKIgamma was capable of blocking the nuclear accumulation of Flag-tagged C subunit in transiently transfected mammalian cells. Finally, the murine PKIgamma gene was found to overlap the murine adenosine deaminase gene on mouse chromosome 2. These results demonstrate that PKIgamma is a novel, functional PKI isoform that accounts for the previously observed discrepancy between PKI activity and PKI mRNA levels in several mammalian tissues.

Absence of continuous epitopes in the house dust mite major allergens Der p I from Dermatophagoides pteronyssinus and Der f I from Dermatophagoides farinae

BACKGROUND

The house dust mite has been shown to be an important source of domestic allergens associated with immediate hypersensitivities. The Group I mite allergens Der p I from Dermatophagoides pteronyssinus and Der f I from D. farinae display extensive amino acid sequence homology and have similarities with cysteine protease enzymes.

OBJECTIVE

The availability of the complete amino acid sequences for these allergens allowed us to search for the allergic determinants within these molecules. The aim of the present investigation was to identify any continuous IgE-binding epitopes within these amino acid sequences. We also sought to test the validity of previously reported Der p I peptide epitope sequences.

METHODS

In order to identify any continuous IgE epitopes, the amino acid sequences of Der p I and Der f I were synthesized as decapeptides overlapping in sequence and coupled to plastic pins. The specific IgE-binding capacity of these peptides was assayed using an enzyme-linked biotin-streptavidin procedure and sera from patients known to be sensitive to these allergens. Previously reported Der p I peptide epitopes were synthesized as free peptides and tested for their ability to inhibit specific IgE binding to allergen extract discs.

RESULTS

None of the pin-coupled Der p I or Der f I peptides was found by the continuous epitope mapping procedure to bind significantly to specific IgE in the sera of hypersensitive patients. The previously reported Der p I peptide epitopes did not inhibit specific IgE binding to mite extract discs.

CONCLUSION

The specific IgE binding epitopes of the house dust mite allergens Der p I and Der f I are discontinuous in nature.