Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN

Genome-wide localization of chromatin and transcription regulators can be detected by a variety of techniques. Here, we describe a novel method ‘greenCUT&RUN’ for genome-wide profiling of transcription regulators, which has a very high sensitivity, resolution, accuracy and reproducibility, whilst assuring specificity. Our strategy begins with tagging of the protein of interest with GFP and utilizes a GFP-specific nanobody fused to MNase to profile genome-wide binding events. By using a GFP-nanobody the greenCUT&RUN approach eliminates antibody dependency and variability. Robust genomic profiles were obtained with greenCUT&RUN, which are accurate and unbiased towards open chromatin. By integrating greenCUT&RUN with nanobody-based affinity purification mass spectrometry, ‘piggy-back’ DNA binding events can be identified on a genomic scale. The unique design of greenCUT&RUN grants target protein flexibility and yields high resolution footprints. In addition, greenCUT&RUN allows rapid profiling of mutants of chromatin and transcription proteins. In conclusion, greenCUT&RUN is a widely applicable and versatile genome-mapping technique.

SABRE and the Stawell Underground Physics Laboratory Dark Matter Research at the Australian National University

The direct detection of dark matter is a key problem in astroparticle physics that generally requires the use of deep-underground laboratories for a low-background environment where the rare signals from dark matter interactions can be observed. This work reports on the Stawell Underground Physics Laboratory – currently under construction and the first such laboratory in the Southern Hemisphere – and the associated research program. A particular focus will be given to ANU’s contribution to SABRE, a NaI:Tl dark matter, direct detection experiment that aims to confirm or refute the long-standing DAMA result. Preliminary measurements of the NaI:Tl quenching factor and characterisation of the SABRE liquid scintillator veto are reported.

Soft X-ray refractive index by reconciling total electron yield with specular reflection: experimental determination of the optical constants of graphite

The complex refractive index of many materials is poorly known in the soft X-ray range across absorption edges. This is due to saturation effects that occur there in total-electron-yield and fluorescence-yield spectroscopy and that are strongest at resonance energies. Aiming to obtain reliable optical constants, a procedure that reconciles electron-yield measurements and reflection spectroscopy by correcting these saturation effects is presented. The procedure takes into account the energy- and polarization-dependence of the photon penetration depth as well as the creation efficiency for secondary electrons and their escape length. From corrected electron-yield spectra the absorption constants and the imaginary parts of the refractive index of the material are determined. The real parts of the index are subsequently obtained through a Kramers-Kronig transformation. These preliminary optical constants are refined by simulating reflection spectra and adapting them, so that measured reflection spectra are reproduced best. The efficacy of the new procedure is demonstrated for graphite. The optical constants that have been determined for linearly polarized synchrotron light incident with p- and s-geometry provide a detailed and reliable representation of the complex refractive index of the material near π- and σ-resonances. They are also suitable for allotropes of graphite such as graphene.

Safety and efficacy of oxandrolone in growth hormone-treated girls with Turner syndrome: evidence from recent studies and recommendations for use

There has been no consensus regarding the efficacy and safety of oxandrolone (Ox) in addition to growth hormone (GH) in girls with Turner syndrome (TS), the optimal age of starting this treatment, or the optimal dose. This collaborative venture between Dutch, UK and US centers is intended to give a summary of the data from three recently published randomized, placebo-controlled, double-blind studies on the effects of Ox. The published papers from these studies were reviewed within the group of authors to reach consensus about the recommendations. The addition of Ox to GH treatment leads to an increase in adult height, on average 2.3–4.6 cm. If Ox dosages<0.06 mg/kg/day are used, side effects are modest. The most relevant safety concerns are virilization(including clitoromegaly and voice deepening) and a transient delay of breast development. We advise monitoring signs of virilization breast development and possibly blood lipids during Ox treatment, in addition to regular follow-up assessments for TS. In girls with TS who are severely short for age, in whom very short adult stature is anticipated,or in whom the growth rate is modest despite good compliance with GH, adjunctive treatment with Ox at a dosage of 0.03–0.05 mg/kg/day starting from the age of 8–10 years onward scan be considered.

Long-term postoperative follow-up in patients with apparently benign pheochromocytoma and paraganglioma

Patients with pheochromocytoma or paraganglioma are at risk of developing tumor recurrences or new tumors after successful resection of the primary tumor. This review summarizes current knowledge concerning the incidence and risk factors for such events. The overall incidence exceeds 15%. Patients with inherited tumors have a higher probability of recurrence or new tumors. Most recurrences are metastatic, particularly in patients with SDHB mutations or nonhereditary tumors. We recommend the determination of plasma or urinary metanephrines (normetanephrine and metanephrine) 1 month after surgery. In patients with sporadic, single tumors ≤5 cm in diameter, clinical and biochemical follow-up should be performed every 2 years. However, this follow-up period can be reduced to yearly, if it is more simple and more convenient for patients and physicians. Patients with larger or multiple but apparently benign tumors and/or inherited disease should be tested 6 months after surgery and then every year for the rest of their lives. Imaging follow-up is also required in patients with inherited or malignant tumors.

Cerebrospinal fluid leakage as complication of treatment with cabergoline for macroprolactinomas

Treatment of patients with prolactinomas consists primarily of dopamine agonists (DA). Cerebrospinal fluid (CSF) leakage has sporadically been reported in patients with macroprolactinomas treated with short-acting DA such as bromocriptine. Little is known on the incidence of this complication in patients treated with the long-acting D2 specific DA cabergoline. We report three patients with CSF leakage shortly after initiation of cabergoline treatment for macroprolactinoma. All three patients responded rapidly to cabergoline (CAB) by shrinkage of the tumor and release of the optic chiasm compression. The CSF leakage occurred within 10 days after initiation of treatment. CAB treatment was not discontinued. In one patient the CSF leakage ceased spontaneously, with no additional therapy. The second patient had a surgical repair of the CSF fistula, permitting cabergoline to be continued without a recurrence of the CSF leakage. The third patient refused surgical repair of the sellar defect. In this patient the cabergoline dosage was temporarily decreased with no effect on the CSF leakage. Four years later, the CSF leakage is unchanged in this patient, whilst no other complications occurred during the follow-up. No infectious complications occurred in these three patients. In conclusion, patients with large, invasive macroprolactinomas are at risk of CSF leakage during medical treatment with CAB. It is advisable to warn these patients for occurrence of this complication and to monitor them closely especially during the first months of treatment.

Letter recognition at low contrast levels: effects of letter size

Contrast variation was used to measure recognition thresholds for lowercase letters, with the aim of obtaining a better understanding of the role that early stages of visual processing play in letter recognition. Frequency-of-recognition curves were measured for alphabets of different letter size. Since variation of the adaptational state of the eye changes the characteristics of primary visual processing in a quantifiable way, recognition thresholds were measured both at a high (150 cd m-2) and at a low (0.9 cd m-2) adaptation level. Thresholds decreased as letter size increased, in a way comparable with data on visual acuity. At the lower adaptation level, recognition thresholds became higher, which is also in accordance with visual acuity data. Furthermore, the slopes of the frequency-of-recognition curves for alphabets as a function of log contrast decreased with decreasing letter size. It is argued that this is mainly caused by an increasing dispersion of internal representations of individual letters on the internal psychological scale as letter size decreases.

Coagulopathy in Ruptured or Dissecting Aortic Aneurysms

A consumption coagulopathy was demonstrated in each of four patients with either ruptured aneurysm of the aorta or a dissecting aortic aneurysm. The most prominent features of this disorder were (1) a prolonged prothrombine time due to a decrease of one or more clotting factors, and (2) formation of fibrin and fibrinogen degradation products. Recognition of this coagulation disorder could be a valuable diagnostic tool to differentiate a ruptured or dissecting aortic aneurysm from other conditions with a similar acute onset. The coagulation disorder could be due to liberation of coagulant material from the aortic wall into the circulation or to an accumulation of clotting factors at the site of the lesion, secondary to the local exposition of tissue factors from the torn arterial wall. The probability of the latter mechanism is suggested by the local increase of radioactivity after the injection of 125I-fibrinogen.