Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz Zentrum Berlin

Fragment screening is a technique that helps to identify promising starting points for ligand design. Given that crystals of the target protein are available and display reproducibly high resolution X ray diffraction properties, crystallography is among the most preferred methods for fragment screening because of its sensitivity. Additionally, it is the only method providing detailed 3D information of the binding mode of the fragment, which is vital for subsequent rational compound evolution. The routine use of the method depends on the availability of suitable fragment libraries, dedicated means to handle large numbers of samples, state of the art synchrotron beamlines for fast diffraction measurements and largely automated solutions for the analysis of the results. Here, the complete practical workflow and the included tools on how to conduct crystallographic fragment screening CFS at the Helmholtz Zentrum Berlin HZB are presented. Preceding this workflow, crystal soaking conditions as well as data collection strategies are optimized for reproducible crystallographic experiments. Then, typically in a one to two day procedure, a 96 membered CFS focused library provided as dried ready to use plates is employed to soak 192 crystals, which are then flash cooled individually. The final diffraction experiments can be performed within one day at the robot mounting supported beamlines BL14.1 and BL14.2 at the BESSY II electron storage ring operated by the HZB in Berlin Adlershof Germany . Processing of the crystallographic data, refinement of the protein structures, and hit identification is fast and largely automated using specialized software pipelines on dedicated servers, requiring little user input. Using the CFS workflow at the HZB enables routine screening experiments. It increases the chances for successful identification of fragment hits as starting points to develop more potent binders, useful for pharmacological or biochemical application

Field-sensitive addressing and control of field-insensitive neutral-atom qubits

The establishment of a scalable scheme for quantum computing with addressable and long-lived qubits would be a scientific watershed, harnessing the laws of quantum physics to solve classically intractable problems. The design of many proposed quantum computational platforms is driven by competing needs: isolating the quantum system from the environment to prevent decoherence, and easily and accurately controlling the system with external fields. For example, neutral-atom optical-lattice architectures provide environmental isolation through the use of states that are robust against fluctuating external fields, yet external fields are essential for qubit addressing. Here we demonstrate the selection of individual qubits with external fields, despite the fact that the qubits are in field-insensitive superpositions. We use a spatially inhomogeneous external field to map selected qubits to a different field-insensitive superposition ("optical MRI"), minimally perturbing unselected qubits, despite the fact that the addressing field is not spatially localized. We show robust single-qubit rotations on neutral-atom qubits located at selected lattice sites. This precise coherent control is an important step forward for lattice-based neutral-atom quantum computation, and is quite generally applicable to state transfer and qubit isolation in other architectures using field-insensitive qubits.Comment: press embarg

Natural Cross Chlamydial Infection between Livestock and Free-Living Bird Species

The study of cross-species pathogen transmission is essential to understanding the epizootiology and epidemiology of infectious diseases. Avian chlamydiosis is a zoonotic disease whose effects have been mainly investigated in humans, poultry and pet birds. It has been suggested that wild bird species play an important role as reservoirs for this disease. During a comparative health status survey in common (Falco tinnunculus) and lesser (Falco naumanni) kestrel populations in Spain, acute gammapathies were detected. We investigated whether gammapathies were associated with Chlamydiaceae infections. We recorded the prevalence of different Chlamydiaceae species in nestlings of both kestrel species in three different study areas. Chlamydophila psittaci serovar I (or Chlamydophila abortus), an ovine pathogen causing late-term abortions, was isolated from all the nestlings of both kestrel species in one of the three studied areas, a location with extensive ovine livestock enzootic of this atypical bacteria and where gammapathies were recorded. Serovar and genetic cluster analysis of the kestrel isolates from this area showed serovars A and C and the genetic cluster 1 and were different than those isolated from the other two areas. The serovar I in this area was also isolated from sheep abortions, sheep faeces, sheep stable dust, nest dust of both kestrel species, carrion beetles (Silphidae) and Orthoptera. This fact was not observed in other areas. In addition, we found kestrels to be infected by Chlamydia suis and Chlamydia muridarum, the first time these have been detected in birds. Our study evidences a pathogen transmission from ruminants to birds, highlighting the importance of this potential and unexplored mechanism of infection in an ecological context. On the other hand, it is reported a pathogen transmission from livestock to wildlife, revealing new and scarcely investigated anthropogenic threats for wild and endangered species

Biomarker candidates of neurodegeneration in Parkinson’s disease for the evaluation of disease-modifying therapeutics

Reliable biomarkers that can be used for early diagnosis and tracking disease progression are the cornerstone of the development of disease-modifying treatments for Parkinson’s disease (PD). The German Society of Experimental and Clinical Neurotherapeutics (GESENT) has convened a Working Group to review the current status of proposed biomarkers of neurodegeneration according to the following criteria and to develop a consensus statement on biomarker candidates for evaluation of disease-modifying therapeutics in PD. The criteria proposed are that the biomarker should be linked to fundamental features of PD neuropathology and mechanisms underlying neurodegeneration in PD, should be correlated to disease progression assessed by clinical rating scales, should monitor the actual disease status, should be pre-clinically validated, and confirmed by at least two independent studies conducted by qualified investigators with the results published in peer-reviewed journals. To date, available data have not yet revealed one reliable biomarker to detect early neurodegeneration in PD and to detect and monitor effects of drug candidates on the disease process, but some promising biomarker candidates, such as antibodies against neuromelanin, pathological forms of α-synuclein, DJ-1, and patterns of gene expression, metabolomic and protein profiling exist. Almost all of the biomarker candidates were not investigated in relation to effects of treatment, validated in experimental models of PD and confirmed in independent studies

ICAR: endoscopic skull‐base surgery

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Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

Off-label psychopharmacologic prescribing for children: History supports close clinical monitoring

The review presents pediatric adverse drug events from a historical perspective and focuses on selected safety issues associated with off-label use of medications for the psychiatric treatment of youth. Clinical monitoring procedures for major psychotropic drug classes are reviewed. Prior studies suggest that systematic treatment monitoring is warranted so as to both minimize risk of unexpected adverse events and exposures to ineffective treatments. Clinical trials to establish the efficacy and safety of drugs currently being used off-label in the pediatric population are needed. In the meantime, clinicians should consider the existing evidence-base for these drugs and institute close clinical monitoring