Accessing DNA damage in chromatin: Preparing the chromatin landscape for base excision repair

DNA damage in chromatin comes in many forms, including single base lesions that induce base excision repair (BER). We and others have shown that the structural location of DNA lesions within nucleosomes greatly influences their accessibility to repair enzymes. Indeed, a difference in the location of uracil as small as one-half turn of the DNA backbone on the histone surface can result in a 10-fold difference in the time course of its removal in vitro. In addition, the cell has evolved several interdependent processes capable of enhancing the accessibility of excision repair enzymes to DNA lesions in nucleosomes, including post-translational modification of histones, ATP-dependent chromatin remodeling and interchange of histone variants in nucleosomes. In this review, we focus on different factors that affect accessibility of BER enzymes to nucleosomal DNA.     

Ventricular noncompaction and long QT syndrome – A deadly double hit for the foetus

Congenital long QT syndrome [LQTS] is a channelopathy characterized by QT prolongation and polymorphic VT. LQTS however need not be a purely electrical disease. Defects in ion channels may cause myocardial architectural disruption leading to ventricular non compaction [VNC]. It is defined as the presence of prominent ventricular trabeculations and deep intertrabecular recesses within the endomyocardium. We describe the in-utero management of a foetus who was later found to have LQTS with VNC. The detection of ventricular tachycardia and complete heart block in utero should arouse the suspicion of LQTS. It would be wise to avoid QT prolonging antiarrhythmics in this subset of patients.     

Locomotor diversity in prosimian primates

An understanding of prosimian movement is basic to many anatomical and paleontological studies in that these studies attempt to correlate movement with anatomy and therefore infer movement in fossil primates. Duke University has a large and diverse collection of prosimian primates, which are housed in cages and enclosures large enough for movement studies. Extant prosimians move in many different ways, and none are so specialized that only one mode of travel is used. The most general locomotor patterns are observed for the cheirogaleids, and thus theirs may best resemble the locomotor patterns of the ancestral euprimate.     

Influence of scale on conservation priority setting – a test on African mammals

Broad-scale priority regions for conservation can be identified usingdatabases on species distribution through the application of site-selectionalgorithms. However, the influence of scale on large-scale priority setting isstill unclear. Using a data set of all 939 sub-Saharan mammal species,we wanted to know if continental conservation priorities derived at the scales of 1°, 2°,4° and 8° latitude–longitude grid cells are consistent. We testedwhether (1) geographical location of minimum sets were nested across scale, (2)the selection sequence (priority) of areas within a minimum set were scaledependent, and (3) these coarse-scale priorities can act as a cost-effectiveshortcut for the identification of fine-scale priorities. We found that minimumsets at smaller scales were largely represented within minimum sets at largerscales, especially when flexibility was considered. However, the geographicallocation of the grid cells with highest priority in the minimum sets was onlyscale independent if ranked by number of endangered species, total speciesrichness or rare quartile species richness, but surprisingly not bycomplementary species richness. Minimum sets at a 1° scale were generallyidentified within the areas of the 2°, 4° and 8° minimum sets.Therefore, coarse-scale priorities may provide a pragmatic basis for immediateassessment of priorities for conservation.     

Rookognise: Acoustic detection and identification of individual rooks in field recordings using multi-task neural networks

Individual-level monitoring is essential in many behavioural and bioacoustics studies. Collecting and annotating those data is costly in terms of human effort, but necessary prior to conducting analysis. In particular, many studies on bird vocalisations also involve manipulating the animals or human presence during observations, which may bias vocal production. Autonomous recording units can be used to collect large amounts of data without human supervision, largely removing those sources of bias. Deep learning can further facilitate the annotation of large amounts of data, for instance to detect vocalisations, identify the species, or recognise the vocalisation types in recordings. Acoustic individual identification, however, has so far largely remained limited to a single vocalisation type for a given species. This has limited the use of those techniques for automated data collection on raw recordings, where many individuals can produce vocalisations of varying complexity, potentially overlapping one another, with the additional presence of unknown and varying background noise. This paper aims at bridging this gap by developing a system to identify individual animals in those difficult conditions. Our system leverages a combination of multi-scale information integration, multi-channel audio and multi-task learning. The multi-task learning paradigm is based the overall task into four sub-tasks, three of which are auxiliary tasks: the detection and segmentation of vocalisations against other noises, the classification of individuals vocalising at any point during a sample, and the sexing of detected vocalisations. The fourth task is the overall identification of individuals. To test our approach, we recorded a captive group of rooks, a Eurasian social corvid with a diverse vocal repertoire. We used a multi-microphone array and collected a large scale dataset of time-stamped and identified vocalisations recorded, and found the system to work reliably for the defined tasks. To our knowledge, the system is the first to acoustically identify individuals regardless of the vocalisation produced. Our system can readily assist data collection and individual monitoring of groups of animals in both outdoor and indoor settings, even across long periods of time, and regardless of a species’ vocal complexity. All data and code used in this article is available online.     

Students’ Alternative Conceptions about the Lotus Effect: To Confront or to Ignore?

At the botanical garden of the University of Würzburg, we conducted practical lessons on bionics, focused on the lotus effect, with 260 students. Those approx. 14 years old, 8th-grade mid-level students were divided into two groups. During an instructional discussion about the topic, one group was confronted with their alternative conceptions (AC), whereas the other group was not (NAC). Both groups were treated equally, following the experimental phase and results discussion. Questionnaires were used to measure conceptual change in a pre-, post- and retention test design. Both groups changed their conceptions in short-term similarly. Over a long-term period, the NAC group showed significantly higher knowledge than the AC group. We discuss that the methodology of the alternative conception confrontation should be selected very carefully by the teacher, as this step is the most delicate within the whole conceptual change process.     

Confusing means with ends: A manager's reflections on experience in agricultural landscapes of Western Australia

Summary Since 'landcare' in its modern form began in Australia during the early 1980s, considerable resources have been focused on applying tools and processes, such as community empowerment, regionalization, integrated catchment management, and facilitation and coordination. While these are valuable tools to achieve goals, they are not themselves goals. Unfortunately, they have frequently become ends in themselves. This confusion of means and ends has hindered landcare achievements in Australia. Examples of this are provided, and then contrasted with management based on goals that emphasize realistic targets, highlight barriers to goal achievement, and facilitate the development of well-targeted actions. The complexity of most natural resource management issues, the lack of technical solutions and the long timescales over which management must be applied have all contributed to the confusion of means and ends.