In mammals, interactions between sequences within topologically associating domains enable control of gene expression across large genomic distances. Yet it is unknown how frequently such contacts ...occur, how long they last and how they depend on the dynamics of chromosome folding and loop extrusion activity of cohesin. By imaging chromosomal locations at high spatial and temporal resolution in living cells, we show that interactions within topologically associating domains are transient and occur frequently during the course of a cell cycle. Interactions become more frequent and longer in the presence of convergent CTCF sites, resulting in suppression of variability in chromosome folding across time. Supported by physical models of chromosome dynamics, our data suggest that CTCF-anchored loops last around 10 min. Our results show that long-range transcriptional regulation might rely on transient physical proximity, and that cohesin and CTCF stabilize highly dynamic chromosome structures, facilitating selected subsets of chromosomal interactions.
Construction of chromosomes 3D models based on single cell Hi-C data constitute an important challenge. We present a reconstruction approach, DPDchrom, that incorporates basic knowledge whether the ...reconstructed conformation should be coil-like or globular and spring relaxation at contact sites. In contrast to previously published protocols, DPDchrom can naturally form globular conformation due to the presence of explicit solvent. Benchmarking of this and several other methods on artificial polymer models reveals similar reconstruction accuracy at high contact density and DPDchrom advantage at low contact density. To compare 3D structures insensitively to spatial orientation and scale, we propose the Modified Jaccard Index. We analyzed two sources of the contact dropout: contact radius change and random contact sampling. We found that the reconstruction accuracy exponentially depends on the number of contacts per genomic bin allowing to estimate the reconstruction accuracy in advance. We applied DPDchrom to model chromosome configurations based on single-cell Hi-C data of mouse oocytes and found that these configurations differ significantly from a random one, that is consistent with other studies.
How the nuclear lamina (NL) impacts on global chromatin architecture is poorly understood. Here, we show that NL disruption in Drosophila S2 cells leads to chromatin compaction and repositioning from ...the nuclear envelope. This increases the chromatin density in a fraction of topologically-associating domains (TADs) enriched in active chromatin and enhances interactions between active and inactive chromatin. Importantly, upon NL disruption the NL-associated TADs become more acetylated at histone H3 and less compact, while background transcription is derepressed. Two-colour FISH confirms that a TAD becomes less compact following its release from the NL. Finally, polymer simulations show that chromatin binding to the NL can per se compact attached TADs. Collectively, our findings demonstrate a dual function of the NL in shaping the 3D genome. Attachment of TADs to the NL makes them more condensed but decreases the overall chromatin density in the nucleus by stretching interphase chromosomes.
Evidence-based management of large carnivores is a crucial step towards their effective conservation. However, monitoring of these populations is demanding and generally requires substantial ...fieldwork effort. Lately, citizen science has become an increasingly important part of wildlife monitoring, but can that endanger studied species? In this paper, we describe our experiences with recruiting and involving volunteers in annual howling surveys of grey wolf (
Canis lupus
) population in Slovenia and present the framework about the use of citizens for collecting data. Huge effort of participants in a 7-year-long monitoring at a national scale has yielded a total of 116 wolf vocal responses, including 53 confirmed litters. Annually, between 5 and 12 reproductive packs were detected and an increasing trend in wolf population throughout the study period was observed. Volunteer-based howling surveys proved to be a cost-effective method for detection of reproductive packs on a large spatial scale, offering an insight into wolf population trends across a longer time period and we provide some recommendations for organisation and coordination of surveys. We also discuss ethical issues raised from our experience in using citizen science for this purpose.
The Eurasian lynx is of special conservation concern based on the European Union's Habitat Directive and its populations need to be maintained or restored at favourable conservation status. To ...evaluate lynx population status, appropriate monitoring needs to be in place. We modelled the distribution dynamics of lynx in the Alps (200 000 km2) during 1994–2014 at a resolution of 100 km2. Lynx distribution and detection probability varied by year, country, forest cover, elevation and distance to the nearest release site. Occupancy of neighbouring quadrats had a strong positive effect on colonization and persistence rates. Our analyses demonstrate the importance of accounting for imperfect detection: the raw data underestimated the lynx range by 55% on average, depending on country and winter. Over the past 20 years the Alpine lynx range has expanded at an average rate of 4% per year, which was partly due to the lynx translocations to new areas. Our approach to large‐scale distribution modelling and analysing trends using site occupancy models can be applied retrospectively and is useful in many cases where a network of trained people is established to report the presence of target species, for example, in Europe where member states of the European Union have to report conservation status of species of community interest. Hence, dynamic occupancy models are an appealing framework for inference about the large‐scale range dynamics based on opportunistic data and a useful tool for large‐scale management and conservation programmes.
We analysed range dynamics of a reintroduced large carnivore, the Eurasian lynx, in the Alps (200 000 km2) over 20 years, combining a cutting edge occupancy model with citizen science. Lynx distribution and detection probability varied by distance to the nearest release site, year, forest cover, elevation and country. Occupancy of neighbouring quadrats had a strong positive effect on colonization and persistence rates. Our analyses demonstrate the importance of accounting for imperfect detection: the raw data underestimated the lynx range by 55% on average. Over the past 20 years the Alpine lynx range expanded at an average rate of 4% per year, which was partly due to the lynx translocations to new areas. Our approach to large‐scale distribution modelling and analysing trends using site occupancy models can be applied retrospectively and is useful in many cases where a network of trained people is established to report the presence of target species.
Inferring the distribution and abundance of a species from field records must deal with false‐negative and false‐positive errors. False‐negative errors occur if a species present goes undetected, ...while false‐positive errors are typically a consequence of species misidentification. False‐positive observations in studies of rare species may cause an overestimation of the distribution or abundance of the species and distort trend indices. We illustrate this issue with the monitoring of the Eurasian lynx in the Alps. We developed a three‐level classification of field records according to their reliability as inferred from whether they were validated or not. The first category (C1) represents ‘hard fact’ data (e.g. dead lynx); the second category (C2) includes confirmed data (e.g. tracks verified by an expert); and the third category (C3) are unconfirmed data (e.g. any kind of direct visual observation). For lynx, which is a comparatively well‐known species in the Alps, we use site‐occupancy modelling to estimate its distribution and show that the inferred lynx distribution is highly sensitive to presence sign category: it is larger if based on C3 records compared with the more reliable C1 and C2 records. We believe that the reason for this is a fairly high frequency of false‐positive errors among C3 records. This suggests that distribution records for many lesser‐known species may be similarly unreliable, because they are mostly or exclusively based on unconfirmed and thus soft data. Nevertheless, such soft data form a considerable part of species assessments as presented, for example in the International Union for Conservation of Nature Red List. However, C3 records can often not be discarded because they may be the only information available. When inferring the distribution of rare carnivores, especially for species with an expanding or shrinking range, we recommend a rigorous discrimination between fully reliable and un‐ or only partly reliable data, in order to identify possible methodological problems in the distribution maps related to false‐positive records.
The aim of this study was to investigate nutritive and sensorial quality of Istrian and Slavonian pork-meat dry-fermented sausages. Sensorial analysis resulted in statistically significant ...differences (p <0.05) between these products in 11 sensorial parameters analysed. Significantly higher protein content was determined in Istrian in comparison with Slavonian dry-fermented sausage, although the latter content significantly varied across the producing households. No significant differences in particular fatty acid esters and saturated, monounsaturated and polyunsaturated fatty acids were obtained. Although some of the nutritional quality indices failed to meet health recommendations, the obtained values are consistent with data published for pork meat products. Keywords: Croatian households, dry-fermented sausages, nutritive properties, sensory properties, traditional pork meat sausages
In species with large geographic ranges, genetic diversity of different populations may be well studied, but differences in loci and sample sizes can make the results of different studies difficult ...to compare. Yet, such comparisons are important for assessing the status of populations of conservation concern. We propose a simple approach of using a single well-studied reference population as a 'yardstick' to calibrate results of different studies to the same scale, enabling comparisons. We use a well-studied large carnivore, the brown bear (Ursus arctos), as a case study to demonstrate the approach. As a reference population, we genotyped 513 brown bears from Slovenia using 20 polymorphic microsatellite loci. We used this data set to calibrate and compare heterozygosity and allelic richness for 30 brown bear populations from 10 different studies across the global distribution of the species. The simplicity of the reference population approach makes it useful for other species, enabling comparisons of genetic diversity estimates between previously incompatible studies and improving our understanding of how genetic diversity is distributed throughout a species range.
Malignant otitis externa is a life-threatening infection of the skull base. Its presentation is not always typical.
We report three cases of malignant otitis externa which illustrate the diversity of ...its clinical manifestations and the difficulties in its diagnosis.
The perception of malignant otitis externa as an infection caused by Pseudomonas aeruginosa in diabetic patients is not always correct. The adoption of diagnostic criteria could be helpful in identifying atypical cases.
Mammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs ...represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes. These maps demonstrate chromatin compartmentalization at the megabase scale and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which closely resembles the TAD profile in the bulk in situ Hi-C data. Over 40% of TAD boundaries are conserved between individual nuclei and possess a high level of active epigenetic marks. Polymer simulations demonstrate that chromatin folding is best described by the random walk model within TADs and is most suitably approximated by a crumpled globule build of Gaussian blobs at longer distances. We observe prominent cell-to-cell variability in the long-range contacts between either active genome loci or between Polycomb-bound regions, suggesting an important contribution of stochastic processes to the formation of the Drosophila 3D genome.
PDF
