Chromatin accessibility dynamics of Chlamydia-infected epithelial cells.

Chlamydia are Gram-negative, obligate intracellular bacterial pathogens responsible for a broad spectrum of human and animal diseases. In humans, Chlamydia trachomatis is the most prevalent bacterial sexually transmitted infection worldwide and is the causative agent of trachoma (infectious blindness) in disadvantaged populations. Over the course of its developmental cycle, Chlamydia extensively remodels its intracellular niche and parasitises the host cell for nutrients, with substantial resulting changes to the host cell transcriptome and proteome. However, little information is available on the impact of chlamydial infection on the host cell epigenome and global gene regulation. Regions of open eukaryotic chromatin correspond to nucleosome-depleted regions, which in turn are associated with regulatory functions and transcription factor binding. We applied formaldehyde-assisted isolation of regulatory elements enrichment followed by sequencing (FAIRE-Seq) to generate temporal chromatin maps of C. trachomatis-infected human epithelial cells in vitro over the chlamydial developmental cycle. We detected both conserved and distinct temporal changes to genome-wide chromatin accessibility associated with C. trachomatis infection. The observed differentially accessible chromatin regions include temporally-enriched sets of transcription factors, which may help shape the host cell response to infection. These regions and motifs were linked to genomic features and genes associated with immune responses, re-direction of host cell nutrients, intracellular signalling, cell-cell adhesion, extracellular matrix, metabolism and apoptosis. This work provides another perspective to the complex response to chlamydial infection, and will inform further studies of transcriptional regulation and the epigenome in Chlamydia-infected human cells and tissues

An integrated biostratigraphy and seismic stratigraphy for the late Neogene continental margin succession in northern Taranaki Basin, New Zealand

Our aim has been to develop an integrated biostratigraphy and seismic stratigraphy for the Pliocene and Pleistocene formations (Ariki, Mangaa, Giant Foresets) in northern Taranaki Basin to better understand the evolution of the modern continental margin offshore central-western North Island, New Zealand. Detailed mapping of seismic reflectors in part of the basin, when compared with correlations of late Neogene stage boundaries between 11 well sections, has highlighted crossover between the datasets. To help resolve this issue, the biostratigraphy of the Pliocene-Pleistocene parts of each of four well sections (Arawa-1, Ariki-1, Kora-1, and Wainui-1) has been re-examined using a dense suite of samples. In addition, the biostratigraphy of seven other well sections (Awatea-1, Kahawai-1, Mangaa-1, Taimana-1, Tangaroa-1, Te Kumi-1, and Turi-1) has been re-evaluated. The crossover is partly attributed to a combination of sampling resolution inherent in exploration well sections, the mixed nature of cuttings samples, and the general scarcity of age-diagnostic planktic foraminifera in the late Neogene formations. The achievement of seismic closure suggests that error in the mapping of the seismic reflectors is not a significant source of the uncertainty (crossover). We have developed a workable time-stratigraphic framework by qualitatively weighting the biostratigraphic data in each of the well sections, thereby identifying the parts of particular well sections with the highest resolution microfossil data and the optimal stratigraphic position of stage boundaries with respect to the mapped seismic horizons/seismic units. Hence, it is possible to assign the known numerical ages for these stage boundaries to reflection horizons/seismic units mapped within the basin. We have applied this information to produce a series of isopach maps for successive stage boundaries that help show the sedimentary evolution of the continental margin succession west of central North Island

Dual RNA sequencing (dRNA-Seq) of bacteria and their host cells

Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA-Seq technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. We pioneered dRNA-Seq to simultaneously capture prokaryotic and eukaryotic expression profiles of cells infected with bacteria, using in vitro Chlamydia-infected epithelial cells as proof of principle. Here we provide a detailed laboratory and bioinformatics protocol for dRNA-seq that is readily adaptable to any host-bacteria system of interest

Spatial and temporal overlaps between leopards (Panthera pardus) and their competitors in the African large predator guild

Understanding the mechanisms facilitating coexistence within species assemblages is a key consideration for conservation as intact assemblages are necessary for maintaining full ecosystem function. The African large predator guild represents one of the few remaining functionally intact large predator assemblages on Earth, and as such, represents a unique study system to understand competitive interactions. Yet, relatively little is known of the coexistence mechanisms between some of its intermediately sized members, particularly leopards (Panthera pardus). Here, we use overlapping spatio‐temporal activity and GPS data on lions (Panthera leo), leopards, African wild dogs (Lycaon pictus) and cheetahs (Acinonyx jubatus) to examine spatial interactions and temporal partitioning between leopards and other guild members in northern Botswana. We found that at the population level, male leopard space use and activity patterns were largely unaffected by intraguild competitors. Leopards showed minimal movement coherence with competitors (avoidance or attraction) when moving through areas of home ranges shared with intraguild species. Moreover, we found evidence to support the hypothesis that guild species’ activity patterns are primarily driven by light availability rather than predator avoidance. Our results suggest predator avoidance has a limited impact on broad‐scale leopard spatio‐temporal niches, with aspects of the leopards’ ecology and life history likely facilitating its ability to thrive in close proximity to competitors. Considered alongside other studies, our results suggest that landscape‐level approaches to conservation may be suitable for aiding leopard conservation

Agreed Definitions and a Shared Vision for New Standards in Stroke Recovery Research: The Stroke Recovery and Rehabilitation Roundtable Taskforce

The first Stroke Recovery and Rehabilitation Roundtable established a game changing set of new standards for stroke recovery research. Common language and definitions were required to develop an agreed framework spanning the four working groups: translation of basic science, biomarkers of stroke recovery, measurement in clinical trials and intervention development and reporting. This paper outlines the working definitions established by our group and an agreed vision for accelerating progress in stroke recovery research

Scent-marking strategies of a solitary carnivore: boundary and road scent marking in the leopard

Scent marking, where individuals deposit signals on objects in the environment, is a common form of chemical signalling in mammals and is thought to play a critical role in maintaining social organisation within wide-ranging, spatially-dispersed populations. Senders, however, can incur scent marking costs through mark production, time investment in patrolling and depositing/maintaining mark sites, and increased risk of detection by predators and prey. To mitigate these costs, senders can adapt spatial patterns of scent marking to increase the probabilities of their scent marking being encountered by intended receivers. Relatively little, however, is known of the spatial scent marking placements of many wide-ranging carnivore species, with most studies focussing on scent mark form and function. Here, we use detailed observational data collected from over seven years of following individual leopards and high-resolution GPS radio collar data to investigate the spatial placements of scent marks within a leopard population in northern Botswana. We found that male leopards within our study area exhibited a boundary scent marking strategy by showing higher investments in the maintenance of marking sites in peripheral areas of their home range. We also found that leopards scent marked over four times as frequently and investigated over three times as frequently when travelling on roads than when travelling along natural routes, suggesting that roads may function as key locations for olfactory information. Compared to leopards from less productive ecosystems, such as the Kalahari, our results (1) suggest that leopards can be highly flexible in their marking strategies, with strategies impacted by the surrounding environment, and (2) provide evidence that human-modifications of the environment now play an important role in facilitating social cohesion within this solitary carnivore

Spatio-temporal factors impacting encounter occurrences between leopards and other large African predators

Encounters between individuals can have implications for a range of processes, including 24 disease transmission, information transfer, and competition. For large carnivores, 25 difficulties in directly observing individuals and historical hardware limitations of GPS 26 collars mean that relatively little is known of the spatio-temporal factors contributing to 27 encounters. The African large predator guild represents one of the few remaining 28 functionally intact guilds of large carnivores on the globe and so represents a unique 29 study system for understanding competitor interactions. We explored the drivers of male 30 leopard (Panthera pardus) encounters with lions (Panthera leo), African wild dogs (Lycaon 31 pictus) and cheetahs (Acinonyx jubatus) in the context of habitat characteristics and 32 temporal activity overlaps. Using high resolution (five minute GPS fixes) data from 48 33 large African carnivores from 2012 to 2018, we quantified encounter occurrences 34 between male leopards and other guild species and related these to habitat type (open vs 35 closed), activity overlaps, and moonlight levels. Leopards met wild dogs 4.56 ± 1.15 36 (standard error), lions 3.11 ± 0.56, and cheetahs 2.27 ± 0.73 times per month. All species 37 instigated encounters, but leopard instigated encounters with dominant competitors 38 appeared to reflect imperfect information on risk, primarily occurring within habitats with 39 limited visibility. Moreover, encounters peaked during periods of high temporal overlap, 40 suggesting that, although previous research indicates temporal activity patterns may not 41 be driven by predator avoidance, temporal overlap has implications for competitor 42 dynamics. Our results show how habitat characteristics and niche overlaps contribute to 43 encounters between competitors and provide an example of how niche shifts within 44 competitor assemblages can impact competition between species

Isolated and dynamical horizons and their applications

Over the past three decades, black holes have played an important role in quantum gravity, mathematical physics, numerical relativity and gravitational wave phenomenology. However, conceptual settings and mathematical models used to discuss them have varied considerably from one area to another. Over the last five years a new, quasi-local framework was introduced to analyze diverse facets of black holes in a unified manner. In this framework, evolving black holes are modeled by dynamical horizons and black holes in equilibrium by isolated horizons. We review basic properties of these horizons and summarize applications to mathematical physics, numerical relativity and quantum gravity. This paradigm has led to significant generalizations of several results in black hole physics. Specifically, it has introduced a more physical setting for black hole thermodynamics and for black hole entropy calculations in quantum gravity; suggested a phenomenological model for hairy black holes; provided novel techniques to extract physics from numerical simulations; and led to new laws governing the dynamics of black holes in exact general relativity.Comment: 77 pages, 12 figures. Typos and references correcte

Tourist photographs as a scalable framework for wildlife monitoring in protected areas.

Protected areas are critical to conservation efforts in the face of rapid biodiversity declines [1]. Yet the resources for conservation are often limited and shared amongst many competing priorities [2]. As a consequence, even basic monitoring surveys are absent within most protected areas [3]. Although a range of wildlife monitoring methods exist, considerable focused survey effort is often required to yield accurate and precise estimates [4]. This makes monitoring difficult to sustain or replicate, limiting access to the data required for evidence-based conservation decisions. Citizen-scientists have been proposed as an important complement to the finite resources available for basic monitoring within protected areas [5]; however, the full potential of this approach has yet to be realised. Wildlife tourists and guides are especially focussed on encountering and photographing fauna and flora, yet the data collected in these efforts is rarely harnessed for conservation monitoring within protected areas. A detailed understanding of photographic tourism's potential role in wildlife monitoring has been lacking, but is essential for the development of new tools to harness the data being collected through tourism. Here, we demonstrate that tourist-contributed data can aid wildlife monitoring in protected areas by providing population estimates of large carnivores comparable to those from traditional survey methods. Our approach could capitalize upon the immense number of wildlife photographs being taken daily as part of the global > 30-billion USD, wildlife-based tourism industry