Note on paramoudra-like carbonate concretions in the Urenui Formation, North Taranaki: possible plumbing system for a Late Miocene methane seep field

A reconnaissance study of calcitic and dolomitic tubular concretions in upper slope mudstone of the Late Miocene Urenui Formation exposed along the north Taranaki coastline indicates that they have a complex diagenetic history involving different phases of carbonate cementation and likely hydrofracturing associated with build up of fluid/gas pressures. The concretions resemble classical paramoudra in the European chalk, but are not siliceous and do not have a trace fossil origin. Stable oxygen and carbon isotope data suggest that the micritic carbonate cements in the Urenui paramoudra were probably sourced primarily from ascending methane fluid/gases, and that they precipitated entirely within the host mudstone below the seafloor. We suggest the paramoudra may mark the subsurface plumbing networks of a Late Miocene cold seep system, in which case they have relevance to the evolution and migration of hydrocarbons in Taranaki Basin, at this site perhaps focussed along the Taranaki Fault. The presence of dislodged and mass-emplaced paramoudra in the axial conglomerate of channels within the Urenui mudstone suggests there could be a connection between the loci of seep field development and slope failure and canyon cutting on the Late Miocene Taranaki margin

Tubular carbonate concretions as hydrocarbon migration pathways? Examples from North Island, New Zealand

Cold seep carbonate deposits are associated with the development on the sea floor of distinctive chemosyn¬thetic animal communities and carbonate minerali¬sation as a consequence of microbially mediated anaerobic oxidation of methane. Several possible sources of the methane exist, identifiable from the carbon isotope values of the carbonate precipitates. In the modern, seep carbonates can occur on the sea floor above petroleum reservoirs where an important origin can be from ascending thermogenic hydrocar¬bons. The character of geological structures marking the ascent pathways from deep in the subsurface to shallow subsurface levels are poorly understood, but one such structure resulting from focused fluid flow may be tubular carbonate concretions. Several mudrock-dominated Cenozoic (especially Miocene) sedimentary formations in the North Island of New Zealand include carbonate concretions having a wide range of tubular morphologies. The concretions are typically oriented at high angles to bedding, and often have a central conduit that is either empty or filled with late stage cements. Stable isotope analyses (δ13C, δ18O) suggest that the carbonate cements in the concretions precipitated mainly from ascending methane, likely sourced from a mixture of deep thermogenic and shallow biogenic sources. A clear link between the tubular concretions and overlying paleo-sea floor seep-carbonate deposits exists at some sites. We suggest that the tubular carbonate concretions mark the subsurface plumbing network of cold seep systems. When exposed and accessible in outcrop, they afford an opportunity to investigate the geochemical evolution of cold seeps, and possibly also the nature of linkages between subsurface and surface portions of such a system. Seep field development has implications for the characterisation of fluid flow in sedimentary basins, for the global carbon cycle, for exerting a biogeochemical influence on the development of marine communities, and for the evaluation of future hydrocarbon resources, recovery, and drilling and production hazards. These matters remain to be fully assessed within a petroleum systems framework for New Zealand’s Cenozoic sedimentary basins

An integrated sequence stratigraphic, palaeoenvironmental, and chronostratigraphic analysis of the Tangahoe Formation, southern Taranaki coast, with implications for mid-Pliocene (c. 3.4–3.0 Ma) glacio-eustatic sea-level changes

Sediments of the mid-Pliocene (c. 3.4–3.0 Ma) Tangahoe Formation exposed in cliffs along the South Taranaki coastline of New Zealand comprise a 270 m thick, cyclothemic shallow-marine succession that has been gently warped into a north to south trending, low angle anticline. This study examines the sedimentologic, faunal, and petrographic characteristics of 10 Milankovitch-scale (6th order), shallow-marine depositional sequences exposed on the western limb of the anticline. The sequences are recognised on the basis of the cyclic vertical stacking of their constituent lithofacies, which are bound by sharp wave cut surfaces produced during transgressive shoreface erosion. Each sequence comprises three parts: (1) a 0.2–2 m thick, deepening upwards, basal suite of reworked bioclastic lag deposits (onlap shellbed) and/or an overlying matrix supported, molluscan shellbed of offshore shelf affinity (backlap shellbed); (2) a 5–20 m thick, gradually shoaling, aggradational siltstone succession; and (3) a 5–10 m thick, strongly progradational, well sorted “forced regressive” shoreline sandstone. The three-fold subdivision corresponds to transgressive, highstand, and regressive systems tracts (TSTs, HSTs, and RSTs) respectively, and represents deposition during a glacio-eustatic sea-level cycle. Lowstand systems tract sediments are not recorded because the outcrop is situated c. 100 km east of the contemporary shelf edge and was subaerially exposed at that time. Well developed, sharp- and gradational-based forced regressive sandstones contain a variety of storm-emplaced sedimentary structures, and represent the rapid and abrupt basinward translation of the shoreline on to a storm dominated, shallow shelf during eustatic sea-level fall. Increased supply of sediment from north-west South Island during “forced regression” is indicated from petrographic analyses of the heavy mineralogy of the sandstones. A chronology based on biostratigraphy and the correlation of a new magnetostratigraphy to the magnetic polarity timescale allows: (1) identification of the Mammoth (C2An.2r) and Kaena (C2An.1r) subchrons; (2) correlation of the coastal section to the Waipipian Stage; and (3) estimation of the age of the coastal section as 3.36–3.06 Ma. Qualitative assessment of foraminiferal census data and molluscan palaeoecology reveals cyclic changes in water depth from shelf to shoreline environments during the deposition of each sequence. Seven major cycles in water depth of between 20 and 50m have been correlated to individual 40 ka glacio-eustatic sea-level cycles on the marine oxygen isotope timescale. The coastal Tangahoe Formation provides a shallow-marine record of global glacio-eustasy prior to the development of significant ice sheets on Northern Hemisphere continents, and supports evidence from marine δ18O archives that changes in Antarctic ice volume were occurring during the Pliocene

The sero-epidemiology of Coxiella burnetii (Q fever) across livestock species and herding contexts in Laikipia County, Kenya

Coxiella burnetii, the causative agent of Query fever (Q fever), is among the most highly infectious zoonotic pathogens transmitted among livestock, with chronic effects challenging to veterinary and medical detection and care systems. Transmission among domestic livestock species can vary regionally due to herd management practices that determine which livestock species are raised, whether or not livestock are in contact with wildlife, and the susceptibility of these livestock to infection. To explore how different livestock management practices are associated with the risk of infection in multispecies environments, we carried out a comparative study of three types of herd management systems in the central Kenyan county of Laikipia: agro‐commercial, mixed conservancy/commercial, and smallholder ranches. We tested C. burnetii antibody seroprevalence in four common livestock species. Across all management types, the highest seroprevalence was in camels (20%), followed by goats (18%), sheep (13%), and cattle (6%). We observed a lower odds of testing seropositive for young compared to adult animals (adjusted OR = 0.44 [95% CI 0.24, 0.76]), and for males compared to females (adjusted OR = 0.52 [95% CI 0.33, 0.80]). Animals from mixed conservancy/commercial and smallholder operations had a higher odds of testing seropositive compared to animals from agro‐commercial ranches (adjusted OR = 5.17 [95% CI 2.71, 10.44] and adjusted OR = 2.21 [95% CI 1.17, 4.43] respectively). These data suggest that herd management practices might affect the transmission dynamics of C. burnetiiin arid African ecosystems like those seen in Kenya where several transmission modes are possible, risk of drought has promoted new livestock species such as camels, and multiple wildlife species may co‐occur with livestock on the landscape. Further longitudinal studies are needed to disentangle the mechanisms underlying these patterns, and further explore transmission patterns between wildlife, domestic animal, and human populations

Type I interferon receptor (IFNAR2) deficiency reveals Zika virus cytopathicity in human macrophages and microglia

Macrophages are key target cells of Zika virus (ZIKV) infection, implicated as a viral reservoir seeding sanctuary sites such as the central nervous system and testes. This rests on the apparent ability of macrophages to sustain ZIKV replication without experiencing cytopathic effects. ZIKV infection of macrophages triggers an innate immune response involving type I interferons (IFN-I), key antiviral cytokines that play a complex role in ZIKV pathogenesis in animal models. To investigate the functional role of the IFN-I response we generated human induced pluripotent stem cell (iPSC)-derived macrophages from a patient with complete deficiency of IFNAR2, the high affinity IFN-I receptor subunit. Accompanying the profound defect of IFN-I signalling in IFNAR2 deficient iPS-macrophages we observed significantly enhanced ZIKV replication and cell death, revealing the inherent cytopathicity of ZIKV towards macrophages. These observations were recapitulated by genetic and pharmacological ablation of IFN-I signalling in control iPS-macrophages and extended to a model of iPS-microglia. Thus, the capacity of macrophages to support noncytolytic ZIKV replication depends on an equilibrium set by IFN-I, suggesting that innate antiviral responses might counterintuitively promote ZIKV persistence via the maintenance of tissue viral reservoirs relevant to pathogenesis

MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking

peer-reviewedMycobacterium bovis, the causative agent of bovine tuberculosis, a major problem for global agriculture, spreads via an airborne route and is taken up by alveolar macrophages (AM) in the lung. Here, we describe the first next-generation sequencing (RNA-seq) approach to temporally profile miRNA expression in primary bovine AMs post-infection with M. bovis. One, six, and forty miRNAs were identified as significantly differentially expressed at 2, 24 and 48 h post-infection, respectively. The differential expression of three miRNAs (bta-miR-142-5p, bta-miR-146a, and bta-miR-423-3p) was confirmed by RT-qPCR. Pathway analysis of the predicted mRNA targets of differentially expressed miRNAs suggests that these miRNAs preferentially target several pathways that are functionally relevant for mycobacterial pathogenesis, including endocytosis and lysosome trafficking, IL-1 signalling and the TGF-β pathway. Over-expression studies using a bovine macrophage cell-line (Bomac) reveal the targeting of two key genes in the innate immune response to M. bovis, IL-1 receptor-associated kinase 1 (IRAK1) and TGF-β receptor 2 (TGFBR2), by miR-146. Taken together, our study suggests that miRNAs play a key role in tuning the complex interplay between M. bovis survival strategies and the host immune response

A peptide-based checkpoint immunomodulator alleviates immune dysfunction in murine polymicrobial sepsis

Sepsis-induced immunosuppression involves both innate and adaptive immunity and is associated with the increased expression of checkpoint inhibitors, such as programmed cell-death protein 1 (PD-1). The expression of PD-1 is associated with poor outcomes in septic patients, and in models of sepsis, blocking PD-1 or its ligands with antibodies increased survival and alleviated immune suppression. While inhibitory antibodies are effective, they can lead to immune-related adverse events (irAEs), in part due to continual blockade of the PD-1 pathway, resulting in hyperactivation of the immune response. Peptide-based therapeutics are an alternative drug modality that provide a rapid pharmacokinetic profile, reducing the incidence of precipitating irAEs. We recently reported that the potent, peptide-based PD-1 checkpoint antagonist, LD01, improves T-cell responses. The goal of the current study was to determine whether LD01 treatment improved survival, bacterial clearance, and host immunity in the cecal-ligation and puncture (CLP)-induced murine polymicrobial sepsis model. LD01 treatment of CLP-induced sepsis significantly enhanced survival and decreased bacterial burden. Altered survival was associated with improved macrophage phagocytic activity and T-cell production of interferon-γ. Further, myeloperoxidase levels and esterase-positive cells were significantly reduced in LD01-treated mice. Taken together, these data establish that LD01 modulates host immunity and is a viable therapeutic candidate for alleviating immunosuppression that characterizes sepsis and other infectious diseases

The NICE-GUT trial protocol:A randomised, placebo controlled trial of oral nitazoxanide for the empiric treatment of acute gastroenteritis among Australian Aboriginal children

Diarrhoeal disease is the second leading cause of death in children under 5 years globally, killing 525 000 annually. Australian Aboriginal and Torres Strait Islander (hereafter Aboriginal) children suffer a high burden of disease. Randomised trials in other populations suggest nitazoxanide accelerates recovery for children with Giardia, amoebiasis, Cryptosporidium, Rotavirus and Norovirus gastroenteritis, as well as in cases where no enteropathogens are found. This double blind, 1:1 randomised, placebo controlled trial is investigating the impact of oral nitazoxanide on acute gastroenteritis in hospitalised Australian Aboriginal children aged 3 months to <5 years. Dosing is based on age-based dosing. The primary endpoint is the time to resolution of 'significant illness' defined as the time from randomisation to the time of clinical assessment as medically ready for discharge, or to the time of actual discharge from hospital, whichever occurs first. Secondary endpoints include duration of hospitalisation, symptom severity during the period of significant illness and following treatment, duration of rehydration and drug safety. Patients will be followed for medically significant events for 60 days. Analysis is based on Bayesian inference. Subgroup analysis will occur by pathogen type (bacteria, virus or parasite), rotavirus vaccination status, age and illness severity. Ethics approval has been granted by the Central Australian Human Research Ethics Committee (HREC-14-221) and the Human Research Ethics Committee of the Northern Territory Department of Health and Menzies School of Health Research (HREC2014-2172). Study investigators will ensure that the trial is conducted in accordance with the principles of the Declaration of Helsinki. Individual participant consent will be obtained. Results will be disseminated via peer-reviewed publication. ACTRN12614000381684

Efficient and long-lived quantum memory with cold atoms inside a ring cavity

Quantum memories are regarded as one of the fundamental building blocks of linear-optical quantum computation and long-distance quantum communication. A long standing goal to realize scalable quantum information processing is to build a long-lived and efficient quantum memory. There have been significant efforts distributed towards this goal. However, either efficient but short-lived or long-lived but inefficient quantum memories have been demonstrated so far. Here we report a high-performance quantum memory in which long lifetime and high retrieval efficiency meet for the first time. By placing a ring cavity around an atomic ensemble, employing a pair of clock states, creating a long-wavelength spin wave, and arranging the setup in the gravitational direction, we realize a quantum memory with an intrinsic spin wave to photon conversion efficiency of 73(2)% together with a storage lifetime of 3.2(1) ms. This realization provides an essential tool towards scalable linear-optical quantum information processing.Comment: 6 pages, 4 figure