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Hydrocarbon contaminated soils resulting from human activities pose a risk to the natural environment, including in the Arctic and Antarctic. Engineered biopiles constructed at Casey Station, Antarctica, have proven to be an effective strategy for remediating hydrocarbon contaminated soils, with active ex-situ remediation resulting in significant reductions in hydrocarbons, even in the extreme Antarctic climate. However, the use of urea-based fertilisers, whilst providing a nitrogen source for bioremediation, has also altered the natural soil chemistry leading to increases in pH, ammonium and nitrite. Monitoring of the urea amended biopiles identified rising levels of nitrite to be of particular interest, which misaligns with the long term goal of reducing contaminant levels and returning soil communities to a 'healthy' state. Here, we combine amplicon sequencing, microfluidic qPCR on field samples and laboratory soil microcosms to assess the impact of persistent nitrite accumulation (up to 60 months) on nitrifier abundances observed within the Antarctic biopiles. Differential inhibition of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) Nitrobacter and Nitrospira in the cold, urea treated, alkaline soils (pH 8.1) was associated with extensive nitrite accumulation (76 ± 57 mg N/kg at 60 months). When the ratio of Nitrospira :AOB dropped below ∼1:1, Nitrobacter was completely inhibited or absent from the biopiles, and nitrite accumulated. Laboratory soil microcosms (incubated at 7 °C and 15 °C for 9 weeks) reproduced the pattern of nitrite accumulation in urea fertilized soil at the lower temperature, consistent with our longer-term observations from the Antarctic biopiles, and with other temperature-controlled microcosm studies. Diammonium phosphate amended soil did not exhibit nitrite accumulation, and could be a suitable alternative biostimulant to avoid excessive nitrite build-up. [Display omitted] • Nitrite accumulation is observed in Antarctic soils stimulated with urea-based fertilizer. • Differential inhibition of ammonia and nitrite oxidizing bacteria is linked to high soil nitrite. • Urea fertilized microcosms reproduced soil nitrite accumulation at lower temperatures. • Diammonium phosphate (DAP) addition did not result in nitrite accumulation. • DAP fertiliser could be a suitable alternative biostimulant to avoid excessive nitrite build-up. [ABSTRACT FROM AUTHOR]

Hydrocarbon polar metabolites are gaining interest from industry and the remediation community due to their ubiquity and uncertainty around their toxicity. In this study, we used headspace-gas chromatography/mass spectrometry (HS-GC/MS) to characterize polar metabolites present in elutriates derived from uncontaminated, freshly hydrocarbon contaminated and partially remediated Antarctic soils. Elutriates represent the bioavailable fraction and may be used as a proxy for leachate runoff in environmental risk assessments. Control and contaminated soil elutriates were analysed for the presence of 12 aldehydes and two ketones, which cover a broad spectrum of metabolites, ranging from nC 2 – nC 12 carbon chain length. A total of nine aldehydes were detected in the soil elutriates. Types of aldehydes present in uncontaminated and hydrocarbon contaminated elutriates were similar. Among the polar metabolites measured in elutriates, acetaldehyde was most abundant in partially remediated soils. Microtox assays were used to determine the potential toxicity of elutriates. In addition, three aldehydes that were present at the highest concentrations in the contaminated and partially remediated soil elutriates (acetaldehyde, octanal and undecanal) were tested as single compounds. Contaminated soil elutriates tested were found to be toxic, with partially remediated elutriates less toxic than freshly contaminated elutriates. None of the three aldehydes tested separately were toxic at levels at which they were measured in elutriates. We infer that high levels of acetaldehyde in partially remediated soil due to hydrocarbon degradation highlight the potential of this metabolite as a useful chemical marker for hydrocarbon degradation under certain conditions. Microtox was sensitive to metabolites and provided a useful initial screening tool for elutriates. Unlabelled Image • Polar metabolites have a higher solubility than their parent hydrocarbons and are potentially bioavailable. • Nine aldehydes ranging from nC 2 -nC 12 were found in hydrocarbon contaminated soil elutriates. • Aldehydes could be potential chemical markers for hydrocarbon degradation. [ABSTRACT FROM AUTHOR]

Somatic hypermutation generates a myriad of Ab mutants in Ag-specific B cells, from which high-affinity mutants are selected. Chickens, sheep, and rabbits use nontemplated point mutations and templated mutations via gene conversion to diversify their expressed Ig loci, whereas mice and humans rely solely on untemplated somatic point mutations. In this study, we demonstrate that, in addition to untemplated point mutations, templated mutagenesis readily occurs at the murine and human Ig loci. We provide two distinct lines of evidence that are not explained by the Neuberger model of somatic hypermutation: 1) across multiple data sets there is significant linkage disequilibrium between individual mutations, especially among close mutations, and 2) among those mutations, those <8 bp apart are significantly more likely to match microhomologous regions in the IgHV repertoire than predicted by the mutation profiles of somatic hypermutation. Together, this supports the role of templated mutagenesis during somatic diversification of Ag-activated B cells. [ABSTRACT FROM AUTHOR]

Reconstructed Holocene lake-level curves from two saline, hydrologically closed maar crater lakes in southwestern Victoria, Australia, show near synchronous lake-level changes throughout the Holocene. We show that lake levels, reconstructed from sediment particle size and ostracod valve chemistry (δ18O and Sr/Ca) have undergone rapid (<100 yr), large (>10 m) fluctuations throughout the Holocene. Finer sampling resolution shows a more sensitive response to Holocene climate than was previously presented for Lake Keilambete. Both maar crater lakes show a short-lived maximum in Holocene lake levels around 7.2 ka. The period of lake filling leading to peak lake levels matches the phase of most effective precipitation (7.4–7.0 ka) reconstructed from a high-resolution speleothem record from northern Tasmania. Water levels declined in both lakes during the mid Holocene, with a more substantive decline after ~5 ka which coincides with the end of the Southern Hemisphere hypsithermal. Water levels continued to oscillate with a periodicity of around 300–700 years, before reaching a late-Holocene nadir around 1.8 ka (Keilambete) and 1.3 ka (Gnotuk). The trend and periodicity of oscillations in the maar water levels show commonalities to δD in the Dome C ice core, and suggest that temperature may be a significant component in influencing the Precipitation/Evaporation (P/E) ratio in southeastern Australia during the Holocene. [ABSTRACT FROM AUTHOR]

Abstract: Reconstructions of primary productivity at low latitudes have been the focus of several studies to better understand how the export of nutrient-rich, intermediate Southern Ocean (SO) waters influences productivity at these latitudes. This was triggered by the general observation of minima in the planktonic foraminiferal δ13C values during deglaciations, which was interpreted as an isotopic signal of intermediate SO waters, together with a concomitant increase in diatom productivity at some equatorial sites. However, the impact of these SO waters on productivity at higher latitudes is not well constrained. Here, we compare a high-resolution planktonic foraminiferal δ13C record with total organic carbon and biomarker records for Proboscia diatoms and haptophytes in marine sediments from offshore Southeastern Australia. The planktonic foraminiferal δ13C record shows distinct minima during deglaciations and the Marine Isotope Stage 4/3 transition, tentatively suggesting that 13C-depleted SO waters reached the coast of Southeastern Australia. However, it did not result in increased productivity during these periods. Instead, the highest primary productivity period, as indicated by total organic carbon and alkenone accumulation rates, occurred during the Last Glacial Maximum while Proboscia diatoms mainly proliferated during interglacials and Marine Isotope Stage 3 matching periods of increased diatom productivity in some sites of the Eastern Equatorial Pacific. Our study suggests that increased primary productivity offshore Southeastern Australia was mainly due to stronger westerly winds during glacial periods while Proboscia diatom productivity was probably controlled by the transport of silicic acid to this area. [Copyright &y& Elsevier]

ABSTRACT Hydrodynamical simulations of star formation have stimulated a need to develop fast and robust algorithms for evaluating radiative cooling. Here we undertake a critical evaluation of what is currently a popular method for prescribing cooling in smoothed particle hydrodynamical simulations, i.e. the polytropic cooling due originally to Stamatellos et al. This method uses the local density and potential to estimate the column density and optical depth to each particle and then uses these quantities to evaluate an approximate expression for the net radiative cooling. We evaluate the algorithm by considering both spherical and disc-like systems with analytic density and temperature structures. In spherical systems, the total cooling rate computed by the method is within around 20 per cent for the astrophysically relevant case of opacity dominated by ice grains and is correct to within a factor of order unity for a range of opacity laws. In disc geometry, however, the method systematically underestimates the cooling by a large factor at all heights in the disc. For the self-gravitating disc studied, we find that the method underestimates the total cooling rate by a factor of ∼ 200. This discrepancy may be readily traced to the method's systematic overestimate of the disc column density and optical depth, since (being based only on the local density and potential) it does not take into account the low column density route for photon escape normal to the disc plane. We note that the discrepancy quoted above applies in the case that the star's potential is not included in the column density estimate and that even worse agreement is obtained if the full (star plus disc) potential is employed. These results raise an obvious caution about the method's use in disc geometry whenever an accurate cooling rate is required, although we note that there are situations where the discrepancies highlighted above may not significantly affect the global outcome of simulations. Finally, we draw attention to our introduction of an analytic self-gravitating disc structure that may be of use in the calibration of future cooling algorithms. [ABSTRACT FROM AUTHOR]

Abstract: A 4m long core taken from the freshwater Blue Lake crater near the township of Mount Gambier in southeastern South Australia provided a high-resolution palaeoclimatic record for the last six millennia. Accelerator Mass Spectrometry (AMS) radiocarbon (14C) dates were obtained from organic plant fibres and biogenic carbonates from the laminated sequence of the core and from a modern water sample. Large discrepancies between the radiocarbon ages determined from plant fibres and biogenic carbonates indicate the presence of a time-variable lacustrine reservoir, which is consistent with what is known of the lake''s hydrology. Ostracod assemblages, associated with stable isotope (δ13C, δ18O) analyses and, in combination with Mg/Ca, Sr/Ca and Na/Ca analyses done on ostracod valves, infer salinity, temperature and water level changes in Blue Lake over the last 6 millenia. The influence of local aquifers through time has also been determined from the Na/Ca of ostracod valves. Approximately 900year cycles are evident in the δ13C record from 5.4ka to 1.8ka. The history of Blue Lake records an initial period of high hydrological variability around 6ka, becoming increasingly deeper as groundwater flowed into the basin. By 4ka, the lake had reached steady state with the lake level fluctuating by as much as 9m, although significant geochemical variations represent temperature fluctuations until European settlement near the lake in 1839. [Copyright &y& Elsevier]

Focuses on the tangent lines of a conic selection. Reference to the work of Mikko Stenlund on parabolas; Inadequacy of certain features of the bisection theorem; Form of the curve; Elimination of the tangent angle; Characterization of a conic section.

Discusses the logarithmic parameter called rapidity and the generalization of rapidity called vibracy. Usefulness of logarithmic parameters in describing translational and gravitational states of some systems; Concept of rapidity; Natural way of getting additive relation.

Overgeneralization and a lack of baseline data for microorganisms in high‐latitude environments have restricted the understanding of the microbial response to climate change, which is needed to establish Antarctic conservation frameworks. To bridge this gap, we examined over 17,000 sequence variants of bacteria and microeukarya across the hyperarid Vestfold Hills and Windmill Islands regions of eastern Antarctica. Using an extended gradient forest model, we quantified multispecies response to variations along 79 edaphic gradients to explore the effects of change and wind‐driven dispersal on community dynamics under projected warming trends. We also analyzed a second set of soil community data from the Windmill Islands to test our predictions of major environmental tipping points. Soil moisture was the most robust predictor for shaping the regional soil microbiome; the highest rates of compositional turnover occurred at 10–12% soil moisture threshold for photoautotrophs, such as Cyanobacteria, Chlorophyta, and Ochrophyta. Dust profiles revealed a high dispersal propensity for Chlamydomonas, a microalga, and higher biomass was detected at trafficked research stations. This could signal the potential for algal blooms and increased nonendemic species dispersal as human activities increase in the region. Predicted increases in moisture availability on the Windmill Islands were accompanied by high photoautotroph abundances. Abundances of rare oligotrophic taxa, such as Eremiobacterota and Candidatus Dormibacterota, which play a crucial role in atmospheric chemosynthesis, declined over time. That photosynthetic taxa increased as soil moisture increased under a warming scenario suggests the potential for competition between primary production strategies and thus a more biotically driven ecosystem should the climate become milder. Better understanding of environmental triggers will aid conservation efforts, and it is crucial that long‐term monitoring of our study sites be established for the protection of Antarctic desert ecosystems. Furthermore, the successful implementation of an improved gradient forest model presents an exciting opportunity to broaden its use on microbial systems globally. [ABSTRACT FROM AUTHOR]

Background We report clinical, epidemiological, and laboratory features of a large diarrhea outbreak caused by a novel Cryptosporidium hominis subtype during British military training in Kenya between February and April 2022. Methods Data were collated from diarrhea cases, and fecal samples were analyzed on site using the multiplex polymerase chain reaction (PCR) BioFire FilmArray. Water was tested using Colilert kits (IDEXX, UK). DNA was extracted from feces for molecular characterization of Cryptosporidium A135 , Lib13 , ssu rRNA , and gp60 genes. Results One hundred seventy-two of 1200 (14.3%) personnel at risk developed diarrhea over 69 days. One hundred six primary fecal samples were tested, and 63/106 (59.4%; 95% CI, 0.49%–0.69%) were positive for Cryptosporidium spp. Thirty-eight had Cryptosporidium spp. alone, and 25 had Cryptosporidium spp. with ≥1 other pathogen. A further 27/106 (25.5%; 95% CI, 0.18%–0.35%) had non- Cryptosporidium pathogens only, and 16/106 (15.1%; 95% CI, 0.09%–0.23%) were negative. C. hominis was detected in 58/63 (92.1%) Cryptosporidium spp.–positive primary samples, but the others were not genotypable. Twenty-seven C. hominis specimens were subtypable; 1 was gp60 subtype IeA11G3T3, and 26 were an unusual subtype, ImA13G1 (GenBank accession OP699729), supporting epidemiological evidence suggesting a point source outbreak from contaminated swimming water. Diarrhea persisted for a mean (SD) of 7.6 (4.6) days in Cryptosporidium spp. cases compared with 2.3 (0.9) days in non- Cryptosporidium cases (P =.001). Conclusions Real-time multiplex PCR fecal testing was vital in managing this large cryptosporidiosis outbreak. The etiology of a rare C. hominis gp60 subtype emphasizes the need for more genotypic surveillance to identify widening host and geographic ranges of novel C. hominis subtypes. [ABSTRACT FROM AUTHOR]

Human activity in the Polar Regions has resulted in petroleum contamination of soils. In this context, subantarctic islands are a unique management challenge for climatic, biological and logistical reasons. In this review we identify the main abiotic factors affecting petroleum-contaminated soils in the subantarctic environment, the primary effects of such contamination on biota, and lessons learned with regards to remediation techniques in this region. The sensitivity of biota to contamination depends on organism life stage, on soil properties, and on the degree of contaminant weathering. Initial studies using species endemic to subantarctic islands suggest that for fresh diesel fuel, sensitivities may range between 103 and 20 000 mg total petroleum hydrocarbons (TPH) kg −1 soil. Diesel that has undergone a short period of weathering is generally more toxic, with sensitivities ranging between 52 and 13 000 mg TPH kg −1 soil for an earthworm and a grass respectively (based on EC 20 and IC 50 values). A sufficient body of data from which to develop remediation targets for existing spills in the region does not yet exist for the region, but there has been a recent increase in research attention to address this data gap. A range of remediation methods have also now been trialled, and techniques such as in-ground aeration and nutrient addition have achieved some success. Passive management techniques such as permeable reactive barriers and phytoremediation are in preliminary stages of investigation for the region and show promise, not least because they cause less collateral disturbance than other methods. [ABSTRACT FROM AUTHOR]

HIV-1 transmission is associated with a severe bottleneck in which a limited number of variants from a pool of genetically diverse quasispecies establishes infection. The IAVI protocol C cohort of discordant couples, female sex workers, other heterosexuals and men who have sex with men (MSM) present varying risks of HIV infection, diverse HIV-1 subtypes and represent a unique opportunity to characterize transmitted/founder viruses (TF) where disease outcome is known. To identify the TF, the HIV-1 repertoire of 38 MSM participants' samples was sequenced close to transmission (median 21 days post infection, IQR 18–41) and assessment of multivariant infection done. Patient derived gag genes were cloned into an NL4.3 provirus to generate chimeric viruses which were characterized for replicative capacity (RC). Finally, an evaluation of how the TF virus predicted disease progression and modified the immune response at both acute and chronic HIV-1 infection was done. There was higher prevalence of multivariant infection compared with previously described heterosexual cohorts. A link was identified between multivariant infection and replicative capacity conferred by gag, whereby TF gag tended to be of lower replicative capacity in multivariant infection (p = 0.02) suggesting an overall lowering of fitness requirements during infection with multiple variants. Notwithstanding, multivariant infection was associated with rapid CD4+ T cell decline and perturbances in the CD4+ T cell and B cell compartments compared to single variant infection, which were reversible upon control of viremia. Strategies aimed at identifying and mitigating multivariant infection could contribute toward improving HIV-1 prognosis and this may involve strategies that tighten the stringency of the transmission bottleneck such as treatment of STI. Furthermore, the sequences and chimeric viruses help with TF based experimental vaccine immunogen design and can be used in functional assays to probe effective immune responses against TF. Author summary: The development of a safe and effective HIV-1 vaccine alongside cure strategies is a major public health concern and requires in-depth knowledge of the HIV-1 populations that establish infection. Here we sequenced the HIV genetic populations present during the acute stage of HIV-1 infection in 38 Men who have sex with men (MSM) and identified the transmitted/founder variant's sequence. We then cloned the gag gene from each patient's transmitted/founder gag sequences in both single and multiple variant infection into a common, lab-adapted virus and measured the replicative capacity it conferred on this virus. Finally, cellular immune responses were compared between single variant and multiple variant infection at 0–3, 6–9 and 24–30 months after infection. We observed a higher frequency of multivariant infection in MSM than has been previously described in heterosexually infected participants, and this was associated with faster decline of CD4+ T cells and perturbances in the CD4+ T cell and the B cell compartment. Moreover, the replicative capacity conferred by gag was lower in multivariant infection, suggesting a less stringent transmission bottleneck that allowed for less fit variants to establish infection. These results suggest that strategies to tighten the stringency of the transmission bottleneck may be of benefit to patients by reducing the likelihood of multivariant transmission and potentially slowing down disease progression. [ABSTRACT FROM AUTHOR]

The HIV-1 reservoir consists of latently infected cells that persist despite antiretroviral therapy (ART). Elucidating the proviral genetic composition of the reservoir, particularly in the context of pre-therapy viral diversity, is therefore important to understanding reservoir formation and the persistence of latently infected cells. Here we investigate reservoir proviral variants from 13 Zambian acutely-infected individuals with additional pre-therapy sampling for a unique comparison to the ART-naïve quasispecies. We identified complete transmitted/founder (TF) viruses from seroconversion plasma samples, and additionally amplified and sequenced HIV-1 from plasma obtained one year post-infection and just prior to ART initiation. While the majority of proviral variants in the reservoir were most closely related to viral variants from the latest pre-therapy time point, we also identified reservoir proviral variants dating to or near the time of infection, and to intermediate time points between infection and treatment initiation. Reservoir proviral variants differing by five or fewer nucleotide changes from the TF virus persisted during treatment in five individuals, including proviral variants that exactly matched the TF in two individuals, one of whom had remained ART-naïve for more than six years. Proviral variants during treatment were significantly less divergent from the TF virus than plasma variants present at the last ART-naïve time point. These findings indicate that reservoir proviral variants are archived throughout infection, recapitulating much of the viral diversity that arises throughout untreated HIV-1 infection, and strategies to target and reduce the reservoir must therefore permit for the clearance of proviruses encompassing this extensive diversity. Author summary: Despite reducing viremia to levels below the limit of detection in standard assays, effective antiretroviral therapy (ART) does not eradicate cells latently infected with HIV-1. These cells serve as a reservoir for viral rebound if therapy is interrupted; thus, understanding the composition of the reservoir may yield further targets for HIV-1 cure strategies. We have taken a genetic approach to elucidating the reservoir in 13 Zambian subtype C seroconvertors who were followed longitudinally through ART initiation and virologic suppression. In five of the 13 individuals, provirus sequences identical to or differing by five or fewer nucleotides from the transmitted/founder virus were detected, indicating archiving and persistence of early infection variants for more than six years following infection. While the majority of proviral variants in latently infected cells were most closely related to plasma virus circulating immediately prior to treatment initiation, additional variants dating to intermediate time points in the infection were also observed. These findings demonstrate that virus is archived during all stages of ART-naïve infection, and these variants persist throughout ART. HIV-1 cure strategies to eliminate the reservoir must address the broad genetic diversity of a within-host proviral quasispecies including variants archived from acute through chronic infection. [ABSTRACT FROM AUTHOR]

Several well-dated and high-resolution, multi-proxy Holocene palaeoclimatic records have recently emerged that permit a cross-continent comparison of climatic changes in Australia. This synthesis seeks to compare these records with recently published records from southern Australia and investigate the role of far-field teleconnections that have played in the mid to late Holocene climatic history of the region. The modern climate of southeastern Australia (SEA) is influenced by the Indian Ocean sector of the Southern Annular Mode (IOS-SAM), the El Niño Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD) and contrasts with southwestern Australia (SWA), which is predominantly influenced by variations in the IOS-SAM. Both regions have undergone a period of increasing aridity through the second half of the Holocene in response to the southerly migration of the mean position of the Inter-Tropical Convergence Zone (ITCZ) and the southerly migration of the IOS-SAM. Comparison of the palaeorecords stemming from both SEA and SWA suggests that the SWA record differs from the climate recorded from SEA from approximately 5.6ka. This difference is ascribed to an increased influence of large-scale climate drivers including the IOD and ENSO variability in SEA, which have negligible impact on the climate of SWA. Throughout the Holocene, the southerly migration of the ITCZ results in a weaker Asian summer monsoon. However, the rate of Asian summer monsoon weakening slowed during the middle Holocene and this coincides with a larger sea-surface temperature gradient across the equatorial Indian Ocean that resulted in a prolonged mode of positive IOD and a period of significantly increased evaporation in SEA. Those phenomena engendered a general decline in the lake levels in SEA, which is not seen in SWA as this region was not significantly affected by the IOD throughout the Holocene. This positive IOD period lasted until ~4.3ka, before a return to the strengthening (weakening) of the Australian (Asian) summer monsoon conditions that resulted in a southward shift of the ITCZ during the austral winter. The southerly shift in the ITCZ was associated with a more southerly mean position of the IOS-SAM and drier conditions for SEA and SWA. The climate affecting SEA after 4.3ka coincides with an increasing incidence and strengthening of the El Niño (non-El Niño or La Niña) mode coupled with positive (negative) modes of the IOD that resulted in a net deficit (excess) of water. The driest phase in SEA occurs at ca. 1.8ka, when far-field palaeoclimate records indicate a peak in El Niño intensity, although the impact of the IOD cannot be discounted. Conversely, both the IOD and ENSO phenomena do not affect the climate of SWA, thus leading to significant differences in the climate across the southern margin of the Australian continent. [ABSTRACT FROM AUTHOR]