Temporal Changes in the Macroinvertebrate Fauna of Two Glacial Lakes, Cootapatamba and Albina, Snowy Mountains, New South Wales

Before 2003, unique assemblages of aquatic invertebrates in Lake Cootapatamba and Lake Albina lived in a fishless environment. A sequence of events in 2003 following a large-scale bushfire in the area allowed the native Mountain Galaxias Galaxias olidus to enter Lake Cootapatamba. This study determines the extent of any temporal changes in the invertebrate assemblages of each lake and whether the introduction of fish into Lake Cootapatamba affected these assemblages. The littoral and benthic fauna of both lakes were found to have changed since the earliest studies of these lakes in 1997/1998 and 1976, respectively. In particular, there has been a large decrease in the abundance of the isopod Metaphreatoicus australis and planarians, and the gastropod Glacidorbis hedleyi and amphipod Neoniphargus sp. have apparently disappeared. The effect is greatest in the benthos and in Lake Cootapatamba, so while fish seemed to have affected some invertebrates in some habitats, other factors may be acting. Sometime since 1976, the exotic worm Lumbriculus variegatus arrived into Lake Albina. Shifts in the representation of other taxa, such as ephemeropterans, plecopterans, tricopterans, dipterans and coleopterans, are thought to reflect natural year-to-year fluctuations but more data are needed

Temporal Changes in the Macroinvertebrate Fauna of Two Glacial Lakes, Cootapatamba and Albina, Snowy Mountains, New South Wales

Before 2003, unique assemblages of aquatic invertebrates in Lake Cootapatamba and Lake Albina lived in a fishless environment. A sequence of events in 2003 following a large-scale bushfire in the area allowed the native Mountain Galaxias Galaxias olidus to enter Lake Cootapatamba. This study determines the extent of any temporal changes in the invertebrate assemblages of each lake and whether the introduction of fish into Lake Cootapatamba affected these assemblages. The littoral and benthic fauna of both lakes were found to have changed since the earliest studies of these lakes in 1997/1998 and 1976, respectively. In particular, there has been a large decrease in the abundance of the isopod Metaphreatoicus australis and planarians, and the gastropod Glacidorbis hedleyi and amphipod Neoniphargus sp. have apparently disappeared. The effect is greatest in the benthos and in Lake Cootapatamba, so while fish seemed to have affected some invertebrates in some habitats, other factors may be acting. Sometime since 1976, the exotic worm Lumbriculus variegatus arrived into Lake Albina. Shifts in the representation of other taxa, such as ephemeropterans, plecopterans, tricopterans, dipterans and coleopterans, are thought to reflect natural year-to-year fluctuations but more data are needed

High expression of IDO1 and TGF-?1 during recurrence and post infection clearance with Chlamydia trachomatis, are independent of host IFN-? response

© 2019 The Author(s). Background: Chlamydia trachomatis infections in women continue to be a major public health concern due to their high prevalence and consequent reproductive morbidities. While antibiotics are usually efficient to clear the Chlamydia, repeat infections are common and may contribute to pathological outcomes. Interferon-gamma (IFN-γ)-mediated immunity has been suggested to be protective against reinfection, and represent an important anti-chlamydial agent, primarily via the induction of indoleamine-2,3 dioxygenase 1 (IDO1) enzyme. IDO1 catalyzes the degradation of tryptophan, which can eliminate C. trachomatis infection in vitro. Here, we sought to measure IDO1 expression levels and related immune markers during different C. trachomatis infection statuses (repeated vs single infection vs post antibiotic treatment), in vitro and in vivo. Methods: In this study, we measured the expression levels of IDO1 and immune regulatory markers, transforming growth factor β1 (TGF-β1) and forkhead box P3 (FoxP3), in vaginal swab samples of C. trachomatis-infected women, with either single or repeated infection. In addition, we used an in vitro co-culture model of endometrial carcinoma cell-line and peripheral blood mononuclear cells (PBMCs) to measure the same immune markers. Results: We found that in women with repeated C. trachomatis infections vaginal IDO1 and TGF-β1 expression levels were significantly increased. Whereas, women who cleared their infection post antibiotic treatment, had increased levels of IDO1 and TGF-β1, as well as FoxP3. Similarly, using the in vitro model, we found significant upregulation of IDO1 and TGF-β1 levels in the co-culture infected with C. trachomatis. Furthermore, we found that in PBMCs infected with C. trachomatis there was a significant upregulation in IDO1 levels, which was independent of IFN-γ. In fact, C. trachomatis infection in PBMCs failed to induce IFN-γ levels in comparison to the uninfected culture. Conclusions: Our data provide evidence for a regulatory immune response comprised of IDO1, TGF-β1 and FoxP3 in women post antibiotic treatment. In this study, we demonstrated a significant increase in IDO1 expression levels in response to C. trachomatis infection, both in vivo and in vitro, without elevated IFN-γ levels. This study implicates IDO1 and TGF-β1 as part of the immune response to repeated C. trachomatis infections, independently of IFN-γ

A cancer cell-line titration series for evaluating somatic classification.

BackgroundAccurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated with normal cells confounding the available evidence for the somatic variants. Furthermore, tumours are heterogeneous so sub-clonal variants are observed at reduced allele frequencies. We present here a cell-line titration series dataset that can be used to evaluate somatic variant calling pipelines with the goal of reliably calling true somatic mutations at low allele frequencies.ResultsCell-line DNA was mixed with matched normal DNA at 8 different ratios to generate samples with known tumour cellularities, and exome sequenced on Illumina HiSeq to depths of >300×. The data was processed with several different variant calling pipelines and verification experiments were performed to assay >1500 somatic variant candidates using Ion Torrent PGM as an orthogonal technology. By examining the variants called at varying cellularities and depths of coverage, we show that the best performing pipelines are able to maintain a high level of precision at any cellularity. In addition, we estimate the number of true somatic variants undetected as cellularity and coverage decrease.ConclusionsOur cell-line titration series dataset, along with the associated verification results, was effective for this evaluation and will serve as a valuable dataset for future somatic calling algorithm development. The data is available for further analysis at the European Genome-phenome Archive under accession number EGAS00001001016. Data access requires registration through the International Cancer Genome Consortium's Data Access Compliance Office (ICGC DACO)

In vitro rescue of genital strains of Chlamydia trachomatis from interferon-γ and tryptophan depletion with indole-positive, but not indole-negative Prevotella spp.

© 2016 The Author(s). Background: The natural course of sexually transmitted infections caused by Chlamydia trachomatis varies between individuals. In addition to parasite and host effects, the vaginal microbiota might play a key role in the outcome of C. trachomatis infections. Interferon-gamma (IFN-γ), known for its anti-chlamydial properties, activates the expression of indoleamine 2,3-dioxygenase (IDO1) in epithelial cells, an enzyme that catabolizes the amino acid L- tryptophan into N-formylkynurenine, depleting the host cell's pool of tryptophan. Although C. trachomatis is a tryptophan auxotroph, urogenital strains (but not ocular strains) have been shown in vitro to have the ability to produce tryptophan from indole using the tryptophan synthase (trpBA) gene. It has been suggested that indole producing bacteria from the vaginal microbiota could influence the outcome of Chlamydia infection. Results: We used two in vitro models (treatment with IFN-γ or direct limitation of tryptophan), to study the effects of direct rescue by the addition of exogenous indole, or by the addition of culture supernatant from indole-positive versus indole-negative Prevotella strains, on the growth and infectivity of C. trachomatis. We found that only supernatants from the indole-positive strains, P. intermedia and P. nigrescens, were able to rescue tryptophan-starved C. trachomatis. In addition, we analyzed vaginal secretion samples to determine physiological indole concentrations. In spite of the complexity of vaginal secretions, we demonstrated that for some vaginal specimens with higher indole levels, there was a link to higher recovery of the Chlamydia under tryptophan-starved conditions, lending preliminary support to the critical role of the IFN-γ-tryptophan-indole axis in vivo. Conclusions: Our data provide evidence for the ability of both exogenous indole as well as supernatant from indole producing bacteria such as Prevotella, to rescue genital C. trachomatis from tryptophan starvation. This adds weight to the hypothesis that the vaginal microbiota (particularly from women with lower levels of lactobacilli and higher levels of indole producing anaerobes) may be intrinsically linked to the outcome of chlamydial infections in some women

Energy-saving compression valve of the rock drill

The relevance of the research is due to the necessity to create pneumatic rock drills with low air consumption. The article analyzes the reasons for low efficiency of percussive machines. The authors state that applying a single distribution body in the percussive mechanism does not allow carrying out a low-energy operating cycle of the mechanism. Using the studied device as an example, it is substantiated that applying a compression valve with two distribution bodies separately operating the working chambers makes it possible to significantly reduce the airflow. The authors describe the construction of a core drill percussive mechanism and the operation of a compression valve. It is shown that in the new percussive mechanism working chambers are cut off the circuit by the time when exhaust windows are opened by the piston and air is not supplied into the cylinder up to 20% of the cycle time. The air flow rate of the new mechanism was 3.8 m3/min. In comparison with the drill PK-75, the overall noise level of the new machine is lower by 8-10 dB, while the percussive mechanism efficiency is 2.3 times higher

Dysbiosis of the vaginal microbiota and higher vaginal kynurenine/tryptophan ratio reveals an association with Chlamydia trachomatis genital infections

© 2018 Ziklo, Vidgen, Taing, Huston and Timms. The natural course of Chlamydia trachomatis urogenital tract infections varies between individuals. While protective immunity can occur, some women can become reinfected, contributing to the development of severe pathology. While the reasons for these differences are unknown, an individual's response to induced interferon-γ (IFN-γ) is suggested to be critical. IFN-γ induction of the enzyme indoleamine 2,3-dioxygenase, which depletes tryptophan, may be the key. One hypothesis suggests that indole-producing bacteria in the vaginal microbiota can provide a substrate for the Chlamydia to synthesize tryptophan, rescuing the Chlamydia from host IFN-γ attack. We studied a cohort of 25 women who were either, Chlamydia negative, Chlamydia positive with a single infection, or Chlamydia positive with repeated infection, to test our hypothesis. We characterized their vaginal microbiota, cytokine response, as well as their tryptophan, kynurenine and indole concentrations directly in vaginal secretions. We found that C. trachomatis urogenital tract infections either initial or repeat infections, were associated with elevated vaginal kynurenine/tryptophan ratios, primarily as a result of elevated kynurenine levels. In addition, vaginal microbiota of community state type (CST) IV showed significantly lower vaginal tryptophan levels compared to CST I and III, which might be related to a higher abundance of indole producers found within this group. Furthermore, we found a higher abundance of indole producers in women who cleared their Chlamydia infection post antibiotic treatment. This study demonstrates for the first time in vivo, the association between high vaginal kynurenine/tryptophan ratios and C. trachomatis infections. In addition, tryptophan depletion was associated with vaginal microbiota of CST IV

Implementation of Pedestrian Meso Models in Portugal. VRU-TOO Deliverable 8.

DRIVE I Project "An Intelligent Traffic System for Vulnerable Road Users" created a computer model WLCAN1, which simulated the crossing behaviour of pedestrians on a length of urban street. Furthermore, a car-based assignment model SATURN was used to assess the effect on cars of pedestrian-friendly policies. The attitude towards this modelling work were very "Northern European" in four important senses: - The technical approach was based upon technology developed in Northern Europe for network models of cars, which are used widely throughout Northern Europe. - The behavioural sub-models used in WLCANl and SATURN were all taken from empirical results obtained in Northern Europe. - All data to feed and calibrate the models was collected at Northern European sites. - All the partners in the DRIVE I project were from Northern Europe, and so the model development automatically followed their way of thinking. The objectives of this deliverable are to assess the transferability of the modelling work of VULCANl (and subsequent updating in DRIVE 11) and SATURN to Portugal. These objectives cover both the transferability of empirically created behavioural sub-models as well as the usefulness of the technology to the practical end user

The Structure of the Littoral Invertebrate Communities of the Kosciuszko Region Lakes

The littoral macroinvertebrate assemblages of Lakes Albina, Blue, Club andCootapatamba in the Mt. Kosciuszko region were sampled by two methods: sweeps and cobble picks. Thirty-six species were collected with total abundance and species richness greatest in Lake Albina. Common species included themolluscs Pisidium kosciusko and Glacidorbis hedleyi, the crustaceans Metaphreatoicus australis and Neoniphragus n. sp., and an unidentified limnephidtrichoperan. Community structure was influenced by the nature of the substrate, with cobble sites having greater richness and abundance than boulder sites. The importance of the major taxonomic groups (crustaceans, insects and molluscs) varied with sampling method and among lakes. Crustaceans (isopods and amphipods) usually dominated in sweeps, with molluscs and insects varying in importance among lakes, while insects mostly dominated in cobble pick samples. Oligotrophic lakes are typically thought to be dominated by insects, however this study shows such lakes may appear to be dominated by insects or crustaceans depending on the sampling method used and the presence of fish