Next-generation sequencing approaches in microbiome research have allowed surveys of microbial communities, their genomes, and their functions with higher sensitivity than ever before. However, this ...sensitivity is a double-edged sword because these tools also efficiently detect contaminant DNA and cross-contamination, which can confound the interpretation of microbiome data. Therefore, there is an urgent need to integrate key controls into microbiome research to improve the integrity of microbiome studies. Here, we review how contaminant DNA and cross-contamination arise within microbiome studies and discuss their negative impacts, especially during the analysis of low microbial biomass samples. We then identify several key measures that researchers can implement to reduce the impact of contaminant DNA and cross-contamination during microbiome research. We put forward a set of minimal experimental criteria, the ‘RIDE’ checklist, to improve the validity of future low microbial biomass research.
There is increasing interest in applying metagenomic techniques to find correlations between microorganisms and disease.
Metagenomic techniques are highly sensitive and can detect contaminant DNA (DNA from sources other than the samples under study) and cross-contamination (DNA exchange between samples).
Recent studies have shown that contaminant DNA and cross-contamination can confound metagenomic studies, especially for sample types that have low microbial biomass.
There is an urgent need for the field to adopt authentication criteria to prevent future metagenomic studies from falling prey to the pitfalls of contaminant DNA and cross-contamination.
Diopside-rich rocks (diopsidites) are interlaminated with nephrite in boulders derived from metasomatic contacts developed between Pounamu Ultramafic meta-serpentinite and country rock Alpine Schist, ...Westland, New Zealand. Petrographic textures indicate that parental tremolite rock, formed by metasomatic diffusion during metamorphism, has been intensely deformed and recrystallised to alternating semi-nephrite and nephrite domains during development of a secondary crenulation cleavage. Nephrites are subsequently sequentially overprinted by porphyroblastic tremolite, diopside, then further tremolite. Crystallisation is controlled by fluctuating activities of SiO
2
, CaO and H
2
O in associated fluids. Pervasive dissolution of nephritic tremolite and crystallisation of diopside generates diopsidites containing accessory epidote, uvarovite and zincian chromite formed in equilibrium with H
2
O-rich fluids. Diopsidites are in turn overgrown by coarse grained (in places > 50 cm long) diopside crystals, interpreted to have infilled an extension fracture that formed during ongoing uplift of the Southern Alps.
The Alpine Dyke Swarm (ADS), intruding Haast Schist in the Southern Alps, New Zealand, comprises dykes, sills and diatremes of alkaline and ultramafic lamprophyres, phonolites and carbonatites. ...Intrusion peaked at ∼25 Ma during inception of dextral transtensional displacement on the Alpine Fault plate boundary. In a chamber beneath Haast River, magmas evolved by fractional crystallisation from primitive lamprophyres to phonolites, and then by liquid immiscibility to carbonatite magmas. Carbonatitic magmas coexisted with a highly sodic fluid that metasomatised adjacent quartzofeldspathic schist to aegirine-albite fenites. Carbonatites fractionated from Ca- to Fe-rich and, under late-stage, hydrothermal conditions, to Ba-Sr-REE-rich varieties. Some lamprophyres rose directly from a highly refractory spinel- or possibly garnet-spinel peridotite mantle that had been extensively metasomatised prior to the low-degree partial melting event and Cr-diopside series nodule entrainment. Al-augite series nodules give ages similar to host lamprophyres and are interpreted as deep-seated cognate cumulates. Compared to the broadly coeval basaltic-basanitic magmas of the Dunedin Volcanic Group (DVG) of East Otago, ADS magmas are enriched in volatiles, LILE, and HFSE (including REE). DVG magmas were derived from a less metasomatised mantle source, and, although undergoing extensive fractionation, failed to achieve the extreme alkali enrichment necessary for silicate melt-carbonatite immiscibility.
Modern management of acne Harris, Victoria Rebecca; Cooper, Alan J
Medical journal of Australia,
01/2017, Volume:
206, Issue:
1
Journal Article
Peer reviewed
Summary
Acne is a chronic inflammatory disease of the pilosebaceous unit resulting from androgen‐induced increased sebum production; altered keratinisation; bacterial colonisation of hair follicles ...on the face, neck, chest and back by Propionibacterium acnes; and an inflammatory response in the skin. The exact way these processes interact and the order in which they occur in the pathogenesis of acne are still unclear.
Scarring that occurs from acne, particularly severe acne, can persist a lifetime and have long lasting psychosocial effects. Depression, social isolation and suicidal ideation are frequent comorbidities in acne.
Despite the plethora of topical and systemic treatments available for acne, there is a relative lack of quality evidence for its application. Of the systemic treatments available, oral isotretinoin remains the most effective well established treatment for acne that targets all the aetiological factors.
Current guidelines for the treatment of acne are based largely on expert consensus and advocate a combination of topical agents in mild to moderate cases and reserve the use of systemic therapies for moderate to severe or refractory cases of acne. However, given the psychosocial impacts of acne, there is a strong argument for early, effective treatment with systemic therapy when topical and general measures have failed.
The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the ...multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace’s Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic.
Abstract The concept of using Photo Response Non-Uniformity (PRNU) as a reliable forensic tool to match an image to a source camera is now well established. Traditionally, the PRNU estimation ...methodologies have centred on a wavelet based de-noising approach. Resultant filtering artefacts in combination with image and JPEG contamination act to reduce the quality of PRNU estimation. In this paper, it is argued that the application calls for a simplified filtering strategy which at its base level may be realised using a combination of adaptive and median filtering applied in the spatial domain. The proposed filtering method is interlinked with a further two stage enhancement strategy where only pixels in the image having high probabilities of significant PRNU bias are retained. This methodology significantly improves the discrimination between matching and non-matching image data sets over that of the common wavelet filtering approach.
Large “anomalous” heat capacity (Δ
C
p) effects are a common feature of the thermodynamics of biomolecular interactions in aqueous solution and, as a result of the improved facility for direct ...calorimetric measurements, there is a growing body of experimental data for such effects in protein folding, protein–protein and protein–ligand interactions. Conventionally such heat capacity effects have been ascribed to hydrophobic interactions, and there are some remarkably convincing demonstrations of the usefulness of this concept. Nonetheless, there is also increasing evidence that hydrophobic interactions are not the only possible source of such effects. Here we re-evaluate the possible contributions of other interactions to the heat capacity changes to be expected for cooperative biomolecular folding and binding processes, with particular reference to the role of hydrogen bonding and solvent water interactions. Simple models based on the hydrogen-bonding propensity of water as a function of temperature give quantitative estimates of Δ
C
p that compare well with experimental observations for both protein folding and ligand binding. The thermodynamic contribution of bound waters in protein complexes is also estimated. The prediction from simple lattice models is that trapping of water in a complex should give more exothermic binding (ΔΔ
H−6 to −12 kJ mol
−1) with lower entropy (ΔΔ
S
0≈−11 J mol
−1 K
−1) and more negative Δ
C
p (by about −75 J mol
−1 K
−1) per water molecule. More generally, it is clear that significant Δ
C
p effects are to be expected for any macromolecular process involving a multiplicity of cooperative weak interactions of whatever kind.
Toxic epidermal necrolysis (TEN) is a severe cutaneous drug reaction with a mortality rate of approximately 30%. The hallmark of TEN is widespread epidermal sloughing due to keratinocyte apoptosis. ...Multiple genetic associations between TEN and specific ethnic populations have been determined. The pathophysiology of TEN has yet to be fully elucidated; however, current pathogenic models implicate Fas ligand, granulysin, and reactive oxygen species. The value of current therapies, such as intravenous immunoglobulin and corticosteroids, remains under evaluation.
Regular biological surveys are essential for informed management of freshwater ecosystems. However, current morphology-based biodiversity surveys can be invasive, time-consuming, and financially ...expensive. Recently, environmental DNA (eDNA) sequencing has been suggested as an alternative non-invasive, time- and cost-effective biological survey tool. However, eDNA sequencing tools require experimental validation in natural ecosystems before confidence in their use can be assumed. In this study, we compare fish community data obtained via eDNA metabarcoding to that of conventional fyke netting within two complex and drought-prone river systems. We also compare different eDNA sampling strategies and genetic markers for detecting rare and threatened fish species. We were able to detect 100% of the fyke net caught-species from eDNA when appropriate sampling strategies were used, including threatened and invasive species. Specifically, we found that two 1L water samples per site were insufficient for detecting less abundant taxa; however, five 1L samples per site enabled a 100% detection rate. Further, sampling eDNA from the water column appeared to be more effective for detecting fish communities than eDNA from sediments. However, on a per site basis, community discrepancies existed between the two methods, highlighting the benefits and limitations of both approaches. We demonstrate that careful interpretation of eDNA data is crucial as bioinformatic identification of sequences, without logical inference or local knowledge, can lead to erroneous conclusions. We discuss these discrepancies and provide recommendations for fish eDNA metabarcoding surveys.
•Fyke net and eDNA surveys of freshwater fish populations were compared.•Five 1L water samples enabled eDNA detection of 100% of fyke net-caught species.•Water eDNA more representative of fyke net-caught species than sediment eDNA•Multiple genetic markers increased detection success.•Discrepancies between the two methods existed on a per site basis.•Inappropriate marker choice and data interpretation can give rise to erroneous data.
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