Marine environments

Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac

Chapter 13 “Marine environments” focuses on different applications of eDNA to study marine biodiversity. After a brief description of the current knowledge on DNA cycle in pelagic and benthic environments, this chapter revisits how DNA metabarcoding, and more generally environmental genomics have revolutionized the field of marine microbiology through the discovery of novel taxa and by unveiling large-scale patterns of diversity for marine bacteria, protists, and viruses. This chapter then presents recent applications of DNA metabarcoding for both basic research or biomonitoring purposes to study marine invertebrates and fish populations and diversity, as well as the detection of invasive species. Current gaps and methodological challenges are also discussed.

2020 ◽  
Author(s):  
Takahiro Nakayama ◽  
Fumie Fujisawa

Despite advances in the treatment of hormone receptor-positive, human epidermal growth factor receptor 2-negative metastatic breast cancer, the disease is rarely curable. In this review, we focus on the use of cyclin-dependent kinase (CDK) 4/6 inhibitors, examining clinical experience and the mechanisms underlying the development of resistance, and evaluating treatment options after failure to respond to CDK4/6 inhibitors. Current basic research supports the use of mammalian target of rapamycin inhibitors after CDK4/6 inhibitor failure; however, more data are needed, particularly regarding treatment sequencing. Real-world data studies may help to fill the current knowledge gap, particularly where large-scale randomized controlled studies are not feasible.


2019 ◽  
Vol 104 (11) ◽  
pp. 5372-5381 ◽  
Author(s):  
Nigel K Stepto ◽  
Alba Moreno-Asso ◽  
Luke C McIlvenna ◽  
Kirsty A Walters ◽  
Raymond J Rodgers

Abstract Context Polycystic ovary syndrome (PCOS) is a common endocrine condition affecting 8% to 13% of women across the lifespan. PCOS affects reproductive, metabolic, and mental health, generating a considerable health burden. Advances in treatment of women with PCOS has been hampered by evolving diagnostic criteria and poor recognition by clinicians. This has resulted in limited clinical and basic research. In this study, we provide insights into the current and future research on the metabolic features of PCOS, specifically as they relate to PCOS-specific insulin resistance (IR), that may affect the most metabolically active tissue, skeletal muscle. Current Knowledge PCOS is a highly heritable condition, yet it is phenotypically heterogeneous in both reproductive and metabolic features. Human studies thus far have not identified molecular mechanisms of PCOS-specific IR in skeletal muscle. However, recent research has provided new insights that implicate energy-sensing pathways regulated via epigenomic and resultant transcriptomic changes. Animal models, while in existence, have been underused in exploring molecular mechanisms of IR in PCOS and specifically in skeletal muscle. Future Directions Based on the latest evidence synthesis and technologies, researchers exploring molecular mechanisms of IR in PCOS, specifically in muscle, will likely need to generate new hypothesis to be tested in human and animal studies. Conclusion Investigations to elucidate the molecular mechanisms driving IR in PCOS are in their early stages, yet remarkable advances have been made in skeletal muscle. Overall, investigations have thus far created more questions than answers, which provide new opportunities to study complex endocrine conditions.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lucia Di Iorio ◽  
Manon Audax ◽  
Julie Deter ◽  
Florian Holon ◽  
Julie Lossent ◽  
...  

AbstractMonitoring the biodiversity of key habitats and understanding the drivers across spatial scales is essential for preserving ecosystem functions and associated services. Coralligenous reefs are threatened marine biodiversity hotspots that are challenging to monitor. As fish sounds reflect biodiversity in other habitats, we unveiled the biogeography of coralligenous reef sounds across the north-western Mediterranean using data from 27 sites covering 2000 km and 3 regions over a 3-year period. We assessed how acoustic biodiversity is related to habitat parameters and environmental status. We identified 28 putative fish sound types, which is up to four times as many as recorded in other Mediterranean habitats. 40% of these sounds are not found in other coastal habitats, thus strongly related to coralligenous reefs. Acoustic diversity differed between geographical regions. Ubiquitous sound types were identified, including sounds from top-predator species and others that were more specifically related to the presence of ecosystem engineers (red coral, gorgonians), which are key players in maintaining habitat function. The main determinants of acoustic community composition were depth and percentage coverage of coralligenous outcrops, suggesting that fish-related acoustic communities exhibit bathymetric stratification and are related to benthic reef assemblages. Multivariate analysis also revealed that acoustic communities can reflect different environmental states. This study presents the first large-scale map of acoustic fish biodiversity providing insights into the ichthyofauna that is otherwise difficult to assess because of reduced diving times. It also highlights the potential of passive acoustics in providing new aspects of the correlates of biogeographical patterns of this emblematic habitat relevant for monitoring and conservation.


2008 ◽  
Vol 20 (3) ◽  
pp. 227-244 ◽  
Author(s):  
Katrin Linse ◽  
Lisa J. Walker ◽  
David K.A. Barnes

AbstractThe Scotia Arc, linking the Magellan region with the Antarctic Peninsula, comprises young and old islands both near continents and isolated, and is the only semi-continuous link between cool temperate and Antarctic environments. It is an ideal region for studies on how marine biodiversity changes across an extended transition zone. Echinoids (sea urchins) and their associated epibionts were found across depths from 91–1045 m, with 19 species from shelf and four from slope depths. The 23 species from 38 trawls represent 31% of all echinoid species known from the Southern Ocean and 38% of the shelf/upper slope echinoids. The specimens collected comprise representatives of the five families Cidaridae, Echinidae, Temnopleuridae, Schizasteridae and Pourtalesiidae. Echinoids are probably a good model for how well we know Antarctic shelf and slope megabenthos; none of the species we report are new to science but we found nine (39%) of our study species present at new localities, some thousands of kilometres from previous findings. New biogeographic ranges are illustrated forCtenocidaris gigantea,C. nutrix,C. spinosa,Abatus curvidens,A. ingens,A. shackletoni,Amphineustes rostratus,Tripylaster philippiandPourtalesia aurorae. Southern Ocean echinoids show eurybathy as the mean depth range of our study species was 1241 m and only one was at less than 500 m. The current view of echinoid dominance of super-abundance in the shallows seems to be not transferable to shelf and slope depths as only one of 38 trawls was dominated by echinoids. Current knowledge on maximum sizes in Antarctic echinoids seems to be good as our morphometric measurements were mainly within known size ranges. Regular echinoids increased predictably in mass with increasing test length, apart fromCtenocidaris spinosa. Tissue mass of cidaroid species was ~17%, but across irregular species varied from 17.7–8.9%. No epibionts were found on irregular echinoids or Echinidae but 70 cidaroids examined carried 51 species representing ten classes. Many of these species are reported as cidaroid epibionts for the first time. Cidaroids and their epibionts constituted > 38% of the total macrofaunal richness in the trawls they were present in. Echinoids and their epibionts clearly contribute significantly to Southern Ocean biodiversity but are minor components of biomass except in the shallows.


2015 ◽  
Vol 8 (7) ◽  
pp. 2153-2165 ◽  
Author(s):  
C. E. Ivey ◽  
H. A. Holmes ◽  
Y. T. Hu ◽  
J. A. Mulholland ◽  
A. G. Russell

Abstract. An integral part of air quality management is knowledge of the impact of pollutant sources on ambient concentrations of particulate matter (PM). There is also a growing desire to directly use source impact estimates in health studies; however, source impacts cannot be directly measured. Several limitations are inherent in most source apportionment methods motivating the development of a novel hybrid approach that is used to estimate source impacts by combining the capabilities of receptor models (RMs) and chemical transport models (CTMs). The hybrid CTM–RM method calculates adjustment factors to refine the CTM-estimated impact of sources at monitoring sites using pollutant species observations and the results of CTM sensitivity analyses, though it does not directly generate spatial source impact fields. The CTM used here is the Community Multiscale Air Quality (CMAQ) model, and the RM approach is based on the chemical mass balance (CMB) model. This work presents a method that utilizes kriging to spatially interpolate source-specific impact adjustment factors to generate revised CTM source impact fields from the CTM–RM method results, and is applied for January 2004 over the continental United States. The kriging step is evaluated using data withholding and by comparing results to data from alternative networks. Data withholding also provides an estimate of method uncertainty. Directly applied (hybrid, HYB) and spatially interpolated (spatial hybrid, SH) hybrid adjustment factors at withheld observation sites had a correlation coefficient of 0.89, a linear regression slope of 0.83 ± 0.02, and an intercept of 0.14 ± 0.02. Refined source contributions reflect current knowledge of PM emissions (e.g., significant differences in biomass burning impact fields). Concentrations of 19 species and total PM2.5 mass were reconstructed for withheld observation sites using HYB and SH adjustment factors. The mean concentrations of total PM2.5 at withheld observation sites were 11.7 (± 8.3), 16.3 (± 11), 8.59 (± 4.7), and 9.2 (± 5.7) μg m−3 for the observations, CTM, HYB, and SH predictions, respectively. Correlations improved for concentrations of major ions, including nitrate (CMAQ–DDM (decoupled direct method): 0.404, SH: 0.449), ammonium (CMAQ–DDM: 0.454, SH: 0.492), and sulfate (CMAQ–DDM: 0.706, SH: 0.730). Errors in simulated concentrations of metals were reduced considerably: 295 % (CMAQ–DDM) to 139 % (SH) for vanadium; and 1340 % (CMAQ–DDM) to 326 % (SH) for manganese. Errors in simulated concentrations of some metals are expected to remain given the uncertainties in source profiles. Species concentrations were reconstructed using SH results, and the error relative to observed concentrations was greatly reduced as compared to CTM-simulated concentrations. Results demonstrate that the hybrid method along with a spatial extension can be used for large-scale, spatially resolved source apportionment studies where observational data are spatially and temporally limited.


2011 ◽  
Vol 59 (1) ◽  
pp. 70 ◽  
Author(s):  
Sapphire J. M. McMullan-Fisher ◽  
Tom W. May ◽  
Richard M. Robinson ◽  
Tina L. Bell ◽  
Teresa Lebel ◽  
...  

Fungi are essential components of all ecosystems in roles including symbiotic partners, decomposers and nutrient cyclers and as a source of food for vertebrates and invertebrates. Fire changes the environment in which fungi live by affecting soil structure, nutrient availability, organic and inorganic substrates and other biotic components with which fungi interact, particularly mycophagous animals. We review the literature on fire and fungi in Australia, collating studies that include sites with different time since fire or different fire regimes. The studies used a variety of methods for survey and identification of fungi and focussed on different groups of fungi, with an emphasis on fruit-bodies of epigeal macrofungi and a lack of studies on microfungi in soil or plant tissues. There was a lack of replication of fire treatment effects in some studies. Nevertheless, most studies reported some consequence of fire on the fungal community. Studies on fire and fungi were concentrated in eucalypt forest in south-west and south-eastern Australia, and were lacking for ecosystems such as grasslands and tropical savannahs. The effects of fire on fungi are highly variable and depend on factors such as soil and vegetation type and variation in fire intensity and history, including the length of time between fires. There is a post-fire flush of fruit-bodies of pyrophilous macrofungi, but there are also fungi that prefer long unburnt vegetation. The few studies that tested the effect of fire regimes in relation to the intervals between burns did not yield consistent results. The functional roles of fungi in ecosystems and the interactions of fire with these functions are explained and discussed. Responses of fungi to fire are reviewed for each fungal trophic group, and also in relation to interactions between fungi and vertebrates and invertebrates. Recommendations are made to include monitoring of fungi in large-scale fire management research programs and to integrate the use of morphological and molecular methods of identification. Preliminary results suggest that fire mosaics promote heterogeneity in the fungal community. Management of substrates could assist in preserving fungal diversity in the absence of specific information on fungi.


PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2157
Author(s):  
Meena Förderer ◽  
Martin R. Langer

Raja Ampat is an archipelago of about 1,500 small islands located northwest off the Bird’s Head Peninsula of Indonesia’s West Papua province. It is part of the Coral Triangle, a region recognized as the “epicenter” of tropical marine biodiversity. In the course of a large-scale survey on shallow benthic foraminifera we have discovered one new genus and five new species of recent miliolid benthic foraminifera from the highly diverse reefal and nearshore environments. The new fischerinid genusDentoplanispirinellais characterized by its planispiral coiling and by the presence of a simple tooth, that differentiate it fromPlanispirinellaWiesner. It is represented in our sample material by the new speciesDentoplanispirinella occulta. The other four species described herein areMiliolinella moia, Miliolinella undina, Triloculina kaweaandSiphonaperta hallocki.All new species are comparatively rare and occur sporadically in the sample material. Detailed morphological descriptions, scanning electron microscopy pictures of complete and dissected specimens as well as micro-computed tomography images are provided.


Micromachines ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 27
Author(s):  
Joon Hyong Cho ◽  
David Cayll ◽  
Dipankar Behera ◽  
Michael Cullinan

The demand for graphene-based devices is rapidly growing but there are significant challenges for developing scalable and repeatable processes for the manufacturing of graphene devices. Basic research on understanding and controlling growth mechanisms have recently enabled various mass production approaches over the past decade. However, the integration of graphene with Micro-Nano Electromechanical Systems (MEMS/NEMS) has been especially challenging due to performance sensitivities of these systems to the production process. Therefore, ability to produce graphene-based devices on a large scale with high repeatability is still a major barrier to the commercialization of graphene. In this review article, we discuss the merits of integrating graphene into Micro-Nano Electromechanical Systems, current approaches for the mass production of graphene integrated devices, and propose solutions to overcome current manufacturing limits for the scalable and repeatable production of integrated graphene-based devices.


Stroke ◽  
2017 ◽  
Vol 48 (suppl_1) ◽  
Author(s):  
Markus D Schirmer ◽  
Adrian V Dalca ◽  
Ramesh Sridharan ◽  
Anne-Katrin Giese ◽  
Joseph P Broderick ◽  
...  

Introduction: White matter hyperintensity volume (WMHv) is an important and highly heritable cerebrovascular phenotype; however, manual or semi-automated approaches to clinically acquired MRI analysis hinder large-scale studies in acute ischemic stroke (AIS). In this work, we develop a high-throughput, fully automated WMHv analysis pipeline for clinical fluid-attenuated inversion recovery (FLAIR) images to facilitate rapid genetic discovery in AIS. Methods: Automated WMHv extraction from multiple subjects relies on significant pre-processing of medical scans, including co-registration of the images. To reduce the effects of anisotropic voxel sizes, each FLAIR image is upsampled using bi-cubic interpolation. Brain extraction is performed using RObust Brain EXtraction (ROBEX). Images are then registered to an in-house FLAIR template using Advanced Normalization Tools (ANTs). The spatial covariation of WMH is learned through principal component analysis (PCA) of manual outlines from 100 subjects. Areas of leukoaraiosis are identified and separated from other lesions using the PCA modes. Volumes are then computed using non-interpolated slices for each subject. Standard deviation (SD) in WMHv (9 subjects; 6 raters each) is calculated as a measure of variability. Good agreement between automated and manual outlines is assessed in 358 subjects (automated WMHv within 3SD of manual WMHv). Results: As part of the MRI - Gen etics I nterface E xploration (MRI-GENIE) study, WMHv were calculated on a set of 2703 FLAIR images of patients from 12 independent AIS cohorts (sites). Results are shown in Figure 1. Comparing manual and automated WMHv shows that 88% of the automated WMHv fall within 3 SD from the manual WMHv, suggesting good agreement. Conclusion: WMHv segmentation using a fully-automated pipeline for analysis of clinical MRIs is both feasible and accurate. Ongoing analysis of the extracted WMHv is expected to advance current knowledge of risks and outcomes in AIS.


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