scholarly journals Simultaneous quantification of Vibrio metoecus and Vibrio cholerae with its O1 serogroup and toxigenic subpopulations in environmental reservoirs

2019 ◽  
Author(s):  
Tania Nasreen ◽  
Nora A. S. Hussain ◽  
Mohammad Tarequl Islam ◽  
Fabini D. Orata ◽  
Paul C. Kirchberger ◽  
...  
Keyword(s):  
Opportunistic Infections ◽  
Limit Of Detection ◽  
Spatial Scales ◽  
Genetic Material ◽  
Size Fraction ◽  
Environmental Water ◽  
Close Relative ◽  
Toxin Gene ◽  
Actual Distribution ◽  
Temporal And Spatial

ABSTRACTVibrio metoecus is a recently described and little studied causative agent of opportunistic infections in humans, often coexisting with V. cholerae in aquatic environments. However, the relative abundance of V. metoecus with V. cholerae and their population dynamics in aquatic reservoirs is still unknown. We developed a multiplex qPCR assay with a limit of detection of three copies per reaction to simultaneously quantify total V. metoecus and V. cholerae abundance, as well as the toxigenic and O1 serogroup subpopulations of V. cholerae from environmental samples. Four different genes were targeted as specific markers for individual Vibrio species or subpopulations; viuB, a gene encoding a vibriobactin utilization protein, was used to quantify the total V. cholerae population. The cholera toxin gene ctxA provided an estimation of toxigenic V. cholerae abundance, while the rfbO1 gene specifically detected and quantified V. cholerae belonging to the O1 serogroup, which includes almost all lineages of the species responsible for the majority of past and ongoing cholera pandemics. To measure V. metoecus abundance, the gene mcp, encoding methyl accepting chemotaxis protein, was used. Marker specificity was confirmed by testing several isolates of V. cholerae and V. metoecus alongside negative controls of isolates within and outside of the Vibrio genus. Analysis of environmental water samples collected from four different geographic locations including cholera-endemic (Dhaka, Kuakata and Mathbaria in Bangladesh) and non-endemic (Oyster Pond in Falmouth, Massachusetts, USA) regions showed that V. metoecus was only present in the USA site, recurring seasonally. Within the coastal USA site, the non-toxigenic O1 serogroup represented up to ∼18% of the total V. cholerae population. V. cholerae toxigenic O1 serogroup was absent or present in low abundance in coastal Bangladesh (Kuakata and Mathbaria) but constituted a relatively high proportion of the total V. cholerae population sustained throughout the year in inland Bangladesh (Dhaka). A preference for host/particle attachment was observed, as the majority of cells from both Vibrio species (>90%) were identified in the largest water size fraction sampled, composed of particles or organisms >63 μm and their attached bacteria. This is the first study to apply a culture-independent method to quantify V. cholerae or V. metoecus directly in environmental reservoirs of areas endemic and non-endemic for cholera on significant temporal and spatial scales.SIGNIFICANCECholera is a life-threatening disease that requires immediate intervention; it is of prime importance to have fast, accurate and sensitive means to detect V. cholerae. Consistent environmental monitoring of the abundance of V. cholerae along with its toxigenic and O1 serogroup subpopulations could facilitate the determination of the actual distribution of this organism in aquatic reservoirs and thus help to predict an outbreak before it strikes. The lack of substantial temporal and spatial environmental sampling, along with specific quantitative measures, has made this goal elusive so far. The same is true for V. metoecus, a close relative of V. cholerae which has been associated with several clinical infections and could likely pose an emerging threat, readily exchanging genetic material with its more famous relative.

Improving Mycobacterium spp. detection in water: a new methodological proposal

2004 ◽  
Vol 4 (2) ◽  
pp. 103-106
Author(s):  
R. Santos ◽  
S. Gonçalves ◽  
F. Macieira ◽  
F. Oliveira ◽  
R. Rodrigues ◽  
...  
Keyword(s):  
Water Samples ◽  
Recovery Rate ◽  
Opportunistic Infections ◽  
Environmental Water ◽  
Environmental Water Samples ◽  
Sample Treatment ◽  
Detection Time ◽  
Fast Detection ◽  
Enrichment Step ◽  
Mycobacterium Spp

In recent years, non-tuberculous mycobacteria (NTM), once considered merely environmental saprophytes, have emerged as a major cause of opportunistic infections. There is no evidence of human-to-human transmission but they have been found in several environmental water samples. It is, therefore, of the utmost importance to develop methods of rapidly and accurately detecting non-tuberculous mycobacteria in water samples. To obtain a maximum recovery rate and a reduction of Mycobacterium spp. detection time in water samples, different decontamination, enrichment procedures and antibiotics supplements were tested before the inoculation into the Bactec® system. The proposed method of sample treatment (decrease in the decontamination time, followed for a peptone pre-enrichment step and an aztreonam and cefepime supplement) before the inoculation into the Bactec® system proved to be a good option for reliable and fast detection of Mycobacterium spp. in water samples.

Larval Feeding: Mechanisms, Rates, and Performance in Nature

2018 ◽  
Keyword(s):  
Marine Invertebrates ◽  
Spatial Scales ◽  
Size Spectrum ◽  
Larval Feeding ◽  
Natural Habitats ◽  
Feeding Mechanism ◽  
Temporal And Spatial ◽  
And Performance ◽  
Bioenergetics Models ◽  
Many Particles

Larvae of many marine invertebrates must capture and ingest particulate food in order to develop to metamorphosis. These larvae use only a few physical processes to capture particles, but implement these processes using diverse morphologies and behaviors. Detailed understanding of larval feeding mechanism permits investigators to make predictions about feeding performance, including the size spectrum of particles larvae can capture and the rates at which they can capture them. In nature, larvae are immersed in complex mixtures of edible particles of varying size, density, flavor, and nutritional quality, as well as many particles that are too large to ingest. Concentrations of all of these components vary on fine temporal and spatial scales. Mechanistic models linking larval feeding mechanism to performance can be combined with data on food availability in nature and integrated into broader bioenergetics models to yield increased understanding of the biology of larvae in complex natural habitats.

Humans and the Environment

2013 ◽  
Keyword(s):  
Spatial Scales ◽  
Empirical Studies ◽  
Human Action ◽  
Cultural Practice ◽  
Environmental Archaeology ◽  
Archaeological Data ◽  
Temporal And Spatial ◽  
Global And Local ◽  
The Relationship ◽  
The Way

The environment has always been a central concept for archaeologists and, although it has been conceived in many ways, its role in archaeological explanation has fluctuated from a mere backdrop to human action, to a primary factor in the understanding of society and social change. Archaeology also has a unique position as its base of interest places it temporally between geological and ethnographic timescales, spatially between global and local dimensions, and epistemologically between empirical studies of environmental change and more heuristic studies of cultural practice. Drawing on data from across the globe at a variety of temporal and spatial scales, this volume resituates the way in which archaeologists use and apply the concept of the environment. Each chapter critically explores the potential for archaeological data and practice to contribute to modern environmental issues, including problems of climate change and environmental degradation. Overall the volume covers four basic themes: archaeological approaches to the way in which both scientists and locals conceive of the relationship between humans and their environment, applied environmental archaeology, the archaeology of disaster, and new interdisciplinary directions.The volume will be of interest to students and established archaeologists, as well as practitioners from a range of applied disciplines.

scholarly journals 8-Day and Daily Maximum and Minimum Air Temperature Estimation via Machine Learning Method on a Climate Zone to Global Scale

2021 ◽  
Vol 13 (12) ◽  
pp. 2355
Author(s):  
Linglin Zeng ◽  
Yuchao Hu ◽  
Rui Wang ◽  
Xiang Zhang ◽  
Guozhang Peng ◽  
...  
Keyword(s):  
Spatial Scale ◽  
Air Temperature ◽  
Spatial Scales ◽  
Model Performance ◽  
Global Scale ◽  
Scale Model ◽  
Validation Dataset ◽  
Daily Maximum ◽  
Climate Zone ◽  
Temporal And Spatial

Air temperature (Ta) is a required input in a wide range of applications, e.g., agriculture. Land Surface Temperature (LST) products from Moderate Resolution Imaging Spectroradiometer (MODIS) are widely used to estimate Ta. Previous studies of these products in Ta estimation, however, were generally applied in small areas and with a small number of meteorological stations. This study designed both temporal and spatial experiments to estimate 8-day and daily maximum and minimum Ta (Tmax and Tmin) on three spatial scales: climate zone, continental and global scales from 2009 to 2018, using the Random Forest (RF) method based on MODIS LST products and other auxiliary data. Factors contributing to the relation between LST and Ta were determined based on physical models and equations. Temporal and spatial experiments were defined by the rules of dividing the training and validation datasets for the RF method, in which the stations selected in the training dataset were all included or not in the validation dataset. The RF model was first trained and validated on each spatial scale, respectively. On a global scale, model accuracy with a determination coefficient (R2) > 0.96 and root mean square error (RMSE) < 1.96 °C and R2 > 0.95 and RMSE < 2.55 °C was achieved for 8-day and daily Ta estimations, respectively, in both temporal and spatial experiments. Then the model was trained and cross-validated on each spatial scale. The results showed that the data size and station distribution of the study area were the main factors influencing the model performance at different spatial scales. Finally, the spatial patterns of the model performance and variable importance were analyzed. Both daytime and nighttime LST had a significant contribution in the 8-day Tmax estimation on all the three spatial scales; while their contribution in daily Tmax estimation varied over different continents or climate zones. This study was expected to improve our understanding of Ta estimation in terms of accuracy variations and influencing variables on different spatial and temporal scales. The future work mainly includes identifying underlying mechanisms of estimation errors and the uncertainty sources of Ta estimation from a local to a global scale.

scholarly journals Sequential modelling of the Earth’s core magnetic field

2020 ◽  
Vol 72 (1) ◽  
Author(s):  
Guillaume Ropp ◽  
Vincent Lesur ◽  
Julien Baerenzung ◽  
Matthias Holschneider
Keyword(s):  
Magnetic Field ◽  
Prior Information ◽  
Spatial Scales ◽  
Model Parameters ◽  
International Geomagnetic Reference Field ◽  
The Earth ◽  
Temporal And Spatial ◽  
Different Sources ◽  
Original Approach ◽  
Modelling Approach

Abstract We describe a new, original approach to the modelling of the Earth’s magnetic field. The overall objective of this study is to reliably render fast variations of the core field and its secular variation. This method combines a sequential modelling approach, a Kalman filter, and a correlation-based modelling step. Sources that most significantly contribute to the field measured at the surface of the Earth are modelled. Their separation is based on strong prior information on their spatial and temporal behaviours. We obtain a time series of model distributions which display behaviours similar to those of recent models based on more classic approaches, particularly at large temporal and spatial scales. Interesting new features and periodicities are visible in our models at smaller time and spatial scales. An important aspect of our method is to yield reliable error bars for all model parameters. These errors, however, are only as reliable as the description of the different sources and the prior information used are realistic. Finally, we used a slightly different version of our method to produce candidate models for the thirteenth edition of the International Geomagnetic Reference Field.

scholarly journals Dissecting the turbulent weather driven by mechanical AGN feedback

2020 ◽  
Vol 498 (4) ◽  
pp. 4983-5002
Author(s):  
D Wittor ◽  
M Gaspari
Keyword(s):  
Feedback Loop ◽  
Spatial Scales ◽  
Self Regulation ◽  
Cosmic Time ◽  
Massive Galaxies ◽  
Temporal And Spatial ◽  
Lagrangian Tracers ◽  
Field Unit ◽  
Integral Field ◽  
Gaseous Halo

ABSTRACT Turbulence in the intracluster, intragroup, and circumgalactic medium plays a crucial role in the self-regulated feeding and feedback loop of central supermassive black holes. We dissect the 3D turbulent ‘weather’ in a high-resolution Eulerian simulation of active galactic nucleus (AGN) feedback, shown to be consistent with multiple multiwavelength observables of massive galaxies. We carry out post-processing simulations of Lagrangian tracers to track the evolution of enstrophy, a proxy of turbulence, and its related sinks and sources. This allows us to isolate in depth the physical processes that determine the evolution of turbulence during the recurring strong and weak AGN feedback events, which repeat self-similarly over the Gyr evolution. We find that the evolution of enstrophy/turbulence in the gaseous halo is highly dynamic and variable over small temporal and spatial scales, similar to the chaotic weather processes on Earth. We observe major correlations between the enstrophy amplification and recurrent AGN activity, especially via its kinetic power. While advective and baroclinc motions are always subdominant, stretching motions are the key sources of the amplification of enstrophy, in particular along the jet/cocoon, while rarefactions decrease it throughout the bulk of the volume. This natural self-regulation is able to preserve, as ensemble, the typically observed subsonic turbulence during cosmic time, superposed by recurrent spikes via impulsive anisotropic AGN features (wide outflows, bubbles, cocoon shocks). This study facilitates the preparation and interpretation of the thermo-kinematical observations enabled by new revolutionary X-ray integral field unit telescopes, such as XRISM and Athena.

Effects of seed dispersal, adult tree and seedling density on the spatial genetic structure of regeneration at fine temporal and spatial scales

2010 ◽  
Vol 7 (1) ◽  
pp. 37-48 ◽  
Author(s):  
Fabrice Sagnard ◽  
Sylvie Oddou-Muratorio ◽  
Christian Pichot ◽  
Giovanni G. Vendramin ◽  
Bruno Fady
Keyword(s):  
Genetic Structure ◽  
Seed Dispersal ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Seedling Density ◽  
Adult Tree ◽  
Temporal And Spatial

Implications of temporal and spatial scale for Atlantic salmon (Salmo salar) research

1998 ◽  
Vol 55 (S1) ◽  
pp. 9-21 ◽  
Author(s):  
Carol L Folt ◽  
Keith H Nislow ◽  
Mary E Power
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Multiple Scales ◽  
Spatial Scales ◽  
Effective Means ◽  
Research Strategies ◽  
Atlantic Salmon Salmo Salar ◽  
Temporal And Spatial ◽  
And Migration ◽  
Dependent Processes

The Atlantic salmon (Salmo salar) is a model species for studying scale issues (i.e., the extent, duration, and resolution of a study or natural process) in ecology. Major shifts in behavior and habitat use over ontogeny, along with a relatively long life span and large dispersal and migration distances, make scale issues critical for effective conservation, management, and restoration of this species. The scale over which a process occurs must be linked to the research design and we illustrate this with a discussion of resource tracking by Atlantic salmon. Identifying scale inconsistencies (e.g., when a process is evident at one scale but not another) is shown to be an effective means by which some scale-dependent processes are understood. We review the literature to assess the temporal and spatial scales used in Atlantic salmon research and find most current studies appear to sacrifice spatial and temporal extent for increased resolution. Finally, we discuss research strategies for expanding the temporal and spatial scales in salmon research, such as conducting multiple scales studies to elucidate scale inconsistencies, identifying mechanisms, and using techniques and approaches to generalize across studies and over time and space.

Crustacean zooplankton species richness: single- and multiple-year estimates

1998 ◽  
Vol 55 (7) ◽  
pp. 1573-1582 ◽  
Author(s):  
Shelley E Arnott ◽  
John J Magnuson ◽  
Norman D Yan
Keyword(s):  
Spatial Scales ◽  
Species Pool ◽  
Crustacean Zooplankton ◽  
Zooplankton Species ◽  
Asymptotic Approach ◽  
Sampling Programme ◽  
Temporal And Spatial ◽  
Shield Lakes ◽  
The Relationship ◽  
Temporal Extent

Richness estimates are dependent on the spatial and temporal extent of the sampling programme and the method used to predict richness. We assessed crustacean zooplankton richness in eight Canadian Shield lakes at different temporal and spatial scales using three methods of estimation: cumulative, asymptotic, and Chao's index. Percent species detected increased with the number of spatial, intraannual, or interannual samples taken. Single samples detected 50% of the annual species pool and 33% of the total estimated species pool. This suggests that previous estimates of zooplankton richness, based on single samples in individual lakes, are too low. Our richness estimates for individual lakes approach the total number of zooplankton found in some regions of Canada, suggesting that each lake has most taxa at some time, the majority being very rare. Single-year richness estimates provided poor predictions of multiple-year richness. The relationship between richness and environmental variables was dependent on the method of estimation and the number of samples used. We conclude that richness should be treated as an "index" rather than an absolute and sampling efforts should be standardized. We recommend an asymptotic approach to estimate zooplankton richness because the number of samples taken influenced it less.

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