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Speleology in Kazakhstan

Shakalov on 04 Jul, 2018
Hello everyone!   I pleased to invite you to the official site of Central Asian Karstic-Speleological commission ("Kaspeko")   There, we regularly publish reports about our expeditions, articles and reports on speleotopics, lecture course for instructors, photos etc. ...

New publications on hypogene speleogenesis

Klimchouk on 26 Mar, 2012
Dear Colleagues, This is to draw your attention to several recent publications added to KarstBase, relevant to hypogenic karst/speleogenesis: Corrosion of limestone tablets in sulfidic ground-water: measurements and speleogenetic implications Galdenzi,

The deepest terrestrial animal

Klimchouk on 23 Feb, 2012
A recent publication of Spanish researchers describes the biology of Krubera Cave, including the deepest terrestrial animal ever found: Jordana, Rafael; Baquero, Enrique; Reboleira, Sofía and Sendra, Alberto. ...

Caves - landscapes without light

akop on 05 Feb, 2012
Exhibition dedicated to caves is taking place in the Vienna Natural History Museum   The exhibition at the Natural History Museum presents the surprising variety of caves and cave formations such as stalactites and various crystals. ...

Did you know?

That hydrostratigraphic unit is see hydrogeologic unit.?

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KarstBase a bibliography database in karst and cave science.

Featured articles from Cave & Karst Science Journals
Chemistry and Karst, White, William B.
See all featured articles
Featured articles from other Geoscience Journals
Karst environment, Culver D.C.
Mushroom Speleothems: Stromatolites That Formed in the Absence of Phototrophs, Bontognali, Tomaso R.R.; D’Angeli Ilenia M.; Tisato, Nicola; Vasconcelos, Crisogono; Bernasconi, Stefano M.; Gonzales, Esteban R. G.; De Waele, Jo
Calculating flux to predict future cave radon concentrations, Rowberry, Matt; Marti, Xavi; Frontera, Carlos; Van De Wiel, Marco; Briestensky, Milos
Microbial mediation of complex subterranean mineral structures, Tirato, Nicola; Torriano, Stefano F.F;, Monteux, Sylvain; Sauro, Francesco; De Waele, Jo; Lavagna, Maria Luisa; D’Angeli, Ilenia Maria; Chailloux, Daniel; Renda, Michel; Eglinton, Timothy I.; Bontognali, Tomaso Renzo Rezio
Evidence of a plate-wide tectonic pressure pulse provided by extensometric monitoring in the Balkan Mountains (Bulgaria), Briestensky, Milos; Rowberry, Matt; Stemberk, Josef; Stefanov, Petar; Vozar, Jozef; Sebela, Stanka; Petro, Lubomir; Bella, Pavel; Gaal, Ludovit; Ormukov, Cholponbek;
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Your search for assay (Keyword) returned 8 results for the whole karstbase:
Fungal communities on speleothem surfaces in Kartchner Caverns, Arizona, USA, , Vaughan Michael J. , Maier Raina M. , Pryor Barry M.

Kartchner Caverns, located near Benson, Arizona, USA, is an active carbonate cave that serves as the major attraction for Kartchner Caverns State Park. Low-impact development and maintenance have preserved prediscovery macroscopic cavern features and minimized disturbances to biological communities within the cave.. The goal of this study was to examine fungal diversity in Kartchner Caverns on actively-forming speleothem surfaces. Fifteen formations were sampled from five sites across the cave. Richness was assessed using standard culture-based fungal isolation techniques. A culture-independent analysis using denaturing gradient gel electrophoresis (DGGE) was used to assay evidence of community homogeneity across the cave through the separation of 18S rDNA amplicons from speleothem community DNA. The culturing effort recovered 53 distinct morphological taxonomic units (MTUs), corresponding to 43 genetic taxonomic units (GTUs) that represented 21 genera. From the observed MTU accumulation curve and the projected total MTU richness curve, it is estimated that 51 percent of the actual MTU richness was recovered. The most commonly isolated fungi belonged to the genera Penicillium, Paecilomyces, Phialophora, and Aspergillus. This culturebased analysis did not reveal significant differences in fungal richness or number of fungi recovered across sites. Cluster analysis using DGGE band profiles did not reveal distinctive groupings of speleothems by sample site. However, canonical correspondence analysis (CCA) analysis of culture-independent DGGE profiles showed a significant effect of sampling site and formation type on fungal community structure. Taken together, these results reveal that diverse fungal communities exist on speleothem surfaces in Kartchner Caverns, and that these communities are not uniformly distributed spatially. Analysis of sample saturation indicated that more sampling depth is required to uncover the full scale of mycological richness across spelothem surfaces.


Morphology of the border cave hominid ulna and humerus, 1996, Pearson O. M. , Grine F. E. ,
Hominid bones from Border Cave (BC) have been the subject of controversy with regard to the question of modern human origins. New dating assays suggest that while some of the BC remains are of comparatively recent age (i.e. < 20 kyr), several postcranial fragments derive from the Middle Stone Age (MSA) layers. Among the latter, a proximal ulna in comparable to one from the MSA at Klasies River Mouth, in that both have an archaic pattern of morphology in the relative height of the coronoid and olecranon processes. This configuration appears to characterize Neandertals, and is displayed also by more ancient African ulnae. The BC humeral diaphysis has moderately thick cortical bone, but us otherwise unremarkable. The proximal ulnar morphology might suggest that the MSA inhabitants of South Africa engaged in activities similar to those of Neandertals and other postcranially archaic hominids. If the modern-looking BC-1 cranium in contemporaneous with the BC postcranial bones, this would bear testament to the mosaic nature of human evolution. Alternatively, if BC-1 proves to be of recent derivation, and the postcrania are as old as the base of the BC MSA sequence has been claimed to be (c. 195 kyr), they might have been associated with more archaic crania (perhaps similar to Florisbad). Final resolution of these questions awaits determination of the absolute ages of the BC-1 cranium and the BC postcranial bones

Occurrence of selected herbicides and herbicide degradation products in Iowa's ground water, 1995, 1997, Kolpin D. W. , Kalkhoff S. J. , Goolsby D. A. , Sneckfahrer D. A. , Thurman E. M. ,
Herbicide compounds were prevalent in ground water across Iowa, being detected in 70% of the 106 municipal wells sampled during the summer of 1995, Herbicide degradation products were three of the four most frequently detected compounds for this study. The degradation product alachlor ethanesulfonic acid was the most frequently detected compound (65.1%), followed by atrazine (40.6%), and the degradation products deethylatrazine (34.9%), and cyanazine amide (19.8%). The corn herbicide acetochlor, first registered for widespread use in the United States in March 1994, was detected in a single water sample, No reported herbicide compound concentrations for this study exceeded current U.S. Environmental Protection Agency's maximum contaminant levels or health advisory levels for drinking water, although the herbicide degradation products examined have get to have such levels established. The occurrence of herbicide compounds had a significant, inverse relation to well depth and a significant, positive relation to dissolved-oxygen concentration. It is felt that both well depth and dissolved oxygen are acting as rough surrogates to ground-water age, with younger ground water being more likely to contain herbicide compounds. The occurrence of herbicide compounds was substantially different among the major aquifer types across Iowa, being detected in 82.5% of the alluvial, 81.8% of the bedrock/ karst region, 40.0% of the glacial-drift, and 25.0% of the bedrock/nonkarst region aquifers. The observed distribution was partially attributed to variations in general ground-water age among these aquifer types. A significant, inverse relation was determined between total herbicide compound concentrations in ground water and the average soil slope within a 2-km radius of sampled wens. Steeper soil slopes may increase the likelihood of surface runoff occurring rather than ground-water infiltration-decreasing the transport of herbicide compounds to ground water. As expected, a significant positive relation was determined between intensity of herbicide use and herbicide concentrations in ground water

Comparison of immunofluorescence assay and immunomagnetic electrochemiluminescence in detection of Cryptosporidium parvum oocysts in karst water samples, 2003, Kuczynska E. , Boyer D. G. , Shelton D. R. ,
Immunofluorescence assay (IFA) and immunomagneticelectrochemiluminescence (IM-ECL) were used for comparison of the percent recovery of Cryptosporidium parvum in environmental water samples obtained from a spring draining a karst basin. The monoclonal antibodies to C. parvum, isotype IgG3 were used for optimization of the IM-ECL protocol. The combination of biotinylated and TAG-labeled anti-C. parvum antibodies with the streptavidin beads gave a linear regression slope for log ECL vs. log fresh oocysts of 0.79 (from 5 to 5000 oocysts), which indicates a constant ECL signal per oocyst. Standard curves gave a dynamic range of 5 to 5000 oocysts/ml (fresh) and 10 to 100,000 cells/ml (4-month-old oocysts) with the maximum limit of linear detection higher than 100,000. The linear slope of 4-month-old oocysts decreased to 0.62, which indicates that ECL signal is a function of oocyst age. The experiment associated with bead storage time shows that even after 4 months of storage of the biotinylated antibodies, the complex retains the ability for binding the oocysts and generating the ECL signal. Based on the IFA results in the experiment evaluating different protocols for oocysts recovery from karst water samples, the most efficient protocol involved dispersion, followed by flotation and immunomagnetic separation (IMS) (24% recovery). The ECL results obtained in that experiment were very similar to the results obtained in the IFA method, which indicates that the IM-ECL method is accurate. Results of the IFA in the study of the prevalence of C. parvum in the groundwater showed that oocysts were present in 78% of 1 L water samples with average number of oocysts of 6.4 5.5 and ranged from 0 (13 samples) to 23.3 (2 samples). The ECL signal generated from these water samples ranged from 3771 to 622 (average 1620 465). However, the background value estimated in groundwater samples with low number of oocysts detected by IFA was highly variable and elevated (from 3702 to 272, average 1503 475). The background value as a result of nonspecific binding to beads by unidentified organic components in the water can inhibit or even completely mask the signal generated by oocysts. Our investigations showed that the IM-ECL method appears to be promising for the qualitative and quantitative detection of C parvum from the environmental water; however, the method requires further development to improve sensitivity and account for background signals. Published by Elsevier Science B.V

Cannibalism within freshwater shrimp populations (Gammarus duebeni - Crustacea: Amphipoda) from spring, riverine and subterranean habitats, Marble Arch Cave System (Northern Ireland), 2007, Wood, Thomas P Worrall And Paul J.
The paper examines cannibalism within Gammarus duebeni (Crustacea: Amphipoda) populations within surface stream, spring and cave habitats. The level of cannibalism was measured via bioassay enclosure experiments in the vicinity of the Marble Arch Cave system. The occurrence of cannibalism was found to be significantly greater within cave populations, compared to epigean spring and riverine populations. The relative length of an individual in relation to its mass (Body Mass Index) was significantly greater for riverine populations when compared to both caves and springs.

Fungal communities on speleothem surfaces in Kartchner Caverns, Arizona, USA, 2011, Vaughan M. J. , Maier R. M. , Pryor B. M.

Kartchner Caverns, located near Benson, Arizona, USA, is an active carbonate cave that serves as the major attraction for Kartchner
Caverns State Park. Low-impact development and maintenance have preserved prediscovery macroscopic cavern features and
minimized disturbances to biological communities within the cave.. The goal of this study was to examine fungal diversity in Kartchner
Caverns on actively-forming speleothem surfaces. Fifteen formations were sampled from five sites across the cave. Richness
was assessed using standard culture-based fungal isolation techniques. A culture-independent analysis using denaturing gradient
gel electrophoresis (DGGE) was used to assay evidence of community homogeneity across the cave through the separation of
18S rDNA amplicons from speleothem community DNA. The culturing effort recovered 53 distinct morphological taxonomic units
(MTUs), corresponding to 43 genetic taxonomic units (GTUs) that represented 21 genera. From the observed MTU accumulation
curve and the projected total MTU richness curve, it is estimated that 51 percent of the actual MTU richness was recovered. The
most commonly isolated fungi belonged to the genera Penicillium, Paecilomyces, Phialophora, and Aspergillus. This culturebased
analysis did not reveal significant differences in fungal richness or number of fungi recovered across sites. Cluster analysis
using DGGE band profiles did not reveal distinctive groupings of speleothems by sample site. However, canonical correspondence
analysis (CCA) analysis of culture-independent DGGE profiles showed a significant effect of sampling site and formation type on
fungal community structure. Taken together, these results reveal that diverse fungal communities exist on speleothem surfaces in
Kartchner Caverns, and that these communities are not uniformly distributed spatially. Analysis of sample saturation indicated that
more sampling depth is required to uncover the full scale of mycological richness across spelothem surfaces.


Development of a Specific Quantitative Real-Time PCR Assay to Monitor Chlorella DNA: A Case Study from Mammoth Cave National Park, Kentucky, USA , 2011, Fowler, Richard F.

Estimates of phytoplankton abundance are important parameters
watched by stewards of water quality and freshwater ecology in rivers, streams, and reservoirs. A targeted phytoplankton assay
for Chlorella DNA was developed to estimate the abundance of the predominant species of green algae in surface waters of Mammoth Cave National Park (MACA) in Kentucky, USA. The phytoplankton community in the Green River in MACA has been shown to consist of 95% Chlorella sp. (Wullschlegger et al., 2003). Chlorella 18S rRNA gene sequences were amplified and quantified using Quantitative Real-Time PCR (qPCR) with primers
specific for the family Chlorellaceae in the class Trebouxiophyceae,
order Chlorellales. Concentrations of Chlorella DNA in river water samples were measured by comparison to a standard curve generated by DNA extracted from a live laboratory culture of C. vulgaris. DNA isolated from other sources including bacteria,
amoebae, fungi, decapods, insects, cave sediment, and a different
green alga, Chlamydomonas, produced no PCR products and thus did not interfere with the detection and quantification of Chlorella DNA. The assay proved quantitative over more than four orders of magnitude with a method detection limit (MDL) of approximately 2.3 x104 cells/L. Presence or absence of Chlorella
DNA could be demonstrated at concentrations ten to 100 times lower than the calculated MDL. Chlorella was detected in lampenflora samples from three tourist trails, and Chlorella was absent from sediment samples off tourist trails that were known to contain high concentrations of bacterial DNA. Demonstration of the utility of the technique was illustrated by a case study in Mammoth Cave National Park to determine Chlorella concentrations
at various sampling sites of karst surface streams where invasive zebra mussels are a threat to native species.


The effects of UV light on the antimicrobial activities of cave actinomycetes, 2013, Rule Devon, Cheeptham Naowarat

The goal of this study was to determine whether actinomycetes isolated from a volcanic cave in western Canada could produce novel antimicrobial compounds against six multidrug- resistant pathogens when exposed to UV light. One hundred and seventy-six actinomycete strains isolated from Helmcken Falls Cave, Wells Gray Provincial Park, BC, were screened against six pathogens using the “plug assay” in UV light and no light conditions. Of the 176 strains tested, 100 or 57% of the cave actinomycete strains had antimicrobial activities against the pathogens in 124 different instances: 35 instances when exposed to UV and no light, 30 when exposed to UV light, and 59 instances when exposed to no light. The metabolites of six actinomycete strains also lost their antimicrobial activities when exposed to UV light. While the metabolites produced by these strains have yet to be determined, exposure to lighted environments may either deactivate or enhance the antimicrobial activities of cave actinomycete strains. This study represents a confirmation that cave actinomycetes are potential sources of novel antimicrobial compounds and also is the first report of the enhancement of antimicrobial activities of some cave bacteria by exposure to UV light. Further investigation of the role of UV light with respect to activation/deactivation of antimicrobial activities of cave actinomycetes is required.


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