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Find video protocols related to scientific articles indexed in Pubmed.
Concentration dynamics and biodegradability of dissolved organic matter in wetland soils subjected to experimental warming.
Sci. Total Environ.
PUBLISHED: 06-14-2013
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Dissolved organic matter (DOM) is the most bioavailable soil organic pool. Understanding how DOM responds to elevated temperature is important for forecasting soil carbon (C) dynamics under climate warming. Here a 4.5-year field microcosm experiment was carried out to examine temporal DOM concentration dynamics in soil pore-water from six different subtropical wetlands. Results are compared between control (ambient temperature) and warmed (+5°C) treatments. UV-visible and fluorescence spectroscopy was performed to reveal DOM structural complexity at the end of the warming incubation. Elevated temperature resulted in initially (1 to 2.5years) high pore-water DOM concentrations in warmed samples. These effects gradually diminished over longer time periods. Of the spectral indices, specific UV absorbance at 280nm and humification index were significantly higher, while the signal intensity ratio of the fulvic-like to humic-like fluorescence peak was lower in warmed samples, compared to the control. Fluorescence regional integration analysis further suggested that warming enhanced the contribution of humic-like substances to DOM composition for all tested wetlands. These spectral fingerprints implied a declined fraction of readily available substrates in DOM allocated to microbial utilization in response to 4.5years of warming. As a negative feedback, decreased DOM biodegradability may have the potential to counteract initial DOM increases and alleviate C loss in water-saturated wetland soils.
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Restoration of blanket peatlands.
J. Environ. Manage.
PUBLISHED: 05-17-2013
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There is concern that ecosystem services provided by blanket peatlands have come under threat due to increasing degradation. Blanket peatlands are subject to a wide range of drivers of degradation and are topographically variable. As a result, many degradation forms can develop, including those resulting from eroding artificial drainage, incising gullies and areas of bare peat. Many degraded blanket peatlands have undergone restoration measures since the turn of the century. However, there has been little formal communication of the techniques used and their success. Using practitioner knowledge and a review of the available literature, this paper discusses the methodologies used for restoring sloping blanket peatlands. It then considers current understanding of the impact of restoration on blanket peatland ecosystem services. There is a paucity of research investigating impacts of several common restoration techniques and much more is needed if informed management decisions are to be made and funding is to be appropriately spent. Where data are available we find that restoration is largely beneficial to many ecosystem services, with improvements being observed in water quality and ecology. However, the same restoration technique does not always result in the same outcomes in all locations. The difference in response is predominantly due to the spatial and temporal heterogeneity inherent in all blanket peatlands. Peatland practitioners must take this variability into account when designing restoration strategies and monitoring impact.
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River Ecosystem Response to Prescribed Vegetation Burning on Blanket peatland.
PLoS ONE
PUBLISHED: 01-01-2013
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Catchment-scale land-use change is recognised as a major threat to aquatic biodiversity and ecosystem functioning globally. In the UK uplands rotational vegetation burning is practised widely to boost production of recreational game birds, and while some recent studies have suggested burning can alter river water quality there has been minimal attention paid to effects on aquatic biota. We studied ten rivers across the north of England between March 2010 and October 2011, five of which drained burned catchments and five from unburned catchments. There were significant effects of burning, season and their interaction on river macroinvertebrate communities, with rivers draining burned catchments having significantly lower taxonomic richness and Simpsons diversity. ANOSIM revealed a significant effect of burning on macroinvertebrate community composition, with typically reduced Ephemeroptera abundance and diversity and greater abundance of Chironomidae and Nemouridae. Grazer and collector-gatherer feeding groups were also significantly less abundant in rivers draining burned catchments. These biotic changes were associated with lower pH and higher Si, Mn, Fe and Al in burned systems. Vegetation burning on peatland therefore has effects beyond the terrestrial part of the system where the management intervention is being practiced. Similar responses of river macroinvertebrate communities have been observed in peatlands disturbed by forestry activity across northern Europe. Finally we found river ecosystem changes similar to those observed in studies of wild and prescribed forest fires across North America and South Africa, illustrating some potentially generic effects of fire on aquatic ecosystems.
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KIT mutations in ocular melanoma: frequency and anatomic distribution.
Mod. Pathol.
PUBLISHED: 04-08-2011
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KIT mutations are known to occur in ~15% of chronic sun damaged cutaneous, mucosal, and acral melanomas. Melanomas with demonstrated activating mutations in KIT or platelet-derived growth factor receptor A (PDGFRA) may benefit from treatment with tyrosine kinase inhibitors. Currently, the limited data regarding KIT mutational status in ocular melanoma suggest that activating mutations are extremely rare. PDGFRA mutational status in ocular melanoma has not been determined. Seventy-five ocular melanomas (53 choroidal, 6 iris, 11 ciliary body, and 5 conjuctival) were selected from the files of the Department of Ophthalmology. High-resolution melting curve analysis and sequencing were performed to detect mutations in KIT exons 9, 11, 13, and 17 and PDGFRA exons 12 and 18. Results of mutational analysis were correlated with anatomical site and KIT (CD117) immunohistochemistry. Eight of 75 (11%) ocular melanomas contained mutations in either the KIT or PDGFRA gene. Five of 53 (9%) choroidal melanomas were associated with mutations (KIT exon 11=3; KIT exon 17=1; PDGFRA intron 18=1). Two of six (33%) iris melanomas and a single (9%) ciliary body melanoma harbored KIT exon 11 mutations. No mutations were identified in conjunctival melanomas. The distribution of KIT and PDGFRA mutations by ocular melanoma anatomical site did not reach statistical significance (P=0.393) CD117 positivity was not predictive of KIT mutational status as only 6 of 58 (10%) CD177-positive tumors harbored KIT mutations. In addition, a KIT exon 17 mutation was identified in one CD117-negative tumor. KIT and PDGFRA mutations do occur in ocular melanomas at a frequency (11%) that is similar to acral and mucosal melanomas. Limited correlation of CD117 positivity with mutational status suggests that all ocular melanomas should undergo mutational analysis to determine if imatinib therapy is appropriate.
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Ditch blocking, water chemistry and organic carbon flux: evidence that blanket bog restoration reduces erosion and fluvial carbon loss.
Sci. Total Environ.
PUBLISHED: 02-21-2011
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The potential for restoration of peatlands to deliver benefits beyond habitat restoration is poorly understood. There may be impacts on discharge water quality, peat erosion, flow rates and flood risk, and nutrient fluxes. This study aimed to assess the impact of drain blocking, as a form of peatland restoration, on an upland blanket bog, by measuring water chemistry and colour, and loss of both dissolved (DOC) and particulate organic carbon (POC). The restoration work was designed to permit the collection of a robust experimental dataset over a landscape scale, with data covering up to 3 years pre-restoration and up to 3 years post-restoration. An information theoretic approach to data analyses provided evidence of a recovery of water chemistry towards more natural conditions, and showed strong declines in the production of water colour. Drain blocking led to increases in the E4:E6 ratio, and declines in specific absorbance, suggesting that DOC released from blocked drains consisted of lighter, less humic and less decomposed carbon. Whilst concentrations of DOC showed slight increases in drains and streams after blocking, instantaneous yields of both DOC and POC declined markedly in streams over the first year post-restoration. Attempts were made to estimate total annual fluvial organic carbon fluxes for the study site, and although errors around these estimates remain considerable, there is strong evidence of a large reduction in aquatic organic carbon flux from the peatland following drain-blocking. Potential mechanisms for the observed changes in water chemistry and organic carbon release are discussed, and we highlight the need for more detailed information, from more sites, to better understand the full impacts of peatland restoration on carbon storage and release.
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Sensitivity of blanket peat vegetation and hydrochemistry to local disturbances.
Sci. Total Environ.
PUBLISHED: 04-16-2010
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At the ecosystem scale, peatlands can be extremely resilient to perturbations. Yet, they are very sensitive to local disturbances, especially mechanical perturbations (e.g. trampling). The effects of these disturbances on vegetation, and potential effects on hydrochemical conditions along the peat surface, however, are largely unknown. We used three research tracks (paths researchers use to access their study sites) differing in time of abandonment to investigate the impact of local disturbance (trampling) on the vegetation and its short-term (< or = 2 year) recovery in a flagship research blanket peatland. Additionally, we examined the effects of local disturbance on fluvial runoff events and the concentrations of dissolved organic carbon (DOC) and particulate organic carbon (POC) in runoff water. Local disturbance heavily impacted peat vegetation, resulting in large areas of scarred and churned peat. Recovery of vascular plants along abandoned tracks was slow, but a functional Sphagnum layer re-established after just one year. The absence of vegetation elicited an increase in the number of runoff events along the tracks, by which POC runoff from the tracks increased. POC concentrations were highest in the surface water from the recently abandoned track, while they were low in the runoff water from the track abandoned longest and the undisturbed control track. We attribute this to the relatively fast recovery of the Sphagnum vegetation. DOC concentrations did not differ significantly either spatially or temporally in surface runoff or soil solution waters. While at an ecosystem scale local disturbances may be negligible in terms of carbon loss, our data points to the need for further research on the potential long-term effects of local disturbance on the vegetation, and significant effects on local scale carbon fluxes. Moreover, the effects of disturbances could be long-lasting and their role on ecosystem processes should not be underestimated.
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Genetic modeling of Li-Fraumeni syndrome in zebrafish.
Dis Model Mech
PUBLISHED: 01-16-2010
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Li-Fraumeni syndrome (LFS) is a highly penetrant, autosomal dominant, human familial cancer predisposition. Although a key role for the tumor suppressor p53 has been implicated in LFS, the genetic and cellular mechanisms underpinning this disease remain unknown. Therefore, modeling LFS in a vertebrate system that is accessible to both large-scale genetic screens and in vivo cell biological studies will facilitate the in vivo dissection of disease mechanisms, help identify candidate genes, and spur the discovery of therapeutic compounds. Here, we describe a forward genetic screen in zebrafish embryos that was used to identify LFS candidate genes, which yielded a p53 mutant (p53(I166T)) that as an adult develops tumors, predominantly sarcomas, with 100% penetrance. As in humans with LFS, tumors arise in heterozygotes and display loss of heterozygosity (LOH). This report of LOH indicates that Knudsons two-hit hypothesis, a hallmark of human autosomal dominant cancer syndromes, can be modeled in zebrafish. Furthermore, as with some LFS mutations, the zebrafish p53(I166T) allele is a loss-of-function allele with dominant-negative activity in vivo. Additionally, we demonstrate that the p53 regulatory pathway, including Mdm2 regulation, is evolutionarily conserved in zebrafish, providing a bona fide biological context in which to systematically uncover novel modifier genes and therapeutic agents for human LFS.
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Composite pheochromocytoma: a clinicopathologic and molecular comparison with ordinary pheochromocytoma and neuroblastoma.
Am. J. Clin. Pathol.
PUBLISHED: 10-30-2009
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Composite pheochromocytoma is a rare adrenal tumor composed of ordinary pheochromocytoma and other components, most frequently neuroblastic elements. Little is known about its biologic potential, therefore creating a clinical dilemma on diagnosis. This study investigates the clinical characteristics and N-myc amplification status of 4 cases of composite pheochromocytoma and compares them with selected cases of ordinary pheochromocytoma and neuroblastoma. The age range of the patients with composite pheochromocytoma was 15 to 40 years with an equal M/F ratio, including 2 patients with syndromes. None of these composite pheochromocytomas demonstrated N-myc amplification, none recurred, and there were no deaths. Of the classic pheochromocytomas, none demonstrated N-myc amplification, 2 recurred, and there were no deaths. Of the neuroblastomas, 5 (50%) of 10 showed significant N-myc amplification, and there were 4 known recurrences and 5 known deaths. These findings suggest that composite pheochromocytoma may be regarded as a histologic variant of classic pheochromocytoma.
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Lack of BRAF activating mutations in prostate adenocarcinoma: a study of 93 cases.
Appl. Immunohistochem. Mol. Morphol.
PUBLISHED: 08-19-2009
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Oncogenic activating mutations in the cytosolic serine/threonine kinase, BRAF, have been reported in a variety of neoplasms. BRAF relays signals from membrane-bound RAS downstream through the MAP/ERK (mitogen-activated protein kinase/extracellular signal-regulated kinase) signaling pathway. The presence of BRAF activating mutations suggests the importance of the MAP/ERK kinase pathway for tumor growth and points to possible therapeutic interventions. Recently, BRAF mutations were reported to characterize a series of prostate adenocarcinomas. In this study, we used DNA melting analysis with high-resolution technology to screen a series of 93 prostate carcinomas for BRAF mutations. None were found. This suggests that BRAF mutations may not play an important role in the oncogenesis or therapy of prostate adenocarcinoma.
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A critical review of hydrological data collection for assessing preservation risk for urban waterlogged archaeology: A case study from the City of York, UK.
J. Environ. Manage.
PUBLISHED: 03-16-2009
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Environmental change caused by urban development, possibly augmented by climate change, may result in accelerated decay of in situ archaeological resources. Damage may be related to changes in hydrological processes. Such archaeological resources have to be considered in environmental planning. In this paper we highlight the need for improved hydrological data from urban archaeological sites using the case study of the City of York, UK, arguably one of the most well studied and well preserved urban archaeological environments globally. We suggest that the quality of hydrological data collected during routine surveys and experimental work must be improved and standardised in order for us to produce reliable archaeological risk models for urban sites.
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Receptor tyrosine kinases in sinonasal undifferentiated carcinomas--evaluation for EGFR, c-KIT, and HER2/neu expression.
Head Neck
PUBLISHED: 03-14-2009
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Our objective was to identify the expression of epidermal growth factor receptor (EGFR), c-KIT (CD117), and HER2/neu in sinonasal undifferentiated carcinoma (SNUC).
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Can carbon offsetting pay for upland ecological restoration?
Sci. Total Environ.
PUBLISHED: 02-19-2009
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Upland peat soils represent a large terrestrial carbon store and as such have the potential to be either an ongoing net sink of carbon or a significant net source of carbon. In the UK many upland peats are managed for a range of purposes but these purposes have rarely included carbon stewardship. However, there is now an opportunity to consider whether management practices could be altered to enhance storage of carbon in upland peats. Further, there are now voluntary and regulated carbon trading schemes operational throughout Europe that mean stored carbon, if verified, could have an economic and tradeable value. This means that new income streams could become available for upland management. The Sustainable Uplands RELU project has developed a model for calculating carbon fluxes from peat soils that covers all carbon uptake and release pathways (e.g. fluvial and gaseous pathways). The model has been developed so that the impact of common management options within UK upland peats can be considered. The model was run for a decade from 1997-2006 and applied to an area of 550 km2 of upland peat soils in the Peak District. The study estimates that the region is presently a net sink of -62 ktonnes CO2 equivalent at an average export of -136 tonnes CO2 equivalent/km2/yr. If management interventions were targeted across the area the total sink could increase to -160 ktonnes CO2/yr at an average export of -219 tonnes CO2 equivalent/km2/yr. However, not all interventions resulted in a benefit; some resulted in increased losses of CO2 equivalents. Given present costs of peatland restoration and value of carbon offsets, the study suggests that 51% of those areas, where a carbon benefit was estimated by modelling for targeted action of management interventions, would show a profit from carbon offsetting within 30 years. However, this percentage is very dependent upon the price of carbon used.
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Histologic, immunohistochemical, and molecular classification of 52 IPMNs of the pancreas.
Appl. Immunohistochem. Mol. Morphol.
PUBLISHED: 01-23-2009
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Intraductal papillary mucinous neoplasms (IPMNs) of the pancreas account for approximately 5% of pancreatic neoplasms. Prognosis is superior to that of pancreatic invasive ductal carcinoma. IPMNs reveal a variety of epithelial linings expressing different mucin staining patterns and may progress along different oncogenic pathways.
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B-RAF V600E mutational analysis of fine needle aspirates correlates with diagnosis of thyroid nodules.
Otolaryngol Head Neck Surg
PUBLISHED: 01-09-2009
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A mutation of B-type RAF kinase (B-RAF) represents the most common genetic alteration in papillary thyroid cancer (PTC), possibly signifying a more aggressive biology. Fine needle aspiration (FNA) represents the most useful initial diagnostic tool of thyroid nodules. Molecular analysis of the mutation status of B-RAF in thyroid nodule FNAs may provide guidance for treatment planning.
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Phosphorus fluxes at the sediment-water interface in subtropical wetlands subjected to experimental warming: a microcosm study.
Chemosphere
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Global warming is increasingly challenging for wetland ecological function. A temperature controlled microcosm system was developed to simulate climate change scenarios of an ambient temperature (control) and an elevated temperature (+5 °C). The effects and associated mechanisms of warming on phosphorus (P) fluxes at the sediment-water interface of six subtropical wetlands were investigated. The results indicated that P fluxes were generally enhanced under the experimental warming as measured by higher P concentrations in the porewater and overlying water as well as higher benthic P fluxes. The release of P from sediment to porewater occurred more strongly and quickly in response to experimental warming compared to the subsequent upward transfer into overlying water. The average accumulative benthic P output from the tested wetlands under the experimental warming was greater by 12.9 ?g cm(-2) y(-1) (28%) for total P and 8.26 ?g cm(-2) y(-1) (25%) for dissolved reactive P, compared to the ambient scenarios. Under warming the redistribution of P fractions in sediments occurred with greater NH(4)Cl-P and lower BD-P (extracted by a bicarbonate buffered dithionite solution) accompanied by greater NaOH-P. The higher temperature enhanced total phospholipid fatty acids. A shift in the microbial community was also observed with a relative dominance of fungi (a 4.7% increase) and a relative decline (by 18%) in bacterial abundance, leading to the higher secretion of phosphatase. Comparing between wetlands, the potential P fluxes in the nutrient-enriched wetlands were less impacted by warming than the other wetland types investigated. Thus wetlands characterized by low or medium concentrations of P in sediments were more susceptible to warming compared to P-rich wetlands.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.