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In JoVE (1)
- Spatial Multiobjective Optimization of Agricultural Conservation Practices using a SWAT Model and an Evolutionary Algorithm
Other Publications (21)
- Chirurgia (Bucharest, Romania : 1990)
- Chirurgia (Bucharest, Romania : 1990)
- Molecular Ecology
- Journal of Proteome Research
- The Journal of Heredity
- Proceedings. Biological Sciences / The Royal Society
- Journal of Proteomics
- Journal of Proteome Research
- Chirurgia (Bucharest, Romania : 1990)
- Current Biology : CB
- Behavioral Ecology : Official Journal of the International Society for Behavioral Ecology
- Nature Methods
- Romanian Journal of Morphology and Embryology = Revue Roumaine De Morphologie Et Embryologie
- Annals of Anatomy = Anatomischer Anzeiger : Official Organ of the Anatomische Gesellschaft
- Journal of Proteomics
- Science (New York, N.Y.)
- Anatomical Record (Hoboken, N.J. : 2007)
Articles by Adriana Valcu in JoVE
Spatial Multiobjective Optimization of Agricultural Conservation Practices using a SWAT Model and an Evolutionary Algorithm
Sergey Rabotyagov1, Todd Campbell2, Adriana Valcu2, Philip Gassman2, Manoj Jha3, Keith Schilling4, Calvin Wolter4, Catherine Kling2
1School of Environmental and Forest Sciences, University of Washington, 2Center for Agricultural and Rural Development, Department of Economics, Iowa State University, 3Department of Civil, Architectural, and Environmental Engineering, North Carolina A&T University, 4Iowa Geological and Water Survey
This work demonstrates an integration of a water quality model with an optimization component utilizing evolutionary algorithms to solve for optimal (lowest-cost) placement of agricultural conservation practices for a specified set of water quality improvement objectives. The solutions are generated using a multi-objective approach, allowing for explicit quantification of tradeoffs.
Other articles by Adriana Valcu on PubMed
Chirurgia (Bucharest, Romania : 1990). Mar-Apr, 1996 | Pubmed ID: 8924797
Chirurgia (Bucharest, Romania : 1990). Sep-Oct, 1996 | Pubmed ID: 9091077
Reduction of Proteins During Sample Preparation and Two-dimensional Gel Electrophoresis of Woody Plant Samples
Proteomics. Mar, 2006 | Pubmed ID: 16456882
Protein extraction procedure and the reducing agent content (DTT, dithioerythritol, tributyl phosphine and tris (2-carboxyethyl) phosphine (TCEP)) of the sample and rehydration buffers were optimised for European beech leaves and roots and Norway spruce needles. Optimal extraction was achieved with 100 mM DTT for leaves and needles and a mixture of 2 mM TCEP and 50 mM DTT for roots. Performing IEF in buffers containing hydroxyethyldisulphide significantly enhanced the quality of separation for all proteins except for acidic root proteins, which were optimally focused in the same buffer as extracted.
Proteomics. Jul, 2006 | Pubmed ID: 16791823
Protein extraction from plant samples is usually challenging due to the low protein content and high level of contaminants. Therefore, the 2-DE pattern resolution is strongly influenced by the procedure of sample preparation. Efficient solubilization of proteins strictly depends on the chaotrope and detergent in the extraction buffer. Despite the large number of detergents that have been developed for the use in protein extraction and IEF, there is no single compound able to efficiently extract proteins from any source. Hence, optimization has to be performed for each type of sample. We tested several chaotrope/detergent combinations to achieve optimal solubilization and separation of proteins from Norway spruce [Picea abies (L.) H. Karst.] needles and European beech (Fagus sylvatica L.) leaves and roots. The same chaotrope mixture (7 M urea, 2 M thiourea) was found to be suitable for the extraction and separation of proteins from all samples. Nonetheless, the efficiency of the surfactants tested varied between samples so that optimal extraction and separation was achieved with different detergents or combination of detergents for each sample. The 2-DE separation of spruce needle proteins was optimal in a mixture of two zwitterionic detergents (2% CHAPS and 2% decyl dimethylammonio propanesulfonate). Beech proteins were best separated in buffers containing sugar-based detergents (2% n-octyl beta-D-glucopiranoside in the case of leaf samples and 2% dodecyl maltoside for the root samples). IEF was performed in buffers with the same composition as the extraction buffer except for the root proteins that were better focused in a buffer containing 2% CHAPS.
Molecular Ecology. Dec, 2006 | Pubmed ID: 17107482
Inbreeding depression, as commonly found in natural populations, should favour the evolution of inbreeding avoidance mechanisms. If natal dispersal, the first and probably most effective mechanism, does not lead to a complete separation of males and females from a common origin, a small-scale genetic population structure may result and other mechanisms to avoid inbreeding may exist. We studied the genetic population structure and individual mating patterns in blue tits (Parus caeruleus). The population showed a local genetic structure in two out of four years: genetic relatedness between individuals (estimated from microsatellite markers) decreased with distance. This pattern was mainly caused by immigrants to the study area; these, if paired with fellow immigrants, were more related than expected by chance. Since blue tits did not avoid inbreeding with their social partner, we examined if individuals preferred less related partners at later stages of the mate choice process. We found no evidence that females or males avoided inbreeding through extra-pair copulations or through mate desertion and postbreeding dispersal. Although the small-scale genetic population structure suggests that blue tits could use a simple rule of thumb to select less related mates, females did not generally prefer more distantly breeding extra-pair partners. However, the proportion of young fathered by an extra-pair male in mixed paternity broods depended on the genetic relatedness with the female. This suggests that there is a fertilization bias towards less related copulation partners and that blue tits are able to reduce the costs of inbreeding through a postcopulatory process.
Journal of Proteome Research. Dec, 2007 | Pubmed ID: 17949049
Reliability of two-dimensional electrophoresis differential display experiments depends on the reproducibility of the separations. The contribution of biological and technical variation to the overall variance of the two-dimensional patterns was estimated based on the factors found to influence spot volume variance. The second dimension and the staining were responsible for most of the spot volume variance, while using pooled samples lowered biological variation to the level of technical variation.
Protein Polymorphism Between 2 Picea Abies Populations Revealed by 2-dimensional Gel Electrophoresis and Tandem Mass Spectrometry
The Journal of Heredity. Jul-Aug, 2008 | Pubmed ID: 18344527
In species with high gene flow and consequent low interpopulation differentiation over wide geographic ranges, differential gene expression along ecological gradients often reveals adaptive significance. We investigated potential differences in protein expression between Picea abies ecotypes adapted to contrasting altitude conditions. Protein expression patterns were compared between needles and roots of 2-month-old P. abies seedlings by means of 2-dimensional electrophoresis. Proteins exhibiting differential expression between the 2 ecotypes were analyzed by tandem mass spectrometry. A total of 19 proteins exhibited qualitative or quantitative polymorphism between the 2 populations. These proteins exhibited organ-specific expression, and the level of interpopulation protein polymorphism was organ dependent. Among differentially expressed proteins, we identified proteins involved in photosynthesis, photorespiration, root tracheary element differentiation, and transmitochondrial membrane transport. Our results show that P. abies seedlings from locally adapted ecotypes exhibit consistent differences in protein expression. The expression polymorphism of some of these proteins has potential adaptive significance.
Proceedings. Biological Sciences / The Royal Society. Oct, 2008 | Pubmed ID: 18628122
Among vertebrates, the sense of smell is mediated by olfactory receptors (ORs) expressed in sensory neurons within the olfactory epithelium. Comparative genomic studies suggest that the olfactory acuity of mammalian species correlates positively with both the total number and the proportion of functional OR genes encoded in their genomes. In contrast to mammals, avian olfaction is poorly understood, with birds widely regarded as relying primarily on visual and auditory inputs. Here, we show that in nine bird species from seven orders (blue tit, Cyanistes caeruleus; black coucal, Centropus grillii; brown kiwi, Apteryx australis; canary, Serinus canaria; galah, Eolophus roseicapillus; red jungle fowl, Gallus gallus; kakapo, Strigops habroptilus; mallard, Anas platyrhynchos; snow petrel, Pagodroma nivea), the majority of amplified OR sequences are predicted to be from potentially functional genes. This finding is somewhat surprising as one previous report suggested that the majority of OR genes in an avian (red jungle fowl) genomic sequence are non-functional pseudogenes. We also show that it is not the estimated proportion of potentially functional OR genes, but rather the estimated total number of OR genes that correlates positively with relative olfactory bulb size, an anatomical correlate of olfactory capability. We further demonstrate that all the nine bird genomes examined encode OR genes belonging to a large gene clade, termed gamma-c, the expansion of which appears to be a shared characteristic of class Aves. In summary, our findings suggest that olfaction in birds may be a more important sense than generally believed.
Heat Induced Changes in Protein Expression Profiles of Norway Spruce (Picea Abies) Ecotypes from Different Elevations
Proteomics. Oct, 2008 | Pubmed ID: 18814337
Although tree species typically exhibit low genetic differentiation between populations, ecotypes adapted to different environmental conditions can vary in their capacity to withstand and recover from environmental stresses like heat stress. Two month old seedlings of a Picea abies ecotype adapted to high elevation showed lower level of thermotolerance and higher level of tolerance to oxidative stress relative to a low elevation ecotype. Protein expression patterns following exposure to severe heat stress of the two ecotypes were compared by means of 2-DE. Several proteins exhibiting ecotype and tissue specific expression were identified by MS/MS. Among them, small heat shock proteins of the HSP 20 family and proteins involved in protection from oxidative stress displayed qualitative and quantitative differences in expression between the ecotypes correlated with the observed phenotypic differences. On the basis of these results, it can be speculated that the observed interpopulation polymorphism of protein regulation in response to heat stress could underlie their different capacities to withstand and recover from heat stress. These local adaptations are potentially relevant for the species adaptation to the conditions predicted by the current models for climate change.
Journal of Proteomics. Mar, 2009 | Pubmed ID: 19167528
Homology-driven proteomics aims at exploring the proteomes of organisms with unsequenced genomes that, despite rapid genomic sequencing progress, still represent the overwhelming majority of species in the biosphere. Methodologies have been developed to enable automated LC-MS/MS identifications of unknown proteins, which rely on the sequence similarity between the fragmented peptides and reference database sequences from phylogenetically related species. However, because full sequences of matched proteins are not available and matching specificity is reduced, estimating protein abundances should become the obligatory element of homology-driven proteomics pipelines to circumvent the interpretation bias towards proteins from evolutionary conserved families.
Journal of Proteome Research. Aug, 2009 | Pubmed ID: 19575529
Defense responses of Fagus sylvatica seedlings elicited by infection with the root pathogen Phytophthora citricola and root or leaf wounding were compared at local and systemic levels in differential display experiments using two-dimensional gel electrophoresis followed by homology-driven mass spectrometric identification of proteins. A total of 68 protein spots were identified representing 51 protein functions related to protein synthesis and processing, energy, primary and secondary metabolism, as well as signal transduction, stress and defense. Changes in the abundance of root and leaf proteins partly overlapped between plant responses to the different stressors. The response to pathogen infection was rather late, weak and unspecific and accompanied by adjustments of the energy and primary metabolism which suggested either a lack of recognition or a suppression of host's defense reaction by the invading pathogen. The response to wounding involved changes in the basal metabolism as well as activation of defense mechanisms. Both types of changes were largely specific to the wounded organ. Similarities between the defense mechanisms activated by root infection and root wounding were also observed.
Oecologia. Mar, 2010 | Pubmed ID: 19924445
In animals, competition for space and resources often results in territorial behaviour. The size of a territory is an important correlate of fitness and is primarily determined by the spatial distribution of resources and by interactions between competing individuals. Both of these determinants, alone or in interaction, could lead to spatial non-independence of territory size (i.e. spatial autocorrelation). We investigated the presence and magnitude of spatial autocorrelation (SAC) in territory size using Monte Carlo simulations of the most widely used territory measures. We found significant positive SAC in a wide array of competition-simulated conditions. A meta-analysis of territory size data showed that SAC is also a feature of territories mapped based on behavioural observations. Our results strongly suggest that SAC is an intrinsic trait of any territory measure. Hence, we recommend that appropriate statistical methods should be employed for the analysis of data sets where territory size is either a dependent or an explanatory variable.
Chirurgia (Bucharest, Romania : 1990). Jan-Feb, 2010 | Pubmed ID: 20405693
We hereby aim to account on a case of actinomycotic infection occurred in a female patient with an intrauterine contraceptive device (IUCD). The infection occurred as a pseudo-tumour which raised differential diagnosis issues with a malignant tumour. The diagnosis has been eventually established following the pathologic examination of paraffin-embedded tissues. Although the infection's gateway was the uterus, the subsequent invasion of the parietal, urinary bladder and lateral rectal walls did not seem to affect the fallopian tubes or the ovaries.
Current Biology : CB. Oct, 2010 | Pubmed ID: 20850324
Associated with a continued global increase in urbanization, anthropogenic light pollution is an important problem. However, our understanding of the ecological consequences of light pollution is limited. We investigated effects of artificial night lighting on dawn song in five common forest-breeding songbirds. In four species, males near street lights started singing significantly earlier at dawn than males elsewhere in the forest, and this effect was stronger in naturally earlier-singing species. We compared reproductive behavior of blue tits breeding in edge territories with and without street lights to that of blue tits breeding in central territories over a 7 year period. Under the influence of street lights, females started egg laying on average 1.5 days earlier. Males occupying edge territories with street lights were twice as successful in obtaining extra-pair mates than their close neighbors or than males occupying central forest territories. Artificial night lighting affected both age classes but had a stronger effect on yearling males. Our findings indicate that light pollution has substantial effects on the timing of reproductive behavior and on individual mating patterns. It may have important evolutionary consequences by changing the information embedded in previously reliable quality-indicator traits.
Behavioral Ecology : Official Journal of the International Society for Behavioral Ecology. 9, 2010 | Pubmed ID: 22476031
Nature Methods. Feb, 2011 | Pubmed ID: 21278720
The Lateral Incisive Canals of the Adult Hard Palate - Aberrant Anatomy of a Minor Form of Clefting?
Romanian Journal of Morphology and Embryology = Revue Roumaine De Morphologie Et Embryologie. 2011 | Pubmed ID: 21892545
Except the oral clefts and their associated dental development disturbances, no other discrete morphologies are reported in the literature as related to altered fusions of the fetal maxilla and premaxilla. We report here two cases related by the persistence in adult of an aberrant canal at the fusion site of the fetal premaxilla and maxilla. The first case presents an anastomosis of the superior anterior alveolar and greater palatine nerves, encountered during the dissection of a human adult male cadaver; that anastomosis, bilaterally present, projected on the aforementioned fusion site and traversed the hard palate to continue within the maxillary sinus wall. The second case evidenced on CT the unilateral presence of aberrant lateral incisive canals (LIC) at the level of the fetal premaxilla and maxilla fusion site; those canals, external (1.5 mm diameter) and internal (1.07 mm diameter), were corresponding as location to that one traversed by the aberrant anastomosis in the first case. Both LIC opened inferiorly but not superiorly, rather seeming to communicate with the bony canals within the nasal fossa floor at that level. We consider that such aberrant canals and nerves may represent very rare forms of clefting, previously undescribed; the possible anastomoses of the superior anterior alveolar and greater palatine nerves can be altered during a Le Fort I fracture and may be the morphology that can explain aberrant clinical nervous distributions at the level of the upper dentoalveolar arch and hard palate.
Annals of Anatomy = Anatomischer Anzeiger : Official Organ of the Anatomische Gesellschaft. Jul, 2012 | Pubmed ID: 22226149
A distinctive stromal cell-type, the telocyte (TC), has recently been described to send specific long prolongations (telopodes) alternating thin segments (podomers) with dilations (podoms). Even though one would expect TCs to be identified in various stromal tissues, there were not yet reported evidence of skin TCs. We aimed to check for the presence of TCs in human skin dermis. Transmission electron microscopy revealed the presence in dermis of TCs projecting specific telopodes. Skin TCs were closely related to or contacting fibroblasts, mast cells, adipocytes, and connective fiber bundles (collagenous and elastic). As it appears, skin TCs exist and are related to other stromal cells. The structural association of TCs to elastic fibers deserves further investigation.
Accounting for Biological Variation in Differential Display Two-dimensional Electrophoresis Experiments
Journal of Proteomics. Jun, 2012 | Pubmed ID: 22521271
Variation of protein expression levels was investigated in the heart, lung and liver from an inbred (C57/BL6) and an outbred (CD-1) mouse line. Based on the measured inter-individual variation, optimal sample sizes for two-dimensional electrophoresis experiments were determined by means of power analysis. For both lines, the level of protein expression variation was in the range of technical variation. Thus, although the differences in protein expression variation were significant between organs and mouse lines, optimal sample sizes were very similar (between 8 for heart proteins from C57/BL6 and 10 for liver proteins of the same line). Proteins with organ expression bias (higher expression in one organ as compared to the other two organs) exhibited higher variation of expression and the proportion of these proteins in each organ explained at least partly inter-organ differences in protein expression variation. The results suggest that proteomic experiments using more heterogeneous mouse samples would not require much larger sample sizes than those using narrowly standardized samples. Experiment designs encompassing a broader genetic variation and thus affording increased relevance of the results can be accessible to proteomics researchers at still affordable sample sizes.
Science (New York, N.Y.). Sep, 2012 | Pubmed ID: 22878501
The functions of sleep remain elusive. Extensive evidence suggests that sleep performs restorative processes that sustain waking brain performance. An alternative view proposes that sleep simply enforces adaptive inactivity to conserve energy when activity is unproductive. Under this hypothesis, animals may evolve the ability to dispense with sleep when ecological demands favor wakefulness. Here, we show that male pectoral sandpipers (Calidris melanotos), a polygynous Arctic breeding shorebird, are able to maintain high neurobehavioral performance despite greatly reducing their time spent sleeping during a 3-week period of intense male-male competition for access to fertile females. Males that slept the least sired the most offspring. Our results challenge the view that decreased performance is an inescapable outcome of sleep loss.
The Mandibular Ridge Oral Mucosa Model of Stromal Influences on the Endothelial Tip Cells: An Immunohistochemical and TEM Study
Anatomical Record (Hoboken, N.J. : 2007). Nov, 2012 | Pubmed ID: 23192856
This study aimed to evaluate by immunohistochemistry and transmission electron microscopy (TEM) the morphological features of the oral mucosa endothelial tip cells (ETCs) and to determine the immune and ultrastructural patterns of the stromal nonimmune cells which could influence healing processes. Immune labeling was performed on bioptic samples obtained from six edentulous patients undergoing surgery for dental implants placement; three normal samples were collected from patients prior to the extraction of the third mandibular molar. The antibodies were tested for CD34, CD117(c-kit), platelet derived growth factor receptor-alpha (PDGFR-Î±), Mast Cell Tryptase, CD44, vimentin, CD45, CD105, alpha-smooth muscle actin, FGF2, Ki67. In light microscopy, while stromal cells (StrCs) of the reparatory and normal oral mucosa, with a fibroblastic appearance, were found positive for a CD34/CD44/CD45/CD105/PDGFR-Î±/vimentin immune phenotype, the CD117/c-kit labeling led to a positive stromal reaction only in the reparatory mucosa. In TEM, non-immune StrCs presenting particular ultrastructural features were identified as circulating fibrocytes (CFCs). Within the lamina propria CFCs were in close contact with ETCs. Long processes of the ETCs were moniliform, and hook-like collaterals were arising from the dilated segments, suggestive for a different stage migration. Maintenance and healing of oral mucosa are so supported by extensive processes of angiogenesis, guided by ETCs that, in turn, are influenced by the CFCs that populate the stromal compartment both in normal and reparatory states. Therefore, CFCs could be targeted by specific therapies, with pro- or anti-angiogenic purposes. Anat Rec, 2012. Â© 2012 Wiley Periodicals, Inc.