Changes
On November 7, 2019 at 10:36:31 PM UTC, eawrdmadmin:
-
Added resource Sgier_et_al_2016.pdf to Data for: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics
f | 1 | { | f | 1 | { |
2 | "author": "[\"Kroll, Alexandra\", \"Sgier, Linn\", \"Zupanic, | 2 | "author": "[\"Kroll, Alexandra\", \"Sgier, Linn\", \"Zupanic, | ||
3 | Anze\", \"Freimann, Remo\"]", | 3 | Anze\", \"Freimann, Remo\"]", | ||
4 | "author_email": null, | 4 | "author_email": null, | ||
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8 | "key": "citation", | 8 | "key": "citation", | ||
9 | "value": "Kroll, A., Sgier, L., Zupanic, A., & Freimann, R. | 9 | "value": "Kroll, A., Sgier, L., Zupanic, A., & Freimann, R. | ||
10 | (2018). <i>Data for: Flow cytometry combined with viSNE for the | 10 | (2018). <i>Data for: Flow cytometry combined with viSNE for the | ||
11 | analysis of microbial biofilms and detection of microplastics</i> | 11 | analysis of microbial biofilms and detection of microplastics</i> | ||
12 | [Data set]. Eawag: Swiss Federal Institute of Aquatic Science and | 12 | [Data set]. Eawag: Swiss Federal Institute of Aquatic Science and | ||
13 | Technology. https://doi.org/10.25678/0000EE" | 13 | Technology. https://doi.org/10.25678/0000EE" | ||
14 | }, | 14 | }, | ||
15 | { | 15 | { | ||
16 | "key": "citation_publication", | 16 | "key": "citation_publication", | ||
17 | "value": "Sgier, L., R. Freimann, A. Zupanic, and A. Kroll | 17 | "value": "Sgier, L., R. Freimann, A. Zupanic, and A. Kroll | ||
18 | (2016), Flow cytometry combined with viSNE for the analysis of | 18 | (2016), Flow cytometry combined with viSNE for the analysis of | ||
19 | microbial biofilms and detection of microplastics, Nature | 19 | microbial biofilms and detection of microplastics, Nature | ||
20 | Communications, 7(1), doi:10.1038/ncomms11587.\n" | 20 | Communications, 7(1), doi:10.1038/ncomms11587.\n" | ||
21 | }, | 21 | }, | ||
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122 | atropurpurea\", \"Botryococcus braunii\", \"Botryococcus spec\", | 122 | atropurpurea\", \"Botryococcus braunii\", \"Botryococcus spec\", | ||
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130 | \"Melosira varians\", \"Meridion circulare\", \"Merismopedia glauca\", | 130 | \"Melosira varians\", \"Meridion circulare\", \"Merismopedia glauca\", | ||
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132 | \"Nitzschia palea\", \"Nitzschia spec\", \"Oedogonium spec\", | 132 | \"Nitzschia palea\", \"Nitzschia spec\", \"Oedogonium spec\", | ||
133 | \"Phormidium autumnale\", \"Phormidium spec\", \"Protozoa\", | 133 | \"Phormidium autumnale\", \"Phormidium spec\", \"Protozoa\", | ||
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135 | acuminatus\", \"Scenedesmus bijugatus\", \"Scenedesmus bimorphus\", | 135 | acuminatus\", \"Scenedesmus bijugatus\", \"Scenedesmus bimorphus\", | ||
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151 | "value": "[\"electric_conductivity\", \"concentration\", | 151 | "value": "[\"electric_conductivity\", \"concentration\", | ||
152 | \"temperature\", \"pH\"]" | 152 | \"temperature\", \"pH\"]" | ||
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158 | "license_id": null, | 158 | "license_id": null, | ||
159 | "license_title": null, | 159 | "license_title": null, | ||
160 | "maintainer": "Zupanic, Anze", | 160 | "maintainer": "Zupanic, Anze", | ||
161 | "maintainer_email": "Anze.Zupanic@eawag.ch", | 161 | "maintainer_email": "Anze.Zupanic@eawag.ch", | ||
162 | "metadata_created": "2019-11-07T22:36:30.178357", | 162 | "metadata_created": "2019-11-07T22:36:30.178357", | ||
163 | "metadata_modified": "2019-11-07T22:36:30.178364", | 163 | "metadata_modified": "2019-11-07T22:36:30.178364", | ||
164 | "name": "data-for-flow-cytometry-combined-with-visne", | 164 | "name": "data-for-flow-cytometry-combined-with-visne", | ||
165 | "notes": "Biofilms serve essential ecosystem functions and are used | 165 | "notes": "Biofilms serve essential ecosystem functions and are used | ||
166 | in different technical applications. Studies from stream ecology and | 166 | in different technical applications. Studies from stream ecology and | ||
167 | waste water treatment have shown that biofilm functionality depends to | 167 | waste water treatment have shown that biofilm functionality depends to | ||
168 | a great extent on community structure. Here we present a fast and | 168 | a great extent on community structure. Here we present a fast and | ||
169 | easy-to-use method for individual cell-based analysis of stream | 169 | easy-to-use method for individual cell-based analysis of stream | ||
170 | biofilms, based on stain-free flow cytometry and visualization of the | 170 | biofilms, based on stain-free flow cytometry and visualization of the | ||
171 | high-dimensional data by viSNE. The method allows the combined | 171 | high-dimensional data by viSNE. The method allows the combined | ||
172 | assessment of community structure, decay of phototrophic organisms and | 172 | assessment of community structure, decay of phototrophic organisms and | ||
173 | presence of abiotic particles. In laboratory experiments, it allows | 173 | presence of abiotic particles. In laboratory experiments, it allows | ||
174 | quantification of cellular decay and detection of survival of larger | 174 | quantification of cellular decay and detection of survival of larger | ||
175 | cells after temperature stress, while in the field it enables | 175 | cells after temperature stress, while in the field it enables | ||
176 | detection of community structure changes that correlate with known | 176 | detection of community structure changes that correlate with known | ||
177 | environmental drivers (flow conditions, dissolved organic carbonDOC, | 177 | environmental drivers (flow conditions, dissolved organic carbonDOC, | ||
178 | calcium) and detection of microplastic contamination. The method can | 178 | calcium) and detection of microplastic contamination. The method can | ||
179 | potentially be applied to other biofilm types, e.g. for inferring | 179 | potentially be applied to other biofilm types, e.g. for inferring | ||
180 | community structure for environmental and industrial research and | 180 | community structure for environmental and industrial research and | ||
181 | monitoring.", | 181 | monitoring.", | ||
n | 182 | "num_resources": 0, | n | 182 | "num_resources": 1, |
183 | "num_tags": 14, | 183 | "num_tags": 14, | ||
184 | "organization": { | 184 | "organization": { | ||
185 | "approval_status": "approved", | 185 | "approval_status": "approved", | ||
186 | "created": "2019-09-18T14:11:47.993320", | 186 | "created": "2019-09-18T14:11:47.993320", | ||
187 | "description": "As the number of different chemicals and | 187 | "description": "As the number of different chemicals and | ||
188 | nanomaterials pollutants in our waters increases and the aquatic | 188 | nanomaterials pollutants in our waters increases and the aquatic | ||
189 | environment is facing many climate related physical and chemical | 189 | environment is facing many climate related physical and chemical | ||
190 | changes in the near future, it is becoming paramount that the paradigm | 190 | changes in the near future, it is becoming paramount that the paradigm | ||
191 | of testing chemical safety on whole animals and plants shifts to cell | 191 | of testing chemical safety on whole animals and plants shifts to cell | ||
192 | culture based high throughput approaches. At the same time, it is | 192 | culture based high throughput approaches. At the same time, it is | ||
193 | necessary to stop looking for adverse effects on single species and | 193 | necessary to stop looking for adverse effects on single species and | ||
194 | instead focus on the effects of pollution on whole ecosystem. Together | 194 | instead focus on the effects of pollution on whole ecosystem. Together | ||
195 | with the development of new experimental systems, mathematical | 195 | with the development of new experimental systems, mathematical | ||
196 | modelling, especially the systems biology approach which tries to | 196 | modelling, especially the systems biology approach which tries to | ||
197 | predict adverse outcomes of chemical on the level of a single cell, is | 197 | predict adverse outcomes of chemical on the level of a single cell, is | ||
198 | of paramount importance. \r\n\r\nIn the Systems Biology group, we | 198 | of paramount importance. \r\n\r\nIn the Systems Biology group, we | ||
199 | are studying how to use mathematical modelling and statistics to | 199 | are studying how to use mathematical modelling and statistics to | ||
200 | integrate different types of ecotoxicological measurements and | 200 | integrate different types of ecotoxicological measurements and | ||
201 | knowledge acquired in the community until now, either available in | 201 | knowledge acquired in the community until now, either available in | ||
202 | public or private data collections. Our goals are to understand the | 202 | public or private data collections. Our goals are to understand the | ||
203 | effects of chemicals on the cellular level, with the aim of later | 203 | effects of chemicals on the cellular level, with the aim of later | ||
204 | connecting this level to tissues, organs, organisms, communities and | 204 | connecting this level to tissues, organs, organisms, communities and | ||
205 | ecosystems. We want to understand, which biological molecules the | 205 | ecosystems. We want to understand, which biological molecules the | ||
206 | chemicals interacts with, what cellular responses this interactions | 206 | chemicals interacts with, what cellular responses this interactions | ||
207 | induce, e.g. in the form of gene expression regulation, and how the | 207 | induce, e.g. in the form of gene expression regulation, and how the | ||
208 | cell adapts or succumbs to the insult. We plan to do this by | 208 | cell adapts or succumbs to the insult. We plan to do this by | ||
209 | integrating our computational efforts with the efforts of our | 209 | integrating our computational efforts with the efforts of our | ||
210 | experimental colleagues, and the vast amount of data gathered in | 210 | experimental colleagues, and the vast amount of data gathered in | ||
211 | different OMICS studies in the past decade. The methods that we use | 211 | different OMICS studies in the past decade. The methods that we use | ||
212 | most are gene expression analysis, network inference, dynamical | 212 | most are gene expression analysis, network inference, dynamical | ||
213 | modelling and metabolic modelling. Understanding the toxic effects on | 213 | modelling and metabolic modelling. Understanding the toxic effects on | ||
214 | the cellular level will help in the assessment of risk of chemical and | 214 | the cellular level will help in the assessment of risk of chemical and | ||
215 | environmental stressors on the organism and the ecosystem level.", | 215 | environmental stressors on the organism and the ecosystem level.", | ||
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243 | "state": "active", | 270 | "state": "active", | ||
244 | "vocabulary_id": null | 271 | "vocabulary_id": null | ||
245 | }, | 272 | }, | ||
246 | { | 273 | { | ||
247 | "display_name": "algae", | 274 | "display_name": "algae", | ||
248 | "id": "51aa6b96-cd9d-40e7-988f-49153f6e6d39", | 275 | "id": "51aa6b96-cd9d-40e7-988f-49153f6e6d39", | ||
249 | "name": "algae", | 276 | "name": "algae", | ||
250 | "state": "active", | 277 | "state": "active", | ||
251 | "vocabulary_id": null | 278 | "vocabulary_id": null | ||
252 | }, | 279 | }, | ||
253 | { | 280 | { | ||
254 | "display_name": "biofilm", | 281 | "display_name": "biofilm", | ||
255 | "id": "6010f5e8-7bfc-4238-89dd-5d045d0ea475", | 282 | "id": "6010f5e8-7bfc-4238-89dd-5d045d0ea475", | ||
256 | "name": "biofilm", | 283 | "name": "biofilm", | ||
257 | "state": "active", | 284 | "state": "active", | ||
258 | "vocabulary_id": null | 285 | "vocabulary_id": null | ||
259 | }, | 286 | }, | ||
260 | { | 287 | { | ||
261 | "display_name": "clustering", | 288 | "display_name": "clustering", | ||
262 | "id": "ebf5c40e-78d9-428d-acf4-d274f17d9ab5", | 289 | "id": "ebf5c40e-78d9-428d-acf4-d274f17d9ab5", | ||
263 | "name": "clustering", | 290 | "name": "clustering", | ||
264 | "state": "active", | 291 | "state": "active", | ||
265 | "vocabulary_id": null | 292 | "vocabulary_id": null | ||
266 | }, | 293 | }, | ||
267 | { | 294 | { | ||
268 | "display_name": "community structure", | 295 | "display_name": "community structure", | ||
269 | "id": "fe460430-63ac-432e-8d0e-9e6402361691", | 296 | "id": "fe460430-63ac-432e-8d0e-9e6402361691", | ||
270 | "name": "community structure", | 297 | "name": "community structure", | ||
271 | "state": "active", | 298 | "state": "active", | ||
272 | "vocabulary_id": null | 299 | "vocabulary_id": null | ||
273 | }, | 300 | }, | ||
274 | { | 301 | { | ||
275 | "display_name": "dissoved phosphorus", | 302 | "display_name": "dissoved phosphorus", | ||
276 | "id": "28b64c25-cf06-42f7-8535-f5a971e6e810", | 303 | "id": "28b64c25-cf06-42f7-8535-f5a971e6e810", | ||
277 | "name": "dissoved phosphorus", | 304 | "name": "dissoved phosphorus", | ||
278 | "state": "active", | 305 | "state": "active", | ||
279 | "vocabulary_id": null | 306 | "vocabulary_id": null | ||
280 | }, | 307 | }, | ||
281 | { | 308 | { | ||
282 | "display_name": "flow cytometry", | 309 | "display_name": "flow cytometry", | ||
283 | "id": "23162fd6-44d3-4b76-8b4b-e700617845fb", | 310 | "id": "23162fd6-44d3-4b76-8b4b-e700617845fb", | ||
284 | "name": "flow cytometry", | 311 | "name": "flow cytometry", | ||
285 | "state": "active", | 312 | "state": "active", | ||
286 | "vocabulary_id": null | 313 | "vocabulary_id": null | ||
287 | }, | 314 | }, | ||
288 | { | 315 | { | ||
289 | "display_name": "microplastics", | 316 | "display_name": "microplastics", | ||
290 | "id": "73a4f1e3-0a59-4374-8d18-7f6a9406eafa", | 317 | "id": "73a4f1e3-0a59-4374-8d18-7f6a9406eafa", | ||
291 | "name": "microplastics", | 318 | "name": "microplastics", | ||
292 | "state": "active", | 319 | "state": "active", | ||
293 | "vocabulary_id": null | 320 | "vocabulary_id": null | ||
294 | }, | 321 | }, | ||
295 | { | 322 | { | ||
296 | "display_name": "nutrients", | 323 | "display_name": "nutrients", | ||
297 | "id": "a3ee6b1e-adaf-4bac-a10f-f95d381e4516", | 324 | "id": "a3ee6b1e-adaf-4bac-a10f-f95d381e4516", | ||
298 | "name": "nutrients", | 325 | "name": "nutrients", | ||
299 | "state": "active", | 326 | "state": "active", | ||
300 | "vocabulary_id": null | 327 | "vocabulary_id": null | ||
301 | }, | 328 | }, | ||
302 | { | 329 | { | ||
303 | "display_name": "organic matter", | 330 | "display_name": "organic matter", | ||
304 | "id": "ae699ede-5dfe-45d2-8d4d-64c8a7359eb5", | 331 | "id": "ae699ede-5dfe-45d2-8d4d-64c8a7359eb5", | ||
305 | "name": "organic matter", | 332 | "name": "organic matter", | ||
306 | "state": "active", | 333 | "state": "active", | ||
307 | "vocabulary_id": null | 334 | "vocabulary_id": null | ||
308 | }, | 335 | }, | ||
309 | { | 336 | { | ||
310 | "display_name": "organic phosphorus", | 337 | "display_name": "organic phosphorus", | ||
311 | "id": "b47b4de4-ad23-430c-8b8d-3efe05c185af", | 338 | "id": "b47b4de4-ad23-430c-8b8d-3efe05c185af", | ||
312 | "name": "organic phosphorus", | 339 | "name": "organic phosphorus", | ||
313 | "state": "active", | 340 | "state": "active", | ||
314 | "vocabulary_id": null | 341 | "vocabulary_id": null | ||
315 | }, | 342 | }, | ||
316 | { | 343 | { | ||
317 | "display_name": "periphyton", | 344 | "display_name": "periphyton", | ||
318 | "id": "eaf89c37-18b9-420a-93a3-11d2296643ef", | 345 | "id": "eaf89c37-18b9-420a-93a3-11d2296643ef", | ||
319 | "name": "periphyton", | 346 | "name": "periphyton", | ||
320 | "state": "active", | 347 | "state": "active", | ||
321 | "vocabulary_id": null | 348 | "vocabulary_id": null | ||
322 | }, | 349 | }, | ||
323 | { | 350 | { | ||
324 | "display_name": "total phosphorus", | 351 | "display_name": "total phosphorus", | ||
325 | "id": "3f02e73e-170d-485b-af32-2a4a0e14e731", | 352 | "id": "3f02e73e-170d-485b-af32-2a4a0e14e731", | ||
326 | "name": "total phosphorus", | 353 | "name": "total phosphorus", | ||
327 | "state": "active", | 354 | "state": "active", | ||
328 | "vocabulary_id": null | 355 | "vocabulary_id": null | ||
329 | } | 356 | } | ||
330 | ], | 357 | ], | ||
331 | "title": "Data for: Flow cytometry combined with viSNE for the | 358 | "title": "Data for: Flow cytometry combined with viSNE for the | ||
332 | analysis of microbial biofilms and detection of microplastics", | 359 | analysis of microbial biofilms and detection of microplastics", | ||
333 | "type": "dataset", | 360 | "type": "dataset", | ||
334 | "url": "https://doi.org/10.25678/0000ee/", | 361 | "url": "https://doi.org/10.25678/0000ee/", | ||
335 | "version": null | 362 | "version": null | ||
336 | } | 363 | } |