| 81. |
- Parducci, Laura, et al.
(författare)
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Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia
- 2013
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 22:13, s. 3511-3524
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Tidskriftsartikel (refereegranskat)abstract
- Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen-based and metabarcoding approaches to explore the Holocene plant composition around two lakes in central Scandinavia. At one site, we also compared barcoding results with those obtained in earlier studies with species-specific primers. The pollen analyses revealed a larger number of taxa (46), of which the majority (78%) was not identified by metabarcoding. The metabarcoding identified 14 taxa (MTUs), but allowed identification to a lower taxonomical level. The combined analyses identified 52 taxa. The barcoding primers may favour amplification of certain taxa, as they did not detect taxa previously identified with species-specific primers. Taphonomy and selectiveness of the primers are likely the major factors influencing these results. We conclude that metabarcoding from lake sediments provides a complementary, but not an alternative, tool to pollen analysis for investigating past flora. In the absence of other fossil evidence, metabarcoding gives a local and important signal from the vegetation, but the resulting assemblages show limited capacity to detect all taxa, regardless of their abundance around the lake. We suggest that metabarcoding is followed by pollen analysis and the use of species-specific primers to provide the most comprehensive signal from the environment.
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| 82. |
- Parducci, Laura, 1965-, et al.
(författare)
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Proxy comparison in ancient peat sediments : pollen, macrofossil and plant DNA
- 2015
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Ingår i: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 370:1660, s. 20130382-
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Tidskriftsartikel (refereegranskat)abstract
- We compared DNA, pollen and macrofossil data obtained from Weichselian interstadial (age more than 40 kyr) and Holocene (maximum age 8400 cal yr BP) peat sediments from northern Europe and used them to reconstruct contemporary floristic compositions at two sites. The majority of the samples provided plant DNA sequences of good quality with success amplification rates depending on age. DNA and sequencing analysis provided five plant taxa from the older site and nine taxa from the younger site, corresponding to 7% and 15% of the total number of taxa identified by the three proxies together. At both sites, pollen analysis detected the largest (54) and DNA the lowest (10) number of taxa, but five of the DNA taxa were not detected by pollen and macrofossils. The finding of a larger overlap between DNA and pollen than between DNA and macrofossils proxies seems to go against our previous suggestion based on lacustrine sediments that DNA originates principally from plant tissues and less from pollen. At both sites, we also detected Quercus spp. DNA, but few pollen grains were found in the record, and these are normally interpreted as long-distance dispersal. We confirm that in palaeoecological investigations, sedimentary DNA analysis is less comprehensive than classical morphological analysis, but is a complementary and important tool to obtain a more complete picture of past flora.
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| 83. |
- Parducci, Laura, et al.
(författare)
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Response to Comment on "Glacial Survival of Boreal Trees in Northern Scandinavia"
- 2012
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 338:6108, s. 742-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Birks et al. question our proposition that trees survived the Last Glacial Maximum (LGM) in Northern Scandinavia. We dispute their interpretation of our modern genetic data but agree that more work is required. Our field and laboratory procedures were robust; contamination is an unlikely explanation of our results. Their description of Endletvatn as ice-covered and inundated during the LGM is inconsistent with recent geological literature.
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| 84. |
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| 85. |
- Pathan, M., et al.
(författare)
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A novel community driven software for functional enrichment analysis of extracellular vesicles data
- 2017
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Ingår i: Journal of Extracellular Vesicles. - : Wiley. - 2001-3078. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture "what the community needs in a tool". Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes. Remarkably, with the enthusiastic participation of the community, we were able to implement 90% of the requested features. FunRich enables plugin for extracellular vesicles wherein users can download and analyse data from Vesiclepedia database. By involving researchers early through community needs software development, we believe that comprehensive analysis tools can be developed in various scientific disciplines.
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| 86. |
- Sardzik, Robert, et al.
(författare)
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Chemoenzymatic Synthesis of O-Mannosylpeptides in Solution and on Solid Phase
- 2012
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 134:10, s. 4521-4524
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Tidskriftsartikel (refereegranskat)abstract
- O-Mannosyl glycans are known to play an important role in regulating the function of alpha-dystroglycan (alpha-DG), as defective glycosylation is associated with various phenotypes of congenital muscular dystrophy. Despite the well-established biological significance of these glycans, questions regarding their precise molecular function remain unanswered. Further biological investigation will require synthetic methods for the generation of pure samples of homogeneous glycopeptides with diverse sequences. Here we describe the first total syntheses of glycopeptides containing the tetrasaccharide NeuNAc alpha 2-3Gal beta 1-4GlcNAc beta 1-2Man alpha, which is reported to be the most abundant O-mannosyl glycan on alpha-DG. Our approach is based on biomimetic stepwise assembly from the reducing end and also gives access to the naturally occurring mono-, di-, and trisaccharide substructures. In addition to the total synthesis, we have developed a one-pot enzymatic cascade leading to the rapid synthesis of the target tetrasaccharide. Finally, solid-phase synthesis of the desired glycopeptides directly on a gold microarray platform is described.
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| 87. |
- Schvartz, D., et al.
(författare)
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The Human Diabetes Proteome Project (HDPP) : The 2014 update
- 2015
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Ingår i: Translational Proteomics. - : Elsevier BV. - 2212-9626. ; 8-9, s. 1-7
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Tidskriftsartikel (refereegranskat)abstract
- Diabetes is an increasing worldwide problem leading to major associated health issues and increased health care costs. In 2012, 9.3% of the American population was affected by diabetes, according to the American Diabetes Association, with 1.7 million of new cases since during the year (www.diabetes.org). Proteome initiatives can provide a deeper understanding of the biology of this disease and help develop more effective treatments. The collaborative effort of the Human Diabetes Proteome Project (HDPP) brings together a wide variety of complementary resources to increase the existing knowledge about both type 1 and type 2 diabetes and their related complications. The goals are to identify proteins and protein isoforms associated with the pathology and to characterize underlying disease-related pathways and mechanisms. Moreover, a considerable effort is being made on data integration and network biology. Sharing these data with the scientific community will be an important part of the consortium. Here we report on: the content of the HDPP session held at the 12th HUPO meeting in Yokohama; recent achievements of the consortium; discussions of several HDPP workshops; as well as future HDPP directions as discussed at the 13th HUPO congress in Madrid, with a special attention given to the lists of prioritized, diabetes-related proteins and the proteomic means to study them.
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| 88. |
- Stutz, Silvina, et al.
(författare)
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Late Holocene climate and environment of the SE Pampa grasslands, Argentina, inferred from biological indicators in shallow, freshwater Lake Nahuel Rucá
- 2010
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Ingår i: Journal of Paleolimnology. - : Springer Science and Business Media LLC. - 0921-2728 .- 1573-0417. ; 44:3, s. 761-775
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Tidskriftsartikel (refereegranskat)abstract
- We analyzed pollen, non-pollen palynomorphs (NPPs), calcareous microfossils, plant macrofossils, diatoms, chrysophyte cysts, opal phytoliths and organic matter content in a 123-cm sediment sequence from Nahuel Ruca Lake, a shallow, freshwater system in the southeastern Pampa grasslands, Argentina. Three stages in the lake evolution were identified. Before 3,680 cal year BP, only pollen, NPPs (dinoflagellate cysts and acritarchs) and ostracods were recovered, suggesting brackish/saline conditions in the lake and nearby areas. Freshwater conditions are, however, indicated by Myriophyllum, Pediastrum and Zygnemataceae. The brackish/saline conditions could have been caused by marine influence during a Holocene sea level high stand that affected the area ca. 6,000 year BP. Between 3,680 and 390 cal year BP, macrophyte pollen and plant macrofossils indicate increasingly freshwater conditions in the lake and the adjacent area. Diatom and ostracod assemblages, however, suggest brackish and oligotrophic conditions, giving way to freshwater and meso-eutrophic conditions toward the end of this period. The relationship between submersed macrophytes (Myriophyllum, Potamogeton, Ceratophyllum, Chara) and planktonic algae (Chlorophyta and diatoms), suggests a shift in the lake from a clear to a turbid state. This turbid state is more evident after 390 cal year BP. High values of Pediastrum, Scenedesmus and diatoms (Cyclotella meneghiniana, Aulacoseira granulata, A. muzzanensis) observed during this stage could have reduced light penetration, with consequent loss of submersed plants. Pollen and plant macrofossils in the uppermost 20 cm indicate a shallow, freshwater lake similar to present, though an increase in brackish/freshwater diatoms suggests an increase in salinity, perhaps related to periodic droughts. Opal phytoliths yield a regional paleoclimatic reconstruction that agrees closely with inferences made using pollen, mammals and sediment characteristics.
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| 89. |
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| 90. |
- Visell, Y., et al.
(författare)
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Sound design and perception in walking interactions
- 2009
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Ingår i: International journal of human-computer studies. - : Elsevier BV. - 1071-5819 .- 1095-9300. ; 67:11, s. 947-959
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Tidskriftsartikel (refereegranskat)abstract
- This paper reviews the state of the art in the display and perception of walking generated sounds and tactile vibrations, and their current and potential future uses in interactive systems. As non-visual information sources that are closely linked to human activities in diverse environments, such signals are capable of communicating about the spaces we traverse and activities we encounter in familial and intuitive ways However, in order for them to be effectively employed in human-computer interfaces, significant knowledge is required in areas including the perception of acoustic signatures of walking, and the design, engineering, and evaluation of interfaces that utilize them. Much of this expertise has accumulated in recent years, although many questions remain to be explored We highlight past work and current research directions in this Multidisciplinary area of investigation, and point to potential future trends.
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