scholarly journals Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

2017 ◽  
Author(s):  
Xiaoyin Chen ◽  
Yu-Chi Sun ◽  
George M Church ◽  
Je Hyuk Lee ◽  
Anthony M Zador
Keyword(s):  
Spatial Resolution ◽  
High Throughput ◽  
Illumina Sequencing ◽  
Lineage Tracing ◽  
List Type ◽  
Padlock Probe ◽  
Gap Filling ◽  
Sequencing Chemistry ◽  
Barcode Sequencing

AbstractCellular DNA/RNA tags (barcodes) allow for multiplexed cell lineage tracing and neuronal projection mapping with cellular resolution. Conventional approaches to reading out cellular barcodes trade off spatial resolution with throughput. Bulk sequencing achieves high throughput but sacrifices spatial resolution, whereas manual cell picking has low throughput. In situ sequencing could potentially achieve both high spatial resolution and high throughput, but current in situ sequencing techniques are inefficient at reading out cellular barcodes. Here we describe BaristaSeq, an optimization of a targeted, padlock probe-based technique for in situ barcode sequencing compatible with Illumina sequencing chemistry. BaristaSeq results in a five-fold increase in amplification efficiency, with a sequencing accuracy of at least 97%. BaristaSeq could be used for barcode-assisted lineage tracing, and to map long-range neuronal projections.Key PointsIn situ sequencing by gap-filling padlock probes is limited by the strand displacement of DNA polymerasesIllumina sequencing chemistry offers superior signal-to-noise ratio in situ compared to sequencing by ligationBaristaSeq as an accurate method for barcode sequencing in situ with improved gap-filling efficiency

scholarly journals Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

2017 ◽  
Vol 46 (4) ◽  
pp. e22-e22 ◽  
Author(s):  
Xiaoyin Chen ◽  
Yu-Chi Sun ◽  
George M Church ◽  
Je Hyuk Lee ◽  
Anthony M Zador
Keyword(s):  
Padlock Probe ◽  
Barcode Sequencing

INDIREKTE PAPIERCHROMATOGRAPHISCHE METHODE ZUR BESTIMMUNG DER HARNOESTROGENE

1961 ◽  
Vol 38 (4) ◽  
pp. 545-562 ◽  
Author(s):  
L. Kecskés ◽  
F. Mutschler ◽  
I. Glós ◽  
E. Thán ◽  
I. Farkas ◽  
...  
Keyword(s):  
Pregnant Women ◽  
Granulosa Cell ◽  
Iron Content ◽  
List Type ◽  
Granulosa Cell Tumour ◽  
Hydrolysis Of ◽  
Phenol Fraction ◽  
Qualitative Determination

ABSTRACT 1. An indirect paperchromatographic method is described for separating urinary oestrogens; this consists of the following steps: acidic hydrolysis, extraction with ether, dissociation of phenol-fractions with partition between the solvents. Previous purification of phenol fraction with the aid of paperchromatography. The elution of oestrogen containing fractions is followed by acetylation. Oestrogen acetate is isolated by re-chromatography. The chromatogram was developed after hydrolysis of the oestrogens 'in situ' on the paper. The quantity of oestrogens was determined indirectly, by means of an iron-reaction, after the elution of the iron content of the oestrogen spot, which was developed by the Jellinek-reaction. 2. The method described above is satisfactory for determining urinary oestrogen, 17β-oestradiol and oestriol, but could include 16-epioestriol and other oestrogenic metabolites. 3. The sensitivity of the method is 1.3–1.6 μg/24 hours. 4. The quantitative and qualitative determination of urinary oestrogens with the above mentioned method was performed in 50 pregnant and 9 non pregnant women, and also in 2 patients with granulosa cell tumour.

Spectro-mechanical Characterization of Aromaticity and Maturity of Kerogens in Oil Shale at 6 nm Spatial Resolution

2018 ◽  
Author(s):  
Devon Jakob ◽  
Le Wang ◽  
Haomin Wang ◽  
Xiaoji Xu
Keyword(s):  
Spatial Resolution ◽  
Oil Shale ◽  
Infrared Imaging ◽  
Mechanical Characterization ◽  
Optical Diffraction ◽  
Chemical Compositions ◽  
Valuable Insight ◽  
Eagle Ford Shale

<p>In situ measurements of the chemical compositions and mechanical properties of kerogen help understand the formation, transformation, and utilization of organic matter in the oil shale at the nanoscale. However, the optical diffraction limit prevents attainment of nanoscale resolution using conventional spectroscopy and microscopy. Here, we utilize peak force infrared (PFIR) microscopy for multimodal characterization of kerogen in oil shale. The PFIR provides correlative infrared imaging, mechanical mapping, and broadband infrared spectroscopy capability with 6 nm spatial resolution. We observed nanoscale heterogeneity in the chemical composition, aromaticity, and maturity of the kerogens from oil shales from Eagle Ford shale play in Texas. The kerogen aromaticity positively correlates with the local mechanical moduli of the surrounding inorganic matrix, manifesting the Le Chatelier’s principle. In situ spectro-mechanical characterization of oil shale will yield valuable insight for geochemical and geomechanical modeling on the origin and transformation of kerogen in the oil shale.</p>

scholarly journals Dendrite-Free and Stable Lithium Metal Battery Achieved by a Model of Stepwise Lithium Deposition and Stripping

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Tiancun Liu ◽  
Jinlong Wang ◽  
Yi Xu ◽  
Yifan Zhang ◽  
Yong Wang
Keyword(s):  
Reduction Method ◽  
Coulombic Efficiency ◽  
List Type ◽  
Lithium Metal ◽  
Metal Anode ◽  
In Situ Raman ◽  
Unique Model ◽  
Li Metal Anode ◽  
Pyridinic N

Highlights A facile method is adopted to obtain cucumber-like lithiophilic composite skeleton. Massive lithiophilic sites in cucumber-like lithiophilic composite skeleton can promote and guide uniform Li depositions. A unique model of stepwise Li deposition and stripping is determined. Abstract The uncontrolled formation of lithium (Li) dendrites and the unnecessary consumption of electrolyte during the Li plating/stripping process have been major obstacles in developing safe and stable Li metal batteries. Herein, we report a cucumber-like lithiophilic composite skeleton (CLCS) fabricated through a facile oxidation-immersion-reduction method. The stepwise Li deposition and stripping, determined using in situ Raman spectra during the galvanostatic Li charging/discharging process, promote the formation of a dendrite-free Li metal anode. Furthermore, numerous pyridinic N, pyrrolic N, and CuxN sites with excellent lithiophilicity work synergistically to distribute Li ions and suppress the formation of Li dendrites. Owing to these advantages, cells based on CLCS exhibit a high Coulombic efficiency of 97.3% for 700 cycles and an improved lifespan of 2000 h for symmetric cells. The full cells assembled with LiFePO4 (LFP), SeS2 cathodes and CLCS@Li anodes demonstrate high capacities of 110.1 mAh g−1 after 600 cycles at 0.2 A g−1 in CLCS@Li|LFP and 491.8 mAh g−1 after 500 cycles at 1 A g−1 in CLCS@Li|SeS2. The unique design of CLCS may accelerate the application of Li metal anodes in commercial Li metal batteries.

scholarly journals Evaluating Machine Learning and Geostatistical Methods for Spatial Gap-filling of Monthly ESA CCI Soil Moisture in China

2021 ◽  
Vol 13 (14) ◽  
pp. 2848
Author(s):  
Hao Sun ◽  
Qian Xu
Keyword(s):  
Machine Learning ◽  
Soil Moisture ◽  
Water Resource Management ◽  
Large Scale ◽  
Gap Filling ◽  
Spatial Continuity ◽  
Study Results ◽  
Data Gaps

Obtaining large-scale, long-term, and spatial continuous soil moisture (SM) data is crucial for climate change, hydrology, and water resource management, etc. ESA CCI SM is such a large-scale and long-term SM (longer than 40 years until now). However, there exist data gaps, especially for the area of China, due to the limitations in remote sensing of SM such as complex topography, human-induced radio frequency interference (RFI), and vegetation disturbances, etc. The data gaps make the CCI SM data cannot achieve spatial continuity, which entails the study of gap-filling methods. In order to develop suitable methods to fill the gaps of CCI SM in the whole area of China, we compared typical Machine Learning (ML) methods, including Random Forest method (RF), Feedforward Neural Network method (FNN), and Generalized Linear Model (GLM) with a geostatistical method, i.e., Ordinary Kriging (OK) in this study. More than 30 years of passive–active combined CCI SM from 1982 to 2018 and other biophysical variables such as Normalized Difference Vegetation Index (NDVI), precipitation, air temperature, Digital Elevation Model (DEM), soil type, and in situ SM from International Soil Moisture Network (ISMN) were utilized in this study. Results indicated that: 1) the data gap of CCI SM is frequent in China, which is found not only in cold seasons and areas but also in warm seasons and areas. The ratio of gap pixel numbers to the whole pixel numbers can be greater than 80%, and its average is around 40%. 2) ML methods can fill the gaps of CCI SM all up. Among the ML methods, RF had the best performance in fitting the relationship between CCI SM and biophysical variables. 3) Over simulated gap areas, RF had a comparable performance with OK, and they outperformed the FNN and GLM methods greatly. 4) Over in situ SM networks, RF achieved better performance than the OK method. 5) We also explored various strategies for gap-filling CCI SM. Results demonstrated that the strategy of constructing a monthly model with one RF for simulating monthly average SM and another RF for simulating monthly SM disturbance achieved the best performance. Such strategy combining with the ML method such as the RF is suggested in this study for filling the gaps of CCI SM in China.

High-throughput cocrystal slurry screening by use of in situ Raman microscopy and multi-well plate

2010 ◽  
Vol 399 (1-2) ◽  
pp. 52-59 ◽  
Author(s):  
Takashi Kojima ◽  
Shunichirou Tsutsumi ◽  
Katsuhiko Yamamoto ◽  
Yukihiro Ikeda ◽  
Toshiya Moriwaki
Keyword(s):  
High Throughput ◽  
Raman Microscopy ◽  
In Situ Raman

scholarly journals Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

2016 ◽  
Vol 82 (15) ◽  
pp. 4757-4766 ◽  
Author(s):  
Caterina R. Giner ◽  
Irene Forn ◽  
Sarah Romac ◽  
Ramiro Logares ◽  
Colomban de Vargas ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
High Throughput ◽  
Relative Abundance ◽  
Ribosomal Dna ◽  
18S Rdna ◽  
High Throughput Sequencing ◽  
454 Sequencing ◽  
Epifluorescence Microscopy ◽  
Environmental Sequencing

ABSTRACTHigh-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescencein situhybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances.IMPORTANCEDirect studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescencein situhybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed.

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