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Ice

Ice is a solid form of water that occurs naturally on Earth.
It can be found in various forms, such as glaciers, icebergs, and sea ice, and plays a crucial role in the Earth's climate and ecosystems.
Ice is an important subject of study in many scientific fields, including climatology, glaciology, and cryobiology.
Reserchers use advanced techniques, such as AI-driven platforms like PubCompare.ai, to optimize their ice-related studies, locate the best protocols, and improve reproducibility and accuracy.
By leveraging the power of these tools, scientists can discover new insights and advance our understanding of this fascinating natural phenomenon.

Most cited protocols related to «Ice»

1
Rapid Detection of Integrative and Conjugative Elements in Bacterial Genomes
Cited 108 times
We have developed a tool, called ICEfinder, available online and as a standalone version for the rapid detection of ICEs and IMEs in bacterial genome sequences. ICEfinder employs a method we called ‘Pattern-based hit co-localization’ (see the Supplementary Methods) that detects the signature sequences of the recombination modules and conjugation modules based on their profile HMMs (19 (link)) (Supplementary Table S2, S3 and Figure S4). It also searches for the oriT region using the approach proposed by oriTfinder (18 (link)). It then co-localizes, filters and groups the corresponding genes. At last, those elements carrying an integrase gene, a relaxase gene and T4SS gene clusters (12 (link),20 (link)) are considered as T4SS-type ICEs, while those without T4SS but with integrase, replication and the AICE translocation-related proteins are thought to be putative AICEs. Those without T4SS but with integrase and relaxase are tagged as putative IMEs. ICEfinder also tries to detect some particular IMEs with integrase and an oriT but no relaxase. ICEfinder employs ARAGORN (21 (link)) with the default parameters to identify the 3′ termini of the tRNA/tmRNA genes as the putative ICE insertion sites. It also uses Vmatch (http://vmatch.de/) with the default options to detect the directed repeats as the tRNA-distal boundaries. The acquired antibiotic resistance genes and virulence factors are also identified by NCBI BLASTp (22 (link)) with the cut-off of Ha-value of 0.64 (12 (link)).
The ICEfinder online tool allows users to submit a GenBank file containing a nucleotide sequence and its annotation as a query. A FASTA format file of a raw nucleotide sequence is also accepted, which is annotated using our gene annotation tool CDSeasy (12 (link)) and is then used as the input for the following ICE detection. ICEfinder uses the CGView circular genome visualization tool (23 (link)) to display the distribution of the predicted T4SS-type ICEs, IMEs and AICEs in the query bacterial genome. In addition, the ICEfinder has a comparison module (Supplementary Figure S5) that allows performing the alignment between the identified ICE loci against the ICEberg-archived ICEs using MultiGeneBlast (24 (link)).
Liu M., Li X., Xie Y., Bi D., Sun J., Li J., Tai C., Deng Z, & Ou H.Y. (2018). ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Research, 47(Database issue), D660-D665.
Publication 2018
Antibiotic Resistance, Microbial Base Sequence DNA Replication Gene Annotation Gene Clusters Genes Genome Genome, Bacterial Hypertelorism, Severe, With Midface Prominence, Myopia, Mental Retardation, And Bone Fragility Ice Icebergs Integrase Proteins Recombination, Genetic tmRNA Transfer RNA Translocation, Chromosomal Virulence Factors
2
Evaluating Linked Population Datasets
Cited 39 times
After record linkage was complete, identifiers (e.g., names) were removed and these anonymized datasets were used to calculate linkage rates and prevalence estimates for linked and unlinked datasets. We examined the number of records linked by deterministic and probabilistic record linkage in each step of the process, as well as the linkage rates over time. The prevalence rates of socio-demographic and geographic characteristics were calculated for the records that did and did not link to the RPDB population (i.e. where an ICES unique identifier could not be attached to the record). Given the very large sample sizes, p-values were not used for statistical testing; instead, prevalence estimates between the linked and unlinked samples were compared using standardized differences to assess systematic bias as suggested by Cohen [31 ], with 0.2, 0.5, and 0.8 representing small, moderate, and large standardized differences, respectively. Data elements of interest in the ORG-VSD data included age at death, sex, cause of death and fiscal year of death. Cause of death was categorized into broad categories of death based on ICD-9 codes. Data elements of interest in the IRCC-PR database included immigrant class, sex, marital status, and age at landing, year of entry into Ontario, as well as geographical attributes such as country of birth. The geographic attributes were grouped into 4 main world regions and 18 sub-regions according to the Standard Classification of Countries and Areas of Interest.
Chiu M., Lebenbaum M., Lam K., Chong N., Azimaee M., Iron K., Manuel D, & Guttmann A. (2016). Describing the linkages of the immigration, refugees and citizenship Canada permanent resident data and vital statistics death registry to Ontario’s administrative health database. BMC Medical Informatics and Decision Making, 16, 135.
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Publication 2016
Childbirth Ice Immigrants
3
Chromatin Immunoprecipitation (ChIP) from Tissue
Cited 30 times

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2009
Bath BP 400 Buffers Cell Extracts Cell Lines Cell Nucleus Cells Chromatin Cytosol Deoxycholate Dietary Fiber DNA Chips Edetic Acid Egtazic Acid Formaldehyde Glycerin HEPES Ice Igepal CA-630 isolation N-lauroylsarcosine Nonidet P-40 Polypropylenes Protease Inhibitors Proteins Sepharose Sodium Chloride Tissues Triton X-100 Tromethamine Trypan Blue
4
Quantitative Determination of CAA and CCA
Cited 27 times
As a reference standard for the quantitative determination of CAA and CCA, a TCA-soluble fraction of S. mansoni adult worm antigen, AWA-TCA (Deelder et al. 1980 (link)), was used in a similar manner as described by Polman et al. (2000) (link). Soluble egg antigen (SEA) was prepared following similar protocols as for AWA, using S. mansoni eggs recovered from the livers of infected hamsters. Soluble crude cercarial antigen preparation (SCAP) was prepared from freshly shed cercariae, collected after precipitation under gravity in ice-cooled water, and subsequently treated similarly to SEA or AWA.
CORSTJENS P.L., DE DOOD C.J., KORNELIS D., FAT E.M., WILSON R.A., KARIUKI T.M., NYAKUNDI R.K., LOVERDE P.T., ABRAMS W.R., TANKE H.J., VAN LIESHOUT L., DEELDER A.M, & VAN DAM G.J. (2014). Tools for diagnosis, monitoring and screening of Schistosoma infections utilizing lateral-flow based assays and upconverting phosphor labels. Parasitology, 141(14), 1841-1855.
Publication 2014
Adult Antigens Antigens, Helminth Cercaria Eggs Gravity Hamsters Ice Liver
5
Metabolite Extraction from Cultured Cells
Cited 22 times

Living cells, cultured on petri dishes or multi-well plates. Cells can be incubated with a labeled tracer (for example: 13C or 15N) for downstream flux analysis

Cells should be confluent in the wells, with a consistent cell number between samples. The amount of cells will vary depending on cell type used, but we have found using around 1 million cells in each well of a 6-well multiwell plate gives good results for both techniques.

0.9% NaCl at room temperature

High purity (MS grade) methanol at −20 °C

High purity (MS grade) chloroform at −20 °C

Millipore or equivalently pure water on ice

Cell scrapers

Eppendorf tube shaker at 4 °C

Centrifuge at 4 °C

Note: This list does not include generic laboratory equipment, which are assumed to be available.

The metabolic profile of a cell can change in as little as a few seconds. Therefore, the most important step in metabolite extraction is the quenching of metabolism; this ensures that the metabolic pathways in the cells do not continue to function, and that the cellular state at the point of extraction is as close as possible to the desired analysis time point [1] (link). This quenching must be performed quickly. There has been much discussion as to which extraction fluids are best for quenching and measuring metabolites [2,3] ; however, it is generally agreed that a mixture of water and methanol provides the best extraction efficiency with minimal loss. Both fluids are added directly to the cells, and should be kept as cold as possible (methanol at −20 °C and water on ice).
Once the metabolic processes have been quenched, the next step is to lyse the cells, separating both the polar and non-polar metabolites from the other cellular substances at the same time. While methanol and water will extract the polar metabolites from a sample, non-polar metabolites must be separated with a non-polar solvent. Therefore, we use chloroform [4] (link) with the methanol/water mixture to separate the polar and non-polar metabolites efficiently. Adherent cells quenched with methanol and water are scraped from the multi-well plates and added to cold chloroform to allow for separation of polar and non-polar phases. These extracts are agitated to complete cell lysis and centrifuged to fully separate the layers.
This is a crucial step for experimental consistency; different amounts of cells in different samples will lead to incorrect comparisons of metabolite levels (which can also occur with cell seeding). Therefore, care should be taken to adequately scrape all wells and transfer as much cellular material as possible from the wells to the chloroform.
After these steps, the cells are shaken to completely lyse the membranes allowing for a more efficient extraction of all possible biomolecules. After shaking, there should be a clear separation between the polar and non-polar phase for the metabolites, with a well-defined interphase containing proteins and nucleic acids.
Sapcariu S.C., Kanashova T., Weindl D., Ghelfi J., Dittmar G, & Hiller K. (2014). Simultaneous extraction of proteins and metabolites from cells in culture. MethodsX, 1, 74-80.
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Publication 2014
Cells Chloroform Cold Temperature Fever Generic Drugs Hyperostosis, Diffuse Idiopathic Skeletal Ice Interphase Metabolic Profile Metabolism Methanol Neoplasm Metastasis Normal Saline Nucleic Acids Proteins Solvents Somatostatin-Secreting Cells Tissue, Membrane

Most recents protocols related to «Ice»

1
Synthesis of 2,5-Difluoro-4-Aminophenyl Piperazine Derivative
Not available on PMC !

Example 161

[Figure (not displayed)]

To a solution of 2-(piperazin-1-yl)ethanol (0.73 g, 5.6 mmol, 1 eq.) in DMF (10 mL) was added K2CO3 (1.56 g, 11.3 mmol, 2 eq.) followed by 1,2,4-trifluoro-5-nitrobenzene (1 g, 5.6 mmol, 1 eq.) and the mixture was stirred at 0° C. for 1 hour. The mixture was poured into ice-water (100 mL), extracted by EA (3×40 mL), and the organic layers were combined, washed with brine (150 mL), concentrated and purified via column chromatography (10-95% CH3CN—H2O) to afford 2-(4-(2,5-difluoro-4-nitrophenyl)piperazin-1-yl)ethanol (0.65 g, 41%) as a yellow solid.

[Figure (not displayed)]

To a solution of 2-(4-(2,5-difluoro-4-nitrophenyl)piperazin-1-yl)ethanol (0.65 g, 2.3 mmol) in MeOH (50 mL) was added Pd/C (100 mg) and the resulting mixture was stirred at r.t. overnight. The Pd/C was removed by filtration and the filtrate was concentrated to afford 2-(4-(4-amino-2,5-difluorophenyl)piperazin-1-yl)ethanol (0.58 g, 99%).

[Figure (not displayed)]

To a suspension of 2-(4-(4-amino-2,5-difluorophenyl)piperazin-1-yl)ethanol (270 mg, 0.88 mmol, 1 eq.) and N-(3-(2-chloroquinazolin-8-yl)phenyl)acrylamide (225 mg, 0.88 mmol, 1 eq.) in n-BuOH (10 mL) was added TFA (0.5 mL, 4.4 mmol, 5 eq.) and the resulting mixture was stirred at 90° C. overnight. The mixture was concentrated, diluted with DCM (20 mL), washed with Na2CO3 solution (20 mL), dried, concentrated and purified via column chromatography (DCM/MeOH=10/1) to afford N-(3-(2-((2,5-difluoro-4-(4-(2-hydroxyethyl)piperazin-1-yl)phenyl)amino)quinazolin-8-yl)phenyl)acrylamide (120 mg, 26%) as yellow solid. LRMS (M+H+) m/z calculated 531.2, found 531.2. 1H NMR (DMSO-d6, 400 MHz) δ 10.18 (s, 1H), 9.37 (s, 1H), 9.17 (s, 1H), 7.97-7.94 (m, 3H), 7.83-7.74 (m, 2H), 7.50-7.39 (m, 3H), 6.90-6.85 (m, 1H), 6.48-6.41 (m, 1H), 6.23 (dd, 1H), 5.73 (dd, 1H), 4.42 (t, 1H), 3.55-3.50 (m, 2H), 2.94-2.91 (m, 4H), 2.55-2.54 (m, 4H), 2.44 (t, 2H).

US11865120B2. Substituted quinazolines for inhibiting kinase activity (2024-01-09). NeuPharma, Inc [US]. Inventors: Xiangping Qian [US], Yong-Liang Zhu [US].
Full text: Click here
Patent 2024
1H NMR Acrylamide brine Chromatography Ethanol Filtration Ice Nitrobenzenes Piperazine potassium carbonate Sulfoxide, Dimethyl
2
Methylation of 15 to Afford 16
Not available on PMC !

Example 19

[Figure (not displayed)]

To a solution of 15 (408 g, 0.77 mol, 1.0 eq.) and methyl iodide (145 mL, 2.32 mol, 3.0 eq.) in THF (4 L) was added sodium hydride (60% dispersion in mineral oil, 62.2 g, 1.55 mol, 2.0 eq.) at 0° C. The resulting mixture was stirred at 0° C. overnight and then poured onto ice-water cooled saturated ammonium chloride (5 L) with vigorous stirring. The mixture was then extracted with EtOAc (3×500 mL) and the organic layers were dried, filtered, concentrated and purified by column chromatography with a gradient of 15-35% EtOAc in petroleum ether to afford product 16 (388 g, 93% yield) as a light yellow oil. 1H NMR (500 MHz, CDCl3) δ 8.09 (s, 1H), 4.95 (d, J=6.6 Hz, 1H), 4.41 (q, J=7.1 Hz, 2H), 3.56 (d, J=9.5 Hz, 1H), 2.98 (s, 3H), 2.27-2.06 (m, 4H), 1.83-1.70 (m, 2H), 1.41 (t, J=7.2 Hz, 3H), 1.29 (ddd, J=8.9, 6.8, 1.6 Hz, 3H), 1.01 (d, J=6.6 Hz, 3H), 0.96 (dt, J=8.0, 2.9 Hz, 15H), 0.92 (d, J=6.6 Hz, 3H), 0.90 (d, J=6.7 Hz, 3H). MS ESI m/z calcd for C25H46N5O4SSi [M+H]+ 540.30, found 540.30.

US11873281B2. Conjugates of cell binding molecules with cytotoxic agents (2024-01-16). HANGZHOU DAC BIOTECH CO., LTD. [CN], None [US], None [CN], None [CN]. Inventors: R. Yongxin Zhao [US], Yue Zhang [CN], Yourang Ma [CN].
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Patent 2024
1H NMR Anabolism Chloride, Ammonium Chromatography Ice Light methyl iodide naphtha Oil, Mineral sodium hydride
3
Synthesis of 5-(p-Chlorophenyl)-6-(1-{[p-(Trifluoromethyl)Phenyl]Methyl}-1H-Pyrazol-4-yl)-4-Pyrimidinylamine Derivative
Not available on PMC !

Example 45

A stirring solution of 5-(p-chlorophenyl)-6-(1-{[p-(trifluoromethyl)phenyl]methyl}-1H-pyrazol-4-yl)-4-pyrimidinylamine (example 4, 150 mg, 0.35 mmol) in THF (1.8 mL) under an inert atmosphere of N2 was treated with sodium hydride (56 mg of a 60% dispersion in oil, 1.40 mmol) and the resulting mixture was stirred for 30 minutes at room temperature. Methanesulfonyl chloride (41 μL, 0.53 mmol) was added via syringe and the resulting mixture was stirred at room temperature for 2 hours. The reaction was carefully poured onto ice/water and the product was extracted with ethyl acetate. The organic layer was washed with 1 N aqueous HCl solution and brine, dried over anhydrous MgSO4, filtered and evaporated. The crude product was purified by silica-gel column chromatography, eluting with hexanes/EtOAc mixture to provide the title compound as a white solid (63 mg, 0.124 mmol, 35%). HPLC/MS (ESI) m/z 508.3 (M++H+). Method 1 retention time=2.70 min.

US11866421B2. Pyrimidine and pyridine amine compounds and usage thereof in disease treatment (2024-01-09). Epigen Biosciences, Inc. [US]. Inventors: Graham Beaton [US], Fabio Tucci [US], Satheesh Ravula [US], Suk Joong Lee [US], Chandravadan Shah [US].
Full text: Click here
Patent 2024
Amines Atmosphere brine Chromatography ethyl acetate Gel Chromatography Hexanes High-Performance Liquid Chromatographies Ice methanesulfonyl chloride pyrazole Retention (Psychology) Silica Gel Silicon Dioxide sodium hydride Sulfate, Magnesium Syringes
4
Synthesis of AM393-A from AM351-A
Not available on PMC !

Example 50

[Figure (not displayed)]

Synthesis of AM393-A.

To a cooled (0° C.) solution of NaH (190 mg, 50% in mineral oil, 4.0 mmol) in DMF (5 mL) was added AM351-A (400 mg, 1.6 mmol) and the mixture was stirred at room temperature for 20 min. The reaction mixture was cooled to 0° C. and methyl iodide was added. The reaction mixture was stirred with slow warming to room temperature for 1 h. The reaction mixture was quenched with ice-cold water (10 mL) and the product was extracted with DCM (20 mL×3). The combined organic layer was washed with brine (20 mL) and dried over anhydrous Na2SO4. The solvent was removed in vacuo and the residue was purified by column chromatography on silica gel (PE:EtOAc=90:10˜85:15) to give AM393-A (360 mg, 85%) as a yellowish gum.

Compound AM393 (120 mg, 99%, a grey solid) was synthesized in a similar procedure used for AM351 from AM351-I)

US11858939B2. Hetero-halo inhibitors of histone deacetylase (2024-01-02). Alkermes, Inc. [US]. Inventors: Martin R. Jefson [US], John A. Lowe, III [US], Fabian Dey [CH], Andreas Bergmann [DE], Andreas Schoop [DE], Nathan Oliver Fuller [US].
Full text: Click here
Patent 2024
Anabolism brine Chromatography Cold Temperature Ice methyl iodide Oil, Mineral Silica Gel Solvents
5
Synthesis of Fluorinated Compound 12b
Not available on PMC !

Example 4

[Figure (not displayed)]

A PTFE bottom reactor was charged with 2 Kg of compound 12a, and 2.1 Kg of concentrated sulfuric acid was added. Then the mixture was heated with stirring for about 4 hours at 45-55° C. (30% aq NaOH scrubber was used to absorb HF generated in the reaction). The mixture was then added dropwise to ice water (5 kg/5 kg). Quench temperature was maintained at 0° C. The organic phase was separated and the aqueous layer was extracted with DCM (2L, 1 V) once. The organic layers were combined together and DCM was removed under vacuum. The crude sample was purified by vacuum distillation. Main fraction of compound 12b was collected at 62-66° C./20 mmHg. 1H NMR (400 MHz, CDCl3): δ=3.89 ppm (s, 6H); 13C NMR (100 MHz, CDCl3): δ=53.95 ppm (—CH3), 105.98 ppm (—CF2—, 1JCF 259.1 Hz), 160.94 ppm (—CO—, 2JCF 30.9 Hz); 19F NMR (188 MHz, CDCl3): δ=−112.05 ppm (s, 2F).

US11873305B2. Processes for synthesis of substituted indole intermediates for the synthesis of serd compounds (2024-01-16). Genentech, Inc. [US], Hoffmann-La Roche Inc. [US]. Inventors: Haiming Zhang [US], Jie Xu [US], Georg Wuitschik [CH], Remy Angelaud [US], Sebastian Herold [DE], Alfred Stutz [CH], Tobias Bruetsch [CH], Johannes Burkhard [CH].
Full text: Click here
Patent 2024
1H NMR Carbon-13 Magnetic Resonance Spectroscopy Distillation Ice Polytetrafluoroethylene sulfuric acid Vacuum

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1
Sas version 9 by SAS Institute
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SAS version 9.4 is a statistical software package. It provides tools for data management, analysis, and reporting. The software is designed to help users extract insights from data and make informed decisions.
2
Trizol by Thermo Fisher Scientific
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TRIzol is a monophasic solution of phenol and guanidine isothiocyanate that is used for the isolation of total RNA from various biological samples. It is a reagent designed to facilitate the disruption of cells and the subsequent isolation of RNA.
3
Cellulase by Merck Group
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Cellulase is a type of enzyme that catalyzes the hydrolysis of cellulose, a major structural component of plant cell walls. It is used in various industrial and research applications.
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The BCA Protein Assay Kit is a colorimetric detection and quantification method for total protein concentration. It utilizes bicinchoninic acid (BCA) for the colorimetric detection and quantification of total protein. The assay is based on the reduction of Cu2+ to Cu1+ by protein in an alkaline medium, with the chelation of BCA with the Cu1+ ion resulting in a purple-colored reaction product that exhibits a strong absorbance at 562 nm, which is proportional to the amount of protein present in the sample.
5
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The UV-mini 1240 PC is a compact UV-Visible spectrophotometer designed for general purpose analysis. It features a wavelength range of 190 to 1100 nm and can be operated via a personal computer. The instrument provides accurate and reliable measurements for a variety of applications.
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Histodenz is a density gradient medium used for the separation and purification of cells, organelles, and other biological particles. It is a non-toxic, non-ionic solute that can be used to create density gradients for centrifugation. Histodenz provides a stable, inert matrix for the separation of a variety of biological samples.
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Pectinase is an enzyme used in laboratory applications. It functions to break down pectin, a complex carbohydrate found in plant cell walls.
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The BCA assay is a colorimetric detection method used to quantify the total protein concentration in a sample. It relies on the reduction of copper ions by proteins in an alkaline environment, which produces a purple-colored complex that can be measured spectrophotometrically.
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Pvdf membrane by Merck Group
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PVDF membranes are a type of laboratory equipment used for a variety of applications. They are made from polyvinylidene fluoride (PVDF), a durable and chemically resistant material. PVDF membranes are known for their high mechanical strength, thermal stability, and resistance to a wide range of chemicals. They are commonly used in various filtration, separation, and analysis processes in scientific and research settings.

More about "Ice"

Ice is a solid, crystalline form of water that is found naturally on Earth.
It plays a crucial role in the planet's climate and ecosystems, and is an important subject of study in fields like climatology, glaciology, and cryobiology.
Researchers use advanced techniques, such as AI-driven platforms like PubCompare.ai, to optimize their ice-related research, locate the best protocols, and improve reproducibility and accuracy.
PubCompare.ai is a leading AI-driven platform that can help scientists discover new insights and advance their understanding of this fascinating natural phenomenon.
By leveraging the power of this tool, researchers can locate the best protocols from literature, pre-prints, and patents using advanced AI comparisons.
This can help improve the reproducibility and accuracy of their ice-related studies, whether they are working with glaciers, icebergs, or sea ice.
Beyond ice research, PubCompare.ai can also be used to optimize studies in other areas, such as those involving SAS version 9.4, TRIzol, Cellulase, BCA protein assay kit, UV-mini 1240 PC, Histodenz, Protease inhibitor cocktail, Pectinase, BCA assay, and PVDF membranes.
By taking advantage of the platform's advanced capabilities, scientists can streamline their workflow, reduce errors, and unlock new discoveries.