Due to the overwhelming sparsity in microbiome datasets, some filtering is required in order to infer microbe-metabolite interactions. We chose to filter out microbes that appear in less than 10 samples, since these microbes don’t have enough information to infer which metabolites are co-occurring with them. In other words the mmvec model has too many degrees of freedom to perform inference on these microbes. For the cystic fibrosis study, there were 172 samples and after filtering there were 138 unique microbial taxa and 462 metabolite features. For the biocrust soils study, there were 19 samples and after filtering there were 466 unique microbial taxa and 85 metabolite features. For the murine high fat diet study, there were 434 samples and after filtering there were 902 microbes and 11978 metabolites. For the IBD dataset, there were 13920 features in the c18 LCMS dataset, 26966 features in the c8 LCMS dataset and 562 taxa. Cross validation was performed across all studies to evaluate overfitting. In the desert biocrust soils experiment, 1 sample out of 19 samples was randomly chosen to be left out for cross-validation. In all of the other studies, 10 samples were randomly chosen to be left out for cross-validation. All of the analyses can be found under https://github.com/knightlab-analyses/multiomic-cooccurences .
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Laboratory Procedure
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Laser Capture Microdissection
Laser Capture Microdissection
Laser Capture Microdissection is a powerful technique that allows researchers to isolate and extract specific cells or tissues from a heterogeneous sample with high precision.
This method uses a laser to selectively remove target cells, enabling in-depth molecular analysis and the study of complex biological processes.
Coupled with advanced analytical tools, Laser Capture Microdissection has become an invaluable tool for a wide range of applications, including cancer research, stem cell biology, and neuroscience.
By providing a means to isolate pure populations of cells, this technqiue enhances reproducibility and enables researchers to gain novel insights into the mechanisms underlying health and disease.
This method uses a laser to selectively remove target cells, enabling in-depth molecular analysis and the study of complex biological processes.
Coupled with advanced analytical tools, Laser Capture Microdissection has become an invaluable tool for a wide range of applications, including cancer research, stem cell biology, and neuroscience.
By providing a means to isolate pure populations of cells, this technqiue enhances reproducibility and enables researchers to gain novel insights into the mechanisms underlying health and disease.
Most cited protocols related to «Laser Capture Microdissection»
Cystic Fibrosis
Diet, High-Fat
Laser Capture Microdissection
Microbial Interactions
Microbiome
Mus
Freezing
Frozen Sections
Gene Expression
Intestinal Polyps
Laser Capture Microdissection
Medical Devices
MicroRNAs
Mus
Polyps
SMAD4 protein, human
Tamoxifen
Tissues
Biopsy
BLOOD
Bones
Core Needle Biopsy
Dreams
Ethics Committees, Research
Freezing
Germ Line
Homo sapiens
Laser Capture Microdissection
Males
Neoplasm Metastasis
Neoplasms
Patients
Prostate Cancer
Tissues
The four GC methods used to predict functional interactions among E. coli proteins were based on: (1) functional linkages among genes which fuse to form a single open reading frame in at least one other genome, i.e., gene fusion [48 (link)]; (2) the mutual information of the coordinated presence or absence of pairs of genes across a set of 440 nonredundant genomes, i.e., phylogenetic profiles [51 (link),97 (link)]; and the natural chromosomal association of bacterial genes in operons as detected by two alternative methods, namely (3) the tendency of genes forming operons to show small intergenic distances [98 (link),99 ], and (4) the conservation of gene order, in which a confidence value for each pair of adjacent genes in the same strand was used as indicator that those genes likely form an operon, as compared with the conservation of adjacent genes in opposite strands [53 (link)]. For the last two methods, subsequent operon rearrangements were detected by genomic mapping of orthologs across 440 nonredundant bacterial genomes [55 (link)].
For all four GC methods, we used the BLAST-BDBHs as an operational definition of orthology (seeProtocol S5 for details). To avoid circularity, the prediction scores of the four GC methods were benchmarked separately using proteins belonging to the same metabolic pathway according to EcoCyc [11 (link)] as positive reference set, and proteins in different pathways as negatives (Protocol S5 ). A single, unified high-confidence functional association network was then constructed by integrating the interaction predictions generated by the four GC methods using the same scoring model [61 (link)] used to integrate the MALDI and LCMS data (Protocol S6 ).
For all four GC methods, we used the BLAST-BDBHs as an operational definition of orthology (see
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Chromosomes
Escherichia coli Proteins
Gene Fusion
Gene Order
Gene Rearrangement
Genes
Genes, Bacterial
Genes, vif
Genome
Genome, Bacterial
Laser Capture Microdissection
Linkage, Genetic
Operon
Proteins
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Aortic Valve Stenosis
Autopsy
Calcinosis
Cell Migration Assays
Cells
CIC protein, human
Disease Progression
Donors
Fibrosis
Gene Expression Profiling
Genes
Homo sapiens
Laser Capture Microdissection
Operative Surgical Procedures
Pathologists
Patients
Peptides
Physical Examination
Proteins
Stenosis
Tissues
Woman
Most recents protocols related to «Laser Capture Microdissection»
Example 7
LC-ESI-HRMS Method for the Determination of Varenicline Nitroso-Drug Substance Related Impurity, U.S. FDA, Aug. 6, 2021, www.fda.gov/media/151470/download (accessed Feb. 27, 2022) can be used to test for impurities.
Other analytical methods for the entire process can be used to test for impurities. The methods are validated as per ICH guideline.
For example, HPLC RS methods are used for quantifying the impurities. The nitrosamines, monomethyl and dimethyl tartaric acid esters are quantified by LCMS methods.
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Esters
High-Performance Liquid Chromatographies
Laser Capture Microdissection
Nitrosamines
Pharmaceutical Preparations
tartaric acid
Varenicline
Example 64
A 1:100 back-dilution from overnight culture of SYN-PKU-2002 was grown to early log phase for 1.5 h before moving to the anaerobic chamber for 4 hours in the presence of 1 mM IPTG and 0.1% arabinose for induction as described herein. To perform activity assay, 1e8 cells were resuspended and incubated in assay buffer (M9 media with 0.5% glucose, 50 mM Phe, and 50 mM MOPS with 50 mM phenylalanine). Supernatant samples were taken over time and TCA (the product of PAL) was measured by absorbance at 290 nm to determine the rate of TCA production/PAL activity. Phenylpyruvate was measured using LCMS methods described herein. Results are shown in FIG. 16A and FIG. 16B.
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3-phenylpyruvate
Arabinose
Biological Assay
Buffers
Cells
Glucose
Isopropyl Thiogalactoside
Laser Capture Microdissection
morpholinopropane sulfonic acid
Phenylalanine
TCL1B protein, human
Technique, Dilution
Example 164
5-(7-Methylpyrazolo[1,5-a]pyridin-6-yl)spiro[3H-benzofuran-2,4′-piperidine] 2HCl was synthesized using tert-butyl 5-(7-methylpyrazolo[1,5-a]pyridin-6-yl)spiro[3H-benzofuran-2,4′-piperidine]-1′-carboxylate and 4 M HCl in dioxane. Analysis: LCMS m/z=320 (M+1); 1H NMR (400 MHz, DMSO-d6) δ: 8.94 (dd, J=4.0, 1.8 Hz, 1H), 8.38 (dd, J=8.3, 1.8 Hz, 1H), 7.75 (d, J=8.8 Hz, 1H), 7.57 (d, J=8.5 Hz, 1H), 7.55-7.52 (m, 1H), 7.47 (d, J=1.5 Hz, 1H), 7.38 (dd, J=8.3, 2.0 Hz, 1H), 6.88 (d, J=8.3 Hz, 1H), 6.01 (s, 2H), 3.91 (s, 3H), 3.57-3.39 (m, 4H), 3.12 (s, 2H), 1.86-1.67 (m, 4H).
Step 2.
5-(7-Methylpyrazolo[1,5-a]pyridin-6-yl)spiro[3H-benzofuran-2,4′-piperidine]-1′-carboxamide was synthesized using 5-(7-methylpyrazolo[1,5-a]pyridin-6-yl)spiro[3H-benzofuran-2,4′-piperidine] 2HCl and trimethylsilyl isocyanate. Analysis: LCMS m/z=363 (M+1); 1H NMR (400 MHz, DMSO-d6) δ: 8.05 (d, J=2.3 Hz, 1H), 7.64 (d, J=8.8 Hz, 1H), 7.27 (d, J=1.5 Hz, 1H), 7.16 (d, J=8.8 Hz, 2H), 6.86 (d, J=8.3 Hz, 1H), 6.68 (d, J=2.3 Hz, 1H), 6.01 (s, 2H), 3.53-3.37 (m, 4H), 3.10 (s, 2H), 2.65 (s, 3H), 1.83-1.67 (m, 4H).
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1H NMR
benzofuran
Dioxanes
Isocyanates
Laser Capture Microdissection
piperidine
Sulfoxide, Dimethyl
TERT protein, human
Example 190
Analysis: LCMS (ESI): 399 (M+H); 1H NMR (400 MHz, methanol-d4) δ 9.13 (d, J=2.3 Hz, 1H), 8.62-8.52 (m, 1H), 8.09-7.98 (m, 2H), 7.85-7.71 (m, 3H), 7.7-7.64 (m, 1H), 7.47-7.34 (m, 2H), 5.59-5.46 (m, 1H), 4.73-4.69 (m, 1H), 4.18-3.77 (m, 4H), 3.74-3.52 (m, 2H), 3.43 (s, 2H), 2.26-1.85 (m, 6H).
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1H NMR
Laser Capture Microdissection
Methanol
tetrahydrofuran
Example 146
This compound was synthesized using CDI, O-(tetrahydro-2H-pyran-2-yl)hydroxylamine, and 6-(3-isoquinolyl)spiro[chromane-2,4′-piperidine] TFA salt. Analysis: LCMS m/z=474 (M+1); 1H NMR (400 MHz, CDCl3) δ: 9.30 (s, 1H), 8.00-7.95 (m, 2H), 7.92 (d, J=2.3 Hz, 1H), 7.88-7.82 (m, 2H), 7.68 (td, J=7.6, 1.1 Hz, 1H), 7.58-7.52 (m, 1H), 7.30 (s, 1H), 6.97 (d, J=8.5 Hz, 1H), 5.01-4.84 (m, 1H), 4.02-3.91 (m, 1H), 3.90-3.78 (m, 2H), 3.71-3.57 (m, 1H), 3.41-3.26 (m, 2H), 2.91 (t, J=6.8 Hz, 2H), 1.95-1.76 (m, 7H), 1.71-1.53 (m, 5H).
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1H NMR
Hydroxylamine
Laser Capture Microdissection
piperidine
Pyrans
Salts
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More about "Laser Capture Microdissection"
Laser Capture Microdissection (LCM) is a powerful analytical technique that enables researchers to precisely isolate and extract specific cells or tissue samples from a heterogeneous population.
This method utilizes a laser to selectively remove target cells, facilitating in-depth molecular analysis and the study of complex biological processes.
LCM is widely used in a variety of applications, including cancer research, stem cell biology, and neuroscience.
By providing a means to isolate pure populations of cells, this technique enhances reproducibility and enables researchers to gain novel insights into the mechanisms underlying health and disease.
LCM can be coupled with advanced analytical tools, such as mass spectrometry (e.g., LCMS-2020, LCMS-IT-TOF, LCMS-8050, LCMS-8040, LCMS-8060, LCMS-IT-TOF) and RNA extraction kits (e.g., RNeasy Micro Kit), to facilitate comprehensive molecular profiling and characterization of the isolated cells.
The precision and selectivity of LCM make it an invaluable tool for researchers, allowing them to focus their analysis on specific cell types or tissues of interest.
This technique has become indispensable in fields like oncology, where the ability to isolate and analyze tumor cells can lead to a better understanding of cancer progression and the development of targeted therapies.
In addition to its scientific applications, LCM has also found use in forensic investigations, where it can be used to isolate and analyze trace evidence from complex samples.
Overall, Laser Capture Microdissection represents a powerful and versatile technique that continues to drive advancements in our understanding of biological systems and disease processes.
By combining LCM with other analytical tools, researchers can unlock new insights and accelerate the pace of scientific discovery.
This method utilizes a laser to selectively remove target cells, facilitating in-depth molecular analysis and the study of complex biological processes.
LCM is widely used in a variety of applications, including cancer research, stem cell biology, and neuroscience.
By providing a means to isolate pure populations of cells, this technique enhances reproducibility and enables researchers to gain novel insights into the mechanisms underlying health and disease.
LCM can be coupled with advanced analytical tools, such as mass spectrometry (e.g., LCMS-2020, LCMS-IT-TOF, LCMS-8050, LCMS-8040, LCMS-8060, LCMS-IT-TOF) and RNA extraction kits (e.g., RNeasy Micro Kit), to facilitate comprehensive molecular profiling and characterization of the isolated cells.
The precision and selectivity of LCM make it an invaluable tool for researchers, allowing them to focus their analysis on specific cell types or tissues of interest.
This technique has become indispensable in fields like oncology, where the ability to isolate and analyze tumor cells can lead to a better understanding of cancer progression and the development of targeted therapies.
In addition to its scientific applications, LCM has also found use in forensic investigations, where it can be used to isolate and analyze trace evidence from complex samples.
Overall, Laser Capture Microdissection represents a powerful and versatile technique that continues to drive advancements in our understanding of biological systems and disease processes.
By combining LCM with other analytical tools, researchers can unlock new insights and accelerate the pace of scientific discovery.