High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine

The lumen of the small intestine (SI) is filled with particulates: microbes, therapeutic particles, and food granules. The structure of this particulate suspension could impact uptake of drugs and nutrients and the function of microorganisms; however, little is understood about how this suspension is re-structured as it transits the gut. Here, we demonstrate that particles spontaneously aggregate in SI luminal fluid ex vivo. We find that mucins and immunoglobulins are not required for aggregation. Instead, aggregation can be controlled using polymers from dietary fiber in a manner that is qualitatively consistent with polymer-induced depletion interactions, which do not require specific chemical interactions. Furthermore, we find that aggregation is tunable; by feeding mice dietary fibers of different molecular weights, we can control aggregation in SI luminal fluid. This work suggests that the molecular weight and concentration of dietary polymers play an underappreciated role in shaping the physicochemical environment of the gut

High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine

The lumen of the small intestine (SI) is filled with particulates: microbes, therapeutic particles, and food granules. The structure of this particulate suspension could impact uptake of drugs and nutrients and the function of microorganisms; however, little is understood about how this suspension is re-structured as it transits the gut. Here, we demonstrate that particles spontaneously aggregate in SI luminal fluid ex vivo. We find that mucins and immunoglobulins are not required for aggregation. Instead, aggregation can be controlled using polymers from dietary fiber in a manner that is qualitatively consistent with polymer-induced depletion interactions, which do not require specific chemical interactions. Furthermore, we find that aggregation is tunable; by feeding mice dietary fibers of different molecular weights, we can control aggregation in SI luminal fluid. This work suggests that the molecular weight and concentration of dietary polymers play an underappreciated role in shaping the physicochemical environment of the gut

Dataset related to "Benzoquinones in the defensive secretion of a bug (Pamillia behrensii): a common chemical trait retrieved in the Heteroptera"

Behavioral and chemical data for a benzoquinone producing bug. Provided DeepLabCut project with behavioral movies, hand labeled frames for network training, neural network, and outputs from DLC and other outputs from custom machine vision pipeline. Also contains endpoint assay chemical readouts from a solid phase micro-extraction deployed during the video runs and analyzed on a GCMS.Related Publication: Benzoquinones in the defensive secretion of a bug (Pamillia behrensii): a common chemical trait retrieved in the Heteroptera Julian M. Wagner Caltech Thomas H. Naragon Adrian Brückner Caltech https://doi.org/10.1101/2020.12.11.421891 en

Benzoquinones in the defensive secretion of a bug (Pamillia behrensii): a common chemical trait retrieved in the Heteroptera

Benzoquinones are a phylogenetically widespread compound class recovered in arthropods and were recover in harvestman, millipedes and insects. While the function of benzoquinones is well studied in the predatory defense and microbial aversion, their entire phylogenetic distribution especially in insects remains to be uncovered. We here report on the metathoracic scent gland secretion of the mirid bug Pamillia behrensii, which is composed of heptan-2-one, 2-heptyl acetate, 2,3-dimethyl-1-4-benzoquinone, 2,3-dimethyl-1-4-hydroquinone as well as one unknown compound. The secretion is released upon disturbance to repel predators and serves as chemical defense. Additional morphological investigation of the gland showed that the benzoquinone-producing gland complex of P. behrensii does not differ from the usual metathoracic scent gland described from other Heteropterans. Overall, our data further underpins the widespread convergent evolution and use of benzoquinones for defense across the Arthropoda, now including the order Hemiptera

Benzoquinones in the defensive secretion of a bug (Pamillia behrensii): a common chemical trait retrieved in the Heteroptera

Benzoquinones are a phylogenetically widespread compound class recovered in arthropods and were recover in harvestman, millipedes and insects. While the function of benzoquinones is well studied in the predatory defense and microbial aversion, their entire phylogenetic distribution especially in insects remains to be uncovered. We here report on the metathoracic scent gland secretion of the mirid bug Pamillia behrensii, which is composed of heptan-2-one, 2-heptyl acetate, 2,3-dimethyl-1-4-benzoquinone, 2,3-dimethyl-1-4-hydroquinone as well as one unknown compound. The secretion is released upon disturbance to repel predators and serves as chemical defense. Additional morphological investigation of the gland showed that the benzoquinone-producing gland complex of P. behrensii does not differ from the usual metathoracic scent gland described from other Heteropterans. Overall, our data further underpins the widespread convergent evolution and use of benzoquinones for defense across the Arthropoda, now including the order Hemiptera

Dataset related to "Enforced specificity of an animal symbiosis"

Data and code (in jupyter notebooks) to generate all main text figures from the upcoming publication "Enforced specificity of an animal symbiosis"&nbsp

Table 3 - source data 1

This zip archive contains the chromatography data that was used to calculate the values displayed in Table 3. “WT_LSI_raw_data.xlsx” contains the data for the wild-type lower small intestine, “KO_LSI_raw_data.xlsx” contains the data for the MUC2 knockout lower small intestine. In both the excel files, RI = refractive index, RALS = Right-angle light scattering, LALS = low-angle light scattering, DP = differential pressure (the viscometer). All values are measured in millivolts except for retention volume, which is measured in milliliters (mL). The file “Table S2 – source data 1.OmnisecArchive” contains all this data, along with the data for the pullulan and dextran standard that were used to calibrate the instrument. This can be used in conjunction with Malvern OMNISEC v10.20 software to reproduce the calculations displayed in the table

Figure 7 - source data 4

This zip archive contains the original z-stacks used for Figure 7, panel G. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows: A7PS318_s1_t1 = 30-µm-filtered Pectin LSI, Dilution factor = 1/4 A7PS318_s2_t1 = 30-µm-filtered Pectin LSI, Dilution factor = 1/8 A7PS318_s3_t1 = 30-µm-filtered Pectin LSI, Dilution factor = 1/16 A7PS318_s4_t1 = 30-µm-filtered Pectin LSI, Dilution factor = 1/32 A7PS318_s5_t1 = 30-µm-filtered Pectin LSI, Dilution factor = 1/64 A7PS318_s6_t1 = 30-µm-filtered Pectin LSI, Dilution factor = 1/128 A7PS314_s25_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1 A7PS314_s26_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/2 A7PS314_s27_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/4 A7PS314_s28_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/8 A7PS314_s29_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/16 A7PS314_s30_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/32 A7PS314_s31_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/64 A7PS314_s32_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/128 A7PS284_s13_t1 = HBSS Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “zstackname_automated_counting_statistics”, where “zstackname” is the title of the associated z-stack. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “zstackname_singlet_IDs”, where “zstackname” is the title of the associated z-stack. These .csv files were used in combination with the Jupyter notebooks (provided with this submission) to generate Figure 7, panel G

Figure 5 - figure supplement 1 - source data 1

This zip archive contains the original z-stacks used for This zip archive contains the original z-stacks used for Figure 5 - figure supplement 1, panels A and C. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows: A7PS302_s1_t1 = WT USI, Dilution factor = 1 A7PS302_s2_t1 = WT USI, Dilution factor = 1/2 A7PS302_s3_t1 = WT USI, Dilution factor = 1/4 A7PS302_s4_t1 = WT USI, Dilution factor = 1/8 A7PS302_s17_t1 = MUC2KO USI, Dilution factor = 1 A7PS302_s18_t1 = MUC2KO USI, Dilution factor = 1/2 A7PS302_s19_t1 = MUC2KO USI, Dilution factor = 1/4 A7PS302_s20_t1 = MUC2KO USI, Dilution factor = 1/8 A7PS284_s13_t1 = HBSS Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “zstackname_automated_counting_statistics”, where “zstackname” is the title of the associated z-stack. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “zstackname_singlet_IDs”, where “zstackname” is the title of the associated z-stack. These .csv files were used in combination with the Jupyter notebooks (provided with this submission) to generate Figure 5 - figure supplement 1, panels A and C

Table S6 - source data 1

This zip archive contains the chromatography data that was used to calculate the values displayed in Table S6. “pectin_USI_raw_data.xlsx” contains the data for the upper small intestine of pectin-fed mice, “Fibersol-2_USI_raw_data.xlsx” contains the data for the upper small intestine of Fibersol-2-fed mice. In both the excel files, RI = refractive index, RALS = Right-angle light scattering, LALS = low-angle light scattering, DP = differential pressure (the viscometer). All values are measured in millivolts except for retention volume, which is measured in milliliters (mL). The file “Table S6 – source data 1” contains all the data, along with the data for the pullulan and dextran standard that were used to calibrate the instrument. This can be used in conjunction with Malvern OMNISEC v10.20 software to reproduce the calculations displayed in the table. LALS data was not used for these calculations because of the noisiness of the signal from the detector