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Artikel ; Online: Diffusion in intact secondary cell wall models of plants at different equilibrium moisture content.

Sarkar, Daipayan / Bu, Lintao / Jakes, Joseph E / Zieba, Jacob K / Kaufman, Isaiah D / Crowley, Michael F / Ciesielski, Peter N / Vermaas, Josh V

Cell surface (Amsterdam, Netherlands)

2023 Band 9, Seite(n) 100105

Abstract: Secondary plant cell walls are composed of carbohydrate and lignin polymers, and collectively represent a significant renewable resource. Leveraging these resources depends in part on a mechanistic understanding for diffusive processes within plant cell ... ...

Abstract	Secondary plant cell walls are composed of carbohydrate and lignin polymers, and collectively represent a significant renewable resource. Leveraging these resources depends in part on a mechanistic understanding for diffusive processes within plant cell walls. Common wood protection treatments and biomass conversion processes to create biorefinery feedstocks feature ion or solvent diffusion within the cell wall. X-ray fluorescence microscopy experiments have determined that ionic diffusion rates are dependent on cell wall hydration as well as the ionic species through non-linear relationships. In this work, we use classical molecular dynamics simulations to map the diffusion behavior of different plant cell wall components (cellulose, hemicellulose, lignin), ions (Na
Sprache	Englisch
Erscheinungsdatum	2023-03-25
Erscheinungsland	Netherlands
Dokumenttyp	Journal Article
ISSN	2468-2330
ISSN (online)	2468-2330
DOI	10.1016/j.tcsw.2023.100105
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Gene Therapy for Genetic Syndromes: Understanding the Current State to Guide Future Care.

Henderson, Marian L / Zieba, Jacob K / Li, Xiaopeng / Campbell, Daniel B / Williams, Michael R / Vogt, Daniel L / Bupp, Caleb P / Edgerly, Yvonne M / Rajasekaran, Surender / Hartog, Nicholas L / Prokop, Jeremy W / Krueger, Jena M

Biotech (Basel (Switzerland))

2024 Band 13, Heft 1

Abstract: Gene therapy holds promise as a life-changing option for individuals with genetic variants that give rise to disease. FDA-approved gene therapies for Spinal Muscular Atrophy (SMA), cerebral adrenoleukodystrophy, β-Thalassemia, hemophilia A/B, retinal ... ...

Abstract	Gene therapy holds promise as a life-changing option for individuals with genetic variants that give rise to disease. FDA-approved gene therapies for Spinal Muscular Atrophy (SMA), cerebral adrenoleukodystrophy, β-Thalassemia, hemophilia A/B, retinal dystrophy, and Duchenne Muscular Dystrophy have generated buzz around the ability to change the course of genetic syndromes. However, this excitement risks over-expansion into areas of genetic disease that may not fit the current state of gene therapy. While in situ (targeted to an area) and ex vivo (removal of cells, delivery, and administration of cells) approaches show promise, they have a limited target ability. Broader in vivo gene therapy trials have shown various continued challenges, including immune response, use of immune suppressants correlating to secondary infections, unknown outcomes of overexpression, and challenges in driving tissue-specific corrections. Viral delivery systems can be associated with adverse outcomes such as hepatotoxicity and lethality if uncontrolled. In some cases, these risks are far outweighed by the potentially lethal syndromes for which these systems are being developed. Therefore, it is critical to evaluate the field of genetic diseases to perform cost-benefit analyses for gene therapy. In this work, we present the current state while setting forth tools and resources to guide informed directions to avoid foreseeable issues in gene therapy that could prevent the field from continued success.
Sprache	Englisch
Erscheinungsdatum	2024-01-03
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article ; Review
ISSN	2673-6284
ISSN (online)	2673-6284
DOI	10.3390/biotech13010001
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Salmonella Typhimurium expansion in the inflamed murine gut is dependent on aspartate derived from ROS-mediated microbiota lysis.

Yoo, Woongjae / Shealy, Nicolas G / Zieba, Jacob K / Torres, Teresa P / Baltagulov, Madi / Thomas, Julia D / Shelton, Catherine D / McGovern, Anna G / Foegeding, Nora J / Olsan, Erin E / Byndloss, Mariana X

Cell host & microbe

2024

Abstract: Inflammation boosts the availability of electron acceptors in the intestinal lumen, creating a favorable niche for pathogenic Enterobacteriaceae. However, the mechanisms linking intestinal inflammation-mediated changes in luminal metabolites and pathogen ...

Abstract	Inflammation boosts the availability of electron acceptors in the intestinal lumen, creating a favorable niche for pathogenic Enterobacteriaceae. However, the mechanisms linking intestinal inflammation-mediated changes in luminal metabolites and pathogen expansion remain unclear. Here, we show that mucosal inflammation induced by Salmonella enterica serovar Typhimurium (S. Tm) infection increases intestinal levels of the amino acid aspartate. S. Tm used aspartate-ammonia lyase (aspA)-dependent fumarate respiration for growth in the murine gut only during inflammation. AspA-dependent growth advantage was abolished in the gut of germ-free mice and restored in gnotobiotic mice colonized with members of the classes Bacteroidia and Clostridia. Reactive oxygen species (ROS) produced during the host response caused lysis of commensal microbes, resulting in the release of microbiota-derived aspartate that was used by S. Tm, in concert with nitrate-dependent anaerobic respiration, to outcompete commensal Enterobacteriaceae. Our findings demonstrate the role of microbiota-derived amino acids in driving respiration-dependent S. Tm expansion during colitis.
Sprache	Englisch
Erscheinungsdatum	2024-05-17
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	2278004-X
ISSN	1934-6069 ; 1931-3128
ISSN (online)	1934-6069
ISSN	1931-3128
DOI	10.1016/j.chom.2024.05.001
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Salmonella enterica serovar Typhimurium uses anaerobic respiration to overcome propionate-mediated colonization resistance.

Shelton, Catherine D / Yoo, Woongjae / Shealy, Nicolas G / Torres, Teresa P / Zieba, Jacob K / Calcutt, M Wade / Foegeding, Nora J / Kim, Dajeong / Kim, Jinshil / Ryu, Sangryeol / Byndloss, Mariana X

Cell reports

2021 Band 38, Heft 1, Seite(n) 110180

Abstract: The gut microbiota benefits the host by limiting enteric pathogen expansion (colonization resistance), partially via the production of inhibitory metabolites. Propionate, a short-chain fatty acid produced by microbiota members, is proposed to mediate ... ...

Abstract	The gut microbiota benefits the host by limiting enteric pathogen expansion (colonization resistance), partially via the production of inhibitory metabolites. Propionate, a short-chain fatty acid produced by microbiota members, is proposed to mediate colonization resistance against Salmonella enterica serovar Typhimurium (S. Tm). Here, we show that S. Tm overcomes the inhibitory effects of propionate by using it as a carbon source for anaerobic respiration. We determine that propionate metabolism provides an inflammation-dependent colonization advantage to S. Tm during infection. Such benefit is abolished in the intestinal lumen of Salmonella-infected germ-free mice. Interestingly, S. Tm propionate-mediated intestinal expansion is restored when germ-free mice are monocolonized with Bacteroides thetaiotaomicron (B. theta), a prominent propionate producer in the gut, but not when mice are monocolonized with a propionate-production-deficient B. theta strain. Taken together, our results reveal a strategy used by S. Tm to mitigate colonization resistance by metabolizing microbiota-derived propionate.
Mesh-Begriff(e)	Anaerobiosis/physiology ; Animals ; Antibiosis/physiology ; Bacteroides thetaiotaomicron/genetics ; Bacteroides thetaiotaomicron/metabolism ; Female ; Gastrointestinal Microbiome/physiology ; Germ-Free Life ; Intestines/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Inbred CBA ; Mice, Knockout ; Nitrates/metabolism ; Propionates/metabolism ; Salmonella Infections, Animal/pathology ; Salmonella typhimurium/growth & development ; Salmonella typhimurium/metabolism
Chemische Substanzen	Nitrates ; Propionates
Sprache	Englisch
Erscheinungsdatum	2021-12-27
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2021.110180
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: An early-life microbiota metabolite protects against obesity by regulating intestinal lipid metabolism.

Cell host & microbe

2023 Band 31, Heft 10, Seite(n) 1604–1619.e10

Abstract: The mechanisms by which the early-life microbiota protects against environmental factors that promote childhood obesity remain largely unknown. Using a mouse model in which young mice are simultaneously exposed to antibiotics and a high-fat (HF) diet, we ...

Abstract	The mechanisms by which the early-life microbiota protects against environmental factors that promote childhood obesity remain largely unknown. Using a mouse model in which young mice are simultaneously exposed to antibiotics and a high-fat (HF) diet, we show that Lactobacillus species, predominant members of the small intestine (SI) microbiota, regulate intestinal epithelial cells (IECs) to limit diet-induced obesity during early life. A Lactobacillus-derived metabolite, phenyllactic acid (PLA), protects against metabolic dysfunction caused by early-life exposure to antibiotics and a HF diet by increasing the abundance of peroxisome proliferator-activated receptor γ (PPAR-γ) in SI IECs. Therefore, PLA is a microbiota-derived metabolite that activates protective pathways in the small intestinal epithelium to regulate intestinal lipid metabolism and prevent antibiotic-associated obesity during early life.
Mesh-Begriff(e)	Humans ; Child ; Animals ; Mice ; Lipid Metabolism ; Pediatric Obesity ; Microbiota ; Diet, High-Fat/adverse effects ; Anti-Bacterial Agents ; Polyesters ; Mice, Inbred C57BL
Chemische Substanzen	Anti-Bacterial Agents ; Polyesters
Sprache	Englisch
Erscheinungsdatum	2023-10-03
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	2278004-X
ISSN	1934-6069 ; 1931-3128
ISSN (online)	1934-6069
ISSN	1931-3128
DOI	10.1016/j.chom.2023.09.002
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Evolutionary Landscape of SOX Genes to Inform Genotype-to-Phenotype Relationships

Underwood, Adam / Rasicci, Daniel T / Hinds, David / Mitchell, Jackson T / Zieba, Jacob K / Mills, Joshua / Arnold, Nicholas E / Cook, Taylor W / Moustaqil, Mehdi / Gambin, Yann / Sierecki, Emma / Fontaine, Frank / Vanderweele, Sophie / Das, Akansha S / Cvammen, William / Sirpilla, Olivia / Soehnlen, Xavier / Bricker, Kristen / Alokaili, Maram /

Green, Morgan / Heeringa, Sadie / Wilstermann, Amy M / Freeland, Thomas M. / Qutob, Dinah / Milsted, Amy / Jauch, Ralf / Triche, Timothy J / Krawczyk, Connie M / Bupp, Caleb P / Rajasekaran, Surender / Francois, Mathias / Prokop, Jeremy W.

Genes (Basel). 2023 Jan. 14, v. 14, no. 1

2023

Abstract: The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype–phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in ... ...

Abstract	The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype–phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in combination with structural dynamics to interpret 3999 gnomAD, 485 ClinVar, 1174 Geno2MP, and 4313 COSMIC human variants. We identified, within the HMG (High Mobility Group)- box, twenty-seven amino acids with changes in multiple SOX proteins annotated to clinical pathologies. These sites were screened through Geno2MP medical phenotypes, revealing novel SOX15 R104G associated with musculature abnormality and SOX8 R159G with intellectual disability. Within gnomAD, SOX18 E137K (rs201931544), found within the HMG box of ~0.8% of Latinx individuals, is associated with seizures and neurological complications, potentially through blood–brain barrier alterations. A total of 56 highly conserved variants were found at sites outside the HMG-box, including several within the SOX2 HMG-box-flanking region with neurological associations, several in the SOX9 dimerization region associated with Campomelic Dysplasia, SOX14 K88R (rs199932938) flanking the HMG box associated with cardiovascular complications within European populations, and SOX7 A379V (rs143587868) within an SOXF conserved far C-terminal domain heterozygous in 0.716% of African individuals with associated eye phenotypes. This SOX data compilation builds a robust genotype-to-phenotype association for a gene family through more robust ortholog data integration.
Schlagwörter	amino acid sequences ; amino acids ; blood-brain barrier ; dimerization ; evolution ; eyes ; genes ; genotype-phenotype correlation ; heterozygosity ; humans ; open reading frames ; transcription factors
Sprache	Englisch
Erscheinungsverlauf	2023-0114
Erscheinungsort	Multidisciplinary Digital Publishing Institute
Dokumenttyp	Artikel ; Online
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14010222
Datenquelle	NAL Katalog (AGRICOLA)

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Artikel ; Online: Evolutionary Landscape of

Green, Morgan / Heeringa, Sadie / Wilstermann, Amy M / Freeland, Thomas M / Qutob, Dinah / Milsted, Amy / Jauch, Ralf / Triche, Timothy J / Krawczyk, Connie M / Bupp, Caleb P / Rajasekaran, Surender / Francois, Mathias / Prokop, Jeremy W

Genes

2023 Band 14, Heft 1

Abstract: The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype-phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in ... ...

Abstract	The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype-phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in combination with structural dynamics to interpret 3999 gnomAD, 485 ClinVar, 1174 Geno2MP, and 4313 COSMIC human variants. We identified, within the HMG (High Mobility Group)- box, twenty-seven amino acids with changes in multiple SOX proteins annotated to clinical pathologies. These sites were screened through Geno2MP medical phenotypes, revealing novel SOX15 R104G associated with musculature abnormality and SOX8 R159G with intellectual disability. Within gnomAD, SOX18 E137K (rs201931544), found within the HMG box of ~0.8% of Latinx individuals, is associated with seizures and neurological complications, potentially through blood-brain barrier alterations. A total of 56 highly conserved variants were found at sites outside the HMG-box, including several within the SOX2 HMG-box-flanking region with neurological associations, several in the SOX9 dimerization region associated with Campomelic Dysplasia, SOX14 K88R (rs199932938) flanking the HMG box associated with cardiovascular complications within European populations, and SOX7 A379V (rs143587868) within an SOXF conserved far C-terminal domain heterozygous in 0.716% of African individuals with associated eye phenotypes. This SOX data compilation builds a robust genotype-to-phenotype association for a gene family through more robust ortholog data integration.
Mesh-Begriff(e)	Humans ; High Mobility Group Proteins/chemistry ; High Mobility Group Proteins/genetics ; High Mobility Group Proteins/metabolism ; SOX Transcription Factors/genetics ; Amino Acid Sequence ; Dimerization ; Genotype ; SOXF Transcription Factors/genetics ; SOXF Transcription Factors/metabolism ; SOXB2 Transcription Factors/genetics ; SOXB2 Transcription Factors/metabolism ; SOXE Transcription Factors/genetics
Chemische Substanzen	High Mobility Group Proteins ; SOX Transcription Factors ; SOX7 protein, human ; SOXF Transcription Factors ; SOX18 protein, human ; SOX14 protein, human ; SOXB2 Transcription Factors ; SOX8 protein, human ; SOXE Transcription Factors
Sprache	Englisch
Erscheinungsdatum	2023-01-14
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14010222
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: High-fat diet-induced colonocyte dysfunction escalates microbiota-derived trimethylamine

Yoo, Woongjae / Zieba, Jacob K / Foegeding, Nora J / Torres, Teresa P / Shelton, Catherine D / Shealy, Nicolas G / Byndloss, Austin J / Cevallos, Stephanie A / Gertz, Erik / Tiffany, Connor R / Thomas, Julia D / Litvak, Yael / Nguyen, Henry / Olsan, Erin E / Bennett, Brian J / Rathmell, Jeffrey C / Major, Amy S / Bäumler, Andreas J / Byndloss, Mariana X

Science (New York, N.Y.)

2021 Band 373, Heft 6556, Seite(n) 813–818

Abstract: A Western-style, high-fat diet promotes cardiovascular disease, in part because it is rich in choline, which is converted to trimethylamine (TMA) by the gut microbiota. However, whether diet-induced changes in intestinal physiology can alter the ... ...

Abstract	A Western-style, high-fat diet promotes cardiovascular disease, in part because it is rich in choline, which is converted to trimethylamine (TMA) by the gut microbiota. However, whether diet-induced changes in intestinal physiology can alter the metabolic capacity of the microbiota remains unknown. Using a mouse model of diet-induced obesity, we show that chronic exposure to a high-fat diet escalates
Mesh-Begriff(e)	Animals ; Cell Hypoxia ; Choline/administration & dosage ; Choline/metabolism ; Colon/cytology ; Colon/physiology ; Diet, High-Fat ; Energy Metabolism ; Epithelial Cells/physiology ; Escherichia coli/genetics ; Escherichia coli/growth & development ; Escherichia coli/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome ; Inflammation ; Intestinal Mucosa/metabolism ; Intestinal Mucosa/physiology ; Male ; Methylamines/blood ; Methylamines/metabolism ; Mice ; Mice, Inbred C57BL ; Mitochondria/metabolism ; Nitrates/metabolism ; Obesity ; Oxygen Consumption
Chemische Substanzen	Methylamines ; Nitrates ; trimethyloxamine (FLD0K1SJ1A) ; Choline (N91BDP6H0X)
Sprache	Englisch
Erscheinungsdatum	2021-08-20
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aba3683
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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