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  1. Article ; 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  Volume 9, Page(s) 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
    Language English
    Publishing date 2023-03-25
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2468-2330
    ISSN (online) 2468-2330
    DOI 10.1016/j.tcsw.2023.100105
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; 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  Volume 13, Issue 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.
    Language English
    Publishing date 2024-01-03
    Publishing country Switzerland
    Document type Journal Article ; Review
    ISSN 2673-6284
    ISSN (online) 2673-6284
    DOI 10.3390/biotech13010001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; 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  Volume 38, Issue 1, Page(s) 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 term(s) 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
    Chemical Substances Nitrates ; Propionates
    Language English
    Publishing date 2021-12-27
    Publishing country United States
    Document type 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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

    Shelton, Catherine D / Sing, Elizabeth / Mo, Jessica / Shealy, Nicolas G / Yoo, Woongjae / Thomas, Julia / Fitz, Gillian N / Castro, Pollyana R / Hickman, Tara T / Torres, Teresa P / Foegeding, Nora J / Zieba, Jacob K / Calcutt, M Wade / Codreanu, Simona G / Sherrod, Stacy D / McLean, John A / Peck, Sun H / Yang, Fan / Markham, Nicholas O /
    Liu, Min / Byndloss, Mariana X

    Cell host & microbe

    2023  Volume 31, Issue 10, Page(s) 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 term(s) Humans ; Child ; Animals ; Mice ; Lipid Metabolism ; Pediatric Obesity ; Microbiota ; Diet, High-Fat/adverse effects ; Anti-Bacterial Agents ; Polyesters ; Mice, Inbred C57BL
    Chemical Substances Anti-Bacterial Agents ; Polyesters
    Language English
    Publishing date 2023-10-03
    Publishing country United States
    Document type 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; 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.
    Keywords amino acid sequences ; amino acids ; blood-brain barrier ; dimerization ; evolution ; eyes ; genes ; genotype-phenotype correlation ; heterozygosity ; humans ; open reading frames ; transcription factors
    Language English
    Dates of publication 2023-0114
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14010222
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Evolutionary Landscape of

    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

    2023  Volume 14, Issue 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 term(s) 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
    Chemical Substances 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
    Language English
    Publishing date 2023-01-14
    Publishing country Switzerland
    Document type 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; 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  Volume 373, Issue 6556, Page(s) 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 term(s) 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
    Chemical Substances Methylamines ; Nitrates ; trimethyloxamine (FLD0K1SJ1A) ; Choline (N91BDP6H0X)
    Language English
    Publishing date 2021-08-20
    Publishing country United States
    Document type 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 27: Show issues Location:
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