US 4399216A
· Axel
· 1983
[cited by applicant]
US 5767063A
· Lee
· 1998
[cited by applicant]
US 20060189526A1
· Podolsky
· 2006
[cited by applicant]
US 20100144618A1
· Podolsky
· 2010
[cited by applicant]
CN 101184507A
· 2008
[cited by applicant]
WO WO2002078640A2
· 2002
[cited by applicant]
WO WO2013050792
· 2013
[cited by applicant]
WO WO2015014973
· 2015
[cited by applicant]
WO WO2016203221
· 2016
[cited by applicant]
WO WO2018187682
· 2018
[cited by applicant]
NCBI reference for WP_014079420.1 (downloaded from https://www.ncbi.nlm.nih.gov/protein/WP_014079420.1?report=genbank&log$=protalign&blast_rank=1&RID=XCKE8H21015; published May 18, 2013) (Year: 2013).
[cited by examiner]
G2T1E5 Uniprot (downloaded from https://www.uniprot.org/uniprot/G2T1E5; last modified Nov. 16, 2011) (Year: 2011).
[cited by examiner]
CN Office Action in Chinese Appln. No. 201880037987.0, mailed on May 31, 2024, 25 pages (with English translation).
[cited by applicant]
KR Office Action in Korean Appln. No. 10-2023-7032575, mailed on May 23, 2024, 13 pages (with English translation).
[cited by applicant]
Altschul et al., “Basic local alignment search tool”, J. Mol. Biol. 215: 403-410, 1990.
[cited by applicant]
Altschul et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs”, Nucleic Acids Res. 25(17): 3389-3402, 1997.
[cited by applicant]
Antonsson et al., “Induction of apoptosis by staurosporine involves the inhibition of expression of the major cell cycle proteins at the G(2)/m checkpoint accompanied by alterations in Erk and Akt kinase activities.” An…
[cited by applicant]
Aroniadis et al. “Fecal microbiota transplantation: past, present and future.” Curr. Opin. Gastroenterol. 29 (1): 79-84, 2013.
[cited by applicant]
Ayoubi et al., “Regulation of gene expression by alternative promoters.”, FASEB J. 10, 453-60, 1996.
[cited by applicant]
Baron et al., “Variation Between Observers in Describing Mucosal Appearances in Proctocolitis”, BMJ, 1: 89, 1964.
[cited by applicant]
Beduneau et al., “A tunable Caco-2/HT29-MTX co-culture model mimicking variable permeabilities of the human intestine obtained by an original seeding procedure.” Eur J Pharm Biopharm., 87 (2): 290-298, 2014.
[cited by applicant]
Behrendt et al., “Lipopolysaccharide binding protein in preterm infants.”, Arch Dis Child Fetal Neonatal Ed 89: F551-554, 2004.
[cited by applicant]
Berge et al., “Pharmaceutical salts”, J. Pharm. Sci. 66: 1-19, 1977.
[cited by applicant]
Berger et al., “Oleic Acid Uptake Reveals the Rescued Enterocyte Phenotype of Colon Cancer Caco-2 by HT29-MTX Cells in Co-Culture Mode”, Int J Mol Sci, 18: 1573, 21 pages, 2017.
[cited by applicant]
Best et al., “Development of a Crohn's disease activity index.”, National Cooperative Crohn's Disease Study, Gastroenterol. 70: 439-444, 1976.
[cited by applicant]
Bibiloni et al.,“VSL#3 probiotic-mixture induces remission in patients with active ulcerative colitis.” Am J Gastroenterol., 100 (7): 1539-1546, 2005.
[cited by applicant]
Boltin et al., Mucin Function in Inflammatory Bowel Disease An Update. J. Clin. Gastroenterol., 47 (2): 106-111, 2003.
[cited by applicant]
Bork, “Powers and pitfalls in sequence analysis: The 70% hurdle,” Genome Research, 2000, 10:398-400.
[cited by applicant]
Botoman et al., “Management of Inflammatory Bowel Disease.” Am Fam Physician 57 (1): 57-68, 1998.
[cited by applicant]
Bowie et al., “Deciphering the message in protein sequences: tolerance to amino acid substitutions”, Science 247: 1306-1310, 1990.
[cited by applicant]
Bratt et al., “A phase 1 trial with transgenic bacteria expressing interleukin-IO in Crohn's disease.” Clinical Gastroenterology and Hepatology 4: 754-759, 2006.
[cited by applicant]
Burgess et al., “Possible Dissociation of the Heparin-binding and Mitogenic Activities of heparin-binding (Acidic Fibroblast) Growth Factor-1 from Its Receptor-binding Activities by Site-directed Mutagenesis of a Single…
[cited by applicant]
Cani et al., “Changes in Gut Micro biota Control Metabolic Endotoxemia-induced Inflammation in High-Fat Diet-Induced Obesity and Diabetes in Mice.” Diabetes 57: 1470-1481, 2008.
[cited by applicant]
Chassaign et al., “Dextran sulfate Sodium(DSS)-Induced Colitis in Mice” Curr Protoc Imunol, Feb. 2014,104: Unit-15.25.
[cited by applicant]
Chelakkot et al., “Mechanisms regulating intestinal barrier integrity and its pathological implications,” Experimental and Molecular Medicine, 2018, 50:103.
[cited by applicant]
Clevelandclinic.org, “Gastrointestinal Disorders” retrieved on Mar. 27, 2020, retrieved from https://my.clevelandclinic.org/health/articles/7040-gastrointestinal-disorders, 16 pages.
[cited by applicant]
Coskun et al., “Intestinal Epithelium in Inflammatory Bowel Disease.” Frontiers in Medicine 1: 24, 2014.
[cited by applicant]
Danese et al., “Etiopathogenesis of inflammatory bowel diseases.” World J. Gastroenterol., 12: 4807-4812, 2006.
[cited by applicant]
Daperno et al., “Results of the 2nd part Scientific Workshop of the ECCO. II: Measures and markers of prediction to achieve, detect, and monitor intestinal healing in inflammatory bowel disease.”, J Crohns Colitis., Oct…
[cited by applicant]
Delzenne et al., “Targeting gut microbiota in obesity: effects of prebiotics and probiotics.” Nature Reviews, 7 (11): 639-646, 2011.
[cited by applicant]
Deutscher, “Maintaining protein stability,” Methods in Enzymology, 1990, 182:83-89.
[cited by applicant]
Dewi et al., “In vitro assessment of human endothelial cell permeability: effects of inflammatory cytokines and dengue virus infection.” J Virol Methods., 121 (2): 171-180, 2004.
[cited by applicant]
Dewi et al., “Peripheral blood mononuclear cells increase the permeability of dengue virus-infected endothelial cells in association with down-regulation of vascular endothelial cadherin”, J. Gen. Virol. 89: 642-652, 20…
[cited by applicant]
Duncan et al., “Proposal of
[cited by applicant]
Durrer et al., “Genetically engineered probiotic for the treatment of phenylketonuria (PKU); assessment of a novel treatment in vitro and in the PAHenu2 mouse model of PKU.” PLoS One., 12(5): e0176286, 17 pages, 2017.
[cited by applicant]
EP European Extended Search Report in Appl. No. 19782209.1, dated May 4, 2021, 8 pages.
[cited by applicant]
EP European Extended Supplemental Search Report in International Appln. A48No. 18781398.5, dated Dec. 22, 2020, 9 pages.
[cited by applicant]
Everard et al., “Cross-talk between
[cited by applicant]
Everard et al., “Responses of Gut Micro biota and Glucose and Lipid Metabolism to Prebiotics in Genetic Obese and Diet-Induced Leptin-Resistant Mice.” Diabetes, 60 (11): 2775-2786, 2011.
[cited by applicant]
Frottin et al., “The Proteomics of N-terminal Methionine Cleavage,” Molecular & Cellular Proteomics 5.12, pp. 2336-2349, 2006.
[cited by applicant]
Gassler et al., “Inflammatory bowel disease is associated with changes of enterocytic junctions.” Am J. Physiol. Gastrointest. Liver Physiol., 28 (1): G216-G228, 2001.
[cited by applicant]
Gaston et al., “S-nitrosylation signaling in cell biology.”, Mol Interv. 3, 253-263, 2003.
[cited by applicant]
GenBank Accession No. AEN96375, hypothetical protein RHOM_06280[
[cited by applicant]
GenBank Accession No. AJ270482, “
[cited by applicant]
GenBank Accession No. CP003040, “
[cited by applicant]
Glozak et al., “Acetylation and deacetylation of non-histone proteins.”, Gene. 363, 15-23, 2005.
[cited by applicant]
Han et al., “Detergent-free biotin switch combined with liquid chromatography/tandem mass spectrometry in the analysis of S-nitrosylated proteins.”, Rapid Commun Mass Spectrom. 22, 1137-1145, 2008.
[cited by applicant]
Hanniffy et al., “Mucosal delivery of a pneumococcal vaccine using
[cited by applicant]
Harvey et al., “A Simple Index of Crohns-Disease Activity”, Lancet 1(8178): 1134-1135, 1980.
[cited by applicant]
Harvey et al., “Measuring Crohn's disease activity,” May 1980, The Lancet, 8178:1134-1135.
[cited by applicant]
Healthline.com, “Liver Diseases,” retrieved on accessed Mar. 27, 2020, pp. 1-14, retrieved from https://www.healthline.com/health/liver-diseases, 14 pages.
[cited by applicant]
Henikoff et al., “Amino acid substitution matrices from protein blocks”, Proc. Natl. Acad. Sci. 89(22): 10915-10919, 1992.
[cited by applicant]
Higgins et al., “CLUSTAL: a package for performing multiple sequence alignment on a microcomputer”, Gene 73: 237-244, 1988.
[cited by applicant]
Horhota et al., “Glycerol nucleoside triphosphates: Synthesis and polymerase substrate activities”, Organic Letters 8: 5345-5347, 2006.
[cited by applicant]
Hsiao et al., “High-frequency transformation of yeast by plasmids containing the cloned yeast ARG4 gene”, Proc. Natl. Acad. Sci. (USA), 76: 3829, 1979.
[cited by applicant]
Huynh et al., “Probiotic preparation VSL#3 induces remission in children with mild to moderate acute ulcerative colitis: a pilot study.” Inflamm Bowel Dis., 15 (5): 760-768, 2009.
[cited by applicant]
Imai et al., “Transcriptional silencing and longevity protein SIR2 is an NADdependent histone deacetylase.”, Nature. 403, 795-800, 2000.
[cited by applicant]
Inouye et al. Cloning and Sequence analysis of cDNA for the luminescent protein aequorin. Proceedings of the National Academy of Sciences, May 1985, 82(10):3154-3158.
[cited by applicant]
International Human Genome Sequencing Consortium, “Finishing the euchromatic sequence of the human genome,” Nature., 2004, 431:931-45.
[cited by applicant]
Irvine et al., “Quality of Life: A Valid and Reliable Measure of Therapeutic Efficacy in the Treatment of Inflammatory Bowel Disease”, Gastroenterology 106: 287-296, 1994.
[cited by applicant]
IUPAC Commission on the Nomenclature of Organic Chemistry (CNOC) and IUPAC-IUB Commission on Biochemical Nomenclature (CBN), Nomenclature of a Amino Acids, (Recommendations 1974), Biochemistry 14: 449-462, 1975.
[cited by applicant]
Jaffrey et al., “The Biotin Switch Method for the Detection of S-Nitrosylated Proteins.”, Sci. STKE. 2001.
[cited by applicant]
Jensen, “Modification-specific proteomics: Characterization of posttranslational modifications by mass spectrometry.”, Curr Opin Chem Biol. 8, 33-41, 2004.
[cited by applicant]
Johansson et al., “Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis.” Gut., 63 (2): 281-291, 2014.
[cited by applicant]
Karlin et al., “Applications and statistics for multiple high-scoring segments in molecular sequences”, Proc. Natl. Acad. Sci. 90: 5873-5877, 1993.
[cited by applicant]
Keown et al., “Methods for Introducing DNA into mammalian cells,” Methods in Enzymology, 1990, 185:527-537.
[cited by applicant]
Kiesler et al., “Experimental Models of Inflammatory Bowel Diseases.”, Cell Mol Gastroenterol Hepatol, vol. 1, No. 2, pp. 154-170, 2015.
[cited by applicant]
Kim et al., “Investigating Intestinal Inflammation in DSS-induced Model of IBD.” Journal of Visualized Experiments, 60: pii: 3678, 171-180, 2012.
[cited by applicant]
Kyte and Doolittle, “A Simple Method for Displaying the Hydropathic Character of a Protein”, J Mol. Biol. 157: 105-132, 1982.
[cited by applicant]
Lazar et al., “Transforming Growth Factor a: Mutation of Aspartic Acid 47 and Leucine 48 Results in Different Biological Activities,” Mol. Cell. Biol., 1988, 8:1247-1252.
[cited by applicant]
Lerner et al., “Dysbiosis may trigger autoimmune diseases via inappropriate posttranslational modification of host proteins.” Frontiers in Microbiology, vol. 7, Article 84, 2016.
[cited by applicant]
Levesque et al., “Converging goals of treatment of inflammatory bowel disease from clinical trials and practice.” Gastroenterology, 148 (1): 37-51.e1, 2015.
[cited by applicant]
Ma, “Animal models of disease,” Modern Drug Discovery, 2004, 7:6.
[cited by applicant]
Machiels et al., “A decrease of the butyrate-producing species
[cited by applicant]
Maloy et al., “Intestinal homeostasis and its breakdown in inflammatory bowel disease.”, Nature 474 (7351): 298-306, 2011.
[cited by applicant]
Mandic et al., “Evaluation of head and neck squamous cell carcinoma invasiveness by the electrical resistance breakdown assay.” Clin Exp Metastasis, 21 (8): 699-704, 2004.
[cited by applicant]
Mansour et al., “Disruption of the proto-oncogene int-2 in mouse embryo-derived stem cells: a general strategy for targeting mutations to non-selectable genes.”, Nature, 336: 348-352, 1988.
[cited by applicant]
Markus et al., “Cytokines in Inflammatory Bowel Disease.” Nature Reviews Immunology, 14 (5): 329-342, 2014.
[cited by applicant]
Martini et al., “Mend Your Fences: The Epithelial Barrier and Its Relationship With Mucosal Immunity in Inflammatory Bowel Disease.” Cellular and Molecular Gastroenterology and Hepatology 4 (1): 33-46, 2017.
[cited by applicant]
Matts, “The value of rectal biopsy in the diagnosis of ulcerative colitis.”, QJM, 30: 393-407, 1961.
[cited by applicant]
Mayo Clinic, “Metabolic syndrome,” retrieved on accessed Mar. 27, 2020, retrieved from https ://www. mayoclinic .org/diseases-conditions/metabolic-syndrome/diagnosis-treatment/drc-20351921, 5 pages.
[cited by applicant]
McCormick et al., “Mucin depletion in inflammatory bowel disease,” Journal of Clinical Pathology, 43: 143-146, 1990.
[cited by applicant]
MedlinePlus, “Neurologic Diseases,” retrieved on accessed Mar. 27, 2020, retrieved from https://medlineplus.gov/neurologicdiseases.html, 8 pages.
[cited by applicant]
[cited by applicant]
Merrifield. J., “Solid Phase Peptide Synthesis. I. The Synthesis of a Tetrapeptide,” Am Chem Soc., 85: 2149-2154, 1963.
[cited by applicant]
Moayyedi et al., “Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial.” Gastroenterology 149 (1): 102-109.e6, 2015.
[cited by applicant]
Molodecky et al., “Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review.” Gastroenterology 142 (1): 46-54.e42, 2012.
[cited by applicant]
Myers et al., “Optimal alignments in linear space”, CABIOS 4: 11-17, 1988.
[cited by applicant]
Narula et al., “Fecal Microbiota Transplantation for Treatment of Active Ulcerative Colitis.” Inflamm Bowel Dis., 23 (10): 1702-1709, 2017.
[cited by applicant]
NCBI Protein Blast for SEQ ID No. 19,downloaded from https://blast.ncbi.nlm.nih.gov/Blast.cgi#alnHdr_ 1473652184 on Oct. 28, 2018, 9 pages.
[cited by applicant]
NCBI reference for WP _014079420.1 (downloaded from https://www.ncbi.nlm.nih.gov/protein/WP 014079420.1?report-genbank&log$=protalign&blast_rank=1&RID=XCKE8H21015; Published May 18, 2013,1 page.
[cited by applicant]
Needleman et al., “A general method applicable to the search for similarities in the amino acid sequence of two proteins”, J. Mol. Biol., 48(3): 444-453, 1970.
[cited by applicant]
Nuerath, “Cytokines in Inflammatory Bowel Disease.” Nature Reviews Immunology 14 (5): 329-342, 2014.
[cited by applicant]
Odenwald et al., “The intestinal epithelial barrier: A therapeutic target?” Nat. Rev. Gastroenterol Hepatol., Jan. 2017, 14:1:9-21.
[cited by applicant]
Paine, “Colonoscopic evaluation in ulcerative colitis.”, Gastroenterol Rep 2: 161-168, 2014.
[cited by applicant]
Pan et al., “Oral administration of
[cited by applicant]
Patterson et al., “Human Gut Symbiont
[cited by applicant]
PCT International Preliminary Report on Patentability in International Appln. No. PCT/US2019/026412, dated Oct. 6, 2020, 5 pages.
[cited by applicant]
PCT International Search Report and Written Opinion in International Appln No. PCT/US 2019/026412, dated Aug. 20, 2019, 10 pages.
[cited by applicant]
PCT International Search Report and Written Opinion, mailed Aug. 23, 2018, for International Application No. PCT/US2018/026447, 17 pages.
[cited by applicant]
Pearson et al., “Improved tools for biological sequence comparison”, Proc. Natl. Acad. Sci. 85: 2444-2448, 1988.
[cited by applicant]
Plovier et al., “A purified membrane protein from
[cited by applicant]
Qazi et al., “The risk of inflammatory bowel disease flares after fecal microbiota transplantation: Systematic review and meta-analysis.” Gut Microbes., 8 (6): 574-588, 2017.
[cited by applicant]
Sands et al., “Infliximab Maintenance Therapy for Fistulizing Crohn's Disease”, N Engl J Med 350 (9): 876-885, 2004.
[cited by applicant]
Sands, “From symptom to diagnosis: clinical distinctions among various forms of intestinal inflammation.” Gastroenterology 126 (6): 1518-1532, 2004.
[cited by applicant]
Sanger et al., “Challenges and prospects for pharmacotherapy in functional gastrointestinal disorders,” Therap Adv. Gastroenterol, Sep. 2010, 3:5:291-305.
[cited by applicant]
Schroeder et al., “Coated Oral 5-Aminosalicyclic Acid Therapy for Mildly to Moderate Active Ulcerative Colitis,” N Eng J Med, 317: 1625-1629, 1987.
[cited by applicant]
Shawki et al. “Mechanisms of Intestinal Epithelial Barrier Dysfunction by Adherent-Invasive
[cited by applicant]
Sheth et al., “Manipulating bacterial communities by in situ microbiome engineering.” Trends in Genetics 32 (4): 189-200, 2016.
[cited by applicant]
Shigemori et al., “Oral delivery of
[cited by applicant]
Simmonds et al., “Paneth cell metaplasia in newly diagnosed inflammatory bowel disease in children.” BMC Gastroenterol., 14: 93, 2014.
[cited by applicant]
Srinivasan et al., “TEER measurement techniques for in vitro barrier model systems.” J Lab Autom., 20 (2): 107-126, 2015.
[cited by applicant]
Srutkova et al., “
[cited by applicant]
Steidler et al., “Treatment of murine colitis by
[cited by applicant]
Strober et al., “Proinflammatory cytokines in the pathogenesis of inflammatory bowel diseases.” Gastroenterology, 140 (6): 1756-1767, 2011.
[cited by applicant]
Sturm et al., “Epithelial restitution and wound healing in inflammatory bowel disease,” World J Gastroenterol, 14(3): 348-353, 2008.
[cited by applicant]
Sutherland et al., “5-Aminosalicylic acid enema in the treatment of distal ulcerative colitis, proctitis, and Proctitis,” Gastroenterology, Jun. 1987, 92:6:1894-1898.
[cited by applicant]
ThermoFisher: www.thermofisher.com/US/en/home/lifo-science/cloning/genesynthesis/geneart-gene-synthesis/geneoptimizerhtm, “Invitrogen GeneArt Gene Synthesis”, 4 pages, 2017.
[cited by applicant]
Thia et al., “Measurement of Disease Activity in Ulcerative Colitis: Interobserver Agreement and Predictors of Severity”, Inflamm Bowel Dis, 17: 1757-1764, 2011.
[cited by applicant]
Tilg et al.,
[cited by applicant]
Travis et al., “Complete Genome Sequence of the Human Gut Symbiont
[cited by applicant]
Travis et al., “Developing an instrument to assess the endoscopic severity of ulcerative colitis: the Ulcerative Colitis Endoscopic Index of Severity (UCEIS)”, Gut, 61: 535-542, 2012.
[cited by applicant]
Ulcerative Colitis: Introduction Johns Hopkins Medicine, found at: www.hopkinsmedicine.org/gastroenterology hepatology / pdfs/small large intestine/ulcerative_ colitis. pdf., 14 pages, 2013.
[cited by applicant]
UniProtKB—G2T1 E5 (G2T1 E5_ROSHA),“Uncharacterized protein—
[cited by applicant]
Van Solingen et al., “Fusion of Yeast Spheroplasts”, J. Bact, 130: 946-947, 1977.
[cited by applicant]
Van Solingen et al., “Fusion of yeast spheroplasts,” J. Bact, May 1977, 130:2:946.
[cited by applicant]
Vandenbroucke et al., “Active delivery of trefoil factors by genetically modified
[cited by applicant]
World Health Organization (WHO) model prescribing information: Drugs used in Bacterial Infections, 2001; report series No. 895: 1-179, 2001.
[cited by applicant]
Yan et al., “Colon-specific delivery of a probiotic-derived soluble protein ameliorates intestinal inflammation in mice through an EGFR-dependent mechanism.” J Clin Invest., 121 (6): 2242-2253, 2011.
[cited by applicant]
Yang et al., “Lysine acetylation: Codified crosstalk with other posttranslational modifications.”, Mol Cell. 31, 449-461, 2008.
[cited by applicant]
Zhang et al., “Cytokines, Inflammation and Pain”, Int. Anesthesiol. Clin. 45(2): 27-37, 2007.
[cited by applicant]
Zhang et al., “Interactions between intestinal microbiota and host immune response in inflammatory bowel disease,” Frontiers in Immunology, Aug. 2017, 8:942:1-13.
[cited by applicant]
Zolotaresky et al., “A membrane-permeant peptide that inhibits MLC kinase restores barrier function in in vitro models of intestinal disease.” Gastroenterology 123 (1): 163-172, 2002.
[cited by applicant]
Walsh-Reitz et al., “AMP-18 protects barrier function of colonic epithelial cells: role of tight junction proteins,” American Journal of Physiology—Gastrointestinal and Liver Physiology, Jul. 2005, 289(1):G163-71.
[cited by applicant]