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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20250612T153000
DTEND;TZID=America/Los_Angeles:20250612T170000
DTSTAMP:20260523T045215
CREATED:20250605T183259Z
LAST-MODIFIED:20250605T190509Z
UID:2507-1749742200-1749747600@saierlab.biosci.ucsd.edu
SUMMARY:Master's thesis defense by Jack Ord
DESCRIPTION:On June 12\, 2025\, our grad student Jack Ord will defend his Master’s thesis entitled “Dynamics of the IS1 Transposase InsAB’ and its Effects on the Directed Mutations Mediated by IS1.” \n  \n  \n  \n  \n 
URL:https://saierlab.biosci.ucsd.edu/event/jack_ord_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2025/06/JackOrd_thesis.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20250609T160000
DTEND;TZID=America/Los_Angeles:20250613T173000
DTSTAMP:20260523T045215
CREATED:20250605T181546Z
LAST-MODIFIED:20250605T190610Z
UID:2504-1749484800-1749835800@saierlab.biosci.ucsd.edu
SUMMARY:Master's thesis defense by Sofia Nicole Smith
DESCRIPTION:On June 9\, 2025\, at 4pm our grad student Sofia Nicole Smith will defend her Master’s thesis entitled “Investigating How Genomic Context and Regulatory Elements Impact IS1 Transposition within the Escherichia coli Genome.” \nAbstract\nInsertion sequences (IS elements) are key drivers of bacterial genome plasticity\, yet the regulation of their transposition remains poorly understood\, even as their relevance grows due to connections with CRISPR/Cas9 systems and gene therapy applications. This study characterizes the internal\, host\, and genomic factors that regulate IS1 transposition at the donor site. Mutations within the IS1 coding region significantly reduce\, but do not abolish\, transposition. Inducing a ribosomal -1 frameshift at the poly A-tract increases transposition over 100-fold; however\, this enhancement is largely reversed by restoring InsA-mediated transcriptional regulation. This study begins to characterize the nature with which disruptions of flanking genomic regions modulate transposition\, a phenomenon that remains very understudied. The effects shown here underscore the importance of genomic context. Finally\, IS1 primarily undergoes replicative transposition\, a mechanism shown here to be independent of transposase levels in the cell. These findings contribute to our understanding of mobile genetic element regulation and potentially offer strategies for mitigating their potentially harmful effects. \n  \n  \n  \n  \n 
URL:https://saierlab.biosci.ucsd.edu/event/sofia_smith_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2025/06/Sofia_title.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20240315T140000
DTEND;TZID=America/Los_Angeles:20240315T150000
DTSTAMP:20260523T045215
CREATED:20240210T224515Z
LAST-MODIFIED:20250605T190700Z
UID:2285-1710511200-1710514800@saierlab.biosci.ucsd.edu
SUMMARY:Master's thesis defense by Sophia Beliaev
DESCRIPTION:At 2pm on March 15\, 2024\, our grad student Sophia Beliaev will defend her master’s thesis entitled “Expansion of the Major Facilitator Superfamily (MFS) with the Sar TMS10 Membrane Protein (S10MP) Family.” The zoom link will be provided before the defense. \nAbstract\nTransport proteins are crucial to essential cellular processes. Databases such as the Transporter Classification Database (TCDB) hold a wealth of hypothetical transport proteins in need of adequate characterization. However\, there are significant challenges to transport protein experimental research in vitro and in vivo due to the physico-chemical properties of transport proteins linked to their membrane-bound nature. Instead\, bioinformatic methods may be utilized to elucidate structural features\, which facilitate the identification of homology between families. If one of the families is well characterized\, it may provide clues to the potential functions and mechanisms of action of the poorly understood family.In this project\, potential homologous relationships were explored between the well-characterized Major Facilitator Superfamily (MFS) and two uncharacterized transport protein families: the Large 14-16 Putative Transporter (LPT) Family and the Sar TMS10 Membrane Protein (S10MP) Family. To infer homology between the families\, we searched for seven types of bioinformatic evidence: 1) sequence similarity\, 2) topology and hydropathy profile compatibility\, 3) shared domains\, 4) conserved motifs\, 5) similarity of hidden Markov model-profiles at the family level\, 6) common 3D structural folds\, and 7) a superfamily tree supporting the proposed relationships. Our results showed that one established MFS family\, The Anion: Cation Symporter (ACS) Family\, generated reliable signals of homology with the S10MP family. Therefore\, we concluded that the S10MP family is a distant member of the MFS. Characteristics of the MFS proteins may extend to S10MP members\, warranting further research. \n \nFigure 1. Transitivity path of homology between the second repeat unit (RU) of ACS and the first RU of S10MP. Hydropathy plots are presented across the homology transitivity path for  both families. The x-axis corresponds to amino acid residues in the protein sequences and the y-axis indicates hydropathy. Panels A-C depict relationships within the ACS family\, panels D-F depict relationships within the S10MP family\, and panel G presents the evidence supporting the relationship between the two families. Cyan (ACS) and orange (S10MP) bars denote TMSs. Thing vertical black lines with wedges delimit the region of a protein involved in an alignment. Wedges with positive hydropathy values indicate the sequence region involved in the sequence alignment displayed in the panel above. Similarly\, black wedges with negative hydropathy values indicate the sequence regions involved in the sequence alignment displayed in the panel below. Interruptions in the hydropathy plots of panels B\, E\, and G indicate gaps in the corresponding sequence alignments. Colored solid horizontal lines depict domains with direct Pfam hits in the annotated protein. Colored dashed horizontal lines depict domains projected onto the protein from the family which had a direct hit with the Pfam domain. A) Hydropathy plots of ACS member Q8I2Z2 (TC: 2.A.1.14.47). B) Hydropathy plot of the alignment (E-value: 4.7e-24) between the ACS member and its homolog. C) Hydropathy plot of ACS homolog CAD8188293. D) Hydropathy plots of S10MP member XP_021337925 (TC: 9.B.442.1.3). E) Hydropathy plots of the alignment (E-value: 9.2e-31) between the S10MP member and its homolog. F. Hydropathy plot of S10MP homolog XP_952262. G) Hydropathy plot of the alignment (E-value: 2.3e-3) between ACS and S10MP homologs. Pfam domain PF07690 in family ACS was projected to the S10MP homolog XP_952262 (E-value: 0.0027; see Methods). \n  \n  \n  \n 
URL:https://saierlab.biosci.ucsd.edu/event/sophia_beliaev_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2024/03/Sophia_thesis.png
END:VEVENT
BEGIN:VEVENT
DTSTART;VALUE=DATE:20231130
DTEND;VALUE=DATE:20240831
DTSTAMP:20260523T045215
CREATED:20231202T004257Z
LAST-MODIFIED:20250605T191111Z
UID:2219-1701302400-1725062399@saierlab.biosci.ucsd.edu
SUMMARY:IJMS special issue
DESCRIPTION:Drs. A Medrano-Soto\, M Saier and G. Moreno-Hagelsieb are guest editors for an upcoming Special Issue  to be published in the International Journal of Molecular Sciences (IJMS). The special issue’s name is: (Meta)genomic\, Functional\, Structural and Evolutionary Analysis of Transport System.  We encourage everyone whose research is related to cellular transport to submit papers before the November 30\, 2023\, deadline. You can find here the Guide for Authors to prepare your submission.\n \nSpecial Issue Information\nMolecular transport systems are essential for life. They move molecules in and out of cells as well as organelles\, thus playing critical roles in organismal physiology\, homeostasis\, and cell–cell communication. Transport proteins include channels\, secondary carriers\, primary active transporters\, group translocators\, and transmembrane electron carriers that selectively allow the passage of substrates through membranes. Whether transport is active or passive (depending on the energy requirements of the process)\, when transporters malfunction there can be catastrophic consequences for a cell. Due to their relevance to human health\, more than 50% of all FDA-approved drugs target integral membrane proteins. This Special Issue presents a collection of papers conveying the state of the art in transport biology. These papers describe research ranging from experimental to bioinformatic approaches\, contributing toward expanding our functional\, evolutionary\, and mechanistic understanding of transport systems in all domains of life. The scope of this Special Issue will cover (but is not limited to) the following areas: \n\nGene mutation and regulatory mechanisms of transport systems.\nBioinformatics approaches to the study of transport systems.\nEcological impact of molecular transport systems.\nGenomic and metagenomic analyses of transport systems.\nThree-dimensional structural approaches to the study of transport systems.\nEvolutionary analyses of transport systems.\n\nKeywords\n\n\nmolecular transport\ntransport mechanisms\nevolution\nfamilies and superfamilies\ngenomics\nmetagenomics\n3D structural insights\nbioinformatics\n\n\nDr. Arturo Medrano-Soto\nDr. Milton Saier\nDr. Gabriel Moreno-Hagelsieb\nGuest Editors
URL:https://saierlab.biosci.ucsd.edu/event/ijms_special_issue/
LOCATION:California
CATEGORIES:Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2023/05/Add.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230601T110000
DTEND;TZID=America/Los_Angeles:20230601T120000
DTSTAMP:20260523T045215
CREATED:20230525T232249Z
LAST-MODIFIED:20250605T191204Z
UID:2213-1685617200-1685620800@saierlab.biosci.ucsd.edu
SUMMARY:Master's thesis defense by Madison Baxter
DESCRIPTION:At 11 am on June 1\, 2023\, our grad student Madison Baxter will defend her master’s thesis entitled “Structural Evidence Supporting the Expansion of the Voltage-gated Ion Channel (VIC) Superfamily with Inclusion of the Ligand-gated Ion Channel (LIC) Family.” The zoom link will be provided before the defense. \nAbstract\nThe Transporter Classification Database (TCDB) provides curated functional\, evolutionary\, and familial classification information on physiologically relevant transporter proteins across all domains of life. The Voltage-gated Ion Channel (VIC) Superfamily is comprised of 7 family members\, and while the Ligand-gated Ion Channel (LIC) Family is not currently a member\, topological similarities between the LIC family and the Glutamate-gated Ion Channel (GIC) Family\, a member of the VIC superfamily\, suggested that the LIC family is a member of the VIC superfamily. To test this hypothesis that the LIC family is a member of the VIC superfamily we used a series of bioinformatic approaches to search for similarities between the LIC family and members of the VIC superfamily. These included 1) sequence similarity\, 2) compatibility of topology and hydropathy profiles\, 3) shared domains\, 4) conserved motifs\, 5) similarity of HMM-based sequence profiles at the family level\, 6) 3D structural similarities\, and 7) protein clustering analysis of all families. Our results showed that two families from the VIC superfamily\, the Glutamate-gated Ion Channel (GIC) Family and the Voltage-gated Proton Channel (VPC) Family\, generated reliable signals of homology with the LIC family. These findings support the conclusion that the LIC family is a distant member of the VIC superfamily. Since classification of transporters into families and superfamilies enables better understanding of transporters and their mechanisms of action\, classification of the LIC family as a member of the VIC superfamily should be useful for further research into the biology and evolution of this superfamily. \nFigure 3: 3D Structural Alignment for 1.A.9 vs 1.A.51. 3D structural superposition of transmembrane regions between LIC member 2MAW (cyan) and VPC member 4G7V (green). Transmembrane α-helices 1-4 for 2MAW\, chain A\, and 4G7V\, chain S\, are labeled and shaded from light to dark in the order they appear in the amino acid sequence. The scores for the alignment are RMSD: 3.66 Å\, TM-align: 0.55317\, and coverage: 91.40%. \n  \n  \n  \n 
URL:https://saierlab.biosci.ucsd.edu/event/madison_baxter_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/jpeg:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2023/05/MadiisonTitle.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230420T160000
DTEND;TZID=America/Los_Angeles:20230420T170000
DTSTAMP:20260523T045215
CREATED:20230403T224556Z
LAST-MODIFIED:20250605T191257Z
UID:2135-1682006400-1682010000@saierlab.biosci.ucsd.edu
SUMMARY:Master's thesis defense by Harry Zhou
DESCRIPTION:At 4 pm on April 20\, 2023\, our grad student Harry Zhou will defend his master’s thesis entitled “Characterizing the fucAO promoter and elucidating the transcriptional mechanism behind IS5-driven activation of the fucAO operon.” The zoom link will be provided before the defense.
URL:https://saierlab.biosci.ucsd.edu/event/harry_zhou_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2023/04/HarryThesis.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230412T110000
DTEND;TZID=America/Los_Angeles:20230412T120000
DTSTAMP:20260523T045215
CREATED:20230320T180733Z
LAST-MODIFIED:20250605T191345Z
UID:2139-1681297200-1681300800@saierlab.biosci.ucsd.edu
SUMMARY:Master's thesis defense by Kevin J. Hendargo
DESCRIPTION:At 11 am on April 12\, 2023\, our grad student Kevin J. Hendargo will defend his master’s thesis entitled “Detection of Sequence Similarity Among Structural Repeats in the Piezo Family of Mechanosensitive Ion Channels.” The room and zoom link will be provided before the defense.
URL:https://saierlab.biosci.ucsd.edu/event/kevin_hendargo_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2023/04/titleslide.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230314T110000
DTEND;TZID=America/Los_Angeles:20230314T110000
DTSTAMP:20260523T045215
CREATED:20230215T233436Z
LAST-MODIFIED:20250605T191433Z
UID:2056-1678791600-1678791600@saierlab.biosci.ucsd.edu
SUMMARY:Master's thesis defense by Aditi Dubey
DESCRIPTION:At 11 am on March 14\, 2023\, our grad student Aditi Dubey will defend her master’s thesis entitled “Expansion of the Voltage-gated Ion Channel (VIC) Superfamily with the Neurotransmitter Receptor\, Cys Loop\, Ligand-gated Ion Channel (LIC) Family of Channel Receptors ” The zoom link will be provided before the defense.
URL:https://saierlab.biosci.ucsd.edu/event/aditi_dubey_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2023/03/Aditi_defense.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230313T150000
DTEND;TZID=America/Los_Angeles:20230313T160000
DTSTAMP:20260523T045215
CREATED:20230210T205751Z
LAST-MODIFIED:20250605T191524Z
UID:2052-1678719600-1678723200@saierlab.biosci.ucsd.edu
SUMMARY:Master's thesis defense by Jianing Wang
DESCRIPTION:At 3 pm on March 13\, 2023\, our grad student Jianing Wang will defend his master’s thesis entitled “Comparative Genomics of Viral Genomes and Identification of Three Novel Viroporin-like Superfamilies” The zoom link will be provided before the defense.
URL:https://saierlab.biosci.ucsd.edu/event/jianin_wang_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2023/03/Jianings_defense.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20221026T103000
DTEND;TZID=America/Los_Angeles:20221026T113000
DTSTAMP:20260523T045215
CREATED:20221015T171626Z
LAST-MODIFIED:20250605T191612Z
UID:1987-1666780200-1666783800@saierlab.biosci.ucsd.edu
SUMMARY:Master's thesis defense by Peter Kopkowski
DESCRIPTION:At 10:30am on October 26\, 2022\, our grad student Peter Kopkoski will defend his master’s thesis entitled “The Effects of DNA-Binding Proteins on IS Elements Insertion Upstream of the bgl Operon in Escherichia coli” The zoom link will be provided before the defense.
URL:https://saierlab.biosci.ucsd.edu/event/peter_kopkowski_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2022/10/PeterThesis-e1666822149391.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20220415T140000
DTEND;TZID=America/Los_Angeles:20220415T160000
DTSTAMP:20260523T045215
CREATED:20220404T232627Z
LAST-MODIFIED:20250605T191747Z
UID:1880-1650031200-1650038400@saierlab.biosci.ucsd.edu
SUMMARY:Master's thesis defense by Katie Jing Kay Lam
DESCRIPTION:At 2pm on April 15\, 2022\, our grad student Katie Jing Kay Lam will defend her master’s thesis entitled “Histone-like Nucleoid Structuring (H-NS) Protein Silences the Beta-Glucoside (bgl) Utilization Operon by Formation of a DNA Loop in Escherichia coli.” The zoom link will be provided before the defense.
URL:https://saierlab.biosci.ucsd.edu/event/katie_lam_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/jpeg:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2022/04/Katie_thesis.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20211105T140000
DTEND;TZID=America/Los_Angeles:20211105T160000
DTSTAMP:20260523T045215
CREATED:20211101T201258Z
LAST-MODIFIED:20250605T191832Z
UID:1791-1636120800-1636128000@saierlab.biosci.ucsd.edu
SUMMARY:Master's thesis defense by Nicholas A. Wong
DESCRIPTION:At 2pm on November 5\, 2021\, our grad student Nicholas A. Wong will defend his master’s thesis entitled “Stages of Early Replication and Membrane Rearrangement in Coronaviruses: The Replication Organelle.” The zoom link will be provided before the defense.
URL:https://saierlab.biosci.ucsd.edu/event/nicholas_wong_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2021/11/NickThesis.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210623T110000
DTEND;TZID=America/Los_Angeles:20210623T110000
DTSTAMP:20260523T045215
CREATED:20210525T012613Z
LAST-MODIFIED:20250605T191957Z
UID:1650-1624446000-1624446000@saierlab.biosci.ucsd.edu
SUMMARY:Master's thesis defense by Dennis Tran
DESCRIPTION:At 11am on June 23\, 2021\, our grad student Dennis Tran will defend his master’s thesis. Zoom link will be sent shortly.
URL:https://saierlab.biosci.ucsd.edu/event/dennis_tran_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2021/05/image.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210508T112000
DTEND;TZID=America/Los_Angeles:20210508T122000
DTSTAMP:20260523T045215
CREATED:20210501T201253Z
LAST-MODIFIED:20210525T011957Z
UID:1629-1620472800-1620476400@saierlab.biosci.ucsd.edu
SUMMARY:Aditi's presentation at the URC 2021
DESCRIPTION:Between 11:20 and 12:20 on May 8\, 2021\, our undergrad student Aditi Dubey will give a talk at the 2021 Undergraduate Research Conference. She will be speaking about a recently published paper that she coauthored describing a comparative genomics analysis within the archaeal Asgard superphylum. If you have a zoom account and would like to listen to her presentation\, please register here. For your convenience\, here’s the PDF with the program of the conference.
URL:https://saierlab.biosci.ucsd.edu/event/aditi_urc2021/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2021/05/Aditi_URC_2021.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210128T140000
DTEND;TZID=America/Los_Angeles:20210128T150000
DTSTAMP:20260523T045215
CREATED:20210120T161517Z
LAST-MODIFIED:20210525T012051Z
UID:725-1611842400-1611846000@saierlab.biosci.ucsd.edu
SUMMARY:Daniel's master's thesis defense
DESCRIPTION:At 2pm on January 28\, 2021\, our grad student Daniel Tyler will defend his master’s thesis. Zoom link will be sent shortly.
URL:https://saierlab.biosci.ucsd.edu/event/daniel_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2021/03/DanielThesisTitle.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210112T130000
DTEND;TZID=America/Los_Angeles:20210112T140000
DTSTAMP:20260523T045215
CREATED:20210103T173230Z
LAST-MODIFIED:20210525T012149Z
UID:721-1610456400-1610460000@saierlab.biosci.ucsd.edu
SUMMARY:Nuo's master's thesis defense
DESCRIPTION:At 1pm on January 12\, 2021\, our grad student Nuo Tian will defend her master’s thesis. Zoom link will be sent shortly.
URL:https://saierlab.biosci.ucsd.edu/event/nuo_thesis/
LOCATION:Zoom meeting\, San Diego\, California
CATEGORIES:Dissertations,Events
ATTACH;FMTTYPE=image/png:https://saierlab.biosci.ucsd.edu/wp-content/uploads/2021/01/NuoThesisTitle.png
END:VEVENT
END:VCALENDAR