Alejandra Yep

ORCID: 0000-0003-1464-4723
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About
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Research Areas
  • Biochemical Acid Research Studies
  • Metabolism and Genetic Disorders
  • Alcoholism and Thiamine Deficiency
  • Enzyme Production and Characterization
  • Glycosylation and Glycoproteins Research
  • Enzyme Structure and Function
  • Carbohydrate Chemistry and Synthesis
  • Urinary Tract Infections Management
  • Antibiotic Resistance in Bacteria
  • Bacterial Genetics and Biotechnology
  • Biochemical and Molecular Research
  • Digestive system and related health
  • Glycogen Storage Diseases and Myoclonus
  • Drug Transport and Resistance Mechanisms
  • Amino Acid Enzymes and Metabolism
  • Bacterial biofilms and quorum sensing
  • Methemoglobinemia and Tumor Lysis Syndrome
  • Diet, Metabolism, and Disease
  • Microbial Metabolic Engineering and Bioproduction
  • Bacillus and Francisella bacterial research
  • Education Methods and Practices
  • Escherichia coli research studies
  • Polyamine Metabolism and Applications
  • Service-Learning and Community Engagement
  • Berberine and alkaloids research

California Polytechnic State University
2016-2021

Cal Poly Corporation
2017

University of Michigan
2006-2014

Brandeis University
2008-2009

Rutgers, The State University of New Jersey
2008-2009

Michigan State University
2003-2009

Urinary catheter use is prevalent in health care settings, and polymicrobial colonization by urease-positive organisms, such as Proteus mirabilis Providencia stuartii, commonly occurs with long-term catheterization. We previously demonstrated that coinfection P. stuartii increased overall urease activity vitro disease severity a model of urinary tract infection (UTI). In this study, we expanded these findings to murine catheter-associated UTI (CAUTI), delineated the contribution enhanced...

10.1128/iai.00808-16 article EN Infection and Immunity 2016-11-29

Background. Catheter-associated urinary tract infections (CaUTIs) are the most common hospital-acquired worldwide and frequently polymicrobial. The urease-positive species Proteus mirabilis Providencia stuartii two of leading causes CaUTIs commonly co-colonize catheters. These can also cause urolithiasis bacteremia. However, impact coinfection on these complications has never been addressed experimentally.

10.1093/infdis/jit663 article EN The Journal of Infectious Diseases 2013-11-26

ABSTRACT The enteric bacterium Proteus mirabilis is a common cause of complicated urinary tract infections. In this study, microarrays were used to analyze P. gene expression in vivo from experimentally infected mice. Urine was collected at 1, 3, and 7 days postinfection, RNA isolated bacteria the urine for transcriptional analysis. Across nine microarrays, 471 genes upregulated 82 downregulated compared vitro broth culture. Genes encoded mannose-resistant -like (MR/P) fimbriae, urease, iron...

10.1128/iai.05152-11 article EN Infection and Immunity 2011-04-20

Escherichia coli glycogen synthase (EcGS, EC 2.4.1.21) is a retaining glycosyltransferase (GT) that transfers glucose from adenosine diphosphate to glucan chain acceptor with retention of configuration at the anomeric carbon. EcGS belongs GT-B structural superfamily. Here we report several x-ray structures together shed considerable light on structure and function these enzymes. The wild-type enzyme bound ADP revealed 15.2 degrees overall domain-domain closure provided for first time...

10.1074/jbc.m809804200 article EN cc-by Journal of Biological Chemistry 2009-02-26

The urinary tract is one of the most common sites infection in humans, and uropathogenic Escherichia coli (UPEC) main causative agent infections. Bacteria colonizing face extremely low iron availability. To counteract this, UPEC expresses a wide variety acquisition systems. exploit as global target for small-molecule inhibition, we developed carried out whole-cell growth-based high throughput screen 149,243 compounds. Our primary assay was under iron-limiting conditions. Hits were assayed...

10.1128/mbio.01089-13 article EN cc-by-nc-sa mBio 2014-02-26

The product of the ARO10 gene from Saccharomyces cerevisiae was initially identified as a thiamine diphosphate‐dependent phenylpyruvate decarboxylase with broad substrate specificity. It suggested that enzyme could be responsible for catabolism aromatic and branched‐chain amino acids, well methionine. In present study, we report overexpression in Escherichia coli first detailed vitro characterization this enzyme. is shown to an efficient 2‐keto acid decarboxylase, consistent it playing major...

10.1111/j.1742-4658.2011.08103.x article EN FEBS Journal 2011-03-24

Benzoylformate decarboxylase from Pseudomonas putida (PpBFDC) is a thiamin diphosphate-dependent enzyme that carries out the nonoxidative decarboxylation of aromatic 2-keto acids. The x-ray structure PpBFDC suggested Ser-26, His-70, and His-281 would play important roles in its catalytic mechanism, S26A, H70A, H281A variants all exhibited greatly impaired activity. Based on stopped-flow studies with alanine mutants, it was proposed histidine residues acted as acid-base catalysts, whereas...

10.1073/pnas.0709657105 article EN Proceedings of the National Academy of Sciences 2008-04-09

Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate- (ThDP-) dependent enzyme acting on aromatic substrates. In addition to its metabolic role in the mandelate pathway, BFDC shows broad substrate specificity coupled with tight stereo control carbon−carbon bond-forming reverse reaction, making it useful biocatalyst for production of chiral α-hydroxy ketones. The reaction methyl benzoylphosphonate (MBP), an analogue natural benzoylformate, results formation stable...

10.1021/bi801950k article EN Biochemistry 2009-03-25

Benzaldehyde lyase (BAL) catalyzes the reversible cleavage of (R)-benzoin to benzaldehyde utilizing thiamin diphosphate and Mg2+ as cofactors. The enzyme is important for chemoenzymatic synthesis a wide range compounds via its carboligation reaction mechanism. In addition principal functions, BAL can slowly decarboxylate aromatic amino acids such benzoylformic acid. It also intriguing mechanistically due paucity acid−base residues at active center that participate in proton transfer steps...

10.1021/bi8004413 article EN Biochemistry 2008-06-21

Glycogen/starch synthase elongates glucan chains and is the key enzyme in synthesis of glycogen bacteria starch plants. Cocrystallization Escherichia coli wild-type (GS) with substrate ADPGlc acceptor mimic HEPPSO produced a closed form GS suggests that domain-domain closure accompanies synthesis. inactive mutant E377A oligosaccharide results first oligosaccharide-bound structure. Four bound oligosaccharides are observed, one interdomain cleft (G6a) three on N-terminal domain surface (G6b,...

10.1021/bi900916t article EN Biochemistry 2009-09-17

Benzoylformate decarboxylase (BFDC) and pyruvate (PDC) are both thiamin diphosphate-dependent enzymes. The two share a common three-dimensional structure catalyze similar chemical reaction, i.e., decarboxylation of 2-keto acids. However, they vary significantly in their substrate utilization pattern. In particular, BFDC has extremely limited activity with pyruvate, while PDC no benzoylformate. Here we report our progress, using semirandom approach, toward converting into an efficient...

10.1021/bi9008402 article EN Biochemistry 2009-07-21

Direct spectroscopic observation of thiamin diphosphate-bound intermediates was achieved on the enzyme benzaldehyde lyase, which carries out reversible and highly enantiospecific conversion ( R)-benzoin to benzaldehyde. The key enamine intermediate could be observed at lambda max 393 nm in benzoin breakdown direction decarboxylase reaction starting with benzoylformate. With as substrate, no detected, only formation 314 nm. To probe rate-limiting step synthesis, (1)H/ (2)H kinetic isotope...

10.1021/bi702302u article EN Biochemistry 2008-03-01

The mechanism of the enzyme benzoylformate decarboxylase (BFDC), which carries out a typical thiamin diphosphate (ThDP)-dependent nonoxidative decarboxylation reaction, was studied with chromophoric alternate substrate (E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid (3-PKB). Addition 3-PKB resulted in appearance two transient intermediates formed consecutively, first one to be predecarboxylation ThDP-bound intermediate λmax at 477 nm, and second corresponding postdecarboxylation enamine 437 nm....

10.1021/bi801810h article EN Biochemistry 2009-01-13

Previous studies showed that deletion of genes c3405 to c3410 from PAI-metV, a genomic island Escherichia coli CFT073, results in strain fails compete with wild-type CFT073 after transurethral cochallenge mice and is deficient the ability independently colonize mouse kidney. Our analysis suggests these constitute an operon role internalization utilization unknown carbohydrate. This not found E. K-12 but present small number pathogenic Shigella boydii strains. One genes, c3406, encodes...

10.1128/jb.00033-11 article EN Journal of Bacteriology 2011-04-16

Mandelamide hydrolase (MAH), a member of the amidase signature family, catalyzes hydrolysis mandelamide to mandelate and ammonia. X-ray structures several members this but not that MAH, have been reported. These reveal nearly superimposable conformations unusual Ser-cisSer-Lys catalytic triad. Conversely, residues involved in substrate recognition are conserved, implying binding pocket could be modified change specificity, perhaps by directed evolution. Here we show MAH is able hydrolyze...

10.1093/protein/gzn073 article EN Protein Engineering Design and Selection 2008-12-10

10.1007/978-1-4939-9601-8_9 article EN Methods in molecular biology 2019-01-01

Synopsis This forward-looking perspective describes the university–elementary bilingual partnership program Nuestra Ciencia. aims to simultaneously tackle two parallel sets of challenges, first related recruitment and retention Latinx into science, technology, engineering mathematics (STEM) fields, second generalized microbiology misconceptions. Latinxs are severely underrepresented in STEM part because they face systemic barriers typically arrive at college with a weaker science foundation...

10.1093/icb/icab117 article EN Integrative and Comparative Biology 2021-05-28
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