Discovery and Optimization of a STING Agonist Platform for Application in Antibody Drug Conjugates.

While STING agonists have proven to be effective preclinically as anti-tumor agents, these promising results have yet to be translated in the clinic. A STING agonist antibody-drug conjugate (ADC) could overcome current limitations by improving tumor accessibility, allowing for systemic administration as well as tumor-localized activation of STING for greater anti-tumor activity and better tolerability. In line with this effort, a STING agonist ADC platform was identified through systematic optimization of the payload, linker, and scaffold based on multiple factors including potency and specificity in both in vitro and in vivo evaluations. The platform employs a potent non-cyclic dinucleotide STING agonist, a cleavable ester-based linker, and a hydrophilic PEG8-bisglucamine scaffold. A tumor-targeted ADC built with the resulting STING agonist platform induced robust and durable anti-tumor activity and demonstrated high stability and favorable pharmacokinetics in nonclinical species.

Comprehension, Utility, and Acceptability of a Multidomain Physical Functioning Report for Systemic Lupus Erythematosus Patients and Their Providers.

OBJECTIVE: Patient-provider discussions about functioning are often outside the scope of usual care for systemic lupus erythematosus (SLE), and tools to facilitate such discussions are lacking. The present study was undertaken to assess the comprehension, utility, and acceptability of a novel, individualized functioning report, the purpose of which is to facilitate patient-provider communication about functioning, in a predominantly Black SLE patient population. METHODS: Individualized reports (including sections with pictorial representations of participants' measured activities of daily living, falls, physical performance, perceived physical functioning, and community mobility from a previous pilot study visit) and surveys were emailed or mailed to 59 SLE patients. Ease of interpretation was dichotomized ("very easy" versus all other responses). Utility and acceptability were assessed by items relating to usefulness for care planning and comfort with discussing the report. RESULTS: Among 47 (79.7%) SLE patients who completed the survey (78.7% Black, 91.5% female, mean age 49.6 years), the reported ease of interpretation ranged from 70.2% to 85.1% across the report sections. Ease of interpretation was lower among those who were older, Black, and female and who had lower cognitive scores (P > 0.05 for all). Most reported that physical functioning domains of the report were useful for treatment or other care planning (70.2-80.5%) and that they felt comfortable discussing the report with a health care provider (93.2-100%). CONCLUSION: We found that a novel functioning report for SLE patients was associated with high comprehension, utility, and acceptability. Future studies can help determine how an individualized functioning report could improve patient-provider communication in the clinic setting.

Discovery of novel polyamide-pyrrolobenzodiazepine hybrids for antibody-drug conjugates.

Pyrrolobenzodiazepine (PBD) dimers are well-known highly potent antibody drug conjugate (ADC) payloads. The corresponding PBD monomers, in contrast, have received much less attention from the ADC community. We prepared several novel polyamide-linked PBD monomers and evaluated their utility as ADC payloads. The unconjugated polyamide-PBD hybrids exhibited potent antiproliferative activity (IC50 range: 10-11-10-8 M) against a variety of HER2-expressing cancer cell lines. Several peptide-linked variants of the lead compound were prepared and conjugated to trastuzumab to afford ADCs with drug-to-antibody (DAR) ratios ranging from 3 to 5. The ADCs exhibited antigen-dependent cytotoxicity in vitro and potently suppressed tumor xenograft growth in vivo in a target-dependent manner. Moreover, the ADCs were well-tolerated in both mouse and rat. This work demonstrates for the first time that PBD polyamide hybrids can serve as effective ADC payloads.

The TechSAge Minimum Battery: A multidimensional and holistic assessment of individuals aging with long-term disabilities.

BACKGROUND: People with disabilities acquired in early to mid-life are living longer, contributing to growing numbers of older adults who are aging with disability, an understudied population likely to be underserved. OBJECTIVES: This paper demonstrates the usefulness of the TechSAge Minimum Battery as a holistic assessment of health for people aging with disabilities. METHODS: Survey data of socio-demographic and health characteristics were collected from 176 older adults with long-term vision, hearing, and/or mobility disabilities. A series of descriptive and bivariate analyses were conducted to illustrate the heterogeneity of the sample. An in-depth analysis of the subsample with vision difficulty was conducted to highlight the tool's value in assessing detailed contextual information for a specific disability. RESULTS: Prevalence of health conditions (M = 4.1; SD = 2.5), prescription medications (M = 4.1; SD = 3.9), and serious functional difficulties (M = 1.6; SD = 0.85) indicated a fair degree of comorbidity, but with considerable variation in number and type among individuals. Subjective health ratings were high overall, but lower scores were correlated with additional comorbidities (r = -0.31-0.40, p =<.001). Analyses of the subsample with vision difficulty demonstrated heterogeneity in functional capacity, degree of impairment, duration, and use of supportive aids. CONCLUSIONS: Findings highlighted the heterogeneity among people aging with disability and demonstrated the importance of capturing multi-dimensional factors inclusive of an individual's capacity, context, and personal factors, which the Minimum Battery provides in an integrated assessment. Potential healthcare applications of the tool are discussed with implications for bridging aging and disability services.

A web-based carepartner-integrated rehabilitation program for persons with stroke: study protocol for a pilot randomized controlled trial.

BACKGROUND: Family carepartner management and support can improve stroke survivor recovery, yet research has placed little emphasis on how to integrate families into the rehabilitation process without increasing negative carepartner outcomes. Our group has developed creative approaches for engaging family carepartners in rehabilitation activities to improve physical and psychosocial health for both the carepartner and stroke survivor. The purpose of this study is to explore a novel, web-based intervention (Carepartner and Constraint-Induced Therapy; CARE-CITE) designed to facilitate positive carepartner involvement during a home-based application of constraint-induced movement therapy (CIMT) for the upper extremity. METHODS: The primary aim of the study is to determine feasibility of CARE-CITE for both stroke survivors and their carepartners. Carepartner mental health, family conflict surrounding stroke recovery, and stroke survivor upper extremity function will be evaluated using an evaluator blinded, two-group experimental design (blocked randomization protocol according to a 2:1 randomization schema) with 32 intervention dyads and 16 control dyads (who will receive CIMT without structured carepartner involvement). CARE-CITE consists of online education modules for the carepartner to review in parallel to the 30-h CIMT that the stroke survivor receives. The intent of CARE-CITE is to enhance the home-based intervention of CIMT, by helping the carepartner support the therapy and create a therapeutic home environment encouraging practice of the weaker arm in functional tasks. DISCUSSION: The CARE-CITE study is testing the feasibility of a family-integrated rehabilitation approach applied in the home environment, and results will provide the foundation for larger clinical studies. The overall significance of this research plan is to increase the understanding and further development of interventions that may serve as models to promote family involvement in the rehabilitation process. TRIAL REGISTRATION: ClinicalTrials.gov, NCT02703532. Registered 9 March 2016.

A Modular, Tn7-Based System for Making Bioluminescent or Fluorescent Salmonella and Escherichia coli Strains.

UNLABELLED: Our goal was to develop a robust tagging method that can be used to track bacterial strains in vivo To address this challenge, we adapted two existing systems: a modular plasmid-based reporter system (pCS26) that has been used for high-throughput gene expression studies in Salmonella and Escherichia coli and Tn7 transposition. We generated kanamycin- and chloramphenicol-resistant versions of pCS26 with bacterial luciferase, green fluorescent protein (GFP), and mCherry reporters under the control of σ(70)-dependent promoters to provide three different levels of constitutive expression. We improved upon the existing Tn7 system by modifying the delivery vector to accept pCS26 constructs and moving the transposase genes from a nonreplicating helper plasmid into a temperature-sensitive plasmid that can be conditionally maintained. This resulted in a 10- to 30-fold boost in transposase gene expression and transposition efficiencies of 10(-8) to 10(-10) in Salmonella enterica serovar Typhimurium and E. coli APEC O1, whereas the existing Tn7 system yielded no successful transposition events. The new reporter strains displayed reproducible signaling in microwell plate assays, confocal microscopy, and in vivo animal infections. We have combined two flexible and complementary tools that can be used for a multitude of molecular biology applications within the Enterobacteriaceae This system can accommodate new promoter-reporter combinations as they become available and can help to bridge the gap between modern, high-throughput technologies and classical molecular genetics. IMPORTANCE: This article describes a flexible and efficient system for tagging bacterial strains. Using our modular plasmid system, a researcher can easily change the reporter type or the promoter driving expression and test the parameters of these new constructs in vitro Selected constructs can then be stably integrated into the chromosomes of desired strains in two simple steps. We demonstrate the use of this system in Salmonella and E. coli, and we predict that it will be widely applicable to other bacterial strains within the Enterobacteriaceae This technology will allow for improved in vivo analysis of bacterial pathogens.

Synthesis and Evaluation of Oxyguanidine Analogues of the Cysteine Protease Inhibitor WRR-483 against Cruzain.

A series of oxyguanidine analogues of the cysteine protease inhibitor WRR-483 were synthesized and evaluated against cruzain, the major cysteine protease of the protozoan parasite Trypanosoma cruzi. Kinetic analyses of these analogues indicated that they have comparable potency to previously prepared vinyl sulfone cruzain inhibitors. Co-crystal structures of the oxyguanidine analogues WRR-666 (4) and WRR-669 (7) bound to cruzain demonstrated different binding interactions with the cysteine protease, depending on the aryl moiety of the P1' inhibitor subunit. Specifically, these data demonstrate that WRR-669 is bound noncovalently in the crystal structure. This represents a rare example of noncovalent inhibition of a cysteine protease by a vinyl sulfone inhibitor.

Periplasmic Acid Stress Increases Cell Division Asymmetry (Polar Aging) of Escherichia coli.

Under certain kinds of cytoplasmic stress, Escherichia coli selectively reproduce by distributing the newer cytoplasmic components to new-pole cells while sequestering older, damaged components in cells inheriting the old pole. This phenomenon is termed polar aging or cell division asymmetry. It is unknown whether cell division asymmetry can arise from a periplasmic stress, such as the stress of extracellular acid, which is mediated by the periplasm. We tested the effect of periplasmic acid stress on growth and division of adherent single cells. We tracked individual cell lineages over five or more generations, using fluorescence microscopy with ratiometric pHluorin to measure cytoplasmic pH. Adherent colonies were perfused continually with LBK medium buffered at pH 6.00 or at pH 7.50; the external pH determines periplasmic pH. In each experiment, cell lineages were mapped to correlate division time, pole age and cell generation number. In colonies perfused at pH 6.0, the cells inheriting the oldest pole divided significantly more slowly than the cells inheriting the newest pole. In colonies perfused at pH 7.50 (near or above cytoplasmic pH), no significant cell division asymmetry was observed. Under both conditions (periplasmic pH 6.0 or pH 7.5) the cells maintained cytoplasmic pH values at 7.2-7.3. No evidence of cytoplasmic protein aggregation was seen. Thus, periplasmic acid stress leads to cell division asymmetry with minimal cytoplasmic stress.

Spirohexenolide A targets human macrophage migration inhibitory factor (hMIF).

Spirohexenolides A and B comprise a unique family of spirotetronate natural products. We report on the identification of their binding to and modulation of human macrophage migration inhibitor factor (hMIF). Using an immunoaffinity-fluorescent labeling method, the properties of this interaction are detailed and evidence is provided that hMIF plays a key role in the cytostatic activity of the spirohexenolides.

New technology-based functional assessment tools should avoid the weaknesses and proliferation of manual functional assessments.

BACKGROUND: Formal functional assessment tools for use with older adults have been in widespread use since the 1960s. Instruments have been designed to assess a wide range of different aspects of a person's everyday life. This article seeks to document the evolution of the tools used in such a way as to inform the development of the field. STUDY DESIGN AND SETTING: The Medline, CINHAL, and Science Direct databases were searched for relevant literature relating to the functional assessment of older adults. After analysis of initial results, a second-stage search was conducted to find literature relating to the use and validation of instruments found initially. RESULTS: Four categories of functional assessment instruments were identified for the purposes of this article: basic activities of daily living (ADLs), instrumental ADL, global health scales, and performance-based tests of functional ability. These categories and several of the most widely used tools therein are discussed chronologically to document the evolution of the field. CONCLUSIONS: With the advancement of technology has come the possibility to perform functional assessments in new ways. This outline of the evolution of functional assessment should be of considerable use as researchers seek to design new functional assessments for older adults.

Older Adults' Use of and Attitudes toward Activity Monitoring Technologies.

Self-management of health is becoming increasingly important in today's healthcare climate. Activity monitoring technologies have the potential to support health self-management by tracking, storing, compiling, and providing feedback about an individual's engagement in movement activities. Older adults represent a fast growing segment of the population who may benefit from such technologies. To understand how to facilitate technology acceptance and adoption, more information is needed about older adults' attitudes and usage of such technologies. Eight older adult participants (M age = 65.0 years; SD = 3.2; range = 61-69) used one of four activity monitoring technologies in their own homes for two weeks. Attitudes and usability issues were assessed and evaluated within a technology acceptance framework. Participants' initial attitudes were positive, but after using the technology for two weeks, attitudes were mixed. Three participants indicated they would continue using the technology, whereas five said they would abandon the technology. These data offer insight into older adults' use of and attitudes toward activity monitoring technologies and provide improvement opportunities for designers. The results suggest that efforts should focus on conveying the usefulness and personal benefits of activity monitoring technologies specific to older adults.

Structure of FD-895 revealed through total synthesis.

The total synthesis of FD-895 was completed through a strategy that featured the use of a tandem esterification ring-closing metathesis (RCM) process to construct the 12-membered macrolide and a modified Stille coupling to append the side chain. These studies combined with detailed analysis of all four possible C16-C17 stereoisomers were used to confirm the structure of FD-895 and identify an analog with an enhanced subnanomolar bioactivity.

Comparison of radiation treatment delivery for pancreatic cancer: Linac intensity-modulated radiotherapy versus helical tomotherapy.

INTRODUCTION: Intensity-modulated radiotherapy (IMRT) has been shown to reduce dose to organs at risk (OAR) while adequately treating tumour volume. This study quantitatively compares the dosimetric differences from step-and-shoot IMRT compared with helical tomotherapy (HT) for pancreatic head cancer. METHODS: Twelve consecutive patients with non-metastatic, stage T3 or T4, unresectable pancreatic head cancer were planned for step-and-shoot IMRT as well as HT. Radiotherapy was planned to deliver 45.9 Gy to the clinical target volume in 30 fractions with an integrated boost to 54 Gy to the gross tumour volume (planning target volume 5400 including a 1-cm set-up margin). The uniformity index (UI) and conformity index (CI) were used to compare the quality of target coverage, while the quality index (QI) compared the dosimetric performance for OAR. RESULTS: Both methods were effective at covering the tumour with no significant difference in UI or CI. However, HT dosimetry exhibited superior sparing of OAR with significantly less stomach (mean QI(StomV30) = 0.84, P = 0.006) and small bowel dosing (mean small bowel QI(SBV30) = 0.84, P = 0.005). HT reduced dose to the kidney receiving the highest dose but the overall volume of kidney receiving 18 Gy was not significantly different between the two systems, indicating that HT spread the dose more uniformly through the kidneys. CONCLUSIONS: Target coverage is equivalent between the two systems; however, HT shows significantly better sparing of the stomach and small bowel. The decreased dose to OAR with HT is likely to improve the therapeutic ratio in the radiotherapy of pancreatic head cancers.

Convergent route to the spirohexenolide macrocycle.

Using key functional dissections, the synthesis of spirohexenolides is examined through a three-component strategy that features a 1,2-addition to couple tetronate and aldehyde components forming the C2-C3 bond and a Stille coupling to install the third sulfone-containing component. The macrocycle is completed by an intramolecular Julia-Kocienski reaction to form the C10-C11 trans-disubstituted olefin. Application of this strategy is described in progress toward the synthesis of (±)-spirohexenolide B.

Responsiveness of a Xenopus laevis cell line to the aryl hydrocarbon receptor ligands 6-formylindolo[3,2-b]carbazole (FICZ) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD).

The aryl hydrocarbon receptor (AHR) mediates the toxic effects of environmental contaminants, such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Frogs are very insensitive to TCDD toxicity, and AHRs from Xenopus laevis (African clawed frog) bind TCDD with >20-fold lower affinity than mouse AHR(b-1). Frog AHRs may nonetheless be highly responsive to structurally distinct compounds, especially putative endogenous ligands. We sought to determine the responsiveness of an X. laevis cell line, XLK-WG, to the candidate endogenous AHR ligand 6-formylindolo[3,2-b]carbazole (FICZ), a tryptophan photoproduct that exhibits high potency in mammalian systems. FICZ readily induced mRNAs for CYP1A6 and CYP1A7. Cells exposed to FICZ for 3h expressed up to 5-fold greater quantities of CYP1A6/7 mRNAs than those exposed for 24h, suggesting FICZ is metabolized following rapid enzyme induction. FICZ appeared more potent than TCDD. Following a 3-h exposure, the EC(50) for CYP1A6 mRNA induction by FICZ was approximately 6nM, while the TCDD response was greater than 174nM. These potencies were lower than those determined for mouse hepatoma cells (Hepa1c1c7; EC(50)= approximately 0.06nM each). The difference in ligand potency between cell lines was confirmed by induction of ethoxyresorufin-O-deethylase (EROD) activity. mRNA from XLK-WG cells treated with 100nM FICZ, 100nM TCDD, or vehicle was also analyzed on expression microarrays. FICZ altered the expression of 105 more transcripts than TCDD, and common targets were altered more dramatically by FICZ. Overall, these studies demonstrate that although FICZ is a less potent CYP1A inducer in frog cells than in mouse cells, the reduction is much less than for TCDD. Relative conservation of the FICZ response in a TCDD-insensitive species suggests its physiological importance as an AHR ligand.

Cytoplasmic acidification and the benzoate transcriptome in Bacillus subtilis.

BACKGROUND: Bacillus subtilis encounters a wide range of environmental pH. The bacteria maintain cytoplasmic pH within a narrow range. Response to acid stress is a poorly understood function of external pH and of permeant acids that conduct protons into the cytoplasm. METHODS AND PRINCIPAL FINDINGS: Cytoplasmic acidification and the benzoate transcriptome were observed in Bacillus subtilis. Cytoplasmic pH was measured with 4-s time resolution using GFPmut3b fluorimetry. Rapid external acidification (pH 7.5 to 6.0) acidified the B. subtilis cytoplasm, followed by partial recovery. Benzoate addition up to 60 mM at external pH 7 depressed cytoplasmic pH but left a transmembrane Delta pH permitting growth; this robust adaptation to benzoate exceeds that seen in E. coli. Cytoplasmic pH was depressed by 0.3 units during growth with 30 mM benzoate. The transcriptome of benzoate-adapted cells was determined by comparing 4,095 gene expression indices following growth at pH 7, +/- 30 mM benzoate. 164 ORFs showed > or = 2-fold up-regulation by benzoate (30 mM benzoate/0 mM), and 102 ORFs showed > or = 2-fold down-regulation. 42% of benzoate-dependent genes are regulated up or down, respectively, at pH 6 versus pH 7; they are candidates for cytoplasmic pH response. Acid-stress genes up-regulated by benzoate included drug resistance genes (yhbI, yhcA, yuxJ, ywoGH); an oligopeptide transporter (opp); glycine catabolism (gcvPA-PB); acetate degradation (acsA); dehydrogenases (ald, fdhD, serA, yrhEFG, yjgCD); the TCA cycle (citZ, icd, mdh, sucD); and oxidative stress (OYE-family yqjM, ohrB). Base-stress genes down-regulated by benzoate included malate metabolism (maeN), sporulation control (spo0M, spo0E), and the SigW alkali shock regulon. Cytoplasmic pH could mediate alkali-shock induction of SigW. CONCLUSIONS: B. subtilis maintains partial pH homeostasis during growth, and withstands high concentrations of permeant acid stress, higher than for gram-negative neutralophile E. coli. The benzoate adaptation transcriptome substantially overlaps that of external acid, contributing to a cytoplasmic pH transcriptome.

Isolation, structure elucidation, and antitumor activity of spirohexenolides A and B.

In this report, we describe the discovery of a pair of bioactive spirotetronates, spirohexenolides A (1) and B (2), that arose from the application of mutagenesis, clonal selection techniques, and media optimization to strains of Streptomyces platensis. The structures of spirohexenolides A (1) and B (2) were elucidated through X-ray crystallography and confirmed by 1D and 2D NMR studies. Under all examined culture conditions, spirohexenolide A (1) was the major metabolite with traces of spirohexenolide B (2) arising in cultures containing increased loads of adsorbent resins. Spirohexenolide A (1) inhibited tumor cell growth with GI(50) values spanning from 0.1 to 17 microM across the NCI 60 cell line panel. An increased activity was observed in leukemia (GI(50) value of 254 nM in RPMI-8226 cells), lung cancer (GI(50) value of 191 nM in HOP-92 cells), and colon cancer (GI(50) value of 565 nM in SW-620 cells) tumor cells. Metabolite 1 was fluorescent and could be examined on a confocal fluorescent microscope with conventional laser excitation and filter sets. Time lapse imaging studies indicated that spirohexenolide A (1) was readily taken up by tumor cells, appearing through the cell immediately after dosing and subcellularly localizing in the lysosomes. This activity, combined with a unique selectivity in NCI 60 cancer cell line screening, indicates that 1 warrants further chemotherapeutic evaluation.

Acid and base stress and transcriptomic responses in Bacillus subtilis.

Acid and base environmental stress responses were investigated in Bacillus subtilis. B. subtilis AG174 cultures in buffered potassium-modified Luria broth were switched from pH 8.5 to pH 6.0 and recovered growth rapidly, whereas cultures switched from pH 6.0 to pH 8.5 showed a long lag time. Log-phase cultures at pH 6.0 survived 60 to 100% at pH 4.5, whereas cells grown at pH 7.0 survived <15%. Cells grown at pH 9.0 survived 40 to 100% at pH 10, whereas cells grown at pH 7.0 survived <5%. Thus, growth in a moderate acid or base induced adaptation to a more extreme acid or base, respectively. Expression indices from Affymetrix chip hybridization were obtained for 4,095 protein-encoding open reading frames of B. subtilis grown at external pH 6, pH 7, and pH 9. Growth at pH 6 upregulated acetoin production (alsDS), dehydrogenases (adhA, ald, fdhD, and gabD), and decarboxylases (psd and speA). Acid upregulated malate metabolism (maeN), metal export (czcDO and cadA), oxidative stress (catalase katA; OYE family namA), and the SigX extracytoplasmic stress regulon. Growth at pH 9 upregulated arginine catabolism (roc), which generates organic acids, glutamate synthase (gltAB), polyamine acetylation and transport (blt), the K(+)/H(+) antiporter (yhaTU), and cytochrome oxidoreductases (cyd, ctaACE, and qcrC). The SigH, SigL, and SigW regulons were upregulated at high pH. Overall, greater genetic adaptation was seen at pH 9 than at pH 6, which may explain the lag time required for growth shift to high pH. Low external pH favored dehydrogenases and decarboxylases that may consume acids and generate basic amines, whereas high external pH favored catabolism-generating acids.

Rapid acid treatment of Escherichia coli: transcriptomic response and recovery.

BACKGROUND: Many E. coli genes show pH-dependent expression during logarithmic growth in acid (pH 5-6) or in base (pH 8-9). The effect of rapid pH change, however, has rarely been tested. Rapid acid treatment could distinguish between genes responding to external pH, and genes responding to cytoplasmic acidification, which occurs transiently following rapid external acidification. It could reveal previously unknown acid-stress genes whose effects are transient, as well as show which acid-stress genes have a delayed response. RESULTS: Microarray hybridization was employed to observe the global gene expression of E. coli K-12 W3110 following rapid acidification of the external medium, from pH 7.6 to pH 5.5. Fluorimetric observation of pH-dependent tetR-YFP showed that rapid external acidification led to a half-unit drop in cytoplasmic pH (from pH 7.6 to pH 6.4) which began to recover within 20 s. Following acid treatment, 630 genes were up-regulated and 586 genes were down-regulated. Up-regulated genes included amino-acid decarboxylases (cadA, adiY, gadA), succinate dehydrogenase (sdhABCD), biofilm-associated genes (bdm, gatAB, and ymgABC), and the Gad, Fur and Rcs regulons. Genes with response patterns consistent with cytoplasmic acid stress were revealed by addition of benzoate, a membrane-permeant acid that permanently depresses cytoplasmic pH without affecting external pH. Several genes (yagU, ygiN, yjeI, and yneI) were up-regulated specifically by external acidification, while other genes (fimB, ygaC, yhcN, yhjX, ymgABC, yodA) presented a benzoate response consistent with cytoplasmic pH stress. Other genes (the nuo operon for NADH dehydrogenase I, and the HslUV protease) showed delayed up-regulation by acid, with expression rising by 10 min following the acid shift. CONCLUSION: Transcriptomic profiling of E. coli K-12 distinguished three different classes of change in gene expression following rapid acid treatment: up-regulation with or without recovery, and delayed response to acid. For eight genes showing acid response and recovery (fimB, ygaC, yhcN, yhjX, ymgABC, yodA), responses to the permeant acid benzoate revealed expression patterns consistent with sensing of cytoplasmic pH. The delayed acid response of nuo genes shows that NADH dehydrogenase I is probably induced as a secondary result of acid-associated metabolism, not as a direct response to cytoplasmic acidification.