Flexible gold standards for transcription factor regulatory interactions in Escherichia coli K-12: architecture of evidence types

Post-genomic implementations have expanded the experimental strategies to identify elements involved in the regulation of transcription initiation. Here, we present for the first time a detailed analysis of the sources of knowledge supporting the collection of transcriptional regulatory interactions (RIs) of Escherichia coli K-12. An RI groups the transcription factor, its effect (positive or negative) and the regulated target, a promoter, a gene or transcription unit. We improved the evidence codes so that specific methods are incorporated and classified into independent groups. On this basis we updated the computation of confidence levels, weak, strong, or confirmed, for the collection of RIs. These updates enabled us to map the RI set to the current collection of HT TF-binding datasets from ChIP-seq, ChIP-exo, gSELEX and DAP-seq in RegulonDB, enriching in this way the evidence of close to one-quarter (1329) of RIs from the current total 5446 RIs. Based on the new computational capabilities of our improved annotation of evidence sources, we can now analyze the internal architecture of evidence, their categories (experimental, classical, HT, computational), and confidence levels. This is how we know that the joint contribution of HT and computational methods increase the overall fraction of reliable RIs (the sum of confirmed and strong evidence) from 49% to 71%. Thus, the current collection has 3912 reliable RIs, with 2718 or 70% of them with classical evidence which can be used to benchmark novel HT methods. Users can selectively exclude the method they want to benchmark, or keep for instance only the confirmed interactions. The recovery of regulatory sites in RegulonDB by the different HT methods ranges between 33% by ChIP-exo to 76% by ChIP-seq although as discussed, many potential confounding factors limit their interpretation. The collection of improvements reported here provides a solid foundation to incorporate new methods and data, and to further integrate the diverse sources of knowledge of the different components of the transcriptional regulatory network. There is no other genomic database that offers this comprehensive high-quality architecture of knowledge supporting a corpus of transcriptional regulatory interactions.

RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12

RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements. We also present a full reconstruction of the RegulonDB computational infrastructure, which has significantly improved data storage, retrieval and accessibility and thus supports a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. RegulonDB version 12.0 can be accessed at https://regulondb.ccg.unam.mx.

The EcoCyc Database (2023)

EcoCyc is a bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists and for biologists who work with related microorganisms. The database includes information pages on each E. coli gene product, metabolite, reaction, operon, and metabolic pathway. The database also includes information on the regulation of gene expression, E. coli gene essentiality, and nutrient conditions that do or do not support the growth of E. coli. The website and downloadable software contain tools for the analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc and can be executed online. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. Data generated from a whole-cell model that is parameterized from the latest data on EcoCyc are also available. This review outlines the data content of EcoCyc and of the procedures by which this content is generated.

A Gold Standard for Transcription Factor Regulatory Interactions in Escherichia coli K-12: Architecture of Evidence Types

Post-genomic implementations have expanded the experimental strategies to identify elements involved in the regulation of transcription initiation. As new methodologies emerge, a natural step is to compare their results with those from established methodologies, such as the classic methods of molecular biology used to characterize transcription factor binding sites, promoters, or transcription units. In the case of Escherichia coli K-12, the best-studied microorganism, for the last 30 years we have continuously gathered such knowledge from original scientific publications, and have organized it in two databases, RegulonDB and EcoCyc. Furthermore, since RegulonDB version 11.0 (1), we offer comprehensive datasets of binding sites from chromatin immunoprecipitation combined with sequencing (ChIP-seq), ChIP combined with exonuclease digestion and next-generation sequencing (ChIP-exo), genomic SELEX screening (gSELEX), and DNA affinity purification sequencing (DAP-seq) HT technologies, as well as additional datasets for transcription start sites, transcription units and RNA sequencing (RNA-seq) expression profiles. Here, we present for the first time an analysis of the sources of knowledge supporting the collection of transcriptional regulatory interactions (RIs) of E. coli K-12. An RI is formed by the transcription factor, its positive or negative effect on a promoter, a gene or transcription unit. We improved the evidence codes so that the specific methods are described, and we classified them into seven independent groups. This is the basis for our updated computation of confidence levels, weak, strong, or confirmed, for the collection of RIs. We compare the confidence levels of the RI collection before and after adding HT evidence illustrating how knowledge will change as more HT data and methods appear in the future. Users can generate subsets filtering out the method they want to benchmark and avoid circularity, or keep for instance only the confirmed interactions. The comparison of different HT methods with the available datasets indicate that ChIP-seq recovers the highest fraction (>70%) of binding sites present in RegulonDB followed by gSELEX, DAP-seq and ChIP-exo. There is no other genomic database that offers this comprehensive high-quality anatomy of evidence supporting a corpus of transcriptional regulatory interactions.

Microaerobic degradation of crude oil and long chain alkanes by a new Rhodococcus strain from Gulf of Mexico

Bacterial degradation of crude oil is a promising strategy for reducing the concentration of hydrocarbons in contaminated environments. In the first part of this study, we report the enrichment of two bacterial consortia from deep sediments of the Gulf of Mexico with crude oil as the sole carbon and energy source. We conducted a comparative analysis of the bacterial community in the original sediment, assessing its diversity, and compared it to the enrichment observed after exposure to crude oil in defined cultures. The consortium exhibiting the highest hydrocarbon degradation was predominantly enriched with Rhodococcus (75%). Bacterial community analysis revealed the presence of other hydrocarbonoclastic members in both consortia. In the second part, we report the isolation of the strain Rhodococcus sp. GOMB7 with crude oil as a unique carbon source under microaerobic conditions and its characterization. This strain demonstrated the ability to degrade long-chain alkanes, including eicosane, tetracosane, and octacosane. We named this new strain Rhodococcus qingshengii GOMB7. Genome analysis revealed the presence of several genes related to aromatic compound degradation, such as benA, benB, benC, catA, catB, and catC; and five alkB genes related to alkane degradation. Although members of the genus Rhodococcus are well known for their great metabolic versatility, including the aerobic degradation of recalcitrant organic compounds such as petroleum hydrocarbons, this is the first report of a novel strain of Rhodococcus capable of degrading long-chain alkanes under microaerobic conditions. The potential of R. qingshengii GOMB7 for applications in bioreactors or controlled systems with low oxygen levels offers an energy-efficient approach for treating crude oil-contaminated water and sediments.

RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12

Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. These datasets are available in public repositories, such as the Gene Expression Omnibus, or ArrayExpress. However, accessing and navigating such a wealth of data is not straightforward. No resource currently exists that offers all available high and low-throughput data on transcriptional regulation in Escherichia coli K-12 to easily use both as whole datasets, or as individual interactions and regulatory elements. RegulonDB (https://regulondb.ccg.unam.mx) began gathering high-throughput dataset collections in 2009, starting with transcription start sites, then adding ChIP-seq and gSELEX in 2012, with up to 99 different experimental high-throughput datasets available in 2019. In this paper we present a radical upgrade to more than 2000 high-throughput datasets, processed to facilitate their comparison, introducing up-to-date collections of transcription termination sites, transcription units, as well as transcription factor binding interactions derived from ChIP-seq, ChIP-exo, gSELEX and DAP-seq experiments, besides expression profiles derived from RNA-seq experiments. For ChIP-seq experiments we offer both the data as presented by the authors, as well as data uniformly processed in-house, enhancing their comparability, as well as the traceability of the methods and reproducibility of the results. Furthermore, we have expanded the tools available for browsing and visualization across and within datasets. We include comparisons against previously existing knowledge in RegulonDB from classic experiments, a nucleotide-resolution genome viewer, and an interface that enables users to browse datasets by querying their metadata. A particular effort was made to automatically extract detailed experimental growth conditions by implementing an assisted curation strategy applying Natural language processing and machine learning. We provide summaries with the total number of interactions found in each experiment, as well as tools to identify common results among different experiments. This is a long-awaited resource to make use of such wealth of knowledge and advance our understanding of the biology of the model bacterium E. coli K-12.

Sensory Systems and Transcriptional Regulation in Escherichia coli

In free-living bacteria, the ability to regulate gene expression is at the core of adapting and interacting with the environment. For these systems to have a logic, a signal must trigger a genetic change that helps the cell to deal with what implies its presence in the environment; briefly, the response is expected to include a feedback to the signal. Thus, it makes sense to think of genetic sensory mechanisms of gene regulation. Escherichia coli K-12 is the bacterium model for which the largest number of regulatory systems and its sensing capabilities have been studied in detail at the molecular level. In this special issue focused on biomolecular sensing systems, we offer an overview of the transcriptional regulatory corpus of knowledge for E. coli that has been gathered in our database, RegulonDB, from the perspective of sensing regulatory systems. Thus, we start with the beginning of the information flux, which is the signal’s chemical or physical elements detected by the cell as changes in the environment; these signals are internally transduced to transcription factors and alter their conformation. Signals transduced to effectors bind allosterically to transcription factors, and this defines the dominant sensing mechanism in E. coli. We offer an updated list of the repertoire of known allosteric effectors, as well as a list of the currently known different mechanisms of this sensing capability. Our previous definition of elementary genetic sensory-response units, GENSOR units for short, that integrate signals, transport, gene regulation, and the biochemical response of the regulated gene products of a given transcriptional factor fit perfectly with the purpose of this overview. We summarize the functional heterogeneity of their response, based on our updated collection of GENSORs, and we use them to identify the expected feedback as part of their response. Finally, we address the question of multiple sensing in the regulatory network of E. coli. This overview introduces the architecture of sensing and regulation of native components in E.coli K-12, which might be a source of inspiration to bioengineering applications.

Transcriptome Analysis Reveals Cr(VI) Adaptation Mechanisms in Klebsiella sp. Strain AqSCr

Klebsiella sp. strain AqSCr, isolated from Cr(VI)-polluted groundwater, reduces Cr(VI) both aerobically and anaerobically and resists up 34 mM Cr(VI); this resistance is independent of the ChrA efflux transporter. In this study, we report the whole genome sequence and the transcriptional profile by RNA-Seq of strain AqSCr under Cr(VI)-adapted conditions and found 255 upregulated and 240 downregulated genes compared to controls without Cr(VI) supplementation. Genes differentially transcribed were mostly associated with oxidative stress response, DNA repair and replication, sulfur starvation response, envelope-osmotic stress response, fatty acid (FA) metabolism, ribosomal subunits, and energy metabolism. Among them, genes not previously associated with chromium resistance, for example, cybB, encoding a putative superoxide oxidase (SOO), gltA2, encoding an alternative citrate synthase, and des, encoding a FA desaturase, were upregulated. The sodA gene encoding a manganese superoxide dismutase was upregulated in the presence of Cr(VI), whereas sodB encoding an iron superoxide dismutase was downregulated. Cr(VI) resistance mechanisms in strain AqSCr seem to be orchestrated by the alternative sigma factors fecl, rpoE, and rpoS (all of them upregulated). Membrane lipid analysis of the Cr(IV)-adapted strain showed a lower proportion of unsaturated lipids with respect to the control, which we hypothesized could result from unsaturated lipid peroxidation followed by degradation, together with de novo synthesis mediated by the upregulated FA desaturase-encoding gene, des. This report helps to elucidate both Cr(VI) toxicity targets and global bacterial response to Cr(VI).

Acetate biostimulation as an effective treatment for cleaning up alkaline soil highly contaminated with Cr(VI)

Stimulation of microbial reduction of Cr(VI) to the less toxic and less soluble Cr(III) through electron donor addition has been regarded as a promising approach for the remediation of chromium-contaminated soil and groundwater sites. However, each site presents different challenges; local physicochemical characteristics and indigenous microbial communities influence the effectiveness of the biostimulation processes. Here, we show microcosm assays stimulation of microbial reduction of Cr(VI) in highly alkaline and saline soil samples from a long-term contaminated site in Guanajuato, Mexico. Acetate was effective promoting anaerobic microbial reduction of 15 mM of Cr(VI) in 25 days accompanied by an increase in pH from 9 to 10. Our analyses showed the presence of Halomonas, Herbaspirillum, Nesterenkonia/Arthrobacter, and Bacillus species in the soil sample collected. Moreover, from biostimulated soil samples, it was possible to isolate Halomonas spp. strains able to grow at 32 mM of Cr(VI). Additionally, we found that polluted groundwater has bacterial species different to those found in soil samples with the ability to resist and reduce chromate using acetate and yeast extract as electron donors.

Transforming the Perioperative Treatment Paradigm in Non-Metastatic RCC-A Possible Path Forward

In 2017, there is no adjuvant systemic therapy proven to increase overall survival in non-metastatic renal cell carcinoma (RCC). The anti-PD-1 antibody nivolumab improves overall survival in metastatic treatment refractory RCC and is generally tolerable. Mouse solid tumor models have revealed a benefit with a short course of neoadjuvant PD-1 blockade compared to adjuvant therapy. Two ongoing phase 2 studies of perioperative nivolumab in RCC patients have shown preliminary feasibility and safety with no surgical delays or complications. The recently opened PROSPER RCC trial (A Phase 3 RandOmized Study Comparing PERioperative Nivolumab vs. Observation in Patients with Localized Renal Cell Carcinoma Undergoing Nephrectomy; EA8143) will examine if the addition of perioperative nivolumab to radical or partial nephrectomy can improve clinical outcomes in patients with high risk localized and locally advanced RCC. With the goal of increasing cure and recurrence-free survival (RFS) rates in non-metastatic RCC, we are executing a three-pronged, multidisciplinary approach of presurgical priming with nivolumab followed by resection and adjuvant PD-1 blockade. We plan to enroll 766 patients with clinical stage ≥T2 or node positive M0 RCC of any histology in this global, randomized, unblinded, phase 3 National Clinical Trials Network study. The investigational arm will receive two doses of nivolumab 240 mg IV prior to surgery followed by adjuvant nivolumab for 9 months. The control arm will undergo the current standard of care: surgical resection followed by observation. Patients are stratified by clinical T stage, node positivity, and histology. The trial is powered to detect a 14.4% absolute benefit in the primary endpoint of RFS from the ASSURE historical control of 55.8% to 70.2% at 5 years (HR = 0.70). The study is also powered to detect a significant overall survival benefit (HR 0.67). Key safety, feasibility, and quality of life endpoints are incorporated. PROSPER RCC exemplifies team science with a host of planned correlative work to investigate the impact of the baseline immune milieu and changes after neoadjuvant priming on clinical outcomes.

Implications of lymph node retrieval in locoregional rectal cancer treated with chemoradiotherapy: a California Cancer Registry Study

BACKGROUND

In contrast to colon cancer, the implications of reduced lymph node retrieval in rectal cancer are unclear.

METHODS

Using the California Cancer Registry, we performed a retrospective cohort study of 4790 patients with stage I - III rectal cancer diagnosed from 2000 to 2007 who underwent tri-modality therapy. Using multivariate Cox proportional hazards models adjusted for age, sex, race, socioeconomic status, T-stage, and lymph node numbers, we evaluated rectal cancer specific survival (RC-SS) in neoadjuvant and adjuvant cohorts in the overall population and amongst those without involved lymph nodes (pN0).

RESULTS

Sixty one percent of evaluable patients were treated with neoadjuvant chemoradiation. Although there was no difference in RC-SS between neoadjuvant and adjuvant chemoradiation cohorts, the median number of lymph nodes examined was reduced after neoadjuvant therapy (8 vs. 11, p < 0.0001). Positive lymph nodes were associated with worse RC-SS regardless of sequence, although the effect was numerically stronger for residual lymph nodes in the neoadjuvant cohort. Compared to at least 12, eight or fewer lymph nodes retrieved was associated with worse outcome in both neoadjuvant and adjuvant cohorts. However, no association between reduced lymph nodes examined and RC-SS was seen in the neoadjuvant cohort when the analysis was restricted to pN0 patients.

CONCLUSIONS

In this large cohort of rectal cancer patients treated with tri-modality therapy, reduced lymph node retrieval in node negative patients did not provide additional prognostic information in patients treated with neoadjuvant therapy.

Infrastructures, treatment modalities, and workload of radiation oncology departments in Spain with special attention to prostate cancer

AIM

The purpose of the study was to describe infrastructures, treatment modalities, and workload in radiation oncology (RO) in Spain, referred particularly to prostate cancer (PC).

METHODS

An epidemiologic, cross-sectional study was performed during 2008-2009. A study-specific questionnaire was sent to the 108 RO-registered departments.

RESULTS

One hundred and two departments answered the survey, and six were contacted by telephone. Centers operated 236 treatment units: 23 (9.7 %) cobalt machines, 37 (15.7 %) mono-energetic linear accelerators, and 176 (74.6 %) multi-energy linear accelerators. Sixty-one (56.4 %) and 33 (30.5 %) departments, respectively, reported intensity-modulated radiation therapy (IMRT) and image-guided RT (IGRT) capabilities; three-dimensional-conformal RT was used in 75.8 % of patients. Virtual simulators were present in 95 departments (88.0 %), 35 use conventional simulators. Fifty-one departments (47.2 %) have brachytherapy units, 38 (35.2 %) perform prostatic implants. Departments saw a mean of 24.9 new patients/week; the number of patients treated annually was 102,054, corresponding to 88.4 % of patients with a RT indication. In 56.5 % of the hospitals, multidisciplinary teams were available to treat PC.

CONCLUSIONS

Results provide an accurate picture of current situation of RO in Spain, showing a trend toward the progressive introduction of new technologies (IMRT, IGRT, brachytherapy).

The hydrogenation of nitroarenes mediated by platinum nanoparticles: an overview

This review reports the most recent advances in the synthesis and application of platinum nanoparticles as catalysts in the hydrogenation reaction of nitroaromatics.

KRAS mutations in non-small-cell lung cancer and colorectal cancer: implications for EGFR-targeted therapies

BACKGROUND

KRAS mutations are associated with diverse biologic functions as well as prognostic and predictive impact in non-small cell-lung cancer (NSCLC) and colorectal cancer (CRC). In CRC, benefit from monoclonal antibody therapies targeting EGFR is generally limited to patients whose tumors have wild-type (WT) KRAS, whereas data suggest that this association is not present for NSCLC. We hypothesized that the unique tobacco-related carcinogenesis of NSCLC results in a divergence of KRAS MT genotype compared with CRC, contributing to differences in outcomes from EGFR-targeted therapies.

MATERIAL AND METHODS

Tumor from 2603 patients (838 CRC and 1765 NSCLC) was analyzed for KRAS mutations. DNA was extracted from microdissected formalin-fixed-paraffin-embedded specimens (FFPE) and 7 different base substitutions in codons 12 and 13 of KRAS were determined.

RESULTS

KRAS mutation genotype differed significantly between NSCLC and CRC in frequency (25% vs. 39%; p<0.001), smoking-associated G>T transversions (73% versus 27%; p<0.001), and ratio of transversions to transitions (3.5 vs. 0.79; p<0.001). In NSCLC GLY12Cys mutations, resulting from a codon 12 GGT>TGT substitution, were observed in 44% compared to 10% for CRC. In contrast, codon 12 or 13 GLY>ASP substitutions (resulting in a G>A transition) were more frequent in CRC (42%) compared with NSCLC (21%).

CONCLUSION

In this large dataset, KRAS mutation patterns are quantitatively and qualitatively distinct between NSCLC and CRC, reflecting in part differences in tobacco-related carcinogenesis. In light of differences in predictive value for EGFR-directed monoclonal antibody therapy and prognosis for specific KRAS mutations between NSCLC and CRC, these data provide an underlying biologic rationale.

The hepatitis B x antigen anti-apoptotic effector URG7 is localized to the endoplasmic reticulum membrane

Hepatitis B x antigen up-regulates the liver expression of URG7 that contributes to sustain chronic virus infection and to increase the risk for hepatocellular carcinoma by its anti-apoptotic activity. We have investigated the subcellular localization of URG7 expressed in HepG2 cells and determined its membrane topology by glycosylation mapping in vitro. The results demonstrate that URG7 is N-glycosylated and located to the endoplasmic reticulum membrane with an Nlumen-Ccytosol orientation. The results imply that the anti-apoptotic effect of URG7 could arise from the C-terminal cytosolic tail binding a pro-apoptotic signaling factor and retaining it to the endoplasmic reticulum membrane.

Encouraging activity of bicalutamide and everolimus in castration-resistant prostate cancer (CRPC): Early results from a phase II clinical trial

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Background: Multiple signaling pathways are involved in the development of CRPC. We previously showed that the mTOR pathway is activated in CRPC cell lines while inhibition of this pathway results in upregulation of androgen receptor (AR) signaling (Wang et al, Oncogene. 2008). Simultaneous blockade of the mTOR and AR pathways synergize in inducing PCa cell death and delaying tumor formation in mouse models. We hypothesize that simultaneous blockade of the AR and mTOR pathways in CRPC patients with bicalutamide and everolimus will result in improved efficacy compared to bicalutamide alone.

Methods: A phase II clinical trial with a lead-in safety phase was designed to determine the efficacy and tolerability of the bicalutamide and everolimus combination in CRPC patients compared with bicalutamide alone. Patients must have histologically confirmed disease and demonstrated disease progression (either by PSA or radiographically) while on androgen deprivation therapy. At the lead-in phase, all patients receive both agents. At the phase II stage, patients are randomized to bicalutamide +/− everolimus. The primary endpoint is PSA response. The second endpoints include progression-free survival, time-to-treatment failure, overall survival and toxicity. Here, we report the results of the lead-in phase.

Results: Eight patients were recruited at the lead-in phase. The bicalutamide/everolimus combination was well tolerated with no unexpected toxicities. Six of 8 patients have had PSA response after at least 8 weeks of therapy and the remaining two patients had stable PSA response. The median time to disease progression was 6.8 months. Nine patients have been recruited at the phase II stage so far. This clinical trial is being subcontracting to the other sites of the California Cancer Consortium. Tumor and blood specimens are being collected for molecular correlative studies of mTOR pathway markers.

Conclusions: The rational combination of bicalutamide and everolimus appears to have promising anti-tumor activity and an acceptable toxicity profile. The randomized phase of the clinical trial is currently ongoing and will be reported. Supported by Novartis.

[Table: see text]

A phase 0 microdosing trial to identify chemoresistance in bladder cancer

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Background: DNA damage is the critical step in cancer cell response to platinum (Pt) chemotherapy. We hypothesize that low levels of Pt-induced DNA damage are predictive of chemoresistance. Accelerator mass spectrometry (AMS) is an ultrasensitive method for measuring radiocarbon. By measuring 14C bound to DNA, AMS can detect carboplatin-induced DNA damage after patients receive one subtoxic microdose of 14C-labeled carboplatin.

Methods: Cancer cells and mice bearing tumor xenografts were treated with one microdose (1/100th of the therapeutic dose) or one therapeutic dose of [14C]carboplatin. Carboplatin-DNA adducts and other relevant parameters such as drug influx/efflux, intracellular drug inactivation, and repair of DNA damage, were measured and correlated with response to chemotherapy.

Results: AMS detected Pt-DNA damage when cancer cells and mice with tumor xenografts were exposed to one microdose of [14C]carboplatin. The levels of microdose-induced DNA damage were linearly proportional to the DNA damage caused by the therapeutic drug dose (R2=0.92, p<0.001); and these levels of DNA damage correlated with chemoresistance. Low DNA damage predicts chemoresistance. Measuring drug uptake/efflux, intracellular inactivation and DNA repair allowed insight into some resistance mechanisms. We have opened a phase 0 microdosing trial to study patients with bladder cancer who are scheduled to receive Pt-based chemotherapy. One subtoxic microdose of 14C-carboplatin will be administered to these patients before biopsy. Pt-induced DNA damage and repair in left-over tumor biopsy specimens and other relevant parameters will be measured and correlated with the response and toxicity of chemotherapy. Molecular analysis of genes such as ERCC1 and RRM1 will be analyzed and compared with this phase 0 results. We have opened a similar phase 0 trial in dog patients with bladder cancer.

Conclusions: The levels of DNA damage induced by nontoxic microdosing carboplatin can potentially predict chemoresistance in cancer cell lines. The clinical data of the phase 0 trial will be presented.

No significant financial relationships to disclose.

Family-based health needs along the Texas-Mexico border

BACKGROUND

The population in the Texas-Mexico border is rapidly increasing and exacerbating a number of public health problems and healthcare services. The needs of this area have been predominantly assessed through a professional lens. To better inform public policy and serve the area, this study assessed the needs of families living along the Texas-Mexico border.

METHODS

Approximately 2000 households along the Texas-Mexico border were interviewed for their basic demographic information and health needs.

RESULTS

It was found that children's healthcare services were the highest reported need among families along the border. The probability of reporting healthcare needs increased by 43% among families with children under the age of 5, whereas the probability of reporting healthcare needs decreased by 40% among families with children 13 and older.

CONCLUSION

The findings from this study suggest child healthcare services, particularly for families with young children, is the most pressing need of the area.

Developing Professional Knowledge and Confidence in Higher Education

The purpose of this paper is to determine the effectiveness of using multiple choice tests in subjects related to the administration and business management. To this end the authors used a multiple-choice test with specific questions to verify the extent of knowledge gained and the confidence and trust in the answers. The analysis made, conducted by tests given out to a group of 200 students, has been implemented in one subject related with investment analysis and has measured the level of knowledge gained and the degree of trust and security in the responses at two different times of the business administration and management course. Measurements were taken into account at different levels of difficulty in the questions asked and the time spent by students to complete the test. Results confirm that students are generally able to obtain more knowledge along the way and get increases in the degree of trust and confidence. It is estimated that improvement in skills learned is viewed favourably by businesses and are important for job placement. Finally, the authors proceed to analyze a multi-choice test using a combination of knowledge and confidence levels.