How efficient is modern peri-urban nitrogen cycling: A case study

Urban centres acquire and accumulate many materials from their hinterland, among these are nutrient elements such as nitrogen (N). The popular North American vision of a peri-urban setting is one where urban food production, composting and re-cycling are assumed to limit urban accumulation of nutrients. This study quantifies this assumption using the Lower Fraser Valley (LFV) of British Columbia as an example, ideal because it is surrounded by mountains, ocean and an international border which collectively delimit the peri-urban boundaries. Nitrogen influxes are dominated by livestock feed imports to support dairy and poultry production (18000 tonnes N), followed by human food imports (9210 tonnes N), as well as 5410 tonnes N as fertilizer and 4690 tonnes N in atmospheric deposition. There is a transfer of 6700 tonnes N from agricultural to urban ecosystems displacing food imports, but food production contributes to the N footprint of the LFV. Nitrogen effluxes are dominated by sewage disposal (10400 tonnes N), solid waste disposal (7020 tonnes N) and atmospheric emissions (9460 tonnes N). The total influx is 15 kg N per person, the net influx is 3.1 kg N per person. Per unit land area, these are a total influx of 24 kg N/ha and a net influx of 4.7 kg N/ha. The atmospheric emissions are 4.7 kg N per person and 7.2 kg/ha. The N in soil is mobile and it is assumed soil N is at a steady state concentration, thus the surplus N is lost from the soil, probably by leaching and runoff. The Fraser River is estimated to acquire and transport 5230 tonnes N from the region into the ocean each year, in addition to 10300 tonnes N from sewage outfall. This is coupled with effluxes of phosphorus (estimated previously), and the result probably has an impact on the coastal waters. There is little reuse of imported N and current waste management practices including composting and combustion do little to improve N efficiency.

Phosphorus flows in a peri-urban region with intensive food production: A case study

Excess phosphorus (P) in peri-urban regions is an emerging issue, whereas there is global depletion of quality mined supplies of P. The flow of P across the landscape leading to regional surpluses and deficits is not well understood. We computed a regional P budget with internal P flows in a fairly discreet peri-urban region (Lower Fraser Valley, BC) with closely juxtaposed agricultural and non-agricultural urban ecosystems, in order to clarify the relationship between food production, food consumption and other activities involving use of P (e.g. keeping pets and horses and using soaps). We hypothesized changes that might notably improve P efficiency in peri-urban settings and wider regions. Livestock feed for the dairy and poultry sectors was the largest influx of P: the peri-urban land is too limited to grow feed grains and they are imported from outside the region. Fertilizer and import of food were the next largest influxes of P and a similar amount of P flows as food from the agricultural to urban ecosystems. Export of horticultural crops (berries and greenhouse crops) and poultry represented agricultural effluxes that partially offset the influxes. P efficiency was lower for horticultural production (21%) than animal production (32%), the latter benefited from importing feed crops, suggesting a regional advantage for animal products. There was 2.0, 3.8, 5.7 and 5.6 tonnes imported P per $ million farm cash receipts for horticulture, dairy, poultry meat and eggs. Eliminating fertilizer for corn and grass would reduce the ratio for the dairy industry. The net influx, dominated by fertilizer, animal feed and food was 8470 tonnes P per year or 3.2 kg P per person per year, and of this the addition to agricultural soils was 3650 tonnes P. The efflux in sewage effluent to the sea was 1150 tonnes P and exported sewage solids was 450 tonnes P. Municipal solid waste disposal was most difficult to quantify and was about 1800 tonnes P, 80% of which was partly reused in the urban regions and partly sequestered in landfill, which may be considered an efflux or a surplus. Reuse of rendering waste for feeding poultry significantly reduced P importation, but no rendering waste is used for cattle due to health concerns. Sensitivity analysis showed that variation in human population and the amount of P consumed per person in chicken and dairy products had the most influence on the total movement of P from agricultural to urban-ecosystems. There are current farm practices that mitigate P surpluses and new technologies are being developed to further reduce farm imbalances. However, current waste management policies that promote practices such composting of home wastes and exporting of poultry manure and biosolids to semiarid rangeland do little to enhance overall P cycling because the P is not returned to the farms producing feed and food for the peri-urban region. Sequestering in landfills may be a better solution until better ways are found to return surplus P.

A Phase 1 dose-finding and pharmacodynamic study of rapamycin in combination with bevacizumab in patients with unresectable hepatocellular carcinoma

BACKGROUND & AIMS

Preclinical studies have demonstrated the additive effect of rapamycin with bevacizumab for hepatocellular carcinoma treatment. We conducted a Phase 1 study to evaluate the safety and pharmacokinetics of the combination in patients with hepatocellular carcinoma.

METHODS

Adult participants with advanced hepatocellular carcinoma received intravenous bevacizumab (5mg/kg every 14 days) and oral rapamycin (1-6 mg/day; 3+3 dose escalation design). Computed tomography assessed tumour response and treatment safety. Pharmacokinetics assessment established rapamycin blood concentrations pre- and post-dose. Dynamic contrast-enhanced computed tomography analysed the tumour region for blood flow, permeability surface area product, fractional intravascular blood volume and extracellular-extravascular volume.

RESULTS

Twenty-four participants were treated. There were two dose limiting toxicities with rapamycin 5mg: grade 3 thrombocytopenia and grade 3 mucositis. The maximally tolerated dose of rapamycin was 4 mg. Adverse events (grade 1-2) included hyperglycaemia (83%), thrombocytopenia (75%), fatigue (46%), mucositis (46%), anorexia (42%), diarrhoea (33%) and proteinuria (12.5%). Of 20 evaluable participants, one reached complete response that lasted 4.5 months, two reached partial response, 14 reached stable disease and three had progressive disease. Median overall survival was 9.4 months; progression-free survival was 5.5 months. Dose level and steady state area under the concentration time curve for hour zero to infinity of rapamycin correlated inversely with blood flow rate and change in permeability-surface area. After 22 days of treatment, there were significant reductions from baseline in blood flow rate, permeability-surface area and fractional intracellular blood volume.

CONCLUSIONS

The recommended Phase 2 dose of rapamycin is 4 mg in combination with bevacizumab. Evidence of anti-vascular activity was observed together with promising clinical activity.

Sunitinib (SUTENT, SU11248) suppresses tumor growth and induces apoptosis in xenograft models of human hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the fifth most common and third deadliest primary neoplasm. Since HCC is a particularly vascular solid tumor, we determined the antitumor and antiangiogenic activities of sunitinib malate, a potent inhibitor of two receptors involved in angiogenesis - vascular endothelial growth factor receptor (VEGFR) and platelet-derived growth factor receptor (PDGFR). In the present study, we reported that treatment of HepG2 and SK-Hep-1 cells with sunitinib led to growth inhibition and apoptosis in a dose-dependent fashion. Sunitinib inhibited phosphorylation of VEGFR-2 at Tyr951 and PDGFR-beta at Tyr1021 both in vitro and in vivo. Sunitinib also suppressed tumor growth of five patient-derived xenografts. Sunitinib-induced tumor growth inhibition was associated with increased apoptosis, reduced microvessel density and inhibition of cell proliferation. This study provides a strong rationale for further clinical investigation of sunitinib in patients with hepatocellular carcinoma.

Phase I study of SIR-sphere plus sorafenib as first-line treatment in patients with nonresectable hepatocellular carcinoma: The Asia-Pacific Hepatocellular Carcinoma Trials Group protocol 05 (AHCC05)

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Background: Sorafenib has been shown to significantly prolong survival in patients with nonresectable hepatocellular carcinoma (HCC) without however significant tumour regression. The addition of radio-ablative therapy could confer additional survival benefit. This phase I trial was carried out to ascertain the toxicities and safety of this combination and was designed as a prelude to a phase II trial. Methods: Eligible patients were administered SIR-sphere (max dose 3 GBq) and subsequently given Sorafenib therapy (400mg bd) either 14 days (Cohort 1: first 3 patients) or 11 days (Cohort 2: subsequent patients) later. Assessment was carried out for 30 days after commencement of Sorafenib. Results: 10 patients were recruited into this phase I trial. The second patient became ineligible for sorafenib therapy after SIR-sphere due to pulmonary bleeding not related to radio-therapy and was excluded from assessment. The characteristics of the patients are in the Table. At the end of the study period, there was no adverse events (AE) of grade 3 or 4 for Cohort 1 and 3 for Cohort 2. The only serious adverse event (SAE) recorded was from Cohort 2. Conclusions: Starting sorafenib 14 days after SIR-sphere therapy is associated fewer AEs and SAEs. The phase II trial has commenced withsorafenib starting 14 days after SIR-sphere. [Table: see text]

[Table: see text]

An exploratory analysis of comprehensive geriatric assessment results and overall survival in 233 consecutive elderly cancer patients

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Background: Performance status (PS) is the main clinical parameter used by most oncologists to assess the ability of elderly cancer patients to tolerate chemotherapy and estimate prognosis. The results of comprehensive geriatric assessment (CGA) for elderly cancer patients were analyzed to investigate the impact of each CGA functional, physical, cognitive, and affective domain on overall survival in relation to performance status. Methods: CGA was used for 233 consecutive elderly cancer patients aged 70 and above. CGA tools included the Katz index of daily activities independence (ADL), instrumental activities of daily living (IADL), mini-mental state examination (MMSE), geriatric depression scale (GDS), Charlson comorbidity risk index, get up and go test, and mini-nutritional assessment. Geriatric syndrome is defined as any high risk of falls, depression, dementia, increased functional dependence, or malnutrition. Eastern Cooperative Oncology Group (ECOG) scale was used to grade PS. Cancer type and stage were also analyzed. Log rank test was used to compare overall survival and hazard ratio (HR) derived using Cox regression method. Univariate and multivariate analyses were done to assess impact of ECOG status, presence of geriatric syndrome, stage of disease and cancer type on overall survival. Results: All 233 patients were included in the analysis, median age 77 (70 - 93), all had solid tumors and predominant tumors comprising 79% of diagnoses were colorectal, lung and breast, 50% had advanced metastatic disease. ECOG grades 2,3,4 (HR 0.28, 95% CI 0.14 - 0.55), dependent IADL status (HR 0.30, 95% CI 0.11 - 0.83), presence of geriatric syndrome (HR 0.42 95% CI 0.26 - 0.69), poor cognition (HR 0.53 95% CI 0.36 - 0.77), or advanced disease (HR 0.30 95% CI 0.14 - 0.65) was associated with inferior overall survival in univariate analysis. Only poor ECOG status, presence of a geriatric syndrome and advanced disease predicted adversely for overall survival in multivariate analysis. Poor cognition (MMSE score <24) in those with borderline ECOG 2 status was associated with poorer survival (HR 0.38 95% CI 0.33 - 0.90). Conclusions: Utility of CGA will improve the assessment of the elderly cancer patient.

No significant financial relationships to disclose.

Predictors of outcome and treatment decisions of older patients with stage III non-small cell lung cancer

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Background: In treating Stage III non-small cell lung cancer in the elderly, oncologists often empirically adjust treatment without clear guidelines. Identifying patient characteristics that impact prognosis will aid in creating better treatment algorithms in this patient population. Methods: A retrospective analysis was done on older patients (age > 70) treated for Stage III NSCLC (excluding “wet” IIIB) at the H. Lee Moffitt Cancer. Cox multivariate analysis identified variables impacting progression free survival, overall survival, treatment chosen, treatment interruptions, and hospitalizations. Correlation and regression tree analysis (CART) was performed to create potential decision making models. Results: 213 patients were evaluable. Multivariate analysis identified ECOG performance status (hazard ratio = 1.52, p = 0.005) and nodal status (HR = 1.36, p = 0.001) as negatively associated with PFS while BMI (HR = 0.96, p = 0.02) was positively associated. ECOG performance status (HR = 2.26, p < 0.0001), nodal status (HR = 1.18, p = 0.08), and CIRS3 (having a comorbidity classified as severity 3; HR = 1.33, p = 0.02) were negatively associated with OS. BMI (HR = 0.95, p = 0.002) and CIRSmean (mean CIRS-G severity score; HR 0.61, p = 0.01) were positively associated with OS. These variables were also identified as the most significant splitters, along with smoking status and pulmonary function, in CART analyses. Trees using PFS and OS as outcomes were created with receiver operating curves (ROC) ranging from 0.64–0.75. A CART analysis targeting treatment modality chosen had ROCs ranging from 0.49–0.78. Conclusions: Our multivariate analysis found ECOG performance status, nodal status, and severe medical comorbidity as negatively associated with survival. Unexpectedly, BMI (at initial treatment), independent of weight loss, was found to be positively associated. Also, the splitter variables identified by CART analysis were very similar to the general multivariate model, but the weights differed in the various analyses and subgroups of patients. The CART analyses suggest that we can create decision making models with a range of applicability comparable to those commonly considered useful for clinical guidelines, i.e. about 60% of straightforward application.

No significant financial relationships to disclose.

Phase II Trial of Gemcitabine and Cisplatin Sequentially Administered in Asian Patients With Unresectable or Metastatic Non-small Cell Lung Cancer

Introduction: The aim of this study was to assess toxicity and response in the sequential administration of gemcitabine followed by cisplatin in unresectable or metastatic non-small cell lung cancer. Materials and Methods: Twenty-three patients were enrolled in this study. Gemcitabine was given at 1250 mg/m2 on days 1 and 8, for four 21-day cycles, followed by cisplatin 40 mg/m2 on days 1, 8 and 15, for three further 28-day cycles. Results: There were 4 patients with partial responses, 5 patients with stable disease and 10 patients with progressive disease, giving a response rate of 21%. The median time to disease progression was 3.3 months. The median overall survival was 14.6 months. Toxicities graded 3 or 4 included anaemia (13.0%), neutropaenia (13.0%), supraventricular tachycardia (4.3%), and nausea and vomiting (4.3%). Conclusion: Although these results show similar efficacy to single-agent treatment regimens, the low toxicity profile and promising survival outcome with this regimen are important points for consideration. Key words: Anaemia, Neutropaenia, Supraventricular tachycardia

Phase II trial of gemcitabine and cisplatin sequentially administered in Asian patients with unresectable or metastatic non-small cell lung cancer

INTRODUCTION

The aim of this study was to assess toxicity and response in the sequential administration of gemcitabine followed by cisplatin in unresectable or metastatic non-small cell lung cancer.

MATERIALS AND METHODS

Twenty-three patients were enrolled in this study. Gemcitabine was given at 1,250 mg/m2 on days 1 and 8, for four 21-day cycles.

RESULTS

There were 4 patients with partial responses. 5 patients with stable disease and 10 patients with progressive disease, giving a response rate of 21%. The median time to disease progression was 3.3 months. The median overall survival was 14.6 months. Toxicities graded 3 or 4 included anaemia (13.0%), neutropaenia (13.0%), supraventricular tachycardia (4.3%), and nausea and vomiting (4.3%).

CONCLUSION

Although these results show similar efficacy to single-agent treatment regimens, the low toxicity profile and promising survival outcome with this regimen are important points for consideration.

Neuroimpairment, activity limitation, and participation restriction among children with cerebral palsy in Hong Kong

OBJECTIVES

To study children with cerebral palsy in Hong Kong, their neuroimpairment, activity limitation, and participation restriction in society. Parents' opinion on current medical and rehabilitation services was also sought.

DESIGN

Systematic survey using questionnaires.

SETTING

Four associations in Hong Kong: Child Assessment Service, Hong Kong Association for Parents of Children with Physical Disabilities, Association of Parents of the Severely Mentally Handicapped, and Hong Kong Physically Handicapped and Able-Bodied Association.

PARTICIPANTS

Parents of children with cerebral palsy.

MAIN OUTCOME MEASURES

Neuroimpairment, activity limitation, and participation restriction.

RESULTS

Information from 181 children with cerebral palsy was analysed. Among them, 56% were boys. The mean age was 7 years 6 months (standard deviation, 3 years 11 months). The most common diagnostic type was spastic cerebral palsy. Co-morbidities in children with cerebral palsy were common. Limitation in daily activities including mobility and self-care tasks was considerable and this posed great stress to parents when taking care of their children. Children's participation in both social and leisure activities was regarded as a low priority. A high percentage (70%) of parents reported difficulty in travelling. The reasons involved problems in transportation, building access (entry and exit), and attitudes of the general public. These environmental factors restricted the social participation of the children and their families. Over 75% of parents were satisfied with the current medical and rehabilitation services.

CONCLUSIONS

Children with cerebral palsy have multiple and complex needs. The findings of this study may serve as a reference for parents, service providers, and policy makers to work in partnership to achieve a more comprehensive health-care service for children with cerebral palsy and to facilitate better integration into the community.

A randomized controlled trial of surgery vs steroid injection for carpal tunnel syndrome

BACKGROUND

Decompressive surgery and steroid injection are widely used forms of treatment for carpal tunnel syndrome (CTS) but there is no consensus on their effectiveness in comparison to each other. The authors evaluated the efficacy of surgery vs steroid injection in relieving symptoms in patients with CTS.

METHODS

The authors conducted a randomized, single blind, controlled trial. Fifty patients with electrophysiologically confirmed idiopathic CTS were randomized and assigned to open carpal tunnel release (25 patients) or to a single injection of steroid (25 patients). Patients were followed up at 6 and 20 weeks. The primary outcome was symptom relief in terms of the Global Symptom Score (GSS), which rates symptoms on a scale of 0 (no symptoms) to 50 (most severe). Nerve conduction studies and grip strength measurements were used as secondary outcome assessments.

RESULTS

At 20 weeks after randomization, patients who underwent surgery had greater symptomatic improvement than those who were injected. The mean improvement in GSS after 20 weeks was 24.2 (SD 11.0) in the surgery group vs 8.7 (SD 13.0) in the injection group (p < 0.001); surgical decompression also resulted in greater improvement in median nerve distal motor latencies and sensory nerve conduction velocity. Mean grip strength in the surgical group was reduced by 1.7 kg (SD 5.1) compared with a gain of 2.4 kg (SD 5.5) in the injection group.

CONCLUSION

Compared with steroid injection, open carpal tunnel release resulted in better symptomatic and neurophysiologic outcome but not grip strength in patients with idiopathic carpal tunnel syndrome over a 20-week period.

Concurrent chemoradiotherapy followed by surgery in locally advanced squamous cell carcinoma of the oesophagus: a single centre experience

INTRODUCTION

Data on combined modality treatment for locally advanced squamous cell carcinoma of the oesophagus involving Asian patients are limited.

MATERIALS AND METHODS

A retrospective study of 56 consecutive patients with this condition treated with concurrent chemoradiotherapy followed by surgery in a single tertiary institution in Singapore was performed.

RESULTS

The median overall survival of the entire cohort was 14.1 months [95% confidence interval (CI); range, 8.6 to 19.6 months]. In patients who underwent successful oesophagectomy after chemoradiotherapy (n = 17), the median survival was 27.8 months compared to 9.8 months for those who did not have surgery (n = 39) (P = 0.046, log-rank test). The median time to first relapse for the entire cohort was 16.1 months (95% CI, 7.7 to 24.5 months). The time to first relapse was 23.9 months in the subgroup of patients with successful surgery and 12.1 months in the group which did not (P = 0.147, log-rank test). The high proportion of patients who were medically unfit for surgery or declined surgery may have conferred a selection bias.

CONCLUSION

Concurrent chemoradiotherapy followed by surgery is feasible in selected patients. The benefit of adding of surgery to chemoradiotherapy is still controversial and we await the results of randomised controlled trials comparing chemoradiotherapy with surgery versus chemoradiotherapy alone.

Two case reports of metastases from colon carcinoma to the thyroid

INTRODUCTION

Secondary malignancy of the thyroid gland is uncommon, but it is a problem requiring ongoing recognition. As it is more common than primary thyroid malignancy, metastatic disease involving the thyroid gland should be actively excluded in a patient with enlarging or abnormal thyroid gland and a previously known primary tumour.

CLINICAL PICTURE

We report 2 cases of primary colon carcinoma with metastasis to the thyroid gland that mimicked thyroid anaplastic carcinoma. In both cases, airway compromise was evident.

TREATMENT AND OUTCOME

Emergency tracheostomy was necessary in the first case with subsequent oxaliplatin-based chemotherapy providing palliation of symptom of breathlessness, with significant reduction in size of thyroidal metastasis. Palliative thyroidectomy relieved airway compromise in the second case.

CONCLUSION

Our case report highlights the importance of early recognition of thyroidal metastases from a colonic primary as life-threatening airway compromise may otherwise rapidly ensue.

Measuring quality of life in Chinese cancer patients: a new version of the Functional Living Index for Cancer (Chinese)

INTRODUCTION

Since its translation into Chinese, the Functional Living Index for Cancer (FLIC) has not been widely received due to some of its difficulties. We modified its visual analogue scale (VAS) to an ordered categorical scale and changed some of the wording in the instrument. This study examined the measurement properties of the modified FLIC.

MATERIALS AND METHODS

The modified version of FLIC and the Functional Assessment of Cancer Therapy (FACT-G Chinese version 4) were filled in by 140 patients recruited from the National Cancer Centre Singapore. The patients' FLIC scores were compared with their clinical characteristics to establish known-group validity. Convergent and divergent validity of FLIC were examined by correlation analysis with FACT-G and its sub-scales. Cronbach's alpha and relative efficiency were also examined.

RESULTS

FLIC and most of its sub-scales could indicate a clear and statistically significant difference of quality of life (QOL) according to patients' performance status and treatment status. FLIC strongly correlated with FACT-G. The Physical, Psychological, and Symptoms sub-scales of FLIC converged to and diverged from FACT-G sub-scales as conceptually expected. Cronbach's alpha indicated a satisfactory level of reliability. FLIC appeared to be more efficient than FACT-G, meaning that a smaller sample size will be required for FLIC than for FACT-G to achieve the same research purpose.

CONCLUSIONS

The modified version of FLIC was found to have achieved satisfactory measurement properties. This is a user-friendly alternative to the original FLIC.

Cloning and characterization of an essential Saccharomyces cerevisiae gene, TAF40, which encodes yTAFII40, an RNA polymerase II-specific TATA-binding protein-associated factor

In this report we describe the cloning and initial characterization of TAF40, a gene that encodes a yeast TATA-binding protein-associated factor (yTAF) of Mr = approximately 40,000. This gene has many similarities to other yTAFs described thus far in that it is present at a single copy per haploid genome, it is essential for viability, and the deduced protein sequence of yTAF40 exhibits similarity to previously described human and Drosophila TAFIIs. Immunological studies confirm that yTAF40 protein is a subunit of a large multiprotein TATA-binding protein-TAF complex that contains a subset of the total number of the yTAFs present in yeast cell extracts. Transcription reactions performed using yeast whole cell extracts reveal that of the three nuclear RNA polymerases only RNA polymerase II function is abrogated when yTAF40 and associated proteins are immunodepleted from solution, indicating that the functionality of the multiprotein complex containing yTAF40 is RNA polymerase II-specific. By these criteria yTAF40 appears to encode a bona fide RNA polymerase II-specific TAF, and thus the protein that it encodes has been termed yTAFII40.

Molecular genetic elucidation of the tripartite structure of the Schizosaccharomyces pombe 72 kDa TFIID subunit which contains a WD40 structural motif

BACKGROUND

The multisubunit general transcription factor termed TFIID is comprised of the TATA box DNA binding protein TBP and several TBP-associated factors termed TAFs. Current arguments regarding the mechanisms of regulation of transcription contend that TFIID makes multiple specific protein-protein interactions with numerous protein factors, and that these interactions are important for the regulation of transcriptional initiation. TAFs contain a variety of potential structural motifs and it has been speculated that these motifs participate directly in TAF function. However, to date the physiological significance of these putative structural motifs has not been systematically analysed in vivo.

RESULTS

The essential gene encoding the Schizosaccharomyces pombe 72 kDa TFIID subunit is termed taf72+, which contains WD40 repeats, was cloned and sequenced. A comparison of the primary structure of this gene with its Drosophila and S. cerevisiae counterparts suggests the presence of regions that might play a role in TFIID function, due to the fact that significant portions of the sequences are highly conserved. Complementation analyses of a series of deletion mutants of this gene revealed that the most evolutionarily conserved regions of taf72+, including the WD40 repeats, are in fact indispensable for the viability.

CONCLUSIONS

The 72 kDa subunit of S. pombe TFIID, which contains putative WD40 repeats, consists of three distinct functional domains separated by intervening regions. The functional significance of the WD40 repeats is demonstrated by this in vivo study.

TBP-associated factors are not generally required for transcriptional activation in yeast

The transcription factor TFIID, a central component of the eukaryotic RNA polymerase II (Pol II) transcription apparatus, comprises the TATA-binding protein (TBP) and approximately ten TBP-associated factors (TAFs). Although the essential role of TBP in all eukaryotic transcription has been extensively analysed in vivo and in vitro, the function of the TAFs is less clear. In vitro, TAFs are dispensable for basal transcription but are required for the response to activators. In addition, specific TAFs may act as molecular bridges between particular activators and the general transcription machinery. In vivo, TAFS are required for yeast and mammalian cell growth, but little is known about their specific transcriptional functions. Using conditional alleles created by a new double-shutoff method, we show here that TAF depletion in yeast cells can reduce transcription from some promoters lacking conventional TATA elements. However, TAF depletion has surprisingly little effect on transcriptional enhancement by several activators, indicating that TAFs are not generally required for transcriptional activation in yeast.

Isolation and characterization of TAF25, an essential yeast gene that encodes an RNA polymerase II-specific TATA-binding protein-associated factor

We describe the cloning and analysis of TAF25, a previously uncharacterized yeast gene that encodes a yeast TATA-binding protein-associated factor or yTAF of Mr = 25,000. The gene encoding yTAF25 is a single copy essential gene, and the protein sequence deduced from TAF25 exhibits sequence similarity to a metazoan hTAFII. The results from immunological studies confirm that yTAF25 is a subunit of a large multiprotein TATA-binding protein-yeast TATA-binding protein-associated factor complex that contains a subset of the total number of the yTAFs present in yeast cell extracts. Both genetic and biochemical analyses demonstrate that yTAF25 can interact directly with itself. Transcriptional data show that the activity of the multiprotein complex containing yTAF25 is RNA polymerase II-specific, thus indicating that TAF25 encodes a bona fide yeast RNA polymerase II TAF. Hence the protein encoded by TAF25 has been termed yTAFII25.

Identification and characterization of a TFIID-like multiprotein complex from Saccharomyces cerevisiae

Although the mechanisms of transcriptional regulation by RNA polymerase II are apparently highly conserved from yeast to man, the identification of a yeast TATA-binding protein (TBP)-TBP-associated factor (TAFII) complex comparable to the metazoan TFIID component of the basal transcriptional machinery has remained elusive. Here, we report the isolation of a yeast TBP-TAFII complex which can mediate transcriptional activation by GAL4-VP16 in a highly purified yeast in vitro transcription system. We have cloned and sequenced the genes encoding four of the multiple yeast TAFII proteins comprising the TBP-TAFII multisubunit complex and find that they are similar at the amino acid level to both human and Drosophila TFIID subunits. Using epitope-tagging and immunoprecipitation experiments, we demonstrate that these genes encode bona fide TAF proteins and show that the yeast TBP-TAFII complex is minimally composed of TBP and seven distinct yTAFII proteins ranging in size from M(r) = 150,000 to M(r) = 25,000. In addition, by constructing null alleles of the cloned TAF-encoding genes, we show that normal function of the TAF-encoding genes is essential for yeast cell viability.

TFIIF-TAF-RNA polymerase II connection

RNA polymerase transcription factor IIF (TFIIF) is required for initiation at most, if not all, polymerase II promoters. We report here the cloning and sequencing of genes for a yeast protein that is the homolog of mammalian TFIIF. This yeast protein, previously designated factor g, contains two subunits, Tfg1 and Tfg2, both of which are required for transcription, essential for yeast cell viability, and whose sequences exhibit significant similarity to those of the mammalian factor. The yeast protein also contains a third subunit, Tfg3, which is less tightly associated and at most stimulatory to transcription, dispensable for cell viability, and has no known counterpart in mammalian TFIIF. Remarkably, the TFG3 gene encodes yeast TAF30, and furthermore, is identical to ANC1, a gene implicated in actin cytoskeletal function in vivo (Welch and Drubin 1994). Tfg3 is also a component of the recently described mediator complex (Kim et al. 1994), whose interaction with the carboxy-terminal repeat domain of RNA polymerase II enables transcriptional activation. Deletion of TFG3 results in diminished transcription in vivo.

Yeast Taf170 is encoded by MOT1 and exists in a TATA box-binding protein (TBP)-TBP-associated factor complex distinct from transcription factor IID

Our characterization of the Saccharomyces cerevisiae TATA box-binding protein (TBP) has led to the identification of nine specific yeast TBP-associated factors (TAFs) ranging in size from 170 to 25 kDa. The amino acid sequence derived from a purified TAF with an apparent M(r) of 170,000 indicates that yeast Taf170 is encoded by the essential yeast gene MOT1. We describe in this report a series of experiments that demonstrate that the protein encoded by MOT1 is a bona fide yeast TAF and that Taf170 forms a separate complex with TBP distinct from the RNA polymerase II-specific multisubunit transcription factor IID TBP-TAF complex. The significance of this unique TBP-Taf170 complex regarding transcriptional regulation is discussed.

Immunopurification of yeast TATA-binding protein and associated factors. Presence of transcription factor IIIB transcriptional activity

The TATA-binding proteins (TBP) from both human and Drosophila have been shown to exist in various distinct multiprotein complexes that are required, respectively, for transcription by all three RNA polymerases. In contrast, in vitro biochemical analyses have suggested that yeast TBP exists as a monomeric 27-kDa protein free in solution. We have examined the oligomerization state of yeast TBP and report here that yeast TBP, like human and Drosophila TBPs, is also stably associated with other proteins in vitro. Using anti-TBP antibodies we have immunopurified yeast TBP and associated factors (TBP-associated factors or TAFs). When this fraction was analyzed by SDS-polyacrylamide gel electrophoresis, polypeptides of approximate relative molecular size ranging from 170 to 60 kDa are prominently represented. Immunoblot analysis revealed that one of these TAFs, TAF70, corresponds to BRF1/TDS4/PCF4, a subunit of transcription factor (TF) IIIB. Furthermore, this highly purified TAF fraction can reconstitute polymerase III transcription when supplemented with purified RNA polymerase III and TFIIIC. Our data indicate that our TAF fraction contains TFIIIB transcription factor activity and that all the subunits of yeast TFIIIB are stably complexed with TBP.

Genetic and biochemical analyses of yeast TATA-binding protein mutants

We have taken a combined genetic and biochemical approach to study TATA-binding protein (TBP) structure-function relationships. Using site-directed mutagenesis coupled with a screen for conditional lethal growth, we have isolated a number of temperature-sensitive TBP alleles in the region of amino acid positions 188, 189, and 190. Conditional growth is not a result of increased TBP turnover as most of the mutant proteins are stable in vivo as evidenced by immunoblot detection of TBP steady-state levels. DNA binding assays reveal that mutations at position 188 do not affect DNA binding activity of these mutants, even at high temperatures. Utilizing whole cell extracts which contain mutant TBPs in in vitro transcription experiments, we confirm that TBP is required for transcription by all three nuclear polymerases. However, certain of our TBP mutants are only compromised for RNA polymerase II transcription.

The conserved carboxy-terminal domain of Saccharomyces cerevisiae TFIID is sufficient to support normal cell growth

We have examined the structure-function relationships of TFIID through in vivo complementation tests. A yeast strain was constructed which lacked the chromosomal copy of SPT15, the gene encoding TFIID, and was therefore dependent on a functional plasmid-borne wild-type copy of this gene for viability. By using the plasmid shuffle technique, the plasmid-borne wild-type TFIID gene was replaced with a family of plasmids containing a series of systematically mutated TFIID genes. These various forms of TFIID were expressed from three different promoter contexts of different strengths, and the ability of each mutant form of TFIID to complement our chromosomal TFIID null allele was assessed. We found that the first 61 amino acid residues of TFIID are totally dispensable for vegetative cell growth, since yeast strains containing this deleted form of TFIID grow at wild-type rates. Amino-terminally deleted TFIID was further shown to be able to function normally in vivo by virtue of its ability both to promote accurate transcription initiation from a large number of different genes and to interact efficiently with the Gal4 protein to activate transcription of GAL1 with essentially wild-type kinetics. Any deletion removing sequences from within the conserved carboxy-terminal region of S. cerevisiae TFIID was lethal. Further, the exact sequence of the conserved carboxy-terminal portion of the molecule is critical for function, since of several heterologous TFIID homologs tested, only the highly related Schizosaccharomyces pombe gene could complement our S. cerevisiae TFIID null mutant. Taken together, these data indicate that all important functional domains of TFIID appear to lie in its carboxy-terminal 179 amino acid residues. The significance of these findings regarding TFIID function are discussed.

Interaction of a liver-specific factor with an enhancer 4.8 kilobases upstream of the phosphoenolpyruvate carboxykinase gene

We have previously identified a series of five DNase-I hypersensitive (HS) sites within and around the rat phosphoenolpyruvate carboxykinase (PEPCK) gene. The far upstream region has now been sequenced, and the tissue-specific HS site has been mapped more precisely at 4,800 base pairs upstream of the transcription start site of the PEPCK gene. DNA fragments that include the HS site were cloned upstream of various promoters to test whether these regions modulate transcription of the chloramphenicol acetyltransferase reporter gene. Chloramphenicol acetyltransferase activity was enhanced when the DNA fragment encompassing the upstream HS site was linked to various lengths of the PEPCK promoter or to the heterologous simian virus 40 promoter. This upstream region in conjunction with the proximal promoter, which may contain a tissue-specific element, conferred maximum activation in H4IIE hepatoma cells, which express the endogenous PEPCK gene. When these experiments were performed in XC cells, in which the gene is not expressed, transcriptional activation by the upstream element was still significant. Evidence of a specific protein-DNA interaction, using DNA mobility shift and DNase I footprinting assays, was obtained only when using H4IIE cell nuclear extracts. Competition assay showed that the interacting factor may be similar or identical to the liver-specific factor HNF3. We suggest that this protein factor binds to DNA within the HS site and interacts with the proximal promoter region to control tissue-specific high-level expression of the PEPCK gene.

Identification and purification of a yeast transcriptional trans-activator. The yeast homolog of the Rous sarcoma virus internal enhancer binding factor

A cis-acting transcriptional activation sequence (IES2) from the Rous sarcoma virus internal enhancer was found to stimulate transcription of a heterologous gene in Saccharomyces cerevisiae. A hamster protein (termed IBF) which binds to IES2 and stimulates transcription in vitro has previously been purified and was found to have a subunit molecular mass of 40,000 (Karnitz, L., Poon, D., Weil, P.A., and Chalkley, R. (1989) Mol. Cell. Biol. 9, 1929-1939). The identification and purification of the yeast homolog of IBF (yIBF) is reported here. Purified yIBF has a subunit molecular mass of 92,000. This protein functions as a trans-activator of transcription in a heterologous HeLa transcription extract in a cis-element sequence-dependent manner in vitro.

Rapid diagnosis of bacterial meningitis by the detection of a fatty acid marker in CSF with gas chromatography-mass spectrometry and selected ion monitoring

A chemical marker of bacterial meningitis was sought by comparing derivatives of sterile cerebrospinal fluid (CSF) with cultures of organisms in spinal fluid and artificial media. The technique of gas chromatography-mass spectrometry with selected ion monitoring (GC-MS-SIM) was used, optimised for the analysis of fatty acids. Twenty candidate ions were screened, and an ion of mass: charge ratio (m/e) 268 was chosen for detection in clinical specimens. The origin of this marker is unknown, but it is probably the molecular ion of a C16:1 fatty acid. In 135 clinical specimens of CSF examined, the m/e 268 ion was found to be a useful marker for the common organisms that cause bacterial meningitis, giving a sensitivity of 88% and a specificity of 98%. The method was more rapid and more sensitive than conventional microscopy and culture, but CSF containing coagulase-negative staphylococci, Mycobacterium tuberculosis, Cryptococcus neoformans and some other uncommon pathogens gave inconsistent results. Many organisms produced characteristic ion profiles with multiple-ion monitoring, and this method of chemical analysis holds promise for the rapid diagnosis of bacterial infections to genus or species level.

Pancreatic beta-cell-type-specific expression of the rat insulin II gene is controlled by positive and negative cellular transcriptional elements

The insulin gene is expressed almost exclusively in pancreatic beta-cells. The DNA sequences that control cell-specific expression are located upstream of the transcription initiation site. To identify the cis-acting transcriptional control regions within the rat insulin II gene that are responsible for this tissue-specific expression pattern, we constructed a series of 5'-flanking deletion mutants and analyzed their expression in vivo in transfected insulin-producing and -nonproducing cell lines. Pancreatic beta-cell-specific expression was shown to be controlled by enhancer sequences lying between nucleotides -342 and -91 relative to the transcription start site. The rat insulin II enhancer appears to be a chimera, composed of a number of distinct cis-acting DNA elements. Both positive and negative transcriptional regulatory elements appear to be responsible for this cell-type-specific expression. We have shown that expression from one element within the enhancer, which is found between nucleotides -100 and -91, is regulated by both positive- and negative-acting cellular transcription factors. Expression from chimeras containing only the enhancer element sequences from -100 to -91 were active only in insulin-producing cells, indicating that the positive-acting factor(s) required for this activity may be active only in beta-cells. In contrast to the enhancer region, the rat insulin II gene promoter did not appear to require cell-specific transcription factors. Promoter mutants with 5'-flanking sequences extending to nucleotides -90 and -73 were constitutively active in both insulin-producing and -nonproducing cells. These results suggest that rat insulin II gene transcription in pancreatic beta-cells is imparted by a combination of both negative- and positive-acting cellular factors interacting with the gene enhancer.