bluuebunny/crossref_metadata_2025 huggingface dataset:
Biology of Desmoplastic Melanoma: A Case-Control Comparison With Other Melanomas
Authors: Livestro Daan P. , Muzikansky Alona , Kaine Emily M. , Flotte Thomas J. , Sober Arthur J. , Mihm Martin C. , Michaelson James S. , Cosimi A. Benedict , Tanabe Kenneth K.
Published: September 2005

Purpose

Previous studies have established that patients with desmoplastic melanoma (DM) have thicker primary tumors. Consequently, comparisons with other forms of melanoma have been strongly biased by differences in Breslow stage. This is the first case-matched control study comparing DM with other forms of melanoma.

Patients and Methods

From a database of 3,202 melanoma patients treated at one institution, 89 patients with DM and 178 case-matched control patients (2:1) were identified by matching for tumor thickness, age, sex, and year of diagnosis. Clinical, pathologic, and outcome information was obtained from chart review.

Results

Controls were matched successfully to patients for tumor thickness, age, sex, and year of diagnosis. Presentation with American Joint Committee on Cancer stage III or IV disease is less common in patients with DM compared to case-matched control patients (5% v 21%; P < .001). Re-excisions to obtain clear surgical margins are required more often in patients with DM compared to case-matched control patients (21% v 6%; P < .001). Risk of positive sentinel nodes is lower in patients with DM compared to case-matched control patients (8% v 34%; P = .013). Despite these differences, survival rates of patients with DM are the same as case-matched control patients.

Conclusion

Use of case-matched control patients matched for tumor thickness avoids biases introduced by the advanced Breslow stage of DMs. DMs are more locally aggressive than thickness-matched controls, and positive sentinel nodes are limited to patients with thick primary tumors. Importantly, patients with DM have survival rates similar to patients with other melanomas of similar thickness.
Use of a Case Definition Approach to Identify Cancer-Related Fatigue in Women Undergoing Adjuvant Therapy for Breast Cancer
Authors: Andrykowski Michael A. , Schmidt John E. , Salsman John M. , Beacham Abbie O. , Jacobsen Paul B.
Published: September 2005

Purpose

Use a proposed case-definition approach to identify the prevalence of cancer-related fatigue (CRF), demographic, clinical and psychosocial predictors of subsequent CRF, and psychosocial factors associated with concurrent CRF.

Patients and Methods

Women (n = 288) undergoing adjuvant therapy for early-stage breast cancer were recruited from two outpatient clinics. Women completed a baseline assessment before adjuvant therapy and a post-treatment assessment at the conclusion of an initial course of adjuvant chemotherapy or radiotherapy. At both assessments, women completed a clinical interview and measures of fatigue, distress, coping, and quality of life (QOL). The clinical interview consisted of modules from the Diagnostic and Statistical Manual of Mental Disorders Fourth Edition (DSM-IV) and a diagnostic interview to identify cases of CRF.

Results

CRF prevalence at the baseline and post-treatment assessments was 10% and 26%, respectively. Multivariate analyses identified factors prospectively associated with greater risk for CRF at the post-treatment assessment, including receipt of adjuvant chemotherapy and a tendency to catastrophize in response to fatigue. Patients with and without CRF differed on a host of concurrent measures of fatigue, depression, functioning, and QOL with mean effect sizes in the range of 1.0 standard deviation.

Conclusion

CRF is a clinical syndrome experienced before and during adjuvant therapy for breast cancer. Results suggest CRF has a multifactorial etiology and support use of the proposed case definition approach to defining CRF. Future research is necessary to determine the scientific value of these criteria for understanding the etiology and management of fatigue in the oncology setting.
Lack of Efficacy of Two Consecutive Treatments of Radioimmunotherapy With 131I-cG250 in Patients With Metastasized Clear Cell Renal Cell Carcinoma
Authors: Brouwers Adrienne H. , Mulders Peter F.A. , de Mulder Pieter H.M. , van den Broek Wim J.M. , Buijs Wilhelmina C.A.M. , Mala Carola , Joosten Frank B.M. , Oosterwijk Egbert , Boerman Otto C. , Corstens Frans H.M. , Oyen Wim J.G.
Published: September 2005

Purpose

A previous activity dose-escalation study using 131I-labeled chimeric monoclonal antibody cG250 in patients with progressive metastatic renal cell carcinoma (RCC) resulted in occasional therapeutic responses. The present study was designed to determine the safety and therapeutic efficacy of two sequential high-dose treatments with 131I-cG250.

Patients and Methods

Patients (n = 29) with progressive metastatic RCC received a low dose of 131I-cG250 for assessment of preferential targeting of metastatic lesions, followed by the first radioimmunotherapy (RIT) with 2220 MBq/m2 131I-cG250 (n = 27) 1 week later. If no grade 4 hematologic toxicity was observed, a second low-dose 131I-cG250 (n = 20) was given 3 months later. When blood clearance was not accelerated, a second RIT of 131I-cG250 was administered at an activity-dose of 1110 MBq/m2 (n = 3) or 1665 MBq/m2 (n = 16). Patients were monitored weekly for toxicity, and tumor size was evaluated by computed tomography once every 3 months intervals.

Results

The maximum-tolerated dose (MTD) of the second RIT was 1,665 MBq/m2 because of dose-limiting hematological toxicity. Based on an intention-to-treat analysis, after two RIT treatments, the disease stabilized in five of 29 patients, whereas it remained progressive in 14 of 29 patients. Two patients received no RIT, and eight of 29 received only one 131I-cG250 RIT because of grade 4 hematologic toxicity, formation of human antichimeric antibodies, or disease progression.

Conclusion

In patients with progressive end-stage RCC, the MTD of the second treatment was 75% of the MTD of the first RIT. In the majority of patients, two cycles of 131I-cG250 could be safely administered without severe toxicity. No objective responses were observed, but occasionally two RIT doses resulted in stabilization of previously progressive disease.
Research-Design Issues in Cancer-Symptom–Management Trials Using Complementary and Alternative Medicine: Lessons From the National Cancer Institute Community Clinical Oncology Program Experience
Authors: Buchanan David R. , White Jeffrey D. , O'Mara Ann M. , Kelaghan Joseph W. , Smith Wendy B. , Minasian Lori M.
Published: September 2005

Purpose

To identify major research-design issues in proposals submitted by investigators in the Community Clinical Oncology Program (CCOP) for clinical trials of complementary and alternative medicine (CAM) for cancer-symptom management.

Methods

We conducted content analysis of all scientific reviews of concepts and protocols submitted by the CCOP to the National Cancer Institute (NCI) to identify research challenges in conducting clinical trials designed to evaluate CAM interventions for cancer-symptom management.

Results

Since the inception of the NCI Office of Cancer Complementary and Alternative Medicine in 1998, a total of 46 symptom-management studies using CAM interventions have been proposed by CCOP investigators, with 20 studies now in progress comprising 22% of the current total CCOP symptom-management portfolio. Proposals fell into four categories: complex natural products; nutritional therapeutics; mind-body interventions; and alternative medical systems. The most significant research-design issues arose as a consequence of the lack of preclinical data for CAM interventions and the lack of quality-control standards comparable with those used in regulating new pharmaceutical agents.

Conclusion

Across the different types of CAM interventions, the most common problems found in proposed research designs are related to unwarranted assumptions about the consistency and standardization of CAM interventions, the need for data-based justifications for the study hypotheses, and the need to implement appropriate quality control and monitoring procedures during the course of the trial. To advance the state of the science, future research must address these critical issues if CAM interventions are to be evaluated rigorously and have a consequent impact on clinical practice and general public awareness.
Racial Disparities in Treatment and Survival Among Women With Early-Stage Breast Cancer
Authors: Hershman Dawn , McBride Russell , Jacobson Judith S. , Lamerato Lois , Roberts Kevin , Grann Victor R. , Neugut Alfred I.
Published: September 2005

Purpose

Black women with breast cancer are known to have poorer survival than white women. Suboptimal treatment may compromise the survival benefits of adjuvant chemotherapy. We analyzed the association of race and survival with duration of treatment and number of treatment cycles among women receiving chemotherapy for early-stage breast cancer.

Patients and Methods

Patients were women in the Henry Ford Health System tumor registry who were diagnosed with stage I/II breast cancer between January 1, 1996, and December 31, 2001, who received adjuvant chemotherapy. We calculated an observed/expected ratio of treatment duration and of completed chemotherapy cycles for each patient. Using Cox proportional hazards models, we analyzed the association of early treatment termination and treatment duration with all-cause mortality, controlling for age, race, stage, hormone receptor status, grade, comorbidity score, and doxorubicin use.

Results

Of 472 eligible patients, 28% (31% black, 23% white; P = .03) received fewer cycles of treatment than expected. Black race, receipt of ≤ 75% of the expected number of cycles, increasing age, hormone receptor negativity, and a comorbidity score of more than 1 were associated with poorer survival. Among the 344 patients receiving the expected number of cycles, 60% experienced delays. These delays did not reduce survival.

Conclusion

This study is the first to find that a substantial fraction of women with early-stage breast cancer terminated their chemotherapy prematurely and that early termination was associated with both black race and poorer survival. A better understanding of the determinants of suboptimal treatment may lead to interventions that can reduce racial disparities and improve breast cancer outcomes for all women.
Randomized Trial of Radiotherapy Versus Concurrent Chemoradiotherapy Followed by Adjuvant Chemotherapy in Patients With American Joint Committee on Cancer/International Union Against Cancer Stage III and IV Nasopharyngeal Cancer of the Endemic Variety
Authors: Wee Joseph , Tan Eng Huat , Tai Bee Choo , Wong Hwee Bee , Leong Swan Swan , Tan Terence , Chua Eu Tiong , Yang Edward , Lee Khai Mun , Fong Kam Weng , Tan Hoon Seng Khoo , Lee Kim Shang , Loong Susan , Sethi Vijay , Chua Eu Jin , Machin David
Published: September 2005

Purpose

The Intergroup 00-99 Trial for nasopharyngeal cancer (NPC) showed a benefit of adding chemotherapy to radiotherapy. However, there were controversies regarding the applicability of the results to patients in endemic regions. This study aims to confirm the findings of the 00-99 Trial and its applicability to patients with endemic NPC.

Patients and Methods

Between September 1997 and May 2003, 221 patients were randomly assigned to receive radiotherapy (RT) alone (n = 110) or chemoradiotherapy (CRT; n = 111). Patients in both arms received 70 Gy in 7 weeks using standard RT portals and techniques. Patients on CRT received concurrent cisplatin (25 mg/m2 on days 1 to 4) on weeks 1, 4, and 7 of RT and adjuvant cisplatin (20 mg/m2 on days 1 to 4) and fluorouracil (1,000 mg/m2 on days 1 to 4) every 4 weeks (weeks 11, 15, and 19) for three cycles after completion of RT. All patients were analyzed by intent-to-treat analysis. The median follow-up time was 3.2 years.

Results

Distant metastasis occurred in 38 patients on RT alone and 18 patients on CRT. The difference in 2-year cumulative incidence was 17% (95% CI, 14% to 20%; P = .0029). The hazard ratio (HR) for disease-free survival was 0.57 (95% CI, 0.38 to 0.87; P = .0093). The 2- and 3-year overall survival (OS) rates were 78% and 85% and 65% and 80% for RT alone and CRT, respectively. The HR for OS was 0.51 (95% CI, 0.31 to 0.81; P = .0061).

Conclusion

This report confirms the findings of the Intergroup 00-99 Trial and demonstrates its applicability to endemic NPC. This study also confirms that chemotherapy improves the distant metastasis control rate in NPC.
Phase II Trial of Carcinoembryonic Antigen Radioimmunotherapy With 131I-Labetuzumab After Salvage Resection of Colorectal Metastases in the Liver: Five-Year Safety and Efficacy Results
Authors: Liersch Torsten , Meller Johannes , Kulle Bettina , Behr Thomas M. , Markus Peter , Langer Claus , Ghadimi B. Michael , Wegener William A. , Kovacs Jacqueline , Horak Ivan D. , Becker Heinz , Goldenberg David M.
Published: September 2005

Purpose

Although complete resection (R0) of liver metastases (LM) remains the treatment of choice for colorectal cancer (CRC) patients amenable to curative therapy, only approximately one third survive for 5 years. The objective of this phase II study was to evaluate the safety and efficacy of radioimmunotherapy (RAIT) after salvage resection of LM.

Patients and Methods

Twenty-three patients who underwent surgery for LM of CRC received a dose of 40 to 60 mCi/m2 of 131I-labetuzumab, which is a humanized monoclonal antibody against carcinoembryonic antigen. Safety (n = 23), disease-free survival (DFS; n = 19), and overall survival (OS; n = 19) were determined.

Results

With a median follow-up of 64 months, the median OS time from the first liver resection for RAIT patients was 68.0 months (95% CI, 46.0 months to infinity), and the median DFS time was 18.0 months (95% CI, 11.0 to 31.0 months). The 5-year survival rate was 51.3%. RAIT benefited patients independently of bilobar involvement, size and number of LM, and resection margins. The major adverse effect was transient myelosuppression, resulting mostly in grade ≤ 3 neutropenia and/or thrombocytopenia.

Conclusion

Because both the median OS and 5-year survival rates seem to be improved with adjuvant RAIT after complete LM resection in CRC, compared with historical and contemporaneous controls not receiving RAIT, these results justify further evaluation of this modality in a multicenter, randomized trial.
Combination of Paclitaxel, Ifosfamide, and Cisplatin Is an Effective Second-Line Therapy for Patients With Relapsed Testicular Germ Cell Tumors
Authors: Kondagunta G. Varuni , Bacik Jennifer , Donadio Alessia , Bajorin Dean , Marion Stephanie , Sheinfeld Joel , Bosl George J. , Motzer Robert J.
Published: September 2005

Purpose

The efficacy of paclitaxel was evaluated in combination with ifosfamide and cisplatin as second-line chemotherapy for patients with relapsed testicular germ cell tumors (GCTs).

Patients and Methods

Forty-six patients with progressive metastatic GCTs were treated with paclitaxel and ifosfamide plus cisplatin (TIP) as second-line therapy. Eligibility required that patients have both a testis primary tumor site and a prior complete response (CR) to a first-line chemotherapy program, which had been identified previously as favorable prognostic factors to conventional-dose salvage chemotherapy.

Results

Thirty-two (70%) of 46 patients achieved a CR to treatment. Three patients (7%) who achieved a CR relapsed after TIP chemotherapy. Twenty-nine patients are continuously disease free at a median follow-up time of 69 months, resulting in a 63% durable CR rate and a 2-year progression-free survival rate of 65% (95% CI, 51% to 79%).

Conclusion

Four cycles of TIP as second-line therapy achieved a durable CR rate in a high proportion of patients with relapsed testicular GCT. The high CR rate emphasizes the importance of patient selection according to prognostic factors to achieve a favorable outcome to conventional-dose salvage therapy.
Prostate-Specific Antigen Nadir and Cancer-Specific Mortality Following Hormonal Therapy for Prostate-Specific Antigen Failure
Authors: Stewart Alexandra J. , Scher Howard I. , Chen Ming-Hui , McLeod David G. , Carroll Peter R. , Moul Judd W. , D'Amico Anthony V.
Published: September 2005

Purpose

For men receiving androgen-suppression therapy (AST) for a rising postoperative or postradiation prostate-specific antigen (PSA), we evaluated whether a PSA nadir of more than 0.2 ng/mL was significantly associated with prostate cancer–specific mortality (PCSM).

Patients and Methods

The study cohort comprised 747 men with rising PSA and negative bone scan after surgery (n = 486) or radiation therapy (n = 261) who were treated with AST. Cox regression was used to evaluate whether a significant association existed between the PSA nadir level after 8 months of AST and the time to PCSM, controlling for treatment and known prognostic factors.

Results

The post-AST PSA nadir (pCox < .0001), the pre-AST PSA doubling time (DT) (pCox = .002), PSA level (P = .0001), and Gleason eight to 10 cancers (pCox = .01) were significantly associated with time to PCSM. The adjusted hazard ratio for PCSM was 20 (95% CI, 7 to 61; pCox < .0001), for men with a PSA nadir of more than 0.2 ng/mL as compared with all others. A PSA DT of less than 3 months was observed in 30% (224 of 747) of the study cohort. Of the 28 observed prostate cancer deaths, 21 (75%) occurred in men whose PSA nadir was more than 0.2 ng/mL and who had a PSA DT of less than 3 months.

Conclusion

A PSA nadir of more than 0.2 ng/mL after 8 months of AST given for postoperative or postradiation PSA failure is significantly associated with PCSM and is clinically significant because it accounted for 75% of the cancer deaths observed in this study.
A Test of the Effectiveness of the Revised Maxillary Suture Obliteration Method in Estimating Adult Age at Death
Authors: Ginter JK
Published: September 2005

The effectiveness of the original maxillary suture method for estimating age at death, introduced in 1987 by Mann and colleagues, has been tested (4,5), but their revised maxillary suture method (1991) has not been subject to similar scrutiny. The purpose of this study is to test the accuracy of the revised maxillary suture method (2) in estimating age at death on a genetically diverse skeletal sample of 155 maxillae (96 males, 59 females, aged 26 to 100 years) of known age at death from the Department of Anatomy and Cell Biology, University of Cape Town, South Africa. Results from a prior study of the original maxillary suture method will be compared. With age category correctly estimated for 83% of this sample, the results of this study indicate that the revised method is more effective in estimating age at death than the original method. The revised method appears to perform best for older individuals and tends to underestimate age for individuals of all age groups. The results suggest that the revised method is useful as a method for age estimation when it is used conjunction with other estimators.
Population Data of 15 STR in Chinese Han Population From North of Guangdong
Authors: Zhu J , Li J , Guo Y , Liu K , Zhu B , Liu Y
Published: September 2005

The samples were obtained from 102 unrelated, healthy individuals of Chinese Han population living in north of Guangdong province of China. Genomic DNA was extracted using the Chelex100 protocol as described by Walsh et al. (1). Fifteen STR loci and Amelogenin locus were co-amplified by using the AmpFLSTR Identifiler kit following the amplification conditions recommended by the manufacturer. Detection and genotyping of all PCR products were accomplished using ABI3100 DNA Genetic Analyzer (Applied Biosystem). Allele designation was done using GeneScan 3.7 and Genotyper 3.7. Evaluation of Hardy—Weinberg equilibrium expectations was carried out using the exact test and further statistical parameters of forensic interest were determined by using Arlequin version 1.1 (2).
Evaluation of Shear Strength Functions Based on Soil Water Characteristic Curves
Authors: Babu GLS , Rao RS , Peter J
Published: September 2005

The objective of this paper is to examine the variation of shear strength with respect to suction and develop a simple method for prediction of suction from shear strength data. The measured values of total suction and the shear strength of the soils are used to predict a fitting parameter that defines the nonlinear variation of suction with shear strength. The equation proposed by Vanapalli and Fredlund is used. The parameter is estimated for two types of soils, red soil and black cotton soil, available in the state of Karnataka, using measured values of total suction and unconfined compressive strength by nonlinear regression analysis. The nonlinear equations developed between suction and unconfined shear strength are useful in unsaturated soil engineering practice.
Mathematical model of real‐time PCR kinetics
Authors: Gevertz Jana L. , Dunn Stanley M. , Roth Charles M.
Published: September 2005

Several real‐time PCR (rtPCR) quantification techniques are currently used to determine the expression levels of individual genes from rtPCR data in the form of fluorescence intensities. In most of these quantification techniques, it is assumed that the efficiency of rtPCR is constant. Our analysis of rtPCR data shows, however, that even during the exponential phase of rtPCR, the efficiency of the reaction is not constant, but is instead a function of cycle number. In order to understand better the mechanisms belying this behavior, we have developed a mathematical model of the annealing and extension phases of the PCR process. Using the model, we can simulate the PCR process over a series of reaction cycles. The model thus allows us to predict the efficiency of rtPCR at any cycle number, given a set of initial conditions and parameter values, which can mostly be estimated from biophysical data. The model predicts a precipitous decrease in cycle efficiency when the product concentration reaches a sufficient level for template–template re‐annealing to compete with primer‐template annealing; this behavior is consistent with available experimental data. The quantitative understanding of rtPCR provided by this model can allow us to develop more accurate methods to quantify gene expression levels from rtPCR data. © 2005 Wiley Periodicals, Inc.
Alternative signaling pathways: When, where and why?
Authors: Gong Yunchen , Zhang Zhaolei
Published: September 2005

Alternative cell signal transduction pathways have been demonstrated in some experimental systems. The importance of their existence has not been completely appreciated. In this review we present the cases of alternative pathways resulted from a survey of the available experimental data. The alternative pathways could show different relationships, i.e., synergistic, redundant, additive, opposite and competitive effects. They could have distinct time courses and cell, organ, sex or species specification. Further, they could happen during physiological or pathological situations, and display differentiated sensitivity. These case studies together imply that alternative signal pathways could be involved in the regulation of cell functions at the pathway level. In‐depth understanding of the importance of the alternative pathways will rely on building and exploration of mathematical models.
Leishmania major thialysine Nε‐acetyltransferase: Identification of amino acid residues crucial for substrate binding
Authors: Lüersen Kai
Published: September 2005

Thialysine N
ε‐acetyltransferases and spermidine/spermine N‐acetyltransferases (SSAT) are closely related members of the GCN5‐related N‐acetyltransferase superfamily. Accordingly, a putative orthologue from the human protozoan parasite Leishmania major exhibits an almost equal similarity to human SSAT and thialysine N
ε‐acetyltransferase. Characterisation of the recombinantly expressed L. major protein indicated that it represents a thialysine N
ε‐acetyltransferase, preferring thialysine (S‐aminoethyl‐l‐cysteine) and structurally related amino acids as acceptor molecules. The known thialysine N
ε‐acetyltransferases contain five conserved amino acid residues that are replaced in SSAT sequences. Kinetic analyses of the respective recombinant mutant proteins suggest that Ser82 and Thr83 of L. major thialysine N
ε‐acetyltransferase are key residues for acceptor binding. In addition, the conserved Leu130 is tentatively involved in specific interaction with the sulphur‐containing side chain of thialysine. The presence of these three amino acid residues is suggested to be a means by which thialysine N
ε‐acetyltransferases can be distinguished from SSAT sequences.
Bovine PrPC directly interacts with αB‐crystalline
Authors: Sun Guihong , Guo Mingxiong , Shen Ao , Mei Fanghua , Peng Xiaoxue , Gong Rui , Guo Deyin , Wu Jianguo , Tien Po , Xiao Gengfu
Published: September 2005

We used a bovine brain cDNA library to perform a yeast two‐hybrid assay with bovine mature PrPC as bait. The screening result showed that αB‐crystalline interacted with PrPC. The interaction was further evaluated both in vivo and in vitro with different methods, such as immunofluorescent colocalization, native polyacrylamide‐gel electrophoresis, and IAsys biosensor assays. The results suggested that αB‐crystalline may have the ability to refold denatured prion proteins, and provided first evidence that αB‐crystalline is directly associated with prion protein.
1.2 Å crystal structure of the S. pneumoniae PhtA histidine triad domain a novel zinc binding fold
Authors: Riboldi-Tunnicliffe A. , Isaacs N.W. , Mitchell T.J.
Published: September 2005

The recently described pneumococcal histidine triad protein family has been shown to be highly conserved within the pneumococcus. As part of our structural genomics effort on proteins from Streptococcus pneumoniae, we have expressed, crystallised and solved the structure of PhtA‐166–220 at 1.2 Å using remote SAD with zinc. The structure of PhtA‐166–220 shows no similarity to any protein structure. The overall fold contains 3β‐strands and a single short α‐helix. The structure appears to contain a novel zinc binding motif. The remaining 4 histidine triad repeats from PhtA have been modelled based on the crystal structure of the PhtA histidine triad repeat 2. From this modelling work, we speculate that only three of the five histidine triad repeats contain the residues in the correct geometry to allow the binding of a zinc ion.
Antioxidants modulate mitochondrial PKA and increase CREB binding to D-loop DNA of the mitochondrial genome in neurons
Authors: Ryu Hoon , Lee Junghee , Impey Soren , Ratan Rajiv R. , Ferrante Robert J.
Published: September 2005

The protein kinase A (PKA) and the cAMP response element (CRE) binding protein (CREB) signaling pathways mediate plasticity and prosurvival responses in neurons through their ability to regulate gene expression. The PKA–CREB signaling mechanism has been well characterized in terms of nuclear gene expression. We show that the PKA catalytic and regulatory subunits and CREB are localized to the mitochondrial matrix of neurons. Mitochondrial CRE sites were identified by using both serial analyses of chromatin occupancy and chromatin immunoprecipitation. Deferoxamine (DFO), an antioxidant and iron chelator known to inhibit oxidative stress-induced death, activated mitochondrial PKA and increased mitochondrial CREB phosphorylation (Ser-133). DFO increased CREB binding to CRE in the mitochondrial D-loop DNA and D-loop CRE-driven luciferase activity. In contrast, KT5720, a specific inhibitor of PKA, reduced DFO-mediated neuronal survival against oxidative stress induced by glutathione depletion. Neuronal survival by DFO may be, in part, mediated by the mitochondrial PKA-dependent pathway. These results suggest that the regulation of mitochondrial function via the mitochondrial PKA and CREB pathways may underlie some of the salutary effects of DFO in neurons.
Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis
Authors: Miyata Tomoko , Suzuki Hirofumi , Oyama Takuji , Mayanagi Kouta , Ishino Yoshizumi , Morikawa Kosuke
Published: September 2005

Ring-shaped sliding clamps and clamp loader ATPases are essential factors for rapid and accurate DNA replication. The clamp ring is opened and resealed at the primer–template junctions by the ATP-fueled clamp loader function. The processivity of the DNA polymerase is conferred by its attachment to the clamp loaded onto the DNA. In eukarya and archaea, the replication factor C (RFC) and the proliferating cell nuclear antigen (PCNA) play crucial roles as the clamp loader and the clamp, respectively. Here, we report the electron microscopic structure of an archaeal RFC–PCNA–DNA complex at 12-Å resolution. This complex exhibits excellent fitting of each atomic structure of RFC, PCNA, and the primed DNA. The PCNA ring retains an open conformation by extensive interactions with RFC, with a distorted spring washer-like conformation. The complex appears to represent the intermediate, where the PCNA ring is kept open before ATP hydrolysis by RFC.
The
MLL
fusion gene,
MLL-AF4
, regulates cyclin-dependent kinase inhibitor
CDKN1B
(p27
kip1
) expression
Authors: Xia Zhen-Biao , Popovic Relja , Chen Jing , Theisler Catherine , Stuart Tara , Santillan Donna A. , Erfurth Frank , Diaz Manuel O. , Zeleznik-Le Nancy J.
Published: September 2005

MLL
, involved in many chromosomal translocations associated with acute myeloid and lymphoid leukemia, has >50 known partner genes with which it is able to form in-frame fusions. Characterizing important downstream target genes of MLL and of MLL fusion proteins may provide rational therapeutic strategies for the treatment of MLL-associated leukemia. We explored downstream target genes of the most prevalent MLL fusion protein, MLL-AF4. To this end, we developed inducible MLL-AF4 fusion cell lines in different backgrounds. Overexpression of MLL-AF4 does not lead to increased proliferation in either cell line, but rather, cell growth was slowed compared with similar cell lines inducibly expressing truncated MLL. We found that in the MLL-AF4-induced cell lines, the expression of the cyclin-dependent kinase inhibitor gene
CDKN1B
was dramatically changed at both the RNA and protein (p27
kip1
) levels. In contrast, the expression levels of
CDKN1A
(p21) and
CDKN2A
(p16) were unchanged. To explore whether
CDKN1B
might be a direct target of MLL and of MLL-AF4, we used chromatin immunoprecipitation (ChIP) assays and luciferase reporter gene assays. MLL-AF4 binds to the
CDKN1B
promoter
in vivo
and regulates
CDKN1B
promoter activity. Further, we confirmed
CDKN1B
promoter binding by ChIP in MLL-AF4 as well as in MLL-AF9 leukemia cell lines. Our results suggest that
CDKN1B
is a downstream target of MLL and of MLL-AF4, and that, depending on the background cell type, MLL-AF4 inhibits or activates
CDKN1B
expression. This finding may have implications in terms of leukemia stem cell resistance to chemotherapy in MLL-AF4 leukemias.
Direct observation of thymine dimer repair in DNA by photolyase
Authors: Kao Ya-Ting , Saxena Chaitanya , Wang Lijuan , Sancar Aziz , Zhong Dongping
Published: September 2005

Photolyase uses light energy to split UV-induced cyclobutane dimers in damaged DNA, but its molecular mechanism has never been directly revealed. Here, we report the direct mapping of catalytic processes through femtosecond synchronization of the enzymatic dynamics with the repair function. We observed direct electron transfer from the excited flavin cofactor to the dimer in 170 ps and back electron transfer from the repaired thymines in 560 ps. Both reactions are strongly modulated by active-site solvation to achieve maximum repair efficiency. These results show that the photocycle of DNA repair by photolyase is through a radical mechanism and completed on subnanosecond time scale at the dynamic active site, with no net change in the redox state of the flavin cofactor.
Rumen development in the calf
Authors: Stobo I. J. F. , Roy J. H. B. , Gaston Helen J.
Published: September 2005

1. Thirty Ayrshire bull calves were used in an experiment to study the effects of diets containing different proportions of concentrates to hay on rumen development at 12 weeks of age. In addition, six milk-fed calves were slaughtered at 3 weeks of age for comparison. 2. Restriction of the maximum daily allowance of concentrates to the lower levels was accompanied by an increase in the voluntary intake of hay, but the performance of calves from 3 to 12 weeks of age was significantly better in calves given the high-concentrate diets. 3. The weight of contents of the reticulo-rumen increased from 0.7 kg at 3 weeks of age in the milk-fed calf to 7.7 kg and 10.9 kg at 12 weeks in calves given the high-concentrate and high-roughage diets respectively. Between 68 and 79% of the total contents of the alimentary tract was contained in the reticulo-rumen of the ruminant calf. The weight of contents of the omasum was significantly greater in calves given 1.36 kg concentrates/day than in those given either 0.45 or 2.27 kg concentrates/day. Equations were developed from the results by which the weight of contents of the various parts of the alimentary tract, and hence empty body weight in the live animal, can be determined from a knowledge of the live weight and daily consumption of concentrates and hay, 4. Volume displacement of the reticulo-rumen tended to increase with increase in the proportion of hay in the diet. The volume displacement of the omasum increased in response to concentrate intake up to a maximum of 1.36 kg/day and thereafter declined, but the nature of the diet had no significant effect on the volume displacement of the abomasum. 5. Calves given the high-concentrate diets had a significantly greater weight of reticulo-rumen tissue at 12 weeks than those given the high-roughage diets. 6. Whereas the thickness of the muscular wall of the rumen did not differ significantly between treatments, there was an increase in the length and density of papillas, particularly in the anterior dorsal and ventral sacs of the rumen, as the intake of concentrates was increased. The results show the marked relationship between the performance of the animal and an advanced stage of development of the rumen papillas.
The relationship in the cow between milk-fat secretion and ruminal volatile fatty acids
Authors: Storry J. E. , Rook J. A. F.
Published: September 2005

1. The effect of reducing the hay and of increasing the proportions of concentrate and flaked maize in the diet of cows on the secretion of milk fat and its component fatty acids and on the proportions of volatile fatty acids in the rumen liquor has been studied. 2. The low-hay diet caused a fall in the milk fat content to about half of the values in the initial control period and the secretion of all the major fatty acids in the milk was reduced. The general pattern of change in the proportions of rumen VFA during the change to the low-hay diet was a decrease in acetic acid, an increase in propionic and n-valeric acids, relatively little change in n-butyric acid and also an increase in the concentration of lactic acid. Approximately 60% of the variation in milk fat content during the change of diet was associated with the increase in propionic acid. 3. In cows established on the low-hay diet there were marked variations in the relative proportions of acetic and propionic acids, but there was no related change in milk fat content. On return of the animals to the high-hay diet, recovery of the initial proportions of acetic, propionic and valeric acids occurred within about 4 days but the recovery in milk fat content was not complete until 2–3 weeks had elapsed. 4. Although the intraruminal infusion of acetic acid in cows on the low-hay diet caused increases and decreases respectively in the molar proportions of acetic and propionic acids in the rumen, an increase in milk fat content was observed amounting to only one-quarter of the loss associated with the transfer to the low-hay diet; therem was no characteristic pattern of increase in the yields of the individual fatty acids of milk fat. No consistent effects of intraruminal infusions of butyric acid, in cows on the low-hay diet, on the yield of milk fat or of the individual fatty acids were observed.
Tissue lipids in calves suffering from muscular dystrophy
Authors: Poukka Ritva
Published: September 2005

1. Lipids of the heart muscle, skeletal muscle and liver were investigated in healthy calves and in calves suffering from enzootic muscular dystrophy with special regard to the fatty acid composition of the phospholipids and triglycerides. 2. Healthy young calves and older calves differed in the fatty acid composition of these tissues. The tissue phospholipids of healthy young calves contained less linoleic acid and more monounsaturated fatty acids than those of older calves. Of the saturated fatty acids, palmitic acid content tended to be higher in young calves and stearic acid content tended to be higher in older calves. 3. The stearic acid content of tissue triglycerides was lower in young calves than in older calves. 4. Fatty aldehydes were present in the phospholipid fraction of the heart muscle and of the skeletal muscle. Stearaldehyde content was higher in older calves than in young calves. 5. In calves with muscular dystrophy definite changes in the fatty acid composition of the phospholipids were found. In young calves the content of linoleic acid was higher and that of monounsaturated fatty acids lower in tissues of diseased animals than in the corresponding tissues of healthy controls. Both in young and older calves arachidonic acid content was higher in the degenerated areas of the skeletal muscle than in the healthy controls. 6. Possible relationships between the tocopherol and arachidonic acid contents of the tissues are discussed. 7. In the triglyceride fraction the differences between diseased and healthy tissues were less significant than in the phospholipid fraction in young calves. In older calves no significant differences were found. 8. An increase in lipid content was found in the degenerated areas of the skeletal muscle and a decrease in livers from diseased animals. An increase in free cholesterol was found in the degenerated areas of the skeletal muscle. The triglyceride content of livers from diseased animals was decreased. The relative proportion of phospholipids was less in skeletal muscle and higher in liver of diseased animals than in the corresponding tissues of healthy controls.
A study of the protein requirements of the mature breeding ewe
Authors: Robinson J. J. , Forbes T. J.
Published: September 2005

1. An experiment was carried out to study more precisely by nitrogen balance techniques the intake of digestible crude protein required for maintenance in the mature non-pregnant ewe. 2. Four isocaloric diets supplying adequate energy, approximately 90 kcal/kg W0.73 metabolizable energy daily, and differing in crude protein content were each given to eight individually penned ewes. The diets provided 2.4, 4.9, 7.7 and 9.5 g digestible N per ewe per day. 3. The average weight of the ewes was 57.4 kg. They were rationed according to metabolic body-weight (W0.73) at a rate of approximately 800 g dry matter per 50 kg ewe per day for a 4-week period before N balance studies were carried out over an 8-day collection period. 4. The mean apparent digestibilities of dry matter were 67.3±0.8, 68.1±0.7, 70.9±1.0 and 68.8±0.8 respectively. The apparent digestibilities of N, increasing with increasing N intake, were 30.6±2.1, 46.3±2.1, 58.2±0.6 and 61.5±1.3 respectively. 5. The intake of apparently digested N required for maintenance was calculated in three ways, from the regressions of apparently digested N on N retention or on urinary N and from the underlying relationship between N retention and urinary N. The estimates so obtained were respectively 0.185±0.037, 0.148±0.020 and 0.150±0.020 g N per kg W0.78 per day, corresponding to 1.16, 0.93 and 0.94 g apparently digestible crude protein per kg W0.73 per day. 6. Metabolic faecal N, determined by the extrapolation method, was 0.629±0.047 g/100 g dry matter consumed. 7. The results are discussed in relation to practical feeding standards and other research findings.
Utilization of salts of volatile fatty acids by growing sheep
Authors: Ørskov E. R. , Allen D. M.
Published: September 2005

1. An experiment was conducted in which sodium and calcium salts of acetic, propionic and butyric acids were given to groups of eight lambs as additions to basal diets of hay and concentrate. Two control groups were included, one group which received only the basal ration and one high-level control group which received sufficient additional concentrate to achieve growth rates greater than those of the groups receiving volatile fatty acid (VFA) salts. 2. With rumen-fistulated sheep, the effect on the rumen VFA composition and the pH of the rumen liquor, of diets supplemented with VFA salts given twice daily, was also investigated and compared with the effect of the basal diet alone. 3. The lambs receiving the VFA salts grew faster and achieved significantly greater empty body and carcass weights than those receiving only the basal rations; the high-level control group had significantly greater empty body and carcass weights than groups receiving salts of VFA. 4. There were no differences approaching significance in the efficiency of the three VFA in promoting gains in live weight, empty body weight and carcass weight. There appeared to be equal efficiency of utilization of the gross energy of the VFA and of the calculatedmetabolizable energy of the concentrates. 5. The effect of twice-daily feeding on the rumen VFA composition was that the concentration of the supple- mentary acid was greatest shortly after feeding, and about 5–6 h after feeding the effect was difficult to detect. There were no differences in the pH of the rumen liquor between animals given diets containing VFA salts and those given the basal ration.
Utilization of salts of volatile fatty acids by growing sheep
Authors: Ørskov† E. R. , Hovell‡ F. D. , Allen D. M.
Published: September 2005

1. In two experiments with growing and fattening lambs sodium and calcium salts of volatile fatty acids (VFA) were added to a basal diet of hay and concentrate. In Expt I the lambs were approaching maturity, and the utilization of salts of acetic, propionic and butyric acids was studied. In Expt 2 the animals were younger; the experimental groups received acetate or propionate, and half of them were implanted with hexoestrol. The chemical composition of the carcass was assessed with the loin as a representative joint. The influence of the VFA salts on the digestibility of the basal ration was also investigated. 2. In both experiments the lambs receiving supplements of VFA salts grew faster, and their empty body weights and carcass weights were significantly greater than in lambs receiving the basal diet. 3. The energy derived from acetate and propionate was utilized more efficiently to promote carcass gains than the calculated metabolizable energy above maintenance of the basal ration. There were no differences in the utilization of energy from the different VFA, except in Expt I in which butyrate was utilized somewhat less efficiently than acetate and propionate. 4. Hexoes-trol implantation resulted in faster growth, and highly significantly greater empty body weights and carcass weights. There was no evidence of an interaction between the VFA and hexoestrol treatments. 5. There were no differences between the VFA treatments in the composition of the carcass gains as judged by the composition of the loins, except in Expt I in which lambs receiving acetate tended to be the fattest. The coefficient of variation in loin fat percentages was large in both experiments, but, in Expt I in which both ewe and wether lambs were used, the coefficient of variation among the wether lambs was four times that of the ewe lambs. 6. Additions of VFA salts to the diet resulted in a significant increase in the excretion of ash.
Some errors in the determination of nitrogen retention of sheep by nitrogen balance studies
Authors: Martin A. K.
Published: September 2005

1. Loss of NH3N from faeces and urine between voiding and collection and also losses in expired air, eructed gas and from the skin of wether sheep 2–3 years old given a ration of 400, 700, 1000 or 1300 g dried grass/day have been measured. 2. Losses of NH3from faeces were negligible, and the loss from urine depended on the temperature and pH at which it was collected. Collection at neutral pH resulted in losses of up to 9.7% of the urinary N as NH3gas if an acid trap were not incorporated in the collection apparatus. The average loss of N on collection of urine at pH values below 2.0 was 1.33% when the ambient temperature was between 25 and 28°, and 0.97% when it was between 15 and 18°. 3. Very little NH3was lost in expired air or eructed gas, but when total NH3loss other than that from urine was determined, an average loss of 3.14±0.55 mg N/kg body-weight per day was found. This loss was independent of food intake and larger than the loss of N in suint which was estimated to range from 0.59 to 2.55 mg N/kg body-weight per day with the rations given. It was concluded that the larger losses found in some experiments were due to splashing of urine on to the fleece during collection and subsequent loss of this urine N as NH3. It was shown that the losses of NH3N due to errors in urine collection and failure to consider dermal losses ranged between 1.2 and 2.6% of the total determined losses in faeces and urine for sheep fed on a variety of diets and that the losses varied inversely with intake of N.
Comparative studies on the digestive physiology of sheep fed on semi-purified or roughage-concentrate diets
Authors: Lawlor M. J. , Giesecke D. , Walser-KÄrst Karin
Published: September 2005

1. The food and water intake and diurnal variations in the rumen contents were measured in sheep with rumen fistulas receiving semi-purified or pelleted roughage-concentrate diets. The rates of secretion and composition of parotid saliva of the sheep on both diets and of sheep fed on hay were determined. The sheep had continuous access to the diet. 2. The mean daily intakes of the semi-purified and roughage-concentrate diets were 920 and 2234 g respectively. The corresponding water intakes were 2.50 and 6.05 1.3. Noneof the sheep ruminated on either diet. The weight of total contents and of dry matter in the rumen was highest in animals on the roughage-concentrate diet, and marked diurnal fluctuations, which reflect the eating habits of these animals, were observed. The semi-purified diet appeared to have a very marked water-retaining capacity in the rumen. 4. The estimated daily total secretion of both parotid glands was 2.7, 5.4 and 11.5 1. in sheep fed on the semi-purified diet, roughage-concentrate and hay respectively. No appreciable differences were observed in the composition of parotid saliva between the three groups of sheep. In sheep receiving hay, saliva secretion was lower during eating than between periods of eating, during part of which time the sheep presumably ruminated. 5. It is concluded that the observed differences in parotid secretion reflected differences in the physical form of the diet.