CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems.

A one-year investigation of the relationship between serum GH levels and the growth of F(4) transgenic and non-transgenic common carp Cyprinus carpio

It has been demonstrated that growth hormone (GH) transgenic fish often posses a trait for fast growth. Here, we investigated the growth of F(4)'all-fish' GH transgenic carp Cyprinus carpio and their serum GH levels for a year. The results showed that F(4) all-fish GH transgenic carp were significantly larger in body mass (c. two-fold, P < 0.001) and body length (c. 1.3 fold, P < 0.001), compared with the non-transgenic group. The discrepancy of serum GH levels between the transgenic carp group and control group is 54 fold, when the water temperature was 12-34 degrees C. When the water temperature decreased to 3.5 degrees C in January, the discrepancy was 256 fold. The serum GH level of the transgenic group was relatively constant, while that of control varied greatly based on month and water temperature. The changes of growth rates between the transgenic group and the control group were similar for a year. Taken together, the results indicated that F(4) all-fish GH transgenic carp had not only higher and constant serum GH levels but also a significant fast-growing effect, compared with the control. To our knowledge, this is the first report on a one-year investigation of growth trait and serum growth hormone level in F(4) all-fish GH transgenic carp.

TS and MTHFR gene polymorphisms in patients (pts) with recurrent or metastatic squamous cell carcinoma of the head or neck (SCCHN) treated with pemetrexed (P) and bevacizumab (B)

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Background: P inhibits multiple enzymes in folate metabolism. We examined polymorphisms in thymidylate synthase (TS) and methylenetetrahydrofolate reductase (MTHFR) in patients with SCCHN treated in a phase II clinical trial with P and B (ASCO 2008; A6069). Methods: All pts were treated with P 500 mg/m2 and B 15 mg/kg, given IV every 21 days until progression. Primary endpoint was time to progression (TTP). DNA was isolated from whole blood samples using commercially available kits. Polymorphisms examined were MTHFR (C677T, A1298C and G1793A) and TS (TS2R3R, TSG2RG and TSmut6). The MTHFR SNPs were detected using TaqMan based SNP genotyping kits from Applied Biosystems, run on the ABI Prism 7700 Sequence Detection systems v 1.7 (Foster City, CA). The TS promoter repeat and promoter SNP polymorphisms and the 3’ untranslated region 6 bp deletion polymorphism were determined using published methods to detect PCR product size and RFLP-PCR assays respectively. Results: 22 pts were genotyped from 34 enrolled. There was no significant difference in characteristics between pts with and without genotype data. For the MTHFR polymorphism C677T, there was a trend towards decreased disease control rate (DCR) (CR/PR/SD) (p = 0.058, Jonckheere-Terpstra trend test) and worse TTP (p = 0.04) transitioning from variant CC to CT to TT; comparing TT genotype versus CT and CC combined, pts with TT had inferior DCR (p = 0.03) and TTP (p = 0.0003); homozygotes with TT had a median TTP of 2.6 months (mo) 95% CI (1.4, NA) versus 5.6 mo (4.2, 11.4) for pts with CT or CC variants. For the MTHFR A1298C SNP, there was no significant difference in DCR between variants, median TTP for homozygotes pts with AA was 4.1 mo (2.6, NA) vs. 6.7 mo (5.1, NA) in pts with AC or CC variants (p = 0.084); median overall survival for AA was 10.2 mo (7.6, NA) and for AC or CC 17.6 mo (17, NA) (p = 0.045). The MTHFR G1793A and TS polymorphisms did not impact DCR, TTP or overall survival. There was no association between any polymorphism and the incidence of grade >2 toxicities. Conclusions: Polymorphisms in MTHFR are potentially associated with antitumor efficacy of P-based therapy in recurrent or metastatic SCCHN. These results warrant validation in larger studies with P in SCCHN.

No significant financial relationships to disclose.

Development and characterization of expressed sequence tag-derived microsatellite markers for the wheat stem rust fungus Puccinia graminis f. sp. tritici

Puccinia graminis f. sp. tritici is the causal agent of stem rust disease in wheat. The rust fungus has caused devastating disease epidemics throughout history and is still posing a potential threat to wheat production in some regions of the world due to the appearance of new races. To develop microsatellite or simple sequence repeat (SSR) markers for use in population genetics studies, a total of 60,579 expressed sequence tag (EST) sequences (reads) generated from P. graminis f. sp. tritici were screened for tandemly repeated di- and tri-nucleotide units using a bioinformatics approach and 708 unisequences containing putative SSR loci with six or more repeat units were identified. Flanking primers were designed for 384 unique SSR loci, which mapped to different locations of the draft genome sequence of the fungus. Of the 384 primer pairs tested, 72 EST-SSR markers were eventually developed, which showed polymorphism among 19 isolates of P. graminis f. sp. tritici and 4 isolates of P. graminis f. sp. secalis evaluated. Thirty-two of the SSR loci were also evaluated in three other rust fungi (P. triticina, P. hordei, and P. coronata f. sp. hordei) for cross-species transferability. These SSR markers derived from ESTs will be useful for characterization of population structures and for gene mapping in P. graminis.

Even distribution of BK polyomavirus subtypes and subgroups in the Japanese Archipelago

BK polyomavirus (BKV) is ubiquitous among humans, infecting children asymptomatically and then persisting in renal tissue. BKV has four subtypes (I-IV) that can be identified by serological and genotyping methods. Subtypes I and IV are most prevalent in all countries examined to date. Based on nucleotide sequence variation, subtype I is further classified into four subgroups (Ia, Ib-1, Ib-2 and Ic), each of which have a close relationship to a particular human population. To clarify the relationships between BKV and human populations, we investigated the distribution patterns of BKV subtypes and subgroups in the modern Japanese population, which was formed from two distinct ethnic groups. Urine samples were collected from immunocompetent elderly patients in six regions along the Japanese Archipelago. The 287-bp VP1 region of the viral genome from these samples was amplified using the polymerase chain reaction. The amplified VP1 regions were sequenced and a neighbor-joining phylogenetic tree was reconstructed to classify the BKV isolates. We observed a similar pattern of subtype distribution throughout the Japanese Archipelago, with subtype I always detected at high rates (67-75%), followed by subtype IV (19-31%), with rare or no detection of subtypes II and III. Based on phylogenetic and single nucleotide polymorphism analyses, the subtype I isolates were divided into subgroups; the percentage of the Ic subgroup was high in all geographic regions (88-100%). These results suggest that BKV subtypes and subgroups are evenly distributed in the Japanese Archipelago. We discuss the implications of these findings for the relationships between BKV and human populations.

Pharmacologic inhibition of epigenetic modifications, coupled with gene expression profiling, reveals novel targets of aberrant DNA methylation and histone deacetylation in lung cancer

Lung cancer is the leading cause of cancer-related deaths in the United States due, in large part, to the lack of early detection methods. Lung cancer arises from a complex series of genetic and epigenetic changes leading to uncontrolled cell growth and metastasis. Unlike genetic changes, epigenetic changes, such as DNA methylation and histone acetylation, are reversible with currently available pharmaceuticals and are early events in lung tumorigenesis detectable by non-invasive methods. In order to better understand how epigenetic changes contribute to lung cancer, and to identify new disease biomarkers, we combined pharmacologic inhibition of DNA methylation and histone deacetylation in non-small cell lung cancer (NSCLC) cell lines, with genome-wide expression profiling. Of the more than 200 genes upregulated by these treatments, three of these, neuronatin, metallothionein 3 and cystatin E/M, were frequently hypermethylated and transcriptionally downregulated in NSCLC cell lines and tumors. Interestingly, four other genes, cylindromatosis, CD9, activating transcription factor 3 and oxytocin receptor, were dominantly regulated by histone deacetylation and were also frequently downregulated in lung tumors. The majority of these genes also suppressed NSCLC growth in culture when ectopically expressed. This study therefore reveals new putative NSCLC growth regulatory genes and epigenetic disease biomarkers that may enhance early detection strategies and serve as therapeutic targets.

Subtype IV of the BK polyomavirus is prevalent in East Asia

BK polyomavirus (BKV) is ubiquitous in human populations, infecting children asymptomatically and then persisting in the kidney. Using either serological or genotyping methods, BKV isolates have been classified into four subtypes (I-IV), with subtype I mainly detected in all countries studied so far. To elucidate the subtype of BKV prevalent in East Asia, we examined BKV-positive urine samples collected from immunocompetent elderly patients in Mongolia, Northeast China, Northwest China, Southeast China, Southwest China, Vietnam and Japan. The 287-bp typing region of the viral genome in each of these samples was PCR-amplified and sequenced, and a phylogenetic tree was constructed. According to the tree, BKV isolates in East Asia were unambiguously classified into subtype I or IV (subtypes II and III were not detected). In Japan, subtype I was mainly detected and subtype IV was rare, whereas in the other regions subtype IV was detected frequently, at rates ranging from 24 to 100%. Thus, East Asia (excluding Japan) is a region in which subtype-IV BKV is prevalent, a finding that requires the view of the geographic distribution of BKV subtypes to be revised. Furthermore, we present evidence that the immunological states of urine donors do not affect the pattern of BKV subtypes.

First Report of a Rust Disease on Ohia Caused by Puccinia psidii in Hawaii

Several species of Metrosideros (Myrtaceae), referred to as ohia in Hawaii, are endemic trees that comprise as much as 80% of the native Hawaiian forests. For centuries, these trees have provided niches for many indigenous and endangered plants and animals and are treasured by Hawaiians for their beauty and role in folklore and legends. During April 2005, a cultivated ohia plant was diagnosed by the Agricultural Diagnostic Service Center at the University of Hawaii at Manoa as infected by a rust fungus. Rust pustules containing abundant urediniospores were observed on leaves, stems, and sepals, causing discolored spots and severe deformity of young leaves and growing tips. By July 2005, a similar rust disease was observed on other plants in the family Myrtaceae; namely Syzygium jambos (L.) Alston, Eugenia koolauensis Degener, E. reinwardtiana (Blume) DC, and Psidium guajava L. Microscopic examination of the uredinia and urediniospores showed that the rust was morphologically similar to Puccinia psidii, which is reported as the guava or eucalyptus rust in Florida and Central and South America (1,2). To confirm the identity of this fungus, DNA was extracted from urediniospores of two isolates collected from ohia plants, and their nuclear ribosomal internal transcribed spacer (ITS) was amplified with two universal primers, ITS4 and ITS5 (3). Sequences of the ITS region of these isolates from ohia were identical to the P. psidii isolates provided by A. Alfenas in Brazil and M. Rayachhetry in Florida. Koch's postulate of the isolates, obtained from ohia, was performed using 1 × 10⁸ spores/ml of urediniospores suspension in distilled water. The suspension was sprayed onto 6-month-old ohia seedlings. These inoculated seedlings were placed in clear plastic chambers maintained at 100% relative humidity and 22°C with a combination of 10-h fluorescent light period and a 14-h dark period. After 48 h of incubation, the seedlings were removed from the chambers and transferred to a greenhouse where the ambient temperature ranged from 20 to 24°C. Rust pustules appeared after 1 to 2 weeks of incubation. Symptoms first appeared as tiny, bright yellow, powdery eruptions that developed into circular, uredinial pustules on the stem and foliage. These pustules later expanded, coalesced, and became necrotic, spreading over the entire leaf and stem surfaces, and then leaves and stems were deformed and tip dieback ensued. These symptoms were the same as those observed on the naturally infected cultivated ohia plant mentioned above. P. psidii is reported to be native to South and Central America that later spread to some Myrtaceous plants in the Caribbean countries (1). It has a very wide host range within the family Myrtaceae (2). To our knowledge, this is the first report of P. psidii in Hawaii. This rust disease may pose a formidable threat to Myrtaceous species that make up the native Hawaiian forests and are grown as ornamental plants or for the production of wood chips. References: (1) T. A. Coutinho et al. Plant Dis. 82:819. 1998. (2) M. B. Rayachhetry et al. Biol. Control 22:38. 2001. (3) T. J. White et al. Page 315 in: PCR Protocols. M. A. Innis et al., eds. 1990.

Comprehensive analysis of risk factors associating with Hepatitis B virus (HBV) reactivation in cancer patients undergoing cytotoxic chemotherapy

For cancer patients with chronic hepatitis B virus (HBV) infection, who receive cytotoxic chemotherapy, HBV reactivation is a well-described complication, which may result in varying degrees of liver damage. Several clinical features and the pre-chemotherapy HBV viral load have been suggested to be associated with an increased risk of developing the condition: (1) to assess the clinical and virological factors in a comprehensive manner and thereby identify those that are associated with the development of HBV reactivation; (2) to develop a predictive model to quantify the risk of HBV reactivation. In all, 138 consecutive cancer patients who were HBV carriers and undergoing chemotherapy were studied, of which 128 patients had sera available for real-time PCR HBV DNA measurement. They were followed up throughout their course of chemotherapy and the HBV reactivation rate was determined. The clinical and virological features between those who did and did not develop viral reactivation were compared. These included age, sex, baseline liver function tests, HBeAg status and viral load (HBV DNA) prior to the chemotherapy, and the use of specific cytotoxic agents. In all, 36 (26%) developed HBV reactivation. Multivariate analysis revealed pre-chemotherapy HBV DNA level, the use of steroids and a diagnosis of lymphoma or breast cancer to be significant factors. Based on real-time HBV DNA PCR assay, detectable baseline HBV DNA prior to the administration of cytotoxic chemotherapy, the use of steroids and a diagnosis of lymphoma or breast cancer are predictive factors for the development of HBV reactivation. A predictive model was developed from the current data, based on a logistic regression method.

High hepatitis B virus (HBV) DNA viral load is an important risk factor for HBV reactivation in breast cancer patients undergoing cytotoxic chemotherapy

Hepatitis B virus (HBV) reactivation during cytotoxic chemotherapy for cancer may complicate treatment and cause liver damage. The complication has been reported to occur in 10% to over 50% of HBV carriers, but the factors that determine which patients will develop reactivation remain unclear. The objective of the study is to test the hypothesis that the prechemotherapy HBV DNA level is a risk factor for the development of HBV reactivation. We studied 41 women undergoing cytotoxic chemotherapy for breast cancer, 17 of whom developed reactivation and 24 who did not. We developed a novel, ultra-sensitive, real-time polymerase chain reaction assay for the measurement of HBV DNA. The sera of 37 patients (16 who developed reactivation and 21 who did not) were available for measurement of HBV DNA using this technique. The results showed that patients in the reactivation group had a significantly higher median HBV DNA load (1.03 x 10(6) copies/mL; range <2.9 x 10(3) to 8.723 x 10(7)) than did the nonreactivation group (<2.9 x 10(3) copies/ml; range <2.9 x 10(3) to 6.331 x 10(7)) (P < 0.001). The optimal cut-off between the two groups was found to be at serum HBV DNA level of 3 x 10(5), which gave a sensitivity of 81.0% and a specificity of 85.0%. In conclusion, for breast cancer patients receiving standard cytotoxic chemotherapy, a high HBV viral load prior to the administration of cytotoxic chemotherapy is a significant predictive factor for the development of HBV reactivation. Such information may be useful in determining which patients would benefit most from prophylactic antiviral therapy during cytotoxic chemotherapy.

The biological response of MCF7 breast cancer cells to proteosome inhibition or gamma-radiation is unrelated to the level of p53 induction

The p53 tumour suppressor is stabilised following exposure to genotoxic agents, such as gamma-radiation. Cell responses to p53 stabilisation include induction of apoptosis and/or cell cycle arrest. Several studies have suggested that gamma-radiation stabilises p53 by blocking ubiquitin mediated proteolysis. Here we have compared the biological activities of p53 stabilized following exposure to gamma-radiation or treatment with the proteosome inhibitor N-acetyl-leucinyl-leucinyl-norleucinal (ALLN) in MCF7 cells with wild type p53. Stabilisation of p53 by ALLN was reversible and was not blocked by caffeine. Although ALLN was a more effective p53 stabilising agent than gamma-radiation, ALLN was not as effective at inducing cell cycle arrest/apoptosis as gamma-radiation. Although p53 stabilised by ALLN and gamma-radiation were both able to bind DNA and activate transcription, ALLN did not increase expression of BAX, which is involved in p53-induced apoptosis. Therefore, p53 stabilised by different agents is not always biologically active to the same extent and additional alterations triggered by gamma-radiation may enable p53 to activate a subset of critical target genes, such as BAX, which are required for p53 responses.

Fabrication and properties of spray-dried nanofeatured spherical Ni(OH)2 materials

Spherical agglomerates of nanostructured beta-phase Ni(OH)2 with the general formula Ni1-xCox(OH)2 (x = 0, 0.1, 0.3) for use as cathode materials were produced by a modified method including coprecipitation of Ni or Ni composite hydroxide and further spray drying of the precipitated and washed slurry. This process leads to the formation of spherical agglomerate particles with a narrow Gaussian-type distribution range. The method permits faster and cheaper production of cathode materials with a higher specific surface area and similar or better capacity and cycle life compared with the materials prepared via conventional technology.

Identification and characterization of DNA markers associated with a locus conferring virulence on barley in the plant pathogenic fungus Cochliobolus sativus

Cochliobolus sativus is a plant pathogenic fungus that causes spot blotch on barley and wheat. Virulence of a pathotype-2 isolate (ND90Pr) on barley cultivar Bowman was previously determined to be controlled by a single locus. To identify DNA markers associated with this virulence locus, amplified fragment length polymorphism (AFLP) analysis was conducted on 104 progeny isolates derived from a cross between isolates ND90Pr (exhibiting high virulence on Bowman) and ND93-1 (exhibiting low virulence on Bowman). Among 115 AFLP markers identified, 14 were linked to the virulence locus VHv1 in isolate ND90Pr, six of which co-segregated with VHv1. Two (E-AG/M-CA-207 and E-AG/M-CG-121) of the six co-segregating AFLP markers were cloned and used to probe genomic DNAs from the fungal parents and progeny. Both markers hybridized only with DNAs from ND90Pr and the virulent progeny. These two cloned markers were also used as probes to survey field isolates of C. sativus collected from different regions of the world and again only hybridized to DNAs from isolates that had the same virulence phenotype as ND90Pr. The results of this study indicate that E-AG/M-CA-207 and E-AG/M-CG-121 are closely linked to VHv1 and are unique to isolates carrying the virulence locus. Development of a linkage group, coupled with the identification of closely linked molecular markers, will facilitate the cloning of the virulence gene VHv1 in C. sativus by map-based cloning.

Effects of long-term enalapril and losartan therapy of hypertension on cardiovascular aldosterone

BACKGROUND

Plasma aldosterone escape is found during long-term angiotensin-converting enzyme inhibitor therapy. Evidence for aldosterone production in cardiovascular tissues raised the question of whether or not aldosterone escape occurs in these tissues.

METHOD

Spontaneously hypertensive rats were treated with enalapril (20 mg/kg/day) and losartan (50 mg/kg/day) for 20 weeks; untreated spontaneously hypertensive and Wistar rats were used as positive and normal controls, respectively. Ex vivo mesenteric artery and heart perfusion, high-performance liquid chromatography, and radioimmunoassay for aldosterone were performed.

RESULTS

The results showed that enalapril failed to significantly inhibit aldosterone production in mesenteric artery, myocardium and plasma. Losartan significantly inhibited aldosterone production to that of Wistar rats in the mesenteric artery, myocardium and plasma.

CONCLUSION

This study provides the first evidence that long-term angiotensin-converting enzyme inhibition therapy induces aldosterone escape in hypertensive cardiovascular tissues, and angiotensin II subtype 1 receptor antagonist does not induce aldosterone escape in mesenteric artery, myocardium and plasma of spontaneously hypertensive rats.

Optical tomographic imaging of dynamic features of dense-scattering media

Methods used in optical tomography have thus far proven to produce images of complex target media (e.g., tissue) having, at best, relatively modest spatial resolution. This presents a challenge in differentiating artifact from true features. Further complicating such efforts is the expectation that the optical properties of tissue for any individual are largely unknown and are likely to be quite variable due to the occurrence of natural vascular rhythms whose amplitudes are sensitive to a host of autonomic stimuli that are easily induced. We recognize, however, that rather than frustrating efforts to validate the accuracy of image features, the time-varying properties of the vasculature can be exploited to aid in such efforts, owing to the known structure-dependent frequency response of the vasculature and to the fact that hemoglobin is a principal contrast feature of the vasculature at near-infrared wavelengths. To accomplish this, it is necessary to generate a time series of image data. In this report we have tested the hypothesis that through analysis of time-series data, independent contrast features can be derived that serve to validate, at least qualitatively, the accuracy of imaging data, in effect establishing a self-referencing scheme. A significant finding is the observation that analysis of such data can produce high-contrast images that reveal features that are mainly obscured in individual image frames or in time-averaged image data. Given the central role of hemoglobin in tissue function, this finding suggests that a wealth of new features associated with vascular dynamics can be identified from the analysis of time-series image data.

PML-RARalpha alleviates the transcriptional repression mediated by tumor suppressor Rb

A fusion between the promyelocytic leukemia (PML) protein and the retinoic acid receptor-alpha (RARalpha) results in the transforming protein of acute promyelocytic leukemia, PML-RARalpha. PML has growth-suppressive properties and is localized within distinct nuclear structures referred to as nuclear bodies. PML participates in numerous cellular functions, including transcriptional activation, apoptosis, and transcriptional repression, whereas PML-RARalpha blocks these functions. However, the role played by PML-RARalpha in leukemogenesis remains unclear. Here we report that PML is required for transcriptional repression mediated by the tumor suppressor Rb. Rb interacts with the histone decaetylase (HDAC) complex containing co-repressors and represses the transcription of the E2F target genes. Overexpression of PML enhanced Rb-mediated repression. The degree of Rb-mediated repression was weakened by injecting anti-PML antibodies and was lower in Pml-deficient mouse embryonic fibroblasts. PML-RARalpha inhibited Rb-mediated repression, and two co-repressor-interacting sites on the PML-RARalpha molecule were required for this activity. Furthermore, PML-RARalpha blocked the interaction between Rb and HDAC. Thus, aberrant binding of PML-RARalpha to co-repressor-HDAC complexes may inhibit their association with Rb, resulting in the abrogation of Rb activity. Thus, the disruption of Rb-mediated repression may be a contributory factor in leukemogenesis.

Histone deacetylase inhibitors induce remission in transgenic models of therapy-resistant acute promyelocytic leukemia

Acute promyelocytic leukemia (APL) is associated with chromosomal translocations, invariably involving the retinoic acid receptor alpha (RAR alpha) gene fused to one of several distinct loci, including the PML or PLZF genes, involved in t(15;17) or t(11;17), respectively. Patients with t(15;17) APL respond well to retinoic acid (RA) and other treatments, whereas those with t(11;17) APL do not. The PML-RAR alpha and PLZF-RAR alpha fusion oncoproteins function as aberrant transcriptional repressors, in part by recruiting nuclear receptor-transcriptional corepressors and histone deacetylases (HDACs). Transgenic mice harboring the RAR alpha fusion genes develop forms of leukemia that faithfully recapitulate both the clinical features and the response to RA observed in humans with the corresponding translocations. Here, we investigated the effects of HDAC inhibitors (HDACIs) in vitro and in these animal models. In cells from PLZF-RAR alpha/RAR alpha-PLZF transgenic mice and cells harboring t(15;17), HDACIs induced apoptosis and dramatic growth inhibition, effects that could be potentiated by RA. HDACIs also increased RA-induced differentiation. HDACIs, but not RA, induced accumulation of acetylated histones. Using microarray analysis, we identified genes induced by RA, HDACIs, or both together. In combination with RA, all HDACIs tested overcame the transcriptional repression exerted by the RAR alpha fusion oncoproteins. In vivo, HDACIs induced accumulation of acetylated histones in target organs. Strikingly, this combination of agents induced leukemia remission and prolonged survival, without apparent toxic side effects.