Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes

Cassava (Manihot esculenta Crantz) is a staple food for over 600 million people in the tropics and subtropics and is increasingly used as an industrial crop for starch production. Cassava has a high growth rate under optimal conditions but also performs well in drought-prone areas and on marginal soils. To increase the tools for understanding and manipulating drought tolerance in cassava, we generated expressed sequence tags (ESTs) from normalized cDNA libraries prepared from dehydration-stressed and control well-watered tissues. Analysis of a total of 18,166 ESTs resulted in the identification of 8,577 unique gene clusters (5,383 singletons and 3,194 clusters). Functional categories could be assigned to 63% of the unigenes, while another approximately 11% were homologous to hypothetical genes with unclear functions. The remaining approximately 26% were not significantly homologous to sequences in public databases suggesting that some may be novel and putatively specific to cassava. The dehydration-stressed library uncovered numerous ESTs with recognized roles in drought-responses, including those that encode late-embryogenesis-abundant proteins thought to confer osmoprotective functions during water stress, transcription factors, heat-shock proteins as well as proteins involved in signal transduction and oxidative stress. The unigene clusters were screened for short tandem repeats for further development as microsatellite markers. A total of 592 clusters contained 646 repeats, representing 3.3% of the ESTs queried. The ESTs presented here are the first dehydration stress transcriptome of cassava and can be utilized for the development of microarrays and gene-derived molecular markers to further dissect the molecular basis of drought tolerance in cassava.

Response to trans-arterial chemoembolization prior to orthotopic liver transplantation or hepatic resection in patients with hepatocellular carcinoma

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Background: Trans-arterial chemoembolization (TACE) is often used as pre-operative therapy for patients with hepatocellular carcinoma (HCC) prior to orthotopic liver transplantation (OLT) or hepatic resection (HR). However, the benefit of response to TACE on overall survival (OS) and progression free survival (PFS) remains unclear. Methods: Complete data was available for 24 patients with HCC who underwent TACE prior to either OLT or HR from 1998–2006. Known prognostic factors including tumor size, histology, number of nodules, Child-Pugh class, Okuda stage, MELD score, CLIP score were recorded. Clinical features before and after TACE were identified and tested by univariate analysis. Results: The mean patient age was age 51 years (range 31–65). Underlying diagnoses included: HBV (17%), HCV (54%), alcohol abuse (63%), cryptogenic (8%), nonalcoholic steotohepatitis (4%). The mean maximum tumor diameter was 6.2 cm (range 1.6–16.1 cm), with 13 tumors (54%) measuring >5 cm. The median number of lesions were 2 (range 1 - 7). The Milan criteria was met in 15 patients (63%). Eighteen subjects underwent OLT, while 6 had HR. Median PFS was 35 months (m) (95% C.I. 17–58 m). One- and three-year OS were 95.8% and 73%, respectively. TACE was performed within a mean time of 2.5 months from diagnosis (range 0.5–9 m). Post-TACE, eleven subjects demonstrated a biologic response, defined as decrease in serum alfa-fetoprotein (AFP) by >50%, or reduction in AFP level to <10 ng/mL. However, biologic response did not predict for improved PFS (p =0.41). Additionally, nine patients had a radiographic response to TACE as measured by RECIST criteria, but this also did not predict for improved PFS (p = 0.79). Only tumor size >5 cm (p = 0.04) and CLIP score (p = 0.01) were found to be independent predictors of improved PFS. Conclusions: Neither radiographic nor biologic responses to TACE appear to serve as selection criteria for OLT or HR. Those patients who fail to demonstrate response to TACE should not necessarily be denied surgical therapy. Larger, prospective trials are needed to better evaluate which patients will benefit most from TACE prior to OLT or HR.

No significant financial relationships to disclose.

Morphological features of TMPRSS2-ERG gene fusion prostate cancer

The TMPRSS2-ETS fusion prostate cancers comprise 50-70% of the prostate-specific antigen (PSA)-screened hospital-based prostate cancers examined to date, making it perhaps the most common genetic rearrangement in human cancer. The most common variant involves androgen-regulated TMPRSS2 and ERG, both located on chromosome 21. Emerging data from our group and others suggests that TMPRSS2-ERG fusion prostate cancer is associated with higher tumour stage and prostate cancer-specific death. The goal of this study was to determine if this common somatic alteration is associated with a morphological phenotype. We assessed 253 prostate cancer cases for TMPRSS2-ERG fusion status using an ERG break-apart FISH assay. Blinded to gene fusion status, two reviewers assessed each tumour for presence or absence of eight morphological features. Statistical analysis was performed to look for significant associations between morphological features and TMPRSS2-ERG fusion status. Five morphological features were associated with TMPRSS2-ERG fusion prostate cancer: blue-tinged mucin, cribriform growth pattern, macronucleoli, intraductal tumour spread, and signet-ring cell features, all with p-values < 0.05. Only 24% (n=30/125) of tumours without any of these features displayed the TMPRSS2-ERG fusion. By comparison, 55% (n=38/69) of cases with one feature (RR=3.88), 86% (n=38/44) of cases with two features (RR=20.06), and 93% (n=14/15) of cases with three or more features (RR=44.33) were fusion positive (p<0.001). To our knowledge, this is the first study that demonstrates a significant link between a molecular alteration in prostate cancer and distinct phenotypic features. The strength of these findings is similar to microsatellite unstable colon cancer and breast cancer involving BRCA1 and BRCA2 mutations. The biological effect of TMPRSS2-ERG overexpression may drive pathways that favour these common morphological features that pathologists observe daily. These features may also be helpful in diagnosing TMPRSS2-ERG fusion prostate cancer, which may have both prognostic and therapeutic implications.

Role of the unfolded protein response in cell death

Unfolded protein response (UPR) is an important genomic response to endoplasmic reticulum (ER) stress. The ER chaperones, GRP78 and Gadd153, play critical roles in cell survival or cell death as part of the UPR, which is regulated by three signaling pathways: PERK/ATF4, IRE1/XBP1 and ATF6. During the UPR, accumulated unfolded protein is either correctly refolded, or unsuccessfully refolded and degraded by the ubiquitin-proteasome pathway. When the unfolded protein exceeds a threshold, damaged cells are committed to cell death, which is mediated by ATF4 and ATF6, as well as activation of the JNK/AP-1/Gadd153-signaling pathway. Gadd153 suppresses activation of Bcl-2 and NF-kappaB. UPR-mediated cell survival or cell death is regulated by the balance of GRP78 and Gadd153 expression, which is coregulated by NF-kappaB in accordance with the magnitude of ER stress. Less susceptibility to cell death upon activation of the UPR may contribute to tumor progression and drug resistance of solid tumors.

Relation of optical coherence tomography and unusual angiographic leakage patterns in central serous chorioretinopathy

PURPOSE

To investigate the anatomic basis of atypical angiographic leaks in central serous chorioretinopathy (CSC) with optical coherence tomography (OCT).

METHODS

Fluorescein angiography (FA) and OCT were performed in three eyes of three patients (two men, one woman) with CSC. The angiographic leaks were treated with transpupillary thermotherapy (TTT) in two patients with long-standing CSC. The investigations were repeated in the treated patients during follow-up visits.

RESULTS

Clinically, all patients demonstrated typical CSC; the female patient had subretinal fibrin under the detachment. FA showed unusual leakage patterns and OCT revealed bridging tissue connecting the pigment epithelial detachment (PED) to the overlying detached retina in all patients. CSC resolved completely in the two patients who underwent TTT along with normalization of the OCT findings. In one patient re-evaluated before complete resolution of CSC, OCT showed a flattened PED with disappearance of the bridging tissue and persistent serous detachment. FA demonstrated conversion of the previously atypical leak into a classic 'smokestack' configuration. Over the next month, leakage resolved completely. CSC and the anatomical findings persisted in the untreated patient.

CONCLUSION

OCT identified a potential anatomic basis for unusual angiographic leakage pattern in all three cases of CSC evaluated.

Surgical outcomes for vitrectomy in Eales' disease

AIM

To present and analyse the anatomical and functional outcomes for vitrectomy in Eales' disease.

METHODS

This retrospective case series enrolled 63 patients (71 eyes) who underwent pars plana vitrectomy (PPV) for the complications of Eales' disease. Indications included nonclearing vitreous haemorrhage (VH) with/without epiretinal membranes in 49 (69%) eyes, and retinal detachments (RD) involving/threatening macula in 22 (31%). Additional procedures (scleral buckling; gas/oil tamponade) were performed at surgeon's discretion. Minimum follow-up was 6 months. The primary outcome measures were change in best-corrected visual acuity (BCVA) and posterior segment status.

RESULTS

The mean age of the patients was 29.6 years (range: 15-70 years); 60 were male (95%). Preoperatively, posterior vitreous detachment (PVD) existed in 28 (39.4%) eyes. Forty (56.3%) eyes underwent only PPV; the rest required additional surgical procedures (q.v.). The mean baseline BCVA (1/60) improved to 6/24 postoperatively (P<0.0001). Fifty-four eyes of 50 patients (76%) showed an improvement of > or =2 equivalent Snellen lines; six eyes (four patients) remained stable (+/-1 line); visual acuity worsened in 11 eyes (nine patients). The mean final BCVA was similar in eyes operated for VH and RD (P=0.08); but the magnitude of change from baseline was greater in the VH group (P=0.009). PVD had a borderline association with final BCVA (P=0.056); but did not influence the functional/anatomical improvement. Thirteen eyes required repeat interventions; 11 (15.49%) eyes experienced surgical failure.

CONCLUSIONS

Although surgical outcomes in Eales' disease depend on preoperative PVD/RD to some extent; good results are possible in the presence of incomplete PVD and tractional sequelae.

Functional roles of immature dendritic cells in impaired immunity of solid tumour and their targeted strategies for provoking tumour immunity

Dendritic cells play a crucial role in initiating tumour immunity as well as in the immune response for invading foreign pathogens such as bacteria and viruses. For bacterial and viral infections, the immature dendritic cells (iDCs) residing in peripheral tissues are efficiently activated and matured by pathogen signals for performing the immune response. In contrast, for self-antigens, the naive T cells are not activated by iDCs but proceed to anergy/deletion, and the generation of regulatory T cells for immune tolerance. The induction of immune response and tolerance is regulated strictly by iDCs as the sensor for homeostasis of immune response in the host. Despite the identification of some tumour antigens, tumour immunity is not provoked successfully. Even though there are some critical obstacles to inhibit effective tumour immunity, tumour cells are able to exploit the functional roles of iDCs for tumour progression, which are induced by tumour-derived soluble factors such as vascular endothelial growth factor (VEGF) and functionally modulated in the microenvironment. The iDCs still remain as the critical target for provoking tumour immunity. In this review, the functional roles of tumour-associated iDCs and the strategy for targeting iDCs in effective tumour immunity for the cancer patient are discussed.

Antisense and nonantisense effects of antisense Bcl-2 on multiple roles of Bcl-2 as a chemosensitizer in cancer therapy

Bcl-2 is an oncoprotein that plays a critical role in inhibiting apoptotic cell death in the mitochondria-dependent pathway in cancer chemotherapy. As a strategy for blocking Bcl-2 for enhancement of the chemotherapeutic effect, antisense Bcl-2 (AS Bcl-2; G3139, oblimersen sodium, Genasense) has shown promise, and there are several ongoing clinical studies with hematological malignancies as well as solid tumors. Although several preclinical and clinical studies have shown the therapeutic efficacy of Bcl-2 in combination with an anticancer drug as a chemosensitizer, in clinical trials the downregulation of Bcl-2 has not been observed with a high frequency in tumor cells. Nevertheless, previous studies showed nonantisense effects such as production of reactive oxygen species and immunostimulatory action through cytosine-phosphate-guanosine-motif in the antisense oligodeoxynucleotides. Further, Bcl-2 is able to inhibit Beclin 1-dependent autophagic cell death, which is a nonapoptotic cell death. The current status and future directions of AS Bcl-2 and the potential mechanisms for multiple roles that Bcl-2 has in cancer therapy are reviewed.

Pilot study of the combination of EGFR and mTOR inhibitors in recurrent malignant gliomas

Malignant gliomas are frequently characterized by amplification of the epidermal growth factor receptor (EGFR) and loss of PTEN tumor suppressor gene. Twenty-eight heavily pretreated patients with recurrent malignant gliomas were administered EGFR inhibitors (gefitinib or erlotinib) in combination with the mTOR (mammalian target of rapamycin) inhibitor sirolimus. The regimens were reasonably well tolerated. Nineteen percent of patients experienced a partial response and 50% had stable disease. Six-month progression-free survival for glioblastoma patients was 25%.

Neoadjuvant dose-dense (DD) concurrent doxorubicin (A) and docetaxel (T) for stage III breast cancer (BC)

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Background: The addition of taxanes to anthracycline therapy results in improved disease-free survival (DFS) in the adjuvant setting, and increased pathologic complete response rates (pCR) in the neoadjuvant setting. DD chemotherapy improves DFS and overall survival (OS). We evaluated neoadjuvant DD concurrent AT. Methods: Eligible patients (pts) with stage III BC were treated with AT q 14 days at 1 of 3 dose levels; L1 = 60 mg/m2 for both drugs (4 pts), L2 = A 75 mg/m2 and T 60 mg/m2 (6 pts) or L3 = 75 mg/m2 for both drugs (7 pts) × 6 cycles with G-CSF. Dexrazoxane was given after a cumulative dose of 300 mg/m2 of A. Pts were stratified to post-operative moderate risk (ModR) (≥ partial response, ≤ 3 lymph nodes (LN)) and received adjuvant IV cyclophosphamide (C) 600 mg/m2, methotrexate 40 mg/m2, 5FU 600 mg/m2 IV q 21 d × 6 (CMF), or high risk (HiR) (≤ minor response +/or ≥ 4 LN) and received C 3 gm/m2 q 14 d x 3. Primary endpoints were clinical and pathologic response rates of neoadjuvant AT. Sample size was 42 pts to estimate pCR and provide 90% confidence the true incidence of severe toxicity is <10%. Results: 17 pts with stage III BC were enrolled between 2/1999 and 7/2001; accrual was halted after data on pre-operative trastuzumab were presented. Median age was 50 yrs [range: 34–69]. 3/17 pts (17.6%) had a pCR, and 3 pts had near pCR (residual foci ≤ 1mm), 4/17 (23.5%) had path (-) LN, 7/17 (41%) had a lumpectomy, 7/17 (41%) required dose reductions of AT due to grade 4 neutropenia (5 pts) and grade 3 neuropathy (2 pts). 3 pts required treatment cessation; 1 pt (L2) for prolonged neutropenic fever and 2 pts (L3) for decreased ejection fraction and for acute renal failure. 15 pts were ModR and received adjuvant CMF, 1/2 pts stratified to high dose C declined it and received CMF. Median follow-up is 63 months [range: 28–80] with 13/17 (76.5%) pts surviving, and 12/17 (70.5%) pts surviving and free of disease. Conclusion: Neoadjuvant DD AT every 2 weeks is well-tolerated, with promising activity and survival in locally advanced BC.

[Table: see text]

Clinical significance of extranuclear expression of hormone receptors in breast cancer

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Background: Hormone receptor (HR)-positive breast cancer cells grow through estrogen receptor (ER)-signaling pathways that mediate both genomic and nongenomic actions, which cross-talk with growth factors associated with resistance to tamoxifen. The aim of this study is to explore the clinical significance of extranuclear expression of ER and PR in the cross-talk between HR and growth factor signaling pathways. Methods: We examined the extranuclear expression of ER and PR in 219 primary breast cancers by immunohistochemical staining. Specimens showing such expression were further examined for the expression of pAkt and aromatase. Due to heterogeneity, staining was scored on the basis of intensity and distribution in the tumors. Results: Extranuclear expression of ER or PR was observed in 21 cases (9.5%), which included 4 cases (19.0%) for ER and 20 cases (95.2%) for PR. Among these patients, HER-2, pAkt, and aromatase-positivity were observed in 14 cases (66.6%), 13 cases (61.9%), and 14 cases (66.6%), respectively. On the basis of nuclear HR expression, 11 of these cases were categorized as ER-positive/PR-negative, while 2 were ER-negative/PR-positive. Of those 13 cases, increased pAkt staining was found in 11 cases (84.6%). In particular, among the 11 ER-positive/PR-negative, elevated pAkt and aromatase were found in 10 (90.9%; p<0.01) and 9 cases (81.8%), respectively. Conclusion: PR is more frequently expressed extranuclearly than ER in primary breast cancer, and extranuclear HRs cross-talk with the Akt/HER-2-signaling pathway and activation of aromatase, providing an explanation for the observation that aromatase inhibitors are more beneficial than tamoxifen for ER-positive/PR-negative patients.

No significant financial relationships to disclose.

Extranuclear expression of hormone receptors in primary breast cancer

BACKGROUND

Hormone receptor (HR)-positive breast cancer cells grow through estrogen receptor (ER)-signaling pathways that mediate both genomic and nongenomic actions, which cross-talk with growth factors associated with resistance to tamoxifen. The aim of this study was to explore the cross-talk between extranuclear expression of ER and progesterone receptor (PR) and growth factor signaling pathways in primary breast cancer.

PATIENTS AND METHODS

The extranuclear expression of ER and PR was examined in 219 primary breast cancers by immunohistochemical staining. Specimens showing such expression were further examined for the expression of pAkt and aromatase. Staining reactions were scored on the basis of intensity and distribution in the tumors.

RESULTS

Extranuclear expression of ER or PR was observed in 21 cases (9.5%), which included four cases for ER and 20 cases for PR. Among these patients, HER-2, pAkt, and aromatase-positivity were observed in 14 cases (66.6%), 13 cases (61.9%), and 14 cases (66.6%), respectively. On the basis of nuclear HR expression, 11 of these cases were categorized as ER-positive/PR-negative, while two were ER-negative/PR-positive. Of these 13 cases, increased pAkt staining was found in 11 cases (84.6%). In particular, among the 11 ER-positive/PR-negative cases, elevated pAkt and aromatase were found in 10 (90.9%; P<0.01) and nine cases (81.8%), respectively.

CONCLUSIONS

PR is expressed extranuclearly more frequently than ER in primary breast cancer, and extranuclear HRs cross-talk with the Akt/HER-2-signaling pathways and activation of aromatase. These observations may explain the more beneficial effects of aromatase inhibitors than tamoxifen for ER-positive/PR-negative patients.

Transpupillary thermotherapy for subfoveal leaks in central serous chorioretinopathy

AIM

To evaluate transpupillary thermotherapy (TTT) for the treatment of subfoveal focal leaks in central serous chorioretinopathy (CSC).

METHODS

The patients presenting with long-standing CSC, but without the features of chronicity, were offered the options of TTT, photodynamic therapy (for subfoveal leaks), photocoagulation (for extrafoveal leaks), or observation. The patients who opted for TTT or observation were enrolled in this study. TTT was performed using a spot diameter of 0.5 mm for 1 min. Best-corrected visual acuity (BCVA), status of macular detachment, and fluorescein angiographic status were evaluated at 1, 3, and 6 months.

RESULTS

This study included 39 patients (40 eyes) with CSC between 4 and 12 months, of whom 25 patients (25 eyes) opted for TTT for subfoveal leaks. Fourteen patients (15 eyes) were followed up without treatment. The groups were comparable in age, sex, and baseline BCVA. Minimum follow-up was 6 months. Within 3 months, TTT resulted in the resolution of the serous detachment in 24 (96%) eyes with a single session; one eye required a repeat treatment. Eight control eyes demonstrated persisting CSC at the last follow-up. Visual acuity improved in 23 (92%) treated and five (33%) control eyes; the difference in outcome was statistically significant (P<0.001). One case developed choroidal neovascularization, which resolved with visual recovery to 20/20 after repeat-TTT.

CONCLUSION

TTT resulted in the resolution of CSC with subfoveal angiographic leaks with significant improvement in visual outcome, in comparison to the natural history of persistent CSC.

The role of apoptotic or nonapoptotic cell death in determining cellular response to anticancer treatment

AIMS

Apoptosis, an early response cell death, is a useful marker for predicting tumour response after anticancer treatment; however, late-response cell death or nonapoptotic cell death, autophagy, can also be observed. This article reviews a rational model for predicting tumour response by assessing the influence of nonapoptotic cell death, and thereby developing a more efficient strategy for enhancing the therapeutic effect of anticancer treatment.

METHOD

Literature search of clinical and experimental studies on "cell death and cancer" using established databases, including PUBMED.

FINDINGS

Although induction of apoptosis may not contribute to overall tumour response, nonapoptotic cell death such as autophagy, which may be triggered by apoptosis, still occurs. Anticancer treatment-induced apoptosis is regulated by the balance of proapoptoic and antiapoptoic proteins through mitochondria, and resistance to apoptosis is mediated by Bcl-2-dependent and Akt-dependent pathways. Bcl-2 partially inhibits nonapoptotic cell death as well as apoptosis, whereas Akt inhibits both apoptotic and nonapoptotic cell death through several target proteins.

CONCLUSIONS

Drug sensitivity is likely correlated with the accumulation of apoptotic and nonapoptotic cell deaths, which may influence overall tumour response in anticancer treatment. The ability to predict overall tumour response from the modulation of several important cell death-related proteins may result in a more efficient strategy for improving the therapeutic effect.

Barrage laser photocoagulation for macula-sparing asymptomatic clinical rhegmatogenous retinal detachments

PURPOSE

To evaluate the efficacy of barrage laser photocoagulation in containing macula-sparing asymptomatic clinical retinal detachments (RD).

METHODS

Consecutive patients presenting with asymptomatic clinical RD were prospectively treated with barrage photocoagulation in 2-3 confluent rows, using frequency-doubled Nd:YAG (532 nm) laser on an indirect-ophthalmoscopic delivery system. The patients were reviewed at 0.5, 1.5, 3, and 6 months, and yearly thereafter. Best-corrected visual acuity (BCVA), and stability/progression of rhegmatous retinal detachment beyond the barrage were noted at each visit.

RESULTS

Nineteen phakic eyes of 17 patients (nine female patients), aged 12-58 years (average: 26 years), underwent barrage laser treatment. Two women had bilateral RD. Most detachments were caused by atrophic holes, and involved at least a quadrant of retina. Seven (37%) extended superiorly with breaks above the horizontal raphe. Three eyes had partial demarcation lines, and five had posterior vitreous detachment at presentation. The minimum follow-up was 6 months (mean: 21 months; range: 6-108 months). Pretreatment anatomical and functional status was maintained in 18 (95%) eyes till the final visit. One superotemporal RD progressed across the laser barrier into macula 5 months after photocoagulation, and BCVA dropped to 6/18. Scleral buckling was performed successfully, with visual recovery to 6/6.

CONCLUSIONS

Barrage photocoagulation may have a place in management of asymptomatic clinical detachments, as an effective and less morbid alternative to scleral buckling.

Regulation and interplay of apoptotic and non-apoptotic cell death

Various death triggers including DNA damage, oxidative stress, and growth factor deprivation promote the loss of mitochondrial membrane potential, leading to the production of reactive oxidative species (ROS) or enhanced permeability of the mitochondrial membrane, otherwise known as mitochondrial membrane permeabilization, by insertion of Bax/Bak into the outer membrane where it interacts with voltage-dependent anion channel (VDAC)/adenine nucleotide transporter (ANT). MMP leads to the release of small pro-apoptotic molecules, which induce caspase-dependent and -independent apoptotic cell death. The production of ROS due to the loss of mitochondrial membrane potential enhances the permeability of lysosomal membranes, resulting in the release of lysosomal proteases, which contribute to mitochondrial membrane permeabilization and the lysosomal degradation mechanism of autophagic cell death. Although defects in apoptotic and non-apoptotic cell death pathways can be carcinogenic, these pathways are more or less preserved within cancer cells and can therefore influence cell death and mediate resistance to cancer treatment. This paper discusses recent advances in determining the molecular mechanisms behind regulation of apoptotic and non-apoptotic cell death, as well as the interplay between these two processes, which may lead to the development of new strategies by which to enhance the therapeutic effects of chemotherapeutic agents.

High-resolution crystals and preliminary X-ray diffraction studies of a catalytic RNA

High-resolution single crystals of a catalytic RNA molecule derived from the sequence of the satellite RNA of tobacco ringspot virus have been obtained. The unit-cell volumes of the RNA crystals vary depending on the crystallization conditions and temperature. The best crystal form, when flash frozen, has space group P1 with unit-cell dimensions a = 53.08, b = 71.81, c = 28.03 A, alpha = 98.43, beta = 104.32 and gamma = 74.54 degrees. This form diffracts to a resolution of 2.4 A. A heavy-atom derivative search is in progress.