Genome sequence of the obligate methanotroph Methylosinus trichosporium strain OB3b.

Methylosinus trichosporium OB3b (for "oddball" strain 3b) is an obligate aerobic methane-oxidizing alphaproteobacterium that was originally isolated in 1970 by Roger Whittenbury and colleagues. This strain has since been used extensively to elucidate the structure and function of several key enzymes of methane oxidation, including both particulate and soluble methane monooxygenase (sMMO) and the extracellular copper chelator methanobactin. In particular, the catalytic properties of soluble methane monooxygenase from M. trichosporium OB3b have been well characterized in context with biodegradation of recalcitrant hydrocarbons, such as trichloroethylene. The sequence of the M. trichosporium OB3b genome is the first reported from a member of the Methylocystaceae family in the order Rhizobiales.

Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds.

Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.

Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment.

We report the genome sequence of Anaeromyxobacter sp. Fw109-5, isolated from nitrate- and uranium-contaminated subsurface sediment of the Oak Ridge Integrated Field-Scale Subsurface Research Challenge (IFC) site, Oak Ridge Reservation, TN. The bacterium's genome sequence will elucidate its physiological potential in subsurface sediments undergoing in situ uranium bioremediation and natural attenuation.

Integration of multimodality imaging data for radiotherapy treatment planning.

This paper describes computational techniques to permit the quantitative integration of magnetic resonance (MR), positron emission tomography (PET), and x-ray computed tomography (CT) imaging data sets. These methods are used to incorporate unique diagnostic information provided by PET and MR imaging into CT-based treatment planning for radiotherapy of intracranial tumors and vascular malformations. Integration of information from the different imaging modalities is treated as a two-step process. The first step is to determine the set of geometric parameters relating the coordinates of two imaging data sets. No universal method for determining these parameters is appropriate because of the diversity of contemporary imaging methods and data formats. Most situations can be handled by one of the four different techniques described. These four methods make use of specific geometric objects contained in the two data sets to determine the parameters. These objects are: (a) anatomical and/or fiducial points, (b) attached line markers, (c) anatomical surfaces, and (d) outlines of anatomical structures. The second step involves using the derived transformation to transfer outlines of treatment volumes and/or anatomical structures drawn on the images of one imaging study to the images of another study, usually the treatment planning CT. Solid modelling and image processing techniques have been adapted and developed further to accomplish this task. Clinical examples and phantom studies are presented which verify the different aspects of these techniques and demonstrate the accuracy with which they can be applied. Clinical use of these techniques for treatment planning has resulted in improvements in localization of treatment volumes and critical structures in the brain. These improvements have allowed greater sparing of normal tissues and more precise delivery of energy to the desired irradiation volume. It is believed that these improvements will have a positive impact on the outcome of radiation therapy.

Dose volume histogram analysis of liver radiation tolerance.

Eleven patients with carcinoma of the pancreas or biliary system received heavy charged particle radiation treatments and whole liver heavy charged particle radiation at Lawrence Berkeley Laboratory. Doses to the whole liver ranged from 10 to 24 Gray-equivalent (the biological equivalent of 10 to 24 Gray of low-LET photon radiation), whereas the dose to the primary lesion ranged from 53.5 to 70 Gray-equivalent (GyE). The fraction size was 2 to 3 GyE. The liver received partial as well as whole organ irradiation. Integral dose volume histograms for the liver were obtained in all 11 patients. An integral dose volume histogram displays on the ordinate the percentage of liver that was irradiated in excess of the dose specified on the abcissa. In this study, the clinical liver radiation tolerance of these patients is correlated with the information contained in an integral dose volume histogram. One patient developed radiation hepatitis. The integral dose volume histogram of this patient differed from the dose volume histograms of the other 10 patients. This difference was greatest in the range of doses between 30 and 40 GyE. Our results suggest that liver doses in excess of 30 to 35 GyE should be limited to 30% of the liver or less when 18 GyE of whole liver radiation is delivered at 2 GyE per fraction in addition to primary radiation of the pancreas or biliary system.

Precision, high dose radiotherapy. II. Helium ion treatment of tumors adjacent to critical central nervous system structures.

In this paper we present a technique for treating relatively small, low grade tumors located very close to critical, radiation sensitive central nervous system structures such as the spinal cord and the brain stem. A beam of helium ions is used to irradiate the tumor. The nearby normal tissues are protected by exploiting the superb dose localization properties of this beam, particularly its well defined and controllable range in tissue, the increased dose deposited near the end of this range (i.e., the Bragg peak), the sharp decrease in dose beyond the Bragg peak, and the sharp penumbra of the beam. To execute this type of treatment, extreme care must be taken in localization of the tumor and normal tissues, as well as in treatment planning and dosimetry, patient immobilization, and verification of treatment delivery. To illustrate the technique, we present a group of 19 patients treated for chordomas, meningiomas and low grade chondrosarcomas in the base of the skull or spinal column. We have been able to deliver high, uniform doses to the target volumes (doses equivalent to 60 to 80 Gy of cobalt-60) while keeping the doses to the nearby critical tissues below the threshold for radiation damage. Follow-up on this group of patients is short, averaging 22 months (2 to 75 months). Currently, 15 patients have local control of their tumor. Two major complications, a spinal cord transection and optic tract damage, are discussed in detail. Our treatment policies have been modified to minimize the risk of these complications in the future, and we are continuing to use this method to treat such patients. We are enthusiastic about this technique, since we believe there is no other potentially curative treatment for these patients.

Treatment of cancer with heavy charged particles.

A clinical radiotherapeutic trial using heavy charged particles in the treatment of human cancers has accrued over 400 patients since 1975, 378 of whom were treated with particles and 28 with low LET photons as control patients. Heavy charged particle radiotherapy offers the potential advantages of improved dose localization and/or enhanced biologic effect, depending on particle selected for treatment. Target sites have included selected head and neck tumors, ocular melanomata, malignant gliomata of the brain, carcinoma of the esophagus, carcinoma of the stomach, carcinoma of the pancreas, selected juxtaspinal tumors and other locally advanced, unresectable tumors. A Phase III prospective clinical trial has been started in carcinoma of the pancreas using helium ions. Phase I-II studies are underway with heavier particles such as carbon, neon and argon ions in order to prepare for prospective Phase III trials. Silicon ions are also under consideration for clinical trial. These studies are supported by the United States Department of Energy and National Institutes of Health.

An automated image-registration technique based on multiple structure matching.

A new image-registration technique that matches multiple structures on complementary imaging data sets (e.g., CT and MRI) has been developed and tested with both phantom and patient data. The algorithm assumes a rigid-body transformation and is suitable for correlating structures within the cranium or at the skull base. The basic premise of the new technique is that an optimum transformation is achieved when the relative volume lying outside of the intersection between a structure and its transformed counterpart is a minimum. This relative volume is calculated numerically using a random sampling approach, and a binary searching algorithm was used to step through the nine-dimensional parameter space consisting of three rotation angles, three scaling factors and three components of a translation vector. For the nine tests using phantom data, the automated structure-matching technique was able to predict the correct rotation angles to within +/- 1 degree. The expected clinical performance of the new technique was assessed by comparing results obtained with the new method to those obtained using other techniques for 12 patients who were treated with charged particles at Lawrence Berkeley Laboratory (LBL) and who had image-registration studies performed as part of their treatment plan. For 9 of the 12 patients considered, the new structure-matching technique produced a significantly better registration than the older methods, as measured by the resultant average relative volume lying outside of the intersection between any structure and its transformed counterpart. For the other three patients, results were not significantly different for the new structure-matching method and the older techniques.

Evaluation of fixed- versus variable-modulation treatment modes for charged-particle irradiation of the gastrointestinal tract.

The clinical usefulness of variable-modulation dose delivery of neon ion and proton beams over fixed-modulation beams is evaluated for several patients with tumors in the gastrointestinal tract by comparing dose distributions, dose volume histograms, and predictions of normal tissue complication probabilities calculated with the two methods. Both techniques provide excellent coverage of the target volume with neon ion and proton beams. The advantage of variable modulation is that less dose is delivered proximal to the target volume. For tumors in the gastrointestinal tract, this implies that less dose is given to the liver, gut, kidneys, and lungs. For the ten patients considered in this study, variable-modulation reduced the total integral dose by an average of 17% for neon ion beams and by 18% for protons as compared to fixed-modulation. If the tumor volume is excluded, the reduction in the integral dose to normal tissues ranged from 15% to 32% for neon ions and from 18% to 34% for proton beams. These gains are larger than those anticipated on the basis of an analytic study by Goitein and Chen [Med. Phys. 10, 831-840 (1983)], which predicted integral dose reductions of the order of 10% for protons and 14% for neon ions. They are also larger than those reported in a similar study by Urie and Goitein [Med. Phys. 16, 593-601 (1989)] for proton irradiation of skull-base tumors. This is probably because the tumors in the GI tract considered in this study were more irregularly shaped than Goitein and Chen's analytic model assumes. The results of this study also suggest that due to increased sparing of normal tissues, the number of different portal directions required to achieve a satisfactory treatment plan will be reduced for variable-modulation beam delivery systems. This implies that variable-modulation treatment plans will be easier to execute than current fixed-modulation plans.

The effect of patient motion on dose uncertainty in charged particle irradiation for lesions encircling the brain stem or spinal cord.

A specialized charged-particle radiotherapy technique developed at Lawrence Berkeley Laboratory (LBL) is applied to patients with lesions abutting or surrounding the spinal cord or brain stem. This technique divides the target into two parts, one partially surrounding the critical structure (brain stem or spinal cord) and a second excluding the critical structure and abutting the first portion of the target. Compensators are used to conform the dose distribution to the distal surface of the target. This technique represents a novel approach in treating unresectable or residual tumors surrounding the spinal cord or brain stem. Since the placement of the patient with respect to beam-shaping devices is critical for divided-target treatments, a method for calculating dose distributions reflecting random patient motion is proposed, and the effects of random patient motion are studied for two divided-target patient examples. Dose-volume histograms and a normal-tissue complication probability model are used in this analysis. For the patients considered in this study, the normal-tissue-complication probability model predicts that random patient motion less than or equal to 0.2 cm is tolerable in terms of spinal cord complications.

Helium charged-particle radiotherapy of locally advanced carcinoma of the esophagus, stomach, and biliary tract.

Sixty-five patients with squamous carcinoma of the esophagus (32 patients), carcinoma of the stomach (18 patients) and carcinoma of the biliary tract (15 patients) received from 6000 to 7000 equivalent rad (60-70 Gray-equivalents) of helium radiotherapy at 2.0 GyE per fraction, four fractions per day, using multiportal, spread-out Bragg peak therapy. All patients had locally advanced disease without evidence of distant metastases. Partial compensation for tissue inhomogeneities was accomplished. Although palliation of symptoms and regression of tumor was commonly seen, local failure occurred in most patients (77%). The median survival was 8 months. It does not appear that an increase in tumor dose relative to normal tissues can be achieved that would be high enough to increase locoregional control rates over historical control rates with low-LET irradiation. Further studies will be carried out with heavier particles such as neon or silicon in hopes of achieving greater biological effect on these difficult-to-control tumors.

Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8.

The complete genome sequence of Methylomicrobium album strain BG8, a methane-oxidizing gammaproteobacterium isolated from freshwater, is reported. Aside from a conserved inventory of genes for growth on single-carbon compounds, M. album BG8 carries a range of gene inventories for additional carbon and nitrogen transformations but no genes for growth on multicarbon substrates or for N fixation.

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1.

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

Helium-ion radiation therapy at the Lawrence Berkeley Laboratory: recent results of a Northern California Oncology Group Clinical Trial.

We report on the first decade of the helium-ion radiotherapy clinical trial being carried out at the Lawrence Berkeley Laboratory. Over 500 patients have now been treated. We have had very good results to date in treating patients with small tumors critically located near a radiation-sensitive organ which would preclude delivering a curative dose with conventional radiotherapy. On the other hand, patients with larger tumors where the tumor dose cannot be increased more than 10% over conventional radiotherapy have not responded well to helium ion radiotherapy. This is illustrated by discussing selected patient groups in detail, namely those with uveal melanoma, small, low-grade tumors near the central nervous system, carcinoma of the pancreas, and carcinoma of the esophagus.

Clinical gain from improved beam delivery systems.

The feasibility of dynamic conformal heavy charged particle radiotherapy has been investigated at UCLBL, and shows high promise of: 1. an improved therapeutic ratio and 2. reduction in the number of treatment portals required for efficient treatment delivery. Assessment of dose to tumor and critical structures for several anatomical sites have been carried out using a normal tissue complication algorithm developed at LBL. For high-LET charged particle treatment delivery, dynamic conformal therapy using a raster scanned beam with variable modulation and multileaf collimator appears to be the optimal technique for treatment delivery.

[Heavy particle radiotherapy at the University of California Lawrence Berkeley Laboratory. Clinical studies by the Northern California Oncology Group]. / Strahlentherapie mit schweren Teilchen am Lawrence Berkeley Laboratory der Universität von Kalifornien. Klinische Untersuchungen der Northern California Oncology Group.

At the university of California Lawrence Berkeley Laboratory, patients have been irradiated for 10 years with heavy ions (He, C, Ne, Si). Due to the biologic efficacy of this type of radiation as well as the possibility of a precise dose application, the tumors can be irradiated with very high doses without exposing the surrounding tissues. The experience gained in the treatment of more than 800 patients is presented. It shows that this radiation can be used to localize tumors situated near to particularly radiosensitive organs such as skull base, paraspinal region, and the eye.

Postmortem examination of 22 pancreatic carcinoma patients treated with helium ion irradiation.

Postmortem findings are available in this report in 22 patients with pancreatic carcinoma treated with helium ions at Lawrence Berkeley Laboratory; California. This represents the largest group evaluated histologically in the literature and is the first report evaluating effects of particle radiation in pancreatic tissue. Patient survival after therapy averaged 9 months. Most died of infection and/or pulmonary emboli. Local control was achieved in 27%. The pancreatic tumors had histologically more severe radiation changes than nontumor bearing pancreas. Irradiated bone marrow was severely hypocellular, and irradiated skin was atrophic. Five patients had radiation injury in the gastrointestinal tract. The spinal cord, liver, and kidneys showed no damage. This study demonstrates the safety of helium particle irradiation with present therapeutic planning. Injury to tumor was seen without excessive damage to adjacent tissues.