A physical map of the human genome.

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

A BAC-based physical map of the major autosomes of Drosophila melanogaster.

We constructed a bacterial artificial chromosome (BAC)-based physical map of chromosomes 2 and 3 of Drosophila melanogaster, which constitute 81% of the genome. Sequence tagged site (STS) content, restriction fingerprinting, and polytene chromosome in situ hybridization approaches were integrated to produce a map spanning the euchromatin. Three of five remaining gaps are in repeat-rich regions near the centromeres. A tiling path of clones spanning this map and STS maps of chromosomes X and 4 was sequenced to low coverage; the maps and tiling path sequence were used to support and verify the whole-genome sequence assembly, and tiling path BACs were used as templates in sequence finishing.

Solid phantom material for the dosimetry of iodine-125 seed ophthalmic plaques.

PURPOSE: A tissue-equivalent solid phantom material, RE-1, closely simulating the radiological attenuation and scattering properties of the human eye for the iodine-125 photon spectrum and their Compton-scattered secondary photons, was fabricated on a polyethylene base with CaCO3 and MgO as inorganic additives. METHODS AND MATERIALS: A 24 mm diameter spherical phantom was made from 1.1 mm thick sheets of RE-1, and holes were drilled in which 1 mm3 TLD cubes were placed. RESULTS: The radial dose function g(r), which determines the dose profile on the transverse axis, was measured in a quasi-infinite phantom of RE-1. CONCLUSION: The values obtained deviate only slightly from those for a quasi-infinite phantom made from water-equivalent material.

Autoradiography for iodine-125 seeds.

To study the interior design of model 6702 and 6711 iodine-125 seeds contact autoradiographs were performed using mammography film. Improved resolution was obtained using a pin-hole camera with a hole of 0.1 mm x 0.1 mm. With these techniques, qualitative determination of the relative activity distribution within each seed was possible. The number of the activated resin spheres and the positions of the centers of these spheres can be exactly determined. A model calculation shows, that variations in the arrangement of the activated spheres within a seed have a moderate influence on the dose distribution at source distances below 10 mm. Knowing the exact source configuration may be useful when comparing dose calculations with measured data for model 6702 125I seeds which are currently employed in ophthalmic plaque and implant therapy of other tumors.

Dosimetry and physical treatment planning for iodine eye plaque therapy.

The dosimetry of eye plaques loaded with iodine-125 seeds (type 6702) was performed by means of computer calculations and measurements with thermoluminescent dosimeters (TLD). Measurements of the depth dose distribution (2-25.5 mm) along the transverse axis of a single seed were performed in water equivalent phantom material. The transverse axis attenuation and geometry factor F(r) was obtained by applying a least squares fit to the measured data. Based on the resulting radial dose function, a computer program was developed which calculates dose distributions within the eye for arbitrary loading and placement of the eye plaque. The computational results were verified by TLD measurements in an eye phantom.

[Aspects of the computer-assisted irradiation planning for the HDR (high dose rate) afterloading technique]. / Aspekte der EDV-Bestrahlungsplanung für das HDR-Afterloadingverfahren.

A mathematical optimization method will be discussed concerning the three dimensional radiation treatment planning of the HDR-afterloading technique. Program libraries of the EDV Center of the University of Essen were used.

[Development and dosimetry of a 125 iodine applicator for brachytherapy of intraocular tumors]. / Entwicklung und Dosimetrie eines 125Jod-Applikators zur Brachytherapie intraokularer Tumoren.

Due to the low gamma energy (27-35 ke V), iodine 125 is especially suitable for brachytherapy of intraocular tumors. 125I is available as encapsulated seeds. Applicators can be individually loaded with these seeds to accommodate the shape of the tumor as much as possible. To measure the depth-dose distribution LiF thermoluminence detectors (TLDs, 1 mm3) are embedded in an RW-1 eye phantom at various distances and directions from the high active plaque positioned at the top of the phantom. To obtain the three-dimensional dose distribution, the TLDs are read after exposure for the appropriate time period. Based on experimental measurements of the 125I plaque, a computer program is developed to calculate the dose distribution within the eye and the radiation time for intraocular tumors. These results are very similar to those obtained when using mathematical equations published in the literature. In summary, three-dimensional dose distribution at various distances from an 125I eye plaque has been experimentally determined using a new method. This is an important prerequisite for introducing 125I plaques into the treatment of intraocular tumors.

[Dosimetry of ruthenium applicators with an eye phantom and small volume thermoluminescence detectors]. / Dosimetrie von Rutheniumapplikatoren mit einem Augenphatom und kleinvolumigen Thermolumineszenzdetektoren (TLD).

Even though 106Ru/106Rh applicators have been in clinical use over more than two decades for the radiotherapy of malignant uveal melanomas, the dosimetry of emitted beta radiation is still a physical problem. The dose rate at the applicator surface and the depth dose in tissue equivalent material can be determined only within +/- 30% error. Using new cubic-shaped thermoluminescence detectors (TLD) with small volume the dose distribution is examined in water equivalent material (RW-1). The spatial resolution is 14 times better compared to the previous technique. From dose measurements in an eye phantom the homogeneity of nuclide deposition and the depth dose distribution of a 106Ru/106Rh applicator are determined.

Inhibition of Nb2 T-lymphoma cell growth by transforming growth factor-beta.

Transforming growth factor-beta (TGF-beta) inhibits proliferation of Nb2 cells, a rat T lymphoma, in response to lactogens and interleukin-2. Prostaglandins may play an important role in the pathway through which TGF-beta exerts its inhibitory actions, because prostaglandin E2 also inhibits proliferation of Nb2 cells, and indomethacin, an inhibitor of prostaglandin synthesis, reverses the inhibitory effects of TGF-beta on Nb2 cell proliferation.

Drug-induced fever.

Humans maintain body temperature within a narrow range. Drug administration can upset the usual balance and cause a fever. The drug may interfere with heat dissipation peripherally, increase the rate of metabolism, evoke a cellular or humoral immune response, mimic endogenous pyrogen, or damage tissues. The fever may be a result of the pharmacological action of the drug or some other unrelated effect. Drug-induced fever is most commonly the result of a hypersensitivity reaction and its characteristics resemble those of an allergic reaction. The fever most commonly occurs after 7 to 10 days of drug administration, persists as long as the drug is continued, disappears soon after stopping the drug, and will rapidly reappear if the drug is restarted. The agents most commonly associated with causing fever include the penicillins, cephalosporins, antituberculars, quinidine, procainamide, methyldopa, and phenytoin.

Direct determination of activities for microorganisms of chesapeake bay populations.

We used three methods in determination of the metabolically active individual microorganisms for Chesapeake Bay surface and near-bottom populations over a period of a year. Synthetically active bacteria were recognized as enlarged cells in samples amended with nalidixic acid and yeast extract and incubated for 6 h. Microorganisms with active electron transport systems were identified by the reduction of a tetrazolium salt electron acceptor. Microorganisms active in uptake of amino acids, thymidine, and acetate were determined by microautoradiography. In conjunction with enumeration of active organisms, a total direct count was made for each sample preparation by epifluorescence microscopy. For the majority of samples, numbers of amino acid uptake-active organisms were greater than numbers of organisms determined to be active by other direct measurements. Within a sample, the numbers of uptake-active organisms (amino acids or thymidine) and electron transport system-active organisms were significantly different for 68% of the samples. Numbers of synthetically active bacteria were generally less than numbers determined by the other direct activity measurements. The distribution of total counts in the 11 samplings showed a seasonal pattern, with significant dependence on in situ water temperature, increasing from March to September and then decreasing through February. Synthetically active bacteria and amino acid uptake-active organisms showed a significant dependence on in situ temperature, independent of the function of temperature on total counts. Numbers of active organisms determined by at least one of the methods used exceeded 25% of the total population of all samplings, and from June through September, >85% of the total population was found to be active by at least one direct activity measurement. Thus, active rather than dormant organisms compose a major portion of the microbial population in this region of Chesapeake Bay.

Inhibitory effect of solar radiation on amino Acid uptake in chesapeake bay bacteria.

The effect of solar radiation on a natural bacterial population from the Chesapeake Bay was evaluated from measured changes in numbers of organisms engaged in amino acid uptake. From July through May, freshly collected water samples were exposed in quartz containers to 3.5 h of total sunlight both with and without UV-absorbing filters. Water samples were subsequently incubated with tritiated amino acids, and the uptake-active bacteria were assayed by microauto-radiography-epifluorescence microscopy. The survival index, defined as the fraction of the uptake-active population that remained active after the exposure to sunlight, ranged from 0.93 to 0.20. Decreased survival was correlated with increased solar intensity. The inhibition of amino acid uptake was attributed not only to the UV-B component of the solar spectrum (280 to 320 nm), but also to longer UV and visible wavelengths.

Improved microautoradiographic method to determine individual microorganisms active in substrate uptake in natural waters.

We report a method which combines epifluorescence microscopy and microautoradiography to determine both the total number of microorganisms in natural water populations and those individual organisms active in the uptake of specific substrates. After incubation with H-labeled substrate, the sample is filtered and, while still on the filter, mounted directly in a film of autoradiographic emulsion on a microscope slide. The microautoradiogram is processed and stained with acridine orange, and, subsequently, the filter is removed before microscopic observation. This novel preparation resulted in increased accuracy in direct counts made from the autoradiogram, improved sensitivity in the recognition of uptake-active (H-labeled) organisms, and enumeration of a significantly greater number of labeled organisms compared with corresponding samples prepared by a previously reported method.

Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples.

Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments.

Improved method for determination of respiring individual microorganisms in natural waters.

A method is reported that combines the microscopic determinations of specific, individual, respiring microorganisms by the detection of electron transport system activity and the total number of organisms of an estuarine population by epifluorescence microscopy. An active cellular electron transport system specifically reduces 2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyl tetrazolium chloride (INT) to INT-formazan, which is recognized as opaque intracellular deposits in microorganisms stained with acridine orange. In a comparison of previously described sample preparation techniques, a loss of >70% of the counts of INT-reducing microorganisms was shown to be due to the dissolution of INT-formazan deposits by immersion oil (used in microscopy). In addition, significantly fewer fluorescing microorganisms and INT-formazan deposits, both

A pressure-retaining deep ocean sampler and transfer system for measurement of microbial activity in the deep sea.

A deep ocean sampler (DOS) has been developed for microbiological sampling and is capable of aseptically collecting 400-ml water samples from any depth in the world oceans. The instrument maintains samples under in situ pressure and temperature. A hyperbaric transfer system has also been developed, enabling transfer of sample volumes up to 150 ml, without decompression or dilution, to pressurized incubation chambers. Utilization of(14)C-glutamate (21 to 96µg/l) and(14)C-acetate (4.6µg/l) by microbial populations in undecompressed water samples from the N.W. Atlantic and the Cape and Angola Basins was recorded over incubation periods of 2 to 18 weeks. Rates of substrate utilization ranged from 1 to 38×10(-2) µg/l/day.

Filterable marine bacteria found in the deep sea: Distribution, taxonomy, and response to starvation.

A significant number of viable colony-forming bacteria were recovered from deep-ocean bottom water samples passed through a 0.45µm filter. However, these bacteria small enough to pass through a 0.45µm membrane filter and termed "filterable bacteria" were less abundant in open-ocean surface water and coastal water samples. The reduced size of bacterial cells present in deep-ocean bottom water samples was documented by scanning electron microscopy. The concentration of ATP in the water samples was found to be correlated with results of direct counts of bacteria.Numerical taxonomy of bacterial strains isolated from water samples collected at two stations in the deep sea yielded taxonomic clusters grouped according to sample and size fraction. The generic composition of bacterial populations of bottom water filtrates was compared with that of bacteria retained by 0.45µ m filters. Strains ofAlcaligenes, Flavobacterium, Pseudomonas, andVibrio spp. were identified among those retained by, as well as passing through, 0.45µm filters.Two marine isolates obtained from the filtrate of a deep-ocean water sample were incubated for 9 weeks in nutrient-free artificial seawater, during which the cells became rounded and reduced in size. After the 9-week incubation period, more than 10% of the viable cells of both cultures were able to pass through a 0.4µm filter. The viable count at 9 weeks wasca. 10% of that of the initial population, although from direct counts the total population number remained relatively constant throughout the incubation period. From the observed reduction in cell size and increased starvation resistance of cells held under low nutrient conditions, it is concluded that a significant relationship exists between decreased cell size and increased survival of marine bacteria in the deep sea.

Barophilic growth of bacteria from intestinal tracts of deep-sea invertebrates.

Digestive tracts of abyssal scavenging amphipods and a deep-sea holothurian were examined for the presence of intestinal microflora capable of rapid proliferation under in situ pressures of 430 to 520 atmospheres (atm) and temperatures of 3-5°C. For two amphipod specimens, population doubling times of 5 and 6 hours were observed under in situ conditions, compared to 8 and 6 hours, respectively, at 1 atm. Growth enhancement under pressure was related inversely to initial population size and directly to concentration of available nutrient. In the case of the deposit-feeding holothurian, attached bacteria scraped from the intestinal lining showed a doubling time, under pressure, of 11 hours, compared to 36 hours for transient sediment bacteria that comprised the gut contents. These data suggest that deep-sea animals possess a commensal gut flora capable of responding to increased nutrient levels, via feeding of the host, without inhibition by the elevated hydrostatic pressures encountered in the deep ocean environment.