Comparison between the polypeptide profile of halophilic bacteria and salt tolerant plants

The endoscopic placement of percutaneous gastrostomy tubes has been an accepted technique for several years but has traditionally been performed by gastroenterologists and general surgeons. Fluoroscopically guided tube placement is now performed by radiologists. Head and neck surgeons have been slow to adopt the responsibility for placing percutaneous gastrostomy tubes despite the fact that most are proficient in both rigid and flexible esophagoscopy and trained in the Seldinger technique. We report on 41 percutaneous endoscopic gastrostomies performed in 39 patients by the Head and Neck Service at Stanford Medical Center between July 1, 1992, and August 30, 1995. There were 28 (71.8%) male and 11 (28.2%) female patients. Eleven (28.2%) procedures were performed in patients at the time of major head and neck resections. Another seven (17.9%) patients underwent percutaneous gastrostomy tube placement at the time of their initial staging panendoscopy before receiving chemotherapy and radiation. Fifteen (38.5%) procedures were performed for severe postsurgical dysphagia. Six (15.4%) patients had neurologic dysfunction, and this procedure was often performed in conjunction with tracheostomy. There were no major complications. Two patients had to undergo intraoperative tube replacement at 7 months and 18 months for chronic infection and tube damage, respectively. The only other complication was local irritation at the surgical site, which occurred in 2 (5.1%) patients. Our experience with percutaneous gastrostomy tube placement confirms that this is a procedure that can be safely performed by head and neck surgeons and should be part of otolaryngology-head and neck surgery training. The ability to provide comprehensive care of head and neck cancer patients as well as a means of supplemental feeding in conjunction with performing tracheostomy in neurologically impaired patients will no doubt improve the service that our specialty can provide.     

Phylogenetic and physiological diversity of sulphate-reducing bacteria isolated from a salt marsh sediment

Xenopus blastula cells activate different mesodermal genes as a concentration-dependent response to activin, which behaves like a morphogen. To understand how cells recognize morphogen concentration, we have bound naturally labeled activin to cells and related this to choice of gene activation. We find that the increasing occupancy of a single receptor type can cause cells to switch gene expression. Cells sense ligand concentration by the absolute number of occupied receptors per cell (100 and 300 molecules of bound activin induce Xbra and Xgsc, respectively, i.e., 2% and 6% of the total receptors) and not by a ratio of occupied to unoccupied receptors. The long duration of occupancy explains a previously described ratchet effect. Our results suggest a new concept of morphogen gradient formation and interpretation that is particularly well suited to the needs of early development.     

Phylogenetic characterization of bacteria in the subsurface microbial culture collection

The Subsurface Microbial Culture Collection (SMCC) was established by the U.S. Dept. of Energy (DOE) and contains nearly 10,000 strains of microorganisms (mostly bacteria) isolated from terrestrial subsurface environments. Selected groups of bacterial isolates from three sample sites situated above geochemically and hydrologically different subsurface environments have been characterized by phylogenetic analysis of 16S ribosomal RNA (rRNA) gene nucleotide sequences. Among these isolates were members of six major phylogenetic groups of bacteria: the high-G+C and low-G+C Gram-positive bacteria; the alpha-, beta-, and gamma-subdivisions of the Proteobacteria; and the Flexibacter/Cytophaga/Bacteroides group. A small number of the SMCC strains may be members of new bacterial genera, but most of them could be placed with reasonable confidence into more than 35 previously described genera. The majority of the Gram-positive isolates were species of Arthrobacter, Bacillus, or Streptococcus, whereas Acinetobacter, Comamonas, Pseudomonas, Sphingomonas, and Variovorax were among the most frequently encountered Gram-negative genera. A high proportion of the strains were placed in fewer than 10 genera, implying that there is substantial duplication within the SMCC at the genus level. When groups of isolates assigned to Acinetobacter, Arthrobacter, or Sphingomonas were analyzed in more detail, however, it was found that each group consisted of subgroups of strains that probably differed at the species level. Restriction endonuclease analysis (applied to the strains from one sample site) indicated that additional diversity was present at the strain level. Most of the SMCC isolates assigned to some genera (e.g., Acinetobacter) were very closely related to previously described species in those genera, but most of the isolates assigned to other genera (e.g., Arthrobacter and Sphingomonas) appeared (or were shown) to be new species, thereby indicating that a reasonable amount of novelty is present within the SMCC at the species level.     

The metabolism of carbohydrates by extremely halophilic bacteria: identification of galactonic acid as a product of galactose metabolism

Cell-free extracts prepared from the extremely halophilic bacterium Halobacterium saccharovorum oxidize galactose and accumulate a product which reacts as if it were a lactone. The product does not act as a reducing sugar and contains all six of the carbon atoms initially present in galactose. The product was jugged to be galactonic acid, based on the behavior of the acetylmethyl ester derivative of the product and the pentaacetyl derivative of the galactonic methyl ester during gas chromatography.     

Influence of salt concentration on the cellular fatty acid composition of the moderately halophilic bacterium Halomonas salina

CONTEXT: Little is known about the problems physicians may be encountering in gaining access to managed care networks and whether the process used by managed care plans to select physicians is discriminatory. OBJECTIVE: To investigate the incidence and predictors of denials or terminations of physicians' managed care contracts and the impact these denials and terminations had on primary care physicians' involvement with managed care. DESIGN: Cross-sectional mail survey of a probability sample of primary care physicians. SETTING: A total of 13 large urban counties in California. PARTICIPANTS: Primary care physicians (family practice, internal medicine, obstetrics and gynecology, or pediatrics) who work in office-based practice. MAIN OUTCOME MEASURES: Denial or termination from a contract with an independent practice association (IPA) or health maintenance organization (HMO) and managed care contracts. RESULTS: Of the 947 respondents (response rate, 71%), 520 were involved in office-based primary care. After adjusting for sampling and response rate, 22% of primary care physicians had been denied or terminated from a contract with an IPA or HMO, but 87% of office-based primary care physicians had at least 1 IPA or direct HMO contract. Solo practice was the strongest predictor of having experienced a denial or termination and of having neither an IPA nor a direct HMO contract. Physician age, sex, and race did not predict the level of involvement with managed care. However, physicians' patient demographics were associated with managed care participation; physicians in managed care had significantly lower percentages of uninsured and nonwhite patients in their practices. Physicians experiencing a denial or termination had fewer capitated patients in their practice. CONCLUSIONS: Denials and terminations, although relatively common, do not preclude most primary care physicians from participating in managed care. Managed care selective contracting does not appear to be systematically discriminatory based on physician characteristics, but it may be biased against physicians who provide greater amounts of care to the underserved.     

Thermo-elasto-visco-plastic finite element analysis on formation and propagation of off-corner subsurface cracks in bloom continuous casting

The formation and propagation of the popular off-corner subsurface cracks in bloom continuous casting were investigated through thermo-mechanical analysis using three coupled thermo-mechanical models.A two-dimensional thermo-elasto-visco-plastic finite element model was developed to predict the mould gap evolution,temperature profiles and deformation behavior of the solidified shell in the mould region.Then,a three-dimensional model was adopted to calculate the shell growth,temperature history and the development of stresses and strains of the shell in the following secondary cooling zones.Finally,another three-dimensional model was used to analyze the stress distributions in the straightening region.The results showed that the off-corner cracks in the shell originated from the mould owing to the tensile strain developed in the crack sensitive regions of the solidification front,and they could be driven deeper by the possible severe surface temperature rebound and the extensive tensile stress in the secondary cooling zone,especially upon the straightening operation of the bloom casting.It is revealed that more homogenous shell temperature and thickness can be obtained through optimization of mould corner radius,casting speed and secondary cooling scheme,which help to decrease stress and strain concentration and therefore prevent the initiation of the cracks.     

Malate dehydrogenase isolated from extremely halophilic bacteria of the Dead Sea. 1. Purification and molecular characterization

The complete purification of malate dehydrogenase (EC 1.1.1.37) from extremely halophilic bacteria of the Dead Sea is described. The purification procedure includes (a) precipitation by ammonium sulfate, (b) fractionation on Sepharose 4B using a decreasing concentration gradient of ammonium sulfate, (c) gel permeation chromatography on Sephadex G-100, (d) chromatography on hydroxylapatite, and (e) affinity chromatography on 8-(6-aminohexyl)amino-NAD+-Sepharose at 4.26 M NaCl. The absorption and fluorescence spectra of the native and denatured enzyme were measured, and the extinction coefficient at 280 nm in 4.26 M NaCl was found to be 0.803 cm2mg-1. The amino acid composition analysis showed an excess of 10.4 mol % of acidic amino acids. The apparent specific "volume" phi' of the active enzyme at 4.26 M NaCl was found to be 0.680 +/- 0.015 mL/g. The molecular weight of the native enzyme was found to be 84 000 +/- 4000 determined in 4.26 M NaCl from equilibrium sedimentation data. The molecular weight of the subunits is 39 000 as measured by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Thus, the native enzyme is composed of two subunits.     

Distribution of butyrylcholinesterase in the human amygdala and hippocampal formation

The distribution of the major cholinergic regulatory enzyme acetylcholinesterase (AChE, EC 3.1.1.7) has been extensively studied in the human brain, but the distribution of the closely related enzyme butyrylcholinesterase (BuChE, EC 3.1.1.8) is largely unknown. Because of the importance of BuChE and AChE in Alzheimer's disease, we have studied the distribution of BuChE in the normal human amygdala and hippocampal formation and compared it with that of AChE by using histochemical techniques. In the amygdala, the distribution of BuChE differed significantly from that of AChE in that BuChE was found primarily in neurons and their dendritic processes, whereas AChE was found predominantly in the neuropil. BuChE-positive neurons were present in up to 10% of the neuronal profiles in lateral, basolateral (basal), basomedial (accessory basal), central, cortical, and medial amygdaloid nuclei. AChE was found primarily in the neuropil in these nuclei with only a few AChE-positive neurons. In the hippocampal formation, BuChE was also found in neurons and not in the neuropil, whereas AChE was found in both neurons and in the neuropil. BuChE and AChE neurons were present in the polymorphic layer of the dentate gyrus, as well as the stratum oriens and stratum pyramidale of the hippocampus proper. There was considerable overlap in shapes, sizes, and numbers of BuChE- and AChE-positive neurons, suggesting that the enzymes were colocalized in neurons of the hippocampal formation. The distinct distribution of BuChE suggests that it may have specific functions including coregulation of cholinergic and noncholinergic neurotransmission in human amygdala and hippocampal formation.     

Distribution of bacteria with the arylsulfate sulfotransferase activity

We herein report a simple method using intestinal clamps to prevent intraoperative contamination during an immediate mucocutaneous suture of the intestinal stoma. Using this technique, a protruded intestinal stoma can be constructed reliably without soiling. The technique can be used both for constructing an end as well as a loop intestinal stoma.     

Differential quantitation of surface and subsurface bacteria of normal skin by the combined use of the cotton swab and the scrub methods

By testing adjacent sites on the hypothenar eminence of the palm, enriched with bacteria by massaging the forehead, we found that the numbers of bacteria recovered from the skin surface by a wet cotton swab in 30 s were not significantly different from the numbers obtained by a brisk scrubbing with a blunted Teflon policeman for 120 s. This was true of aerobes (gram-positive cocci) and anaerobes (propionibacteria). If the same site on the palm was swabbed two times for 15 s each time, 67 to 94% of the total recovered bacteria were obtained on the first swab. Differential localization of bacteria into surface and subsurface populations was accomplished by first swabbing a test skin site to assay the surface flora and then scrubbing the same site to test for subsurface organisms. On the palm the swab yielded more aerobes and anaerobes than did the subsequent scrub. On the forehead the scrub yielded three to eight times as many anaerobes as the preceding swab. In some tests gram-positive cocci were distributed on the forehead like propionibacteria (large excess in scrub specimen); in other tests their numbers were similar in the swab and scrub specimens or there was a large excess in the swab specimen. These results indicate that there was no substantial subsurface flora on the palm. On the forehead propionibacteria were predominantly in deeper locations in all tests; gram-positive cocci were variable: in some test sites they were largely at the surface, whereas at other sites a predominance of cocci was in subsurface locations.     

Distribution of desmin and fibronectin in chick embryo gonad during testicular cord formation

In order to compare PCR with rapid virus culture for the early detection of CMV in bronchoalveolar lavage (BAL) after bone marrow transplantation, 26 asymptomatic patients were routinely evaluated for the presence of CMV on day 35 using these two techniques. Concurrent blood samples were also analyzed in all cases. CMV was detected synchronously by both culture and PCR in six of 26 (23%) BAL and in five of 26 (19%) blood specimens. Among these positive specimens, three BAL and blood samples were positive in the same patients. Five (19%) BAL and five (19%) blood samples were culture-negative but PCR-positive. No BAL or blood specimens were positive by culture alone. When considering matched BAL-blood samples, five were positive in only one fluid, BAL (n = 3) or blood (n = 2) using culture, while seven were positive in only one fluid, BAL (n = 4) or blood (in = 3) using PCR. Overall, six of 26 (23%) patients had culture-negative but PCR-positive results. Three of these six patients were positive only in BAL and two of them subsequently received antiviral therapy for development of symptoms suggestive of CMV infection. We suggest that asymptomatic patients with negative-culture but PCR-positive results on day 35 in BAL should be subsequently closely monitored for the presence of CMV.     

Distribution, diversity, and host specificity of Bartonella in rodents from the Southeastern United States

Of 215 leuconostocs isolated from field grass, natural whey cultures and water-buffalo milk, 178 were identified as Leuconostoc mesenteroides ssp. mesenteroides while 37 strains could not be identified. Biochemical characterization allowed seven groups to be defined. Representative strains of each group and different habitat and nine reference strains were selected for further analyses. Protein profiles appeared suitable for species discrimination, but did not differentiate between the three subspecies of Leuc. mesenteroides. The technique also showed some differences among equivocal strains. DNA fingerprinting for most strains of Leuc. mesenteroides ssp. mesenteroides examined showed a different restriction pattern from that of the type strain. Ribotyping was not useful for discriminating species and subspecies of the genus Leuconostoc: Leuc. mesenteroides ssp. mesenteroides and ssp. dextranicum showed the same ribopattern as Leuc. lactis while Leuc. mesenteroides ssp. cremoris exhibited a pattern distinct from all the other species examined. On the basis of ARDRA-PCR, two main groups could be distinguished: the larger group included Leuc. mesenteroides, Leuc. lactis, Leuc. pseudomesenteroides and some unidentifiable strains; the second one included Leuc. citreum, Leuc. fallax, Weissella paramesenteroides and some unidentified strains.     

Distribution of genetic diversity in relation to chromosomal inversions in the malaria mosquito Anopheles gambiae

The epidemiology of malaria in Africa is complicated by the fact that its principal vector, the mosquito Anopheles gambiae, constitutes a complex of six sibling species. Each species is characterized by a unique array of paracentric inversions, as deduced by karyotypic analysis. In addition, most of the species carry a number of polymorphic inversions. In order to develop an understanding of the evolutionary histories of different parts of the genome, we compared the genetic variation of areas inside and outside inversions in two distinct inversion karyotypes of A. gambiae. Thirty-five cDNA clones were mapped on the five arms of the A. gambiae chromosomes with divisional probes. Sixteen of these clones, localized both inside and outside inversions of chromosome 2, were used as probes in order to determine the nucleotide diversity of different parts of the genome in the two inversion karyotypes. We observed that the sequence diversity inside the inversion is more than three-fold lower than in areas outside the inversion and that the degree of divergence increases gradually at loci at increasing distance from the inversion. To interpret the data we present a selectionist and a stochastic model, both of which point to a relatively recent origin of the studied inversion and may suggest differences between the evolutionary history of inversions in Anopheles and Drosophila species.     

Distribution, diversity and evolution of the bacterial mercury resistance (mer) operon

Mercury and its compounds are distributed widely across the earth. Many of the chemical forms of mercury are toxic to all living organisms. However, bacteria have evolved mechanisms of resistance to several of these different chemical forms, and play a major role in the global cycling of mercury in the natural environment. Five mechanisms of resistance to mercury compounds have been identified, of which resistance to inorganic mercury (HgR) is the best understood, both in terms of the mechanisms of resistance to mercury and of resistance to heavy metals in general. Resistance to inorganic mercury is encoded by the genes of the mer operon, and can be located on transposons, plasmids and the bacterial chromosome. Such systems have a worldwide geographical distribution, and furthermore, are found across a wide range of both Gram-negative and Gram-positive bacteria from both natural and clinical environments. The presence of mer genes in bacteria from sediment cores suggest that mer is an ancient system. Analysis of DNA sequences from mer operons and genes has revealed genetic variation both in operon structure and between individual genes from different mer operons, whilst analysis of bacteria which are sensitive to inorganic mercury has identified a number of vestigial non-functional operons. It is hypothesised that mer, due to its ubiquity with respect to geographical location, environment and species range, is an ancient system, and that ancient bacteria carried genes conferring resistance to mercury in response to increased levels of mercury in natural environments, perhaps resulting from volcanic activity. Models for the evolution of both a basic mer operon and for the Tn21-related family of mer operons and transposons are suggested. The study of evolution in bacteria has recently become dominated by the generation of phylogenies based on 16S rRNA genes. However, it is important not to underestimate the roles of horizontal gene transfer and recombinational events in evolution. In this respect mer is a suitable system for evaluating phylogenetic methods which incorporate the effects of horizontal gene transfer. In addition, the mer operon provides a model system in the study of environmental microbiology which is useful both as an example of a genotype which is responsive to environmental pressures and as a generic tool for the development of new methodology for the analysis of bacterial communities in natural environments.     

Is intracellular pH and/or intracellular bicarbonate a determinant of bile salt independent canalicular bile formation? The subject revisited

Canalicular bile formation is a complex process that involves basolateral and apical cell membrane transport, paracellular transport and vesicular transport, all of which may be subject to regulation by pH. We review the concept that apical cell membrane bicarbonate secretion promotes bile salt independent canalicular bile formation. We show that the presence of paracellular electrolyte transport imposes a severe restriction in interpreting data from ion substitution experiments aimed at demonstrating pH or bicarbonate dependent bile formation. Furthermore, we report on experiments that all show stimulation of bile flow under three disparate experimental conditions: i) intracellular alkalinization in the absence of [HCO3-]i or associated with a decrease of [HCO3-]i, ii) intracellular alkalinization with an increase of [HCO3-]i, and iii) intracellular acidification with increase of [HCO3-]i. It is suggested that both, intracellular pH and intracellular bicarbonate may modulate canalicular bile salt independent bile formation, but it remains conjectural which mechanism is the prevailing one under a given experimental setting.     

Bacterial diversity in a deep-subsurface clay environment

The presence of bacteria in a deep clay sediment was analyzed in a 20-m-long core horizontally drilled from a mine gallery at a depth of 224 m in the Boom clay formation (Mol, Belgium). This clay deposit is the result of a marine sedimentary process that occurred 35 million years ago. Bacterial activities were estimated by measuring respiration on [14C]glucose. Using the same samples, universal primers for the genes coding for eubacterial 16S rRNA were used to amplify extracted DNA. PCR products were then cloned, sequenced, and analyzed by molecular phylogeny. Our data showed a decrease in bacterial densities as a function of distance from the gallery, with few bacteria detectable by culture at more than 80 cm from the gallery wall. PCR experiments showed the presence of bacteria in all samples, and phylogenetic analyses were then used to tentatively identify these organisms. Because of low bacterial densities in deep clay samples, direct counts and enumeration of viable bacteria on diverse culture media remained negative. All experiments, both cultures and PCR, demonstrated the difficulty of analyzing samples that contain only a few poorly active bacteria as it is difficult to avoid a small contamination by active bacteria during sampling. Since the porosity of the Boom clay formation is less than the expected size of bacteria, it is possible that some of the bacteria present in this 35-million-year-old deep clay deposit derive from cells initially trapped during the sedimentation process.