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Publication
Journal: PLoS Genetics
April/21/2016
Abstract
Salmonella enterica serovar Agona has caused multiple food-borne outbreaks of gastroenteritis since it was first isolated in 1952. We analyzed the genomes of 73 isolates from global sources, comparing five distinct outbreaks with sporadic infections as well as food contamination and the environment. Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and subsequently underwent a major population expansion in the 1960s. Homologous recombination with other serovars of S. enterica imported 42 recombinational tracts (360 kb) in 5/143 nodes within the genealogy, which resulted in 3,164 additional SNPs. In contrast to this paucity of genetic diversity, Agona is highly diverse according to pulsed-field gel electrophoresis (PFGE), which is used to assign isolates to outbreaks. PFGE diversity reflects a highly dynamic accessory genome associated with the gain or loss (indels) of 51 bacteriophages, 10 plasmids, and 6 integrative conjugational elements (ICE/IMEs), but did not correlate uniquely with outbreaks. Unlike the core genome, indels occurred repeatedly in independent nodes (homoplasies), resulting in inaccurate PFGE genealogies. The accessory genome contained only few cargo genes relevant to infection, other than antibiotic resistance. Thus, most of the genetic diversity within this recently emerged pathogen reflects changes in the accessory genome, or is due to recombination, but these changes seemed to reflect neutral processes rather than Darwinian selection. Each outbreak was caused by an independent clade, without universal, outbreak-associated genomic features, and none of the variable genes in the pan-genome seemed to be associated with an ability to cause outbreaks.
Publication
Journal: Journal of Structural Biology
April/13/2000
Abstract
Cryo-electron tomography was used to study the structural organization of whole frozen-hydrated mitochondria from Neurospora crassa. Unlike mitochondria from many other species and tissues, in this case the cristae form a three-dimensional network of interconnected lamellae. Basically, the three-dimensional structure of ice-embedded mitochondria from this species is consistent with previous descriptions of mitochondria prepared by chemical fixation and resin embedding. Nonetheless, ice-embedded mitochondria display some important differences: the outer surface of the mitochondria was found to be rather smooth, the intermembrane space was constant in width, and distinct contact sites between the membranes were clearly revealed. Furthermore ATP synthase particles on the outer surface of an "inside-out vesicle" were visible in 3-D reconstructions. Thus, cryo-electron tomography can provide detailed insights into these organelles with minimal perturbations of the physiological state. This indicates that it is a realistic goal to achieve "molecular resolution" with rather large biological specimens in the near future, ultimately allowing the identification and localization of macromolecules in their cellular context.
Publication
Journal: Reproduction, Fertility and Development
September/5/1996
Abstract
New research on the cooling and cryopreservation of mammalian spermatozoa is reviewed in the context of the older literature. Cryoinjury to a variety of cell organelles is regarded as being due to the two major stresses of cryopreservation, i.e., the change in temperature, and the formation and dissolution of ice and its consequences. Since the cryopreservation process involves departure of the cells from and return to body temperature, both cold shock and warm shock are included as potential stresses to be considered, as well as the stages involving cooling below the freezing point of the medium. The causes of cryoinjury are reconsidered and new concepts concerning the influence of osmotic stress are presented. Heterogeneity of the sperm population is discussed in the context of the success with which spermatozoa can be cryopreserved between and within ejaculates and individuals. The functional state of frozen and thawed spermatozoa is examined on the basis of published results of structural and functional tests of sperm competence. The hypothesis is advanced that cryopreserved mammalian spermatozoa are in a state resembling capacitation, which accounts for their relatively reduced longevity and their readiness to undergo egg penetration without incubation. The importance of this to the utilization of cryopreserved spermatozoa is examined, and proposals are made for new avenues of research to overcome these problems.
Authors
Publication
Journal: International Journal of Food Microbiology
October/14/1996
Abstract
Aeromonas spp. are Gram-negative rods of the family Vibrionaceae. They are normal water inhabitants and are part of the regular flora of poiquilotherm and homeotherm animals. They can be isolated from many foodstuffs (green vegetables, raw milk, ice cream, meat and seafood). Mesophilic Aeromonas spp. have been classified following the AeroKey II system (Altwegg et al., 1990; Carnahan et al., 1991). The major human diseases caused by Aeromonas spp. can be classified in two major groups: septicemia (mainly by strains of A. veronii subsp. sobria and A. hydrophila), and gastroenteritis (any mesophilic Aeromonas spp. but principally A. hydrophila and A. veronii). Most epidemiological studies have shown Aeromonas spp. in stools to be more often associated with diarrhea than with the carrier state; an association with the consumption of untreated water was also conspicuous. Acute self-limited diarrhea is more frequent in young children, in older patients chronic enterocolitis may also be observed. Fever, vomiting, and fecal leukocytes or erythrocytes (colitis) may be present (Janda, 1991). The main putative virulence factors are: exotoxins, endotoxin (LPS), presence of S-layers, fimbriae or adhesins and the capacity to form capsules.
Publication
Journal: Nature
May/13/2002
Abstract
Amino acids are the essential molecular components of living organisms on Earth, but the proposed mechanisms for their spontaneous generation have been unable to account for their presence in Earth's early history. The delivery of extraterrestrial organic compounds has been proposed as an alternative to generation on Earth, and some amino acids have been found in several meteorites. Here we report the detection of amino acids in the room-temperature residue of an interstellar ice analogue that was ultraviolet-irradiated in a high vacuum at 12 K. We identified 16 amino acids; the chiral ones showed enantiomeric separation. Some of the identified amino acids are also found in meteorites. Our results demonstrate that the spontaneous generation of amino acids in the interstellar medium is possible, supporting the suggestion that prebiotic molecules could have been delivered to the early Earth by cometary dust, meteorites or interplanetary dust particles.
Publication
Journal: Current Opinion in Biotechnology
January/7/2003
Abstract
Aerial plant surfaces harbor large numbers of microbes, some of which are deleterious to plants whereas others are benign or beneficial. Commercial formulations of bacteria antagonistic to plant pathogenic microbes and ice nucleation active bacteria have been utilized as an environmentally safe method to manage plant disease and to prevent frost damage. Molecular genetic tools, microscopic examination and whole-cell bacterial biosensors have provided extensive information on these microbes, their complex associations and their habitat. The aerial habitat influenced by plants, termed the phyllosphere, is particularly amenable to studies of microbial ecology and the information gained should lead to more effective means of plant protection.
Publication
Journal: Journal of Magnetic Resonance Imaging
February/1/2012
Abstract
OBJECTIVE
To present the use of a quality control ice-water phantom for diffusion-weighted magnetic resonance imaging (DW-MRI). DW-MRI has emerged as an important cancer imaging biomarker candidate for diagnosis and early treatment response assessment. Validating imaging biomarkers through multicenter trials requires calibration and performance testing across sites.
METHODS
The phantom consisted of a center tube filled with distilled water surrounded by ice water. Following preparation of the phantom, ≈30 minutes was allowed to reach thermal equilibrium. DW-MRI data were collected at seven institutions, 20 MRI scanners from three vendors, and two field strengths (1.5 and 3T). The phantom was also scanned on a single system on 16 different days over a 25-day period. All data were transferred to a central processing site at the University of Michigan for analysis.
RESULTS
Results revealed that the variation of measured apparent diffusion coefficient (ADC) values between all systems tested was ±5%, indicating excellent agreement between systems. Reproducibility of a single system over a 25-day period was also found to be within ±5% ADC values. Overall, the use of an ice-water phantom for assessment of ADC was found to be a reasonable candidate for use in multicenter trials.
CONCLUSIONS
The ice-water phantom described here is a practical and universal approach to validate the accuracy of ADC measurements with ever changing MRI sequence and hardware design and can be readily implemented in multicenter clinical trial designs.
Publication
Journal: Trends in Microbiology
November/3/2004
Abstract
As do many temperate bacteriophages, integrating conjugative elements (ICEs) recruit the SOS DNA damage response to mobilize themselves from the bacterial chromosome and infect other cells. This transfers resistance to multiple antibiotics. Several commonly used antibiotics induce the SOS response, potentially hastening genetic change and the evolution to resistance of pathogenic populations. The use of such antibiotics should be reconsidered.
Publication
Journal: Journal of Biological Chemistry
October/9/1996
Abstract
Previous studies indicate that activation of c-Jun kinase (JNK) is necessary for apoptosis of trophic factor-deprived PC12 cells and that death in this system is suppressed by multiple agents, including BCL2, inhibitors of the interleukin-1-converting enzyme (ICE) family of proteases, blockers of transcription, and a variety of small molecules with differing modes of action. Here, we determine the order in which these agents block apoptosis relative to JNK activation. Overexpression of BCL2 promotes PC12 cell survival and blocks JNK activation caused by trophic factor withdrawal. Similarly, the survival-promoting agents aurintricarboxylic acid, N-acetylcysteine, the nitric oxide generator diethylenetriamine nitric oxide, 8-bromo-cGMP, and 8-(4-chlorophenylthio)-cAMP act upstream to inhibit JNK activation. In contrast, zVAD-fluoromethylketone (a permeant ICE family inhibitor), actinomycin D, and the G1/S cell cycle inhibitor deferoxamine, all promote survival after trophic factor withdrawal, but do not affect JNK activation. These findings are consistent with the presence of an ordered cell death pathway triggered by trophic factor deprivation in which 1) BCL2 and a number of survival-promoting agents act upstream of JNK, 2) ICE family protease actions, regulated genes required for cell death, and certain cell cycle blockers lie either downstream of JNK or on independent pathways required for apoptotic death.
Publication
Journal: Journal of Cell Biology
November/19/1997
Abstract
Many cells (e.g., epithelial cells) require attachment to the extracellular matrix (ECM) to survive, a phenomenon known as anchorage-dependent cell survival. Disruption of the cell-ECM interactions mediated by the integrin receptors results in apoptosis. Focal adhesion kinase (FAK), a 125-kD protein tyrosine kinase activated by integrin engagement, appears to be involved in mediating cell attachment and survival. Proline-rich tyrosine kinase 2 (PYK2), also known as cellular adhesion kinase beta (CAKbeta) and related adhesion focal tyrosine kinase, is a second member of the FAK subfamily and is activated by an increase in intracellular calcium levels, or treatment with TNFalpha and UV light. However, the function of PYK2 remains largely unknown. In this study, we show that over-expression of PYK2, but not FAK, in rat and mouse fibroblasts leads to apoptotic cell death. Using a series of deletion mutants and chimeric fusion proteins of PYK2/FAK, we determined that the NH2-terminal domain and tyrosine kinase activity of PYK2 were required for the efficient induction of apoptosis. Furthermore, the apoptosis mediated by PYK2 could be suppressed by over-expressing catalytically active v-Src, c-Src, phosphatidylinositol-3-kinase, or Akt/protein kinase B. In addition, it could also be suppressed by overexpressing an ICE or ICE-like proteinase inhibitor, crmA, but not Bcl2. Collectively, our results suggest that PYK2 and FAK, albeit highly homologous in primary structure, appear to have different functions; FAK is required for cell survival, whereas PYK2 induces apoptosis in fibroblasts.
Publication
Journal: Chemistry & biology
January/13/1998
Abstract
The transmissible spongiform encephalopathies pose an increasing problem for animal, and perhaps human, health. The infectious agent seems to lack a nucleic acid component, posing the question of how it can reproduce. A model of reproduction by nucleated polymerization suggests a number of novel approaches to the problem.
Publication
Journal: Blood
April/8/1998
Abstract
Interleukin-18 (IL-18) is a costimulatory factor for interferongamma (IFNgamma) production. Processing of pro-IL-18 by IL-1beta-converting enzyme (ICE) leads to the release of bioactive IL-18. Compared with wild-type (WT) mice, splenocytes from ICE-deficient mice produced low IFNgamma after lipopolysaccharide (LPS) or zymosan (50% and 80% reduction). In contrast, IFNgamma production was unimpaired in ICE-deficient mice using Concanavalin A (Con A). Comparable results were obtained when endogenous IL-18 was blocked with a neutralizing antibody. LPS-induced IFNgamma was also reduced by an ICE inhibitor. Exogenous IL-18 augmented zymosan-induced IFNgamma production in WT mice. In ICE-deficient cells, IFNgamma production was only partially restored by IL-18. The reduced levels of IFNgamma in ICE-deficient mice were not due to a lack of IL-12, because zymosan induced IL-12 equally in WT and in ICE-deficient mice. IFNgamma is an important regulator of cell proliferation. In accordance, splenocytes from ICE-deficient mice proliferated more when stimulated with LPS, but not with Con A. Furthermore, in ovalbumin-sensitized ICE-deficient mice, proliferation of lymph node cells in response to the specific antigen was not altered. Exogenous IFNgamma inhibited, whereas blockade of endogenous IFNgamma or IL-18 increased, LPS induced splenocyte proliferation both in WT and in ICE-deficient mice. Our results show that IL-18 is an IL-12-independent regulator of IFNgamma production and of cell proliferation induced by microbial stimuli. However, ICE-dependent processing of IL-18 is not needed for response to mitogens or antigens.
Publication
Journal: Clinical and diagnostic laboratory immunology
December/3/2001
Abstract
Cell-mediated immunity appears to be critical for the prevention and control of varicella-zoster virus (VZV) infection and complications arising from zoster. Current assays of VZV-specific cell-mediated immunity are cumbersome or lack sensitivity. We have developed a gamma interferon ELISPOT assay that provides a direct measure of the number of T cells secreting a cytokine following stimulation with antigen. This assay is extremely sensitive and specific, with the ability to detect gamma interferon spot-forming cells (SFC) in the range of 10 to 1,000 SFC per million peripheral blood mononuclear cells (PBMCs). This assay has been validated by demonstrating the following: (i) the response detected is mediated almost entirely by CD4+ T cells, (ii) ELISPOT responses from fresh-frozen PBMCs are equivalent to those from freshly isolated cells, (iii) frozen PBMCs can be shipped on dry ice for up to 48 h without loss of activity, (iv) frozen PBMC samples can be stored in liquid nitrogen over long periods (>22 months) without any significant change in response, and (v) the numbers of ELISPOTs counted using a computer-based imaging system are equivalent to those counted by humans but have lower variability. The ability to use frozen cells is facilitated by the use of a recombinant nuclease (Benzonase) that can prevent cell clumping when samples are thawed. Frozen PBMC samples can be cycled through multiple changes in storage between liquid nitrogen and dry ice without any change in response being detected. This facilitates collection of samples at one site and testing performed at a remote location. This VZV ELISPOT assay provides a new versatile tool for monitoring cellular immune responses either during a herpes zoster disease outbreak or following vaccination.
Publication
Journal: Journal of Biological Chemistry
March/20/1989
Abstract
Incubation of the reconstituted H+-ATPase from chromaffin granules on ice resulted in inactivation of the proton-pumping and ATPase activities of the enzyme. Inactivation was dependent on the presence of Mg2+, Cl-, and ATP during the incubation at low temperature. Approximately 1 mM ATP, 1 mM Mg2+, and 200 mM Cl- were required for maximum inactivation. Incubation for about 10 min on ice was required to achieve 50% inactivation. A much smaller decline in activity was observed when the enzyme was incubated at room temperature with the same chemicals. Inactivation in the cold resulted in the release of five polypeptides from the membrane with apparent molecular masses of 72, 57, 41, 34, and 33 kDa on sodium dodecyl sulfate gels. Three of the polypeptides of 72, 57, and 34 kDa were identified as subunits of vacuolar H+-ATPases by antibody cross-reactivity. Similar results were obtained with several other vacuolar H+-ATPases including those from plant sources. It was concluded that the catalytic sector of the enzyme is released from the H+-ATPase complex by cold treatment, resulting in inactivation of the enzyme.
Publication
Journal: Molecular Microbiology
June/27/2004
Abstract
Diversification of bacterial species and pathotypes is largely caused by horizontal transfer of diverse DNA elements such as plasmids, phages and genomic islands (e.g. pathogenicity islands, PAIs). A PAI called high-pathogenicity island (HPI) carrying genes involved in siderophore-mediated iron acquisition (yersiniabactin system) has previously been identified in Yersinia pestis, Y. pseudotuberculosis and Y. enterocolitica IB strains, and has been characterized as an essential virulence factor in these species. Strikingly, an orthologous HPI is a widely distributed virulence determinant among Escherichia coli and other Enterobacteriaceae which cause extraintestinal infections. Here we report on the HPI of E. coli strain ECOR31 which is distinct from all other HPIs described to date because the ECOR31 HPI comprises an additional 35 kb fragment at the right border compared to the HPI of other E. coli and Yersinia species. This part encodes for both a functional mating pair formation system and a DNA-processing region related to plasmid CloDF13 of Enterobacter cloacae. Upon induction of the P4-like integrase, the entire HPI of ECOR31 is precisely excised and circularised. The HPI of ECOR31 presented here resembles integrative and conjugative elements termed ICE. It may represent the progenitor of the HPI found in Y. pestis and E. coli, revealing a missing link in the horizontal transfer of an element that contributes to microbial pathogenicity upon acquisition.
Publication
Journal: Nature
May/13/2002
Abstract
The delivery of extraterrestrial organic molecules to Earth by meteorites may have been important for the origin and early evolution of life. Indigenous amino acids have been found in meteorites-over 70 in the Murchison meteorite alone. Although it has been generally accepted that the meteoritic amino acids formed in liquid water on a parent body, the water in the Murchison meteorite is depleted in deuterium relative to the indigenous organic acids. Moreover, the meteoritical evidence for an excess of laevo-rotatory amino acids is hard to understand in the context of liquid-water reactions on meteorite parent bodies. Here we report a laboratory demonstration that glycine, alanine and serine naturally form from ultraviolet photolysis of the analogues of icy interstellar grains. Such amino acids would naturally have a deuterium excess similar to that seen in interstellar molecular clouds, and the formation process could also result in enantiomeric excesses if the incident radiation is circularly polarized. These results suggest that at least some meteoritic amino acids are the result of interstellar photochemistry, rather than formation in liquid water on an early Solar System body.
Publication
Journal: ChemPhysChem
July/11/2007
Abstract
In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.
Publication
Journal: Journal of Evolutionary Biology
September/14/2006
Abstract
Currently many attempts are made to reconstruct the colonization history of plant species after the last ice age. A surprising finding is that during the colonization phase genetic diversity did not decrease as much as expected. In this paper we examine whether long distance seed dispersal events could play a role in the unexpected maintenance of genetic diversity during range expansion. This study is based on simulations carried out with a maternally inherited haploid locus using a cellular automaton. The simulations reveal a close relationship between the frequency of long distance seed dispersal events and the amount of genetic diversity preserved during colonization. In particular, when the colonized region is narrow, a complete loss of genetic diversity results from the occurrence of very rare long distance dispersal (LDD) events. We call this phenomenon the 'embolism effect'. However, slightly higher rates of LDD events reverse this effect, up to the point that diversity is better preserved than in a pure diffusion model. This phenomenon is linked to the reorganization of the genetic structure during colonization and is called the 'reshuffling effect'.
Publication
Journal: Acta crystallographica. Section D, Biological crystallography
September/14/2005
Abstract
Flash-cooling of protein crystals is the best known method to effectively mitigate radiation damage in macromolecular crystallography. To prevent physical damage to crystals upon cooling, suitable cryoprotectants must usually be found, a process that is time-consuming and in some cases unsuccessful. A method is described to cool protein crystals in high-pressure helium gas without the need for penetrative cryoprotectants. The method involves mounting protein crystals from the native mother liquor in a cryoloop with a droplet of oil, pressurizing the crystal to 200 MPa in He gas, cooling the crystal under pressure and then releasing the pressure. The crystal is then removed from the apparatus under liquid nitrogen and handled thereafter like a normal cryocooled crystal. Results are presented from three representative proteins. Dramatic improvement in diffraction quality in terms of resolution and mosaicity was observed in all cases. A mechanism for the pressure cooling is proposed involving high-density amorphous (HDA) ice which is produced at high pressure and is metastable at room pressure and 110 K.
Publication
Journal: Journal of Biological Chemistry
April/13/1997
Abstract
The pivotal discovery that Fas-associated death domain protein (FADD) interleukin-1beta-converting enzyme (FLICE)/MACH was recruited to the CD95 signaling complex by virtue of its ability to bind the adapter molecule FADD established that this protease has a role in initiating the death pathway (Boldin, M. P., Goncharov, T. M. , Goltsev, Y. V., and Wallach, D. (1996) Cell 85, 803-815; Muzio, M., Chinnaiyan, A. M., Kischkel, K. C., O'Rourke, K., Shevchenko, A., Ni, J., Scaffidi, C., Bretz, J. D., Zhang, M., Gentz, R., Mann, M., Krammer, P. H., Peter, M. E., and Dixit, V. M. (1996) Cell 85, 817-827). In this report, we describe the cloning and characterization of a new member of the caspase family, a homologue of FLICE/MACH, and Mch4. Since the overall architecture and function of this molecule is similar to that of FLICE, it has been designated FLICE2. Importantly, the carboxyl-terminal half of the small catalytic subunit that includes amino acids predicted to be involved in substrate binding is distinct. We show that the pro-domain of FLICE2 encodes a functional death effector domain that binds to the corresponding domain in the adapter molecule FADD. Consistent with this finding, FLICE2 is recruited to both the CD95 and p55 tumor necrosis factor receptor signaling complexes in a FADD-dependent manner. A functional role for FLICE2 is suggested by the finding that an active site mutant of FLICE2 inhibits CD95 and tumor necrosis factor receptor-mediated apoptosis. FLICE2 is therefore involved in CD95 and p55 signal transduction.
Publication
Journal: Plant Physiology
June/28/2010
Abstract
Heterogeneous ice nuclei are necessary, and the common epiphytic ice nucleation active (INA) bacteria Pseudomonas syringae van Hall and Erwinia herbicola (Löhnis) Dye are sufficient to incite frost injury to sensitive plants at -5 degrees C. The ice nucleation activity of the bacteria occurs at the same temperatures at which frost injury to sensitive plants occurs in nature. Bacterial ice nucleation on leaves can be detected at about -2 degrees C, whereas the leaves themselves, i.e. without INA bacteria, contain nuclei active only at much lower temperatures. The temperature at which injury to plants occurs is predictable on the basis of the ice nucleation activity of leaf discs, which in turn depends on the number and ice nucleation activity of their resident bacteria. Bacterial isolates which are able to incite injury to corn at -5 degrees C are always active as ice nuclei at -5 degrees C. INA bacteria incited frost injury to all of the species of sensitive plants tested.
Publication
Journal: Microbial Ecology
July/29/2002
Abstract
Heterotrophic bacteria in sea <em>ice</em> play a key role in carbon cycling, but little is known about the predominant players at the phylogenetic level. In a study of both algal bands and clear <em>ice</em> habitats within summertime Arctic pack <em>ice</em> from the Chukchi Sea, we determined the abundance of total bacteria and actively respiring cells in melted <em>ice</em> samples using epifluorescence microscopy and the stains 4', 6'-diamidino-2-phenylindole 2HCl (DAPI) and 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), respectively. Organic-rich and -poor culturing media were used to determine culturable members by plating (at 0 degrees C and 5 degrees C) and most-probable-number (MPN) analyses (at -1 degrees C). Total bacterial counts ranged from 5.44 x 10(4) ml(-1) in clear <em>ice</em> to 2.41 x 10(6) ml(-1) in algal-band <em>ice</em> samples, with 2-27% metabolically active by CTC stain. Plating and MPN results revealed a high degree of culturability in both types of media, but greater success in oligotrophic media (to 62% of total abundance) and from clear <em>ice</em> samples. The bacterial enumeration anomaly, commonly held to mean <or= 0.01% cultured, was not demonstrated in any of our samples. Denaturing gradient gel electrophoresis was used to check the purity of 44 isolates and select representatives for subsequent sequencing. Phylogenetic analyses based on 16S rRNA sequences indicated close relationships exclusively to known marine psychrophiles within two bacterial divisions, Proteobacteria (in the genera Alteromonas, Colwellia, Glaciecola, Octadecabacter, Pseudoaltermonas and Shewanella) and Cytophaga-Flexibacter-Bacteroides (Cytophaga, Flavobacterium, Gelidibacter and Polaribacter). All cultures from the clear <em>ice</em> sample with highest (62%) culturability were closely related to each other or to psychrophilic Cytophaga-Flexibacter-Bacteroides (94.9-99.6% sequence similarities). Overall, these findings suggest limited, heterotrophic bacterial diversity at cold temperatures and may provide insight into the recent evolution of psychrophilic bacteria.
Publication
Journal: Structure
February/10/1997
Abstract
BACKGROUND
Antifreeze proteins are found in certain fish inhabiting polar sea water. These proteins depress the freezing points of blood and body fluids below that of the surrounding sea water by binding to and inhibiting the growth of seed ice crystals. The proteins are believed to bind irreversibly to growing ice crystals in such a way as to change the curvature of the ice-water interface, leading to freezing point depression, but the mechanism of high-affinity ice binding is not yet fully understood.
RESULTS
The solution structure of the type III antifreeze protein was determined by multidimensional NMR spectroscopy. Twenty-two structures converged and display a root mean square difference from the mean of 0.26 A for backbone atoms and 0.62 A for all non-hydrogen atoms. The protein exhibits a compact fold with a relatively large hydrophobic core, several short and irregular beta sheets and one helical turn. The ice-binding site, which encompasses parts of the C-terminal sheet and a loop, is planar and relatively nonpolar. The site is further characterized by the low solvent accessibilities and the specific spatial arrangement of the polar side-chain atoms of the putative ice-binding residues Gln9, Asn14, Thr15, Thr18 and Gln44.
CONCLUSIONS
In agreement with the adsorption-inhibition mechanism of action, interatomic distances between active polar protein residues match the spacing of water molecules in the prism planes (¿10&1macr;0¿) of the hexagonal ice crystal. The particular side-chain conformations, however, limit the number and strength of possible proten-ice hydrogen bonds. This suggests that other entropic and enthalpic contributions, such as those arising from hydrophobic groups, could play a role in the high-affinity protein-ice adsorption.
Publication
Journal: Journal of Clinical Oncology
March/27/2002
Abstract
OBJECTIVE
To investigate the efficacy of chemotherapy followed by low-dose involved-field radiotherapy for the treatment of intracranial germ cell tumors (GCTs).
METHODS
Thirty-three patients with GCTs, including 16 pure germinomas, 11 human chorionic gonadotropin-beta (HCG-beta)-secreting germinomas, three mixed GCTs composed of immature teratomas plus germinomas (IMT/G), and three highly malignant mixed GCTs, were treated. Etoposide and cisplatin (EP) were used for the treatment of solitary pure germinomas, and ifosfamide, cisplatin, and etoposide (ICE) were used for the treatment of other GCTs. The dose schedule was 24 Gy for germinomas and 40 to 54 Gy for other GCTs. An involved-field set-up was used except for highly malignant GCTs, in which craniospinal irradiation was used. The median follow-up was 58 months (range, 18 to 102 months).
RESULTS
Disease-related, overall, and relapse-free survival rates at 5 years were 100%, 93%, and 69% for all patients, 100%, 100%, and 86% for patients with pure germinomas, and 100%, 75%, and 44% for patients with HCG-beta-secreting germinomas, respectively. All six patients with nongerminomatous GCTs were alive at the last follow-up. All eight relapses (one pure germinoma, five HCG-beta-secreting germinomas, and two IMT/G), except one in a course of salvage treatment, were salvaged and free of disease at the last follow-up. No decline was observed in the full-scale, verbal, or performance intelligence quotient at 12 to 51 months after the treatment in 11 patients.
CONCLUSIONS
Our results support an excellent prognosis after EP and ICE regimens followed by radiotherapy. Dose and volume can be reduced to 24 Gy in 12 fractions and involve a field set-up after EP chemotherapy for the treatment of pure germinomas.
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