Analysis of the Soehner-Dmochowski strain of Moloney murine sarcoma virus

The Soehner-Dmochowski strain of murine sarcoma virus (MuSV-SD) was derived from a bone tumor of a New Zealand Black (NZB) rat infected with the Moloney strain of MuSV, which carries the gene encoding the v-mos protein. Serial passage of cell-free tumor extracts both decreased the latent period and resulted in osteosarcomas. Cells from a late passage tumor were established in culture, cell-free extracts frozen, and later inoculated into newborn NZB rats. One of the resulting bone tumors was established in culture and clonal cell lines derived, of which S4 was selected for the present study. The objectives of the study were two-fold: an examination of the genetic organization of MuSV-SD, and an examination of the biochemical characteristics of the viral proteins, since this is an acutely transforming virus which may yield insights into the mechanism of transformation caused by the v-mos protein. Blot hybridization of digested S4 genomic DNA reveals three candidate MuSV-SD integrated viral DNAs. The largest of these, MuSV-SD-6.5, was cloned from an S4 cosmid library, and the complete MuSV-SD-mos sequence was determined. The predicted amino acid sequence of the v-mos protein was compared to that of MuSV-124 and Ht-1, which show a 96.5% and 97.1% similarity, respectively. To characterize the MuSV-SD-mos protein further, immunochemical assays were performed using anti-mos antisera. The immunoblot analysis and immunoprecipitation assays demonstrated that similar levels of the v-mos protein were present in cells chronically infected with either MuSV-SD or MuSV-124; however, the immune complex kinase assay revealed greatly reduced in vitro serine kinase activity of the MuSV-SD-mos protein compared to that of MuSV-124. Sequence analysis demonstrated that the serine at amino acid residue 358 of the MuSV-SD-mos protein, like that of MuSV-Ht-1, had been mutated to a glycine. Mutations of this serine residue have been shown to affect the detectable in vitro kinase activity, however, v-mos proteins containing this mutation still retain transforming properties. Therefore, although the characteristic in vitro kinase activity of the MuSV-SD-mos protein has not been demonstrated, it is clear that this virus is a potent transforming agent. ^

Characterization of the beta-lactamase gene from {\it Enterococcus faecalis\/} strain HH22

The plasmid-encoded, constitutively produced $\beta$-lactamase gene from Enterococcus faecalis strain HH22 was genetically characterized. A restriction endonuclease map of the 5.1 kb EcoRI fragment encoding the enterococcal $\beta$-lactamase was prepared and compared with the restriction map of a cloned staphylococcal $\beta$-lactamase gene (from the naturally-occurring staphylococcal $\beta$-lactamase plasmid pI258). Comparison and hybridization studies showed that there were identical restriction sites in the region of the $\beta$-lactamase structural gene but not in the region surrounding this gene. Also the enterococcal $\beta$-lactamase plasmid did not encode resistance to mercury or cadmium which is encoded by the small, transducible staphylococcal $\beta$-lactamase plasmids. The nucleotide sequence of the enterococcal gene was shown to be identical to the published sequences of three of four staphylococcal type A $\beta$-lactamase genes; more differences were seen with the genes for staphylococcal type C and D enzymes. One hundred-forty nucleotides upstream of the $\beta$-lactamase start codon were also determined for the inducible staphylococcal $\beta$-lactamase gene on pI258; this sequence was identical to that of the constitutively expressed enterococcal gene indicating that the changes resulting in constitutive expression are not due to changes in the promoter or operator region. Moreover, complementation studies indicated that production of the enterococcal enzyme could be repressed. The gene for the enterococcal $\beta$-lactamase and an inducible staphylococcal $\beta$-lactamase were each cloned into a shuttle vector and then transformed into enterococcal and staphylococcal recipients. The major difference between the two host backgrounds was that more enzyme was produced by the staphylococcal host, regardless of the source of the gene but no qualitative difference was seen between the two genera. Also a difference in the level of resistance to ampicillin was seen between the two backgrounds with the cloned enzymes by MIC and time-kill studies. The location of the enzyme was found to be host dependent since each cloned gene generated extracellular (free) enzyme in the staphylococcus and cell bound enzyme in the enterococcus. Based on the identity of the enterococcal $\beta$-lactamase and several staphylococcal $\beta$-lactamases, these data suggest recent spread of $\beta$-lactamase to enterococci and also suggest loss of a functional repressor. ^

The physical map of {\it Escherichia coli\/} K-12 strain MG1655: Construction, comparison with other strains and implications for mechanisms controlling oligonucleotide frequency

Complete NotI, SfiI, XbaI and BlnI cleavage maps of Escherichia coli K-12 strain MG1655 were constructed. Techniques used included: CHEF pulsed field gel electrophoresis; transposon mutagenesis; fragment hybridization to the ordered $\lambda$ library of Kohara et al.; fragment and cosmid hybridization to Southern blots; correlation of fragments and cleavage sites with EcoMap, a sequence-modified version of the genomic restriction map of Kohara et al.; and correlation of cleavage sites with DNA sequence databases. In all, 105 restriction sites were mapped and correlated with the EcoMap coordinate system.^ NotI, SfiI, XbaI and BlnI restriction patterns of five commonly used E. coli K-12 strains were compared to those of MG1655. The variability between strains, some of which are separated by numerous steps of mutagenic treatment, is readily detectable by pulsed-field gel electrophoresis. A model is presented to account for the difference between the strains on the basis of simple insertions, deletions, and in one case an inversion. Insertions and deletions ranged in size from 1 kb to 86 kb. Several of the larger features have previously been characterized and some of the smaller rearrangements can potentially account for previously reported genetic features of these strains.^ Some aspects of the frequency and distribution of NotI, SfiI, XbaI and BlnI cleavage sites were analyzed using a method based on Markov chain theory. Overlaps of Dam and Dcm methylase sites with XbaI and SfiI cleavage sites were examined. The one XbaI-Dam overlap in the database is in accord with the expected frequency of this overlap. The occurrence of certain types of SfiI-Dcm overlaps are overrepresented. Of the four subtypes of SfiI-Dcm overlap, only one has a partial inhibitory effect on the activity of SfiI. Recognition sites for all four enzymes are rarer than expected based on oligonucleotide frequency data, with this effect being much stronger for XbaI and BlnI than for NotI and SfiI. The latter two enzyme sites are rare mainly due to apparent negative selection against GGCC (both) and CGGCCG (NotI). The former two enzyme sites are rare mainly due to effects of the VSP repair system on certain di-tri- and tetranucleotides, most notably CTAG. Models are proposed to explain several of the anomalies of oligonucleotide distribution in E. coli, and the biological significance of the systems that produce these anomalies is discussed. ^

Derived Bedrock Elevations, Strain Rates and Stresses from Measured Surface Elevations and Velocities - Jakobshavns-Isbrae, Greenland

Jakobshavns Isbrae (69 degrees 10'N, 49 degrees 5'W) drains about 6.5% of the Greenland ice sheet and is the fastest ice stream known. The Jakobshavns Isbrae basin of about 10 000 km(2) was mapped photogrammetrically from four sets of aerial photography, two taken in July 1985 and two in July 1986. Positions and elevations of several hundred natural features on the ice surface were determined for each epoch by photogrammetric block-aerial triangulation, and surface velocity vectors were computed from the positions. The two flights in 1985 yielded the best results and provided most common points (716) for velocity determinations and are therefore used in the modeling studies. The data from these irregularly spaced points were used to calculate ice elevations and velocity vectors at uniformly spaced grid paints 3 km apart by interpolation. The field of surface strain rates was then calculated from these gridded data and used to compute the field of surface deviatoric stresses, using the flow law of ice, for rectilinear coordinates, X, Y pointing eastward and northward. and curvilinear coordinates, L, T pointing longitudinally and transversely to the changing ice-flow direction. Ice-surface elevations and slopes were then used to calculate ice thicknesses and the fraction of the ice velocity due to basal sliding. Our calculated ice thicknesses are in fair agreement with an ice-thickness map based on seismic sounding and supplied to us by K. Echelmeyer. Ice thicknesses were subtracted from measured ice-surface elevations to map bed topography. Our calculation shows that basal sliding is significant only in the 10-15 km before Jakobshavns Isbrae becomes afloat in Jakobshavns IsfJord.

Metamorphism, Transient Mid-Crustal Rheology, Strain Localization and the Exhumation of High-Grade Metamorphic Rocks

We present a series of three-dimensional numerical models investigating the effects of metamorphic strengthening and weakening on the geodynamic evolution of convergent orogens that are constrained by observations from an exposed mid-crustal section in the New England Appalachians. The natural mid-crustal section records evidence for spatially and temporally variable mid-crustal strength as a function of metamorphic grade during prograde polymetamorphism. Our models address changes in strain rate partitioning and topographic uplift as a function of strengthening/weakening in the middle crust, as well as the resultant changes in deformation kinematics and potential exhumation patterns of high-grade metamorphic rock. Results suggest that strengthening leads to strain rate partitioning around the zone and suppressed topographic uplift rates whereas weakening leads to strain rate partitioning into the zone and enhanced topographic uplift rates. Deformation kinematics recorded in the orogen are also affected by strengthening/weakening, with complete reversals in shear sense occurring as a function of strengthening/weakening without changes in plate boundary kinematics.

Relating Crevassing to Non-Linear Strain in the Floating Part of Jakobshavn Isbrae, West Greenland

Jakobshavn Isbrae is a major ice stream that drains the west-central Greenland ice sheet and becomes afloat in Jakobshavn Isfiord (69degreesN, 49degreesW), where it has maintained the world's fastest-known sustained velocity and calving rate (7 km a(-1)) for at least four decades. The floating portion is approximately 12 km long and 6 km wide. Surface elevations and motion vectors were determined photogrammetrically for about 500 crevasses on the floating ice, and adjacent grounded ice, using aerial photographs obtained 2 weeks apart in July 1985. Surface strain rates were computed from a mesh of 399 quadrilateral elements having velocity measurements at each corner. It is shown that heavy crevassing of floating ice invalidates the assumptions of linear strain theory that (i) surface strain in the floating ice is homogeneous in both space and time, (ii) the squares and products of strain components are nil, and (iii) first- and second-order rotation components are small compared to strain components. Therefore, strain rates and rotation rates were also computed using non-linear strain theory. The percentage difference between computed linear and non-linear second invariants of strain rate per element were greatest (mostly in the range 40-70%) where crevassing is greatest. Isopleths of strain rate parallel and transverse to flow and elevation isopleths relate crevassing to known and inferred pinning points.

Genome Sequences of Two Klebsiella pneumoniae Isolates from Different Geographical Regions, Argentina (Strain JHCK1) and the United States (Strain VA360)

We report the sequences of two Klebsiella pneumoniae clinical isolates, strains JHCK1 and VA360, from a newborn with meningitis in Buenos Aires, Argentina, and from a tertiary care medical center in Cleveland, OH, respectively. Both isolates contain one chromosome and at least five plasmids; isolate VA360 contains the Klebsiella pneumoniae carbapenemase (KPC) gene

Microfabric memory of vein quartz for strain localization in detachment faults: A case study on the Simplon fault zone

This manuscript deals with the adaptation of quartz-microfabrics to changing physical deformation conditions, and discusses their preservation potential during subsequent retrograde deformation. Using microstructural analysis, a sequence of recrystallization processes in quartz, ranging from Grain-Boundary Migration Recrystallization (GBM) over Subgrain-Rotation Recrystallization (SGR) to Bulging Nucleation (BLG) is detected for the Simplon fault zone (SFZ) from the low strain rim towards the internal high strain part of the large-scale shear zone. Based on: (i) the retrograde cooling path; (ii) estimates of deformation temperatures; and (iii) spatial variation of dynamic recrystallization processes and different microstructural characteristics, continuous strain localization with decreasing temperature is inferred. In contrast to the recrystallization microstructures, crystallographic preferred orientations (CPO) have a longer memory. CPO patterns indicative of prism and rhomb glide systems in mylonitic quartz veins, overprinted at low temperatures (�400 �C), suggest inheritance of a high-temperature deformation. In this way, microstructural, textural and geochemical analyses provide information for several million years of the deformation history. The reasons for such incomplete resetting of the rock texture is that strain localization is caused by change in effective viscosity contrasts related to temporal large- and small-scale temperature changes during the evolution of such a long-lived shear zone. The spatially resolved, quantitative investigation of quartz microfabrics and associated recrystallization processes therefore provide great potential for an improved understanding of the geodynamics of large-scale shear zones.

Tracking a tuberculosis outbreak over 21 years: strain-specific single nucleotide polymorphism-typing combined with targeted whole genome sequencing.

BACKGROUND  Whole genome sequencing (WGS) is increasingly used in molecular-epidemiological investigations of bacterial pathogens, despite cost- and time-intensive analyses. We combined strain-specific single nucleotide polymorphism (SNP)-typing and targeted WGS to investigate a tuberculosis cluster spanning 21 years in Bern, Switzerland. METHODS  Based on genome sequences of three historical outbreak Mycobacterium tuberculosis isolates, we developed a strain-specific SNP-typing assay to identify further cases. We screened 1,642 patient isolates, and performed WGS on all identified cluster isolates. We extracted SNPs to construct genomic networks. Clinical and social data were retrospectively collected. RESULTS  We identified 68 patients associated with the outbreak strain. Most were diagnosed in 1991-1995, but cases were observed until 2011. Two thirds belonged to the homeless and substance abuser milieu. Targeted WGS revealed 133 variable SNP positions among outbreak isolates. Genomic network analyses suggested a single origin of the outbreak, with subsequent division into three sub-clusters. Isolates from patients with confirmed epidemiological links differed by 0-11 SNPs. CONCLUSIONS  Strain-specific SNP-genotyping allowed rapid and inexpensive identification of M. tuberculosis outbreak isolates in a population-based strain collection. Subsequent targeted WGS provided detailed insights into transmission dynamics. This combined approach could be applied to track bacterial pathogens in real-time and at high resolution.

Compressive strength of elderly vertebrae is reduced by disc degeneration and additional flexion

Computer tomography (CT)-based finite element (FE) models assess vertebral strength better than dual energy X-ray absorptiometry. Osteoporotic vertebrae are usually loaded via degenerated intervertebral discs (IVD) and potentially at higher risk under forward bending, but the influences of the IVD and loading conditions are generally overlooked. Accordingly, magnetic resonance imaging was performed on 14 lumbar discs to generate FE models for the healthiest and most degenerated specimens. Compression, torsion, bending, flexion and extension conducted experimentally were used to calibrate both models. They were combined with CT-based FE models of 12 lumbar vertebral bodies to evaluate the effect of disc degeneration compared to a loading via endplates embedded in a stiff resin, the usual experimental paradigm. Compression and lifting were simulated, load and damage pattern were evaluated at failure. Adding flexion to the compression (lifting) and higher disc degeneration reduces the failure load (8–14%, 5–7%) and increases damage in the vertebrae. Under both loading scenarios, decreasing the disc height slightly increases the failure load; embedding and degenerated IVD provides respectively the highest and lowest failure load. Embedded vertebrae are more brittle, but failure loads induced via IVDs correlate highly with vertebral strength. In conclusion, osteoporotic vertebrae with degenerated IVDs are consistently weaker—especially under lifting, but clinical assessment of their strength is possible via FE analysis without extensive disc modelling, by extrapolating measures from the embedded situation.

International Clostridium difficile animal strain collection and large diversity of animal associated strains

BACKGROUND Clostridium difficile is an important cause of intestinal infections in some animal species and animals might be a reservoir for community associated human infections. Here we describe a collection of animal associated C. difficile strains from 12 countries based on inclusion criteria of one strain (PCR ribotype) per animal species per laboratory. RESULTS Altogether 112 isolates were collected and distributed into 38 PCR ribotypes with agarose based approach and 50 PCR ribotypes with sequencer based approach. Four PCR ribotypes were most prevalent in terms of number of isolates as well as in terms of number of different host species: 078 (14.3% of isolates; 4 hosts), 014/020 (11.6%; 8 hosts); 002 (5.4%; 4 hosts) and 012 (5.4%; 5 hosts). Two animal hosts were best represented; cattle with 31 isolates (20 PCR ribotypes; 7 countries) and pigs with 31 isolates (16 PCR ribotypes; 10 countries). CONCLUSIONS This results show that although PCR ribotype 078 is often reported as the major animal C. difficile type, especially in pigs, the variability of strains in pigs and other animal hosts is substantial. Most common human PCR ribotypes (014/020 and 002) are also among most prevalent animal associated C. difficile strains worldwide. The widespread dissemination of toxigenic C. difficile and the considerable overlap in strain distribution between species furthers concerns about interspecies, including zoonotic, transmission of this critically important pathogen.