Temporal focusing multiphoton microscopy with cross-modality multi-stage 3D U-Net for fast and clear bioimaging

Temporal focusing multiphoton excitation microscopy (TFMPEM) enables fast widefield biotissue imaging with optical sectioning. However, under widefield illumination, the imaging performance is severely degraded by scattering effects, which induce signal crosstalk and a low signal-to-noise ratio in the detection process, particularly when imaging deep layers. Accordingly, the present study proposes a cross-modality learning-based neural network method for performing image registration and restoration. In the proposed method, the point-scanning multiphoton excitation microscopy images are registered to the TFMPEM images by an unsupervised U-Net model based on a global linear affine transformation process and local VoxelMorph registration network. A multi-stage 3D U-Net model with a cross-stage feature fusion mechanism and self-supervised attention module is then used to infer in-vitro fixed TFMPEM volumetric images. The experimental results obtained for in-vitro drosophila mushroom body (MB) images show that the proposed method improves the structure similarity index measures (SSIMs) of the TFMPEM images acquired with a 10-ms exposure time from 0.38 to 0.93 and 0.80 for shallow- and deep-layer images, respectively. A 3D U-Net model, pretrained on in-vitro images, is further trained using a small in-vivo MB image dataset. The transfer learning network improves the SSIMs of in-vivo drosophila MB images captured with a 1-ms exposure time to 0.97 and 0.94 for shallow and deep layers, respectively.

A virally inactivated functional growth factor preparation from human platelet concentrates

BACKGROUND

Human platelet growth factors (HPGF) are essential for tissue regeneration and may replace fetal bovine serum (FBS) in cell therapy. No method for the manufacture of standardized virally inactivated HPGF has been developed yet.

STUDY DESIGN AND METHODS

Platelet concentrates (PC) were subjected to solvent/detergent (S/D) treatment (1% TnBP/1% Triton X-45), oil extraction, hydrophobic interaction chromatography and sterile filtration. Platelet-derived growth factor (PDGF)-AB, -BB and -AA, transforming growth factor-beta1 (TGF-beta1), epidermal growth factor (EGF), insulin-like growth factor-1 (IGF-1) and vascular endothelium growth factor (VEGF) were measured by ELISA. Composition in proteins and lipids was determined, protein profiles were obtained by SDS-PAGE, and TnBP and Triton X-45 were assessed by gas chromatography and high-performance liquid chromatography, respectively. Cell growth promoting activity of HPGF was evaluated by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay using human embryonic kidney (HEK293A) fibroblast and Statens Seruminstitute rabbit corneal (SIRC) epithelial cell lines.

RESULTS

The GF preparation contained a mean of 16.66, 2.04, 1.53, 72.19, 0.33, 48.59 and 0.44 ng/ml of PDGF-AB, -BB, -AA, TGF-beta1, EGF, IGF-1 and VEGF, respectively. The protein profile was typical of platelet releasates and had less than 2 p.p.m. of residual S/D agents. MTS assay of HEK293A and SIRC cultures showed that the GF preparation at 10% and 0.1% (v/v), respectively, could successfully replace 10% FBS for cell proliferation. Cell-stimulating activity of HPGF on HEK293A was over twice that of PC releasates.

CONCLUSION

STANDARDIZED and functional virally inactivated HPGF can be prepared from human PC for possible applications in cell therapy and regenerative medicine.

Phylogenetic and structural analyses of the oxa1 family of protein translocases

Mitochondrial Oxa1p homologs have been shown to function in protein export and membrane insertion in bacteria, mitochondria and chloroplasts, but their mode of action, organismal distribution and evolutionary origins are poorly understood. All sequenced homologs of Oxa1p were retrieved from the databases and multiply aligned. All organisms with a fully sequenced genome possess at least one Oxa1p homolog showing that the family is truly ubiquitous. Most prokaryotes possess just one Oxa1p homolog, but several Gram-positive bacteria and one archaeon possess two, and eukaryotes may have as many as six. Although these proteins vary in length over a 5-fold range, they exhibit a common hydrophobic core region of about 200 residues. Multiple sequence alignments reveal conserved residues and provide the basis for structural and phylogenetic analyses that serve to characterize the Oxa1 family.

Plasmids carrying cloned fragments of RF DNA from the filamentous phage (phi)Lf can be integrated into the host chromosome via site-specific integration and homologous recombination

Different regions of RF DNA from the filamentous bacteriophage phiLf were cloned in Escherichia coli vectors that can not be maintained in Xanthomonas. After introduction into X. campestris pv. campestris 17 (Xc17), most of these constructs were found to integrate into the host chromosome, either by recA-dependent homologous recombination or recA-independent site-specific integration. Mutations in himA, which codes for the alpha-subunit of the Integration Host Factor, does not affect the integration. Integration occurs into a chromosomal region which harbors a copy of a defective phage (4445 bp) that shares a high degree of identity with the phiLf genome. While various parts of the 4445-bp region are susceptible to homologous recombination, site-specific integration requires the attB sequence on the chromosome and the phage attP. The attB shows a high level of sequence identity (22 out of 28 bp) to the dif site required for E. coli Xer site-specific recombination, including the 6-bp central region, and 8/11 identity in both the left XerC-binding arm and the right XerD-binding arm, with the innermost 5 nt of the arms forming a dyad symmetry that is also present in dif. The attP has the same central region and shows 10/11 identity to the dif site in the left arm, but the sequence of the right arm is less conserved than that of attB. The smallest regions still capable of mediating integration are a cloned 72-bp phiLf attP-containing sequence and a 51-bp Xc17 attB-containing sequence, which was reinserted into the Xc17 chromosome after the 4445-bp region had been deleted, indicating that accessory sequences are not necessary and that the integrase required for site-specific integration is neither specified by the 4445-bp Xc17 chromosomal region nor encoded by the phiLf genome.

Sequence, transcriptional analysis and chromosomal location of the Xanthomonas campestris pv. campestris uvrB gene

The uvrB gene of Xanthomonas campestris pv. campestris, a Gram-negative plant pathogenic bacterium inhabiting soil and infected plants, was cloned and sequenced. This gene has the capacity to encode a polypeptide of 673 amino acid residues with a calculated molecular mass of 75.9 kDa. Its deduced amino acid sequence shows a high degree of similarity and possesses domain conservation to those of bacterial UvrB. The uvrB mutant, isolated by gene replacement, is extremely sensitive to ultraviolet irradiation. Like the situation in the X. campestris pv. campestris recA gene, no SOS box is present upstream of the uvrB gene. Northern blotting and transcriptional fusion assay with lacZ indicated that X. campestris pv. campestris uvrB is expressed constitutively at high levels and cannot be further induced by UV irradiation. These results suggest a regulatory mechanism different from that for the expression of Escherichia coli uvrB. Using a gene-tagging strategy in conjunction with pulsed-field gel electrophoresis, the uvrB gene was located near 1 o'clock on the X. campestris pv. campestris 17 chromosome (4.8 Mb) map, which is far apart from the lexA-recA-recX cluster near 5 o'clock.

UDP-glucose dehydrogenase gene of Xanthomonas campestris is required for virulence

Xanthomonas campestris pv. campestris (Xc) is the casual agent of black rot in crucifers. The Xc gene (udgH) coding for UDP-glucose dehydrogenase, an enzyme catalyzing the conversion of UDP-glucose to UDP-glucuronic acid, was previously shown to be required for the biosynthesis of xanthan gum, a substance necessary for the bacterium to cause disease. In this study, the transcription start site of the udgH was determined and the promoter activity monitored by the xylE reporter system indicated that expression of the udgH increases following cell growth and that the udgH gene may possess a second promoter that is responsive to stationary-phase change retaining high levels of expression. Results of Southern hybridization suggest that the udgH gene may be ubiquitous in Xanthomonas, coincident with the notion that members of this genus are capable of xanthan gum biosynthesis. Mutation of the udgH gene in Xc and X. campestris pv. vesicatoria, the casual agent of leaf spot in pepper and tomato, was found to cause a loss of virulence.

Characterization of stress-responsive genes, hrcA-grpE-dnaK-dnaJ, from phytopathogenic Xanthomonas campestris

Sequencing of a 6.4-kb DNA fragment, cloned from the plant pathogenic bacterium Xanthomonas campestris pv. campestris 17 revealed five ORFs whose deduced amino acid sequences show strong similarities to the bacterial HrcA, GrpE, DnaK, DnaJ, and PdxK. The four heat shock genes are organized in the order hrcA-grpE-dnaK-dnaJ, a genome organization found in many gram-positive bacteria, but only in one gram-negative species (Xylella fastidiosa). These observations suggest that the HrcA-CIRCE system, comprising at least four genes arranged in this order, already existed for the regulation of stress responses before bacteria diverged into gram-negative and gram-positive groups. Primer-extension results suggested the presence of promoters at the regions upstream of grpE and dnaK. In the presence of stress, heat or ethanol (4%), the X. campestris pv. campestris 17 grpE and dnaK promoters were induced two- to three-fold over controls. Since the grpE and dnaK promoters possess E. coli sigma(32) promoter-like sequences, they are functional in E. coli, although at levels much lower than in X. campestris pv. campestris 17. Furthermore, expression of the X. campestris pv. campestris 17 dnaK promoter in E. coli was elevated by the cloned X. campestris sigma(32) gene, indicating that the cognate sigma(32) works more efficiently for the X. campestris promoters.

The early stages of filamentous phage phiLf infection require the host transcription factor, Clp

Xanthomonas campestris pv. campestris produces great amounts of an exopolysaccharide (EPS), xanthan gum. Eight eps loci involved in biosynthesis of the EPS were previously located in the chromosome map of strain Xc17. In this study, the eps8 region was cloned, sequenced and found to contain a crp homologue whose deduced amino acid sequence possesses similarity to that of the cyclic AMP receptor protein of bacteria, with the highest identity (97%) being shared with the X. campestris pv. campestris B-1459 clp gene previously shown to be involved in pathogenicity and regulation of the production of xanthan, extracellular enzymes, and pigment (de Crecy-Lagard V., Glaser P., Lejeune P., Sismeiro O., Barber C.E., Daniels M.J., and Danchin A., J. Bacteriol. 172:5877-5883, 1990). Based on sequence identity, pleiotropic effects of the mutation, the ability to complement an Escherichia coli cya crp mutant, and Southern hybridization detecting a single copy in the chromosome, we propose this eps8 gene to be the Xc17 clp. In addition to the previously reported properties, a clp mutant (AU56E) cannot be plaqued with filamentous phage phiLf, although it retains the capability to support phiLf DNA replication and release authentic phage particles upon electroporation of the RF DNA. Infective center assays demonstrated that the frequency of infection is 460- to 7,500-fold lower in AU56E compared to that in the wild-type Xc17. Electron microscopy, which showed no surface appendages other than the monotrichous flagellum, confirmed that AU56E drastically diminishes in the efficiency of phage adsorption. These results suggest Clp to be regulating the biosynthesis of the primary receptor, most likely a type IV pilus. Upstream to clp is a homologue of the E. coli speD gene required for spermidine synthesis. Mutation of the clp flanking regions and transcriptional analyses suggest clp to be monocistronic and the only gene contained at the eps8 locus.

Regulation of growth and tumorigenicity of breast cancer cells by the low molecular weight GTPase Rad and nm23

Rad is the prototypic member of a family of novel Ras-related GTPases that is normally expressed in heart, skeletal muscle, and lung and that has been shown to exhibit a novel form of bi-directional interaction with the nm23 metastasis suppressor. In the present study, we have investigated the expression of Rad in normal and neoplastic breast tissues by Western blot and immunohistochemistry and the functional effect of altered Rad expression in breast cancer cell lines. We found that, although Rad is frequently expressed in normal breast tissue (23/30 Rad+ve), expression is usually lost in adjacent invasive carcinoma (8/30 Rad+ve; P < 0.0001). However, where Rad expression persists in a small proportion of tumors, it is associated with higher grade, larger size, and extensive axillary nodal involvement (n = 48; P = 0.035, P = 0.016, P = 0.022, respectively). Furthermore, Rad is also highly expressed in a breast cancer cell line with high tumorigenic and metastatic potential (MDA-MB231). To further examine the role of Rad in breast cancer, we stably transfected a Rad-ve breast cancer cell line (MDA-MB435). We observed an increase in growth and marked increased colony formation in soft agar in vitro (P < 0.05) and an increase in tumor growth rate in nude mice (P < 0.05). Moreover, coexpression of nm23 with wild-type Rad inhibited the effect of Rad on growth of these cells in culture and markedly inhibited tumor growth in vivo. Additional transfection studies with mutated Rad cDNAs revealed that the growth-promoting effects of Rad appeared to be mediated through its NH2- and COOH-terminal regions, rather than its GTPase domain, and might involve acceleration of cell cycle transition. These findings suggest that Rad may act as an oncogenic protein in breast tissues and demonstrate a potential mechanism by which interaction between Rad and nm23 may regulate growth and tumorigenicity of breast cancer.

Challenges of implementing intervention research in persons with dementia: example of a glider swing intervention

Intervention studies for persons with dementia present many challenges. This article describes challenges encountered in conducting a glider swing intervention study for persons with dementia and the strategies used to manage the problems encountered. The overall purpose of a quasi-experimental study was to explore the effects of a glider swing intervention on emotions, relaxation, and aggressive behaviors in nursing home residents with dementia. Suggestions for investigators conducting intervention studies for persons with dementia are provided.

Characterization of the IncW cryptic plasmid pXV2 from Xanthomonas campestris pv. vesicatoria

The gram-negative plant pathogen Xanthomonas campestris pv. vesicatoria strain Xv2 harbors an indigenous, cryptic plasmid pXV2 of 14.6 kb. This plasmid can only be maintained in Xanthomonas and is incapable of self-transmission. However, incompatibility testing classified it in IncW, a group containing the smallest number of naturally occurring, broad-host-range, conjugative plasmids. A pXV2 derivative containing only a 5.5-kb PstI fragment is stably maintained. Deletion of a 3.0-kb region from the PstI fragment causes a loss of plasmid stability. Nucleotide sequencing of the 2. 1-kb region essential for autonomous replication revealed a repA gene and a downstream noncoding region containing four iterons, two 17- and two 19-nt direct repeats, and an AT-rich region lying between the two sets of iterons. The sequence of the deduced RepA and the iterons shows homology to the RepA (39% identity) and the iterons, respectively, of the IncW plasmid pSa. Maxicell expression of the repA gene produced a protein of 35 kDa, a size similar to that deduced from the nucleotide sequence. Trans-complementation test confirmed that the repA gene and the iterons are indeed the essential elements for pXV2 replication.

Dominant negative mutants of the yeast splicing factor Prp2 map to a putative cleft region in the helicase domain of DExD/H-box proteins

The Prp2 protein of Saccharomyces cerevisiae is an RNA-dependent ATPase required before the first transesterification reaction in pre-mRNA splicing. Prp2 binds to the spliceosome in the absence of ATP and is released following ATP hydrolysis. We determined what regions in Prp2 are essential for release from the spliceosome by analyzing dominant negative mutants in vivo and in vitro. We made mutations in conserved motif II (DExH) and motif VI (QRxGR) of the helicase (H) domain. Mutations that inactivated PRP2 had a dominant negative phenotype when overexpressed in vivo. To test whether mutations outside of the H domain could confer a dominant negative phenotype, we mutagenized a GAL1-PRP2 construct and screened for mutants unable to grow on galactose-containing media. Five dominant negative mutants were characterized; three mapped within the H domain and two mapped downstream of motif VI, indicating that an extended helicase domain is required for release of Prp2 from the spliceosome. Most mutants stalled in the spliceosome in vitro. However, not all mutants that were dominant negative in vivo were dominant negative in vitro, indicating that multiple mechanisms may cause a dominant negative phenotype. Structural modeling of the H domain of Prp2 suggests that mutants map to a cleft region found in helicases of known structure.

Sequence and molecular analysis of the rpoA cluster genes from Xanthomonas campestris pv. campestris

The Xanthomonas campestris rpsM (S13)-rpsK (S11)-rpsD (S4)-rpoA (alpha)-rplQ (L17) cluster, encoding RNA polymerase alpha-subunit and four ribosomal proteins, reside in a 3164-bp DNA region. The N-terminal sequence of the authentic alpha-protein determined chemically matches that predicted from the nucleotide sequence. rplQ is monocistronic, instead of being co-transcribed with the other genes as in Escherichia coli. Antiserum against the His-tagged alpha-protein cross-reacted with the E. coli alpha-protein.

Use of presence in the critical care unit

Nurses have used the intervention of presence for centuries, but only recently has attention been given to defining and describing this intervention that conveys much of the caring aspect of nursing. Presence is more than a nurse's being with a patient physically. Researchers have found that patients recognize and value nurses who are present with their whole beings and are attuned to patients' needs and concerns. When critical care nurses use the intervention of presence, findings have shown that they make a connection with the patient that can lead to earlier identification of patients' problems. Further, critical care nurses can use presence in interactions with patients to avoid the perception by patients and their families that the nurse is emotionally distant or is there just to do a job. By incorporating presence as an integral part of all patient interactions, critical care nurses have the privilege of transforming a technical, potentially impersonal setting into a humane, healing place.

Isolation and characterization of a novel phytase from Penicillium simplicissimum

Eighty-three isolates from different soil samples exhibited the potential for producing active extracellular phytase. The most active fungal isolate with phytase activity was identified as Penicillium simplicissimum. In shaking culture with enrichment medium, the highest extracellular phytase activity of the producing strain was 3.8 U/mL. The crude enzyme filtrate was purified to homogeneity using ultrafiltration. IEC and gel filtration chromatography. The molar mass of the purified enzyme was estimated to be 65 kDa on SDS-PAGE. The saccharide identification with periodic acid-Schiff reagent (PAS) and activity recognition by 1-naphthyl phosphate was all positive. The isoelectric point of the enzyme, as deduced by isoelectric focusing, was pH 5.8, the optimum pH and temperature being pH 4.0 and 55 degrees C, respectively. The purified enzyme revealed broad substrate specificity and was strongly inhibited by Fe2+, Fe3+ and Zn2+; however, no inhibition was found by EDTA and PMSF. Phytase activity was inhibited when 2 mmol/L of dodecasodium phytate was added and the Km for it was determined to be 813 mmol/L.

Interaction of the Ras-related protein associated with diabetes rad and the putative tumor metastasis suppressor NM23 provides a novel mechanism of GTPase regulation

Rad is the prototypic member of a new class of Ras-related GTPases. Purification of the GTPase-activating protein (GAP) for Rad revealed nm23, a putative tumor metastasis suppressor and a development gene in Drosophila. Antibodies against nm23 depleted Rad-GAP activity from human skeletal muscle cytosol, and bacterially expressed nm23 reconstituted the activity. The GAP activity of nm23 was specific for Rad, was absent with the S105N putative dominant negative mutant of Rad, and was reduced with mutations of nm23. In the presence of ATP, GDP.Rad was also reconverted to GTP.Rad by the nucleoside diphosphate (NDP) kinase activity of nm23. Simultaneously, Rad regulated nm23 by enhancing its NDP kinase activity and decreasing its autophosphorylation. Melanoma cells transfected with wild-type Rad, but not the S105N-Rad, showed enhanced DNA synthesis in response to serum; this effect was lost with coexpression of nm23. Thus, the interaction of nm23 and Rad provides a potential novel mechanism for bidirectional, bimolecular regulation in which nm23 stimulates both GTP hydrolysis and GTP loading of Rad whereas Rad regulates activity of nm23. This interaction may play important roles in the effects of Rad on glucose metabolism and the effects of nm23 on tumor metastasis and developmental regulation.

Identification of a novel beta-lactamase produced by Xanthomonas campestris, a phytopathogenic bacterium

The Xanthomonas campestris pv. campestris 11 chromosome encodes a periplasmic beta-lactamase of 30 kDa. Gene replacement and complementation confirmed the presence of this enzyme. Its deduced amino acid sequence shows identity and conserved domains between it and Stenotrophomonas maltophilia L2 and other Ambler class A/Bush group 2 beta-lactamases. Southern hybridization detected a single homologous fragment in each of 12 other Xanthomonas strains, indicating that the presence of a beta-lactamase gene is common among xanthomonads.

The adsorption protein genes of Xanthomonas campestris filamentous phages determining host specificity

Gene III (gIII) of phiLf, a filamentous phage specifically infecting Xanthomonas campestris pv. campestris, was previously shown to encode a virion-associated protein (pIII) required for phage adsorption. In this study, the transcription start site for the gene and the N-terminal sequence of the protein were determined, resulting in the revision of the translation initiation site from the one previously predicted for this gene. For comparative study, the gIII of phiXv, a filamentous phage specifically infecting X. campestris pv. vesicatoria, was cloned and sequenced. The deduced amino acid sequences of these two pIIIs exhibit a high degree of identity in their C-terminal halves and possess the structural features typical of the adsorption proteins of filamentous phages: a signal sequence in the N terminus, a long glycine-rich region near the center, and a hydrophobic membrane anchorage domain in the C terminus. The regions between gIII and the upstream gVIII, 128 nucleotides in both phages, are larger than those of other filamentous phages. A hybrid phage of phiXv, consisting of the phiLf pIII and all the other components derived from phiXv, was able to infect X. campestris pv. campestris but not X. campestris pv. vesicatoria, indicating that gIII is the gene specifying host specificity and demonstrating the interchangeability of the pIIIs.

Chromosome map of Xanthomonas campestris pv. campestris 17 with locations of genes involved in xanthan gum synthesis and yellow pigmentation

No plasmid was detected in Xanthomonas campestris pv. campestris 17, a strain of the causative agent of black rot in cruciferous plants isolated in Taiwan. Its chromosome was cut by PacI, PmeI, and SwaI into five, two, and six fragments, respectively, and a size of 4.8 Mb was estimated by summing the fragment lengths in these digests. Based on the data obtained from partial digestion and Southern hybridization using probes common to pairs of the overlapping fragments or prepared from linking fragments, a circular physical map bearing the PacI, PmeI, and SwaI sites was constructed for the X. campestris pv. campestris 17 chromosome. Locations of eight eps loci involved in exopolysaccharide (xanthan gum) synthesis, two rrn operons each possessing an unique I-CeuI site, one pig cluster required for yellow pigmentation, and nine auxotrophic markers were determined, using mutants isolated by mutagenesis with Tn5(pfm)CmKm. This transposon contains a polylinker with sites for several rare-cutting restriction endonucleases located between the chloramphenicol resistance and kanamycin resistance (Kmr) genes, which upon insertion introduced additional sites into the chromosome. The recA and tdh genes, with known sequences, were mapped by tagging with the polylinker-Kmr segment from Tn5(pfm)CmKm. This is the first map for X. campestris and would be useful for genetic studies of this and related Xanthomonas species.

Transcriptional regulation of interleukin-1beta gene by interleukin-1beta itself is mediated in part by Oct-1 in thymic stromal cells

Interleukin (IL)-1 is involved in many processes, including thymic development. However, control of IL-1 expression in thymic-derived stromal cells (TSC) has not been reported. We found that IL-1beta increased steady-state mRNA levels for IL-1alpha and IL-1beta in TSC-936 and TSC-2C4 cells; stability was not a major determinant of this effect. To study transcriptional regulation of IL-1beta, we functionally characterized 4 kilobase pairs of the 5'-flanking region and first intron of the bovine IL-1beta gene. The -470/+14 fragment was sufficient to confer maximal responsiveness to IL-1beta upon transfection into these cell lines. Progressive 5' deletions identified several IL-1beta-responsive regions, including -308 to -226, which we further characterized. Electrophoretic mobility shift and supershift analyses showed that IL-1beta induced the ability to form multiple protein complexes with -261/-226 and that one of these contained nuclear factor Oct-1. A competitor containing a mutated Oct consensus site failed to compete not only for this complex but others as well, suggesting that this sequence regulates binding of other proteins to this region. Functional analysis confirmed that this element was essential for maximal induction of transcription. These findings document a heretofore undescribed mechanism utilized by TSC for regulation of IL-1beta transcription by IL-1beta itself.

Sequence analysis and expression of the filamentous phage phi Lf gene I encoding a 48-kDa protein associated with host cell membrane

One viral strand of phi Lf, a filamentous phage of Xanthomonas campestris pv.campestris, the open reading frame (ORF440) behind gene VI was identified as gene I. This gene codes for pI protein (440 aa, 48 kDa) which was shown to be membrane-bound in the phi Lf-infected host cell by Western blot analysis using the antibody raised against the protein expressed in Escherichia coli. Its predicted amino acid sequence has a nucleotide-binding motif in the N-terminal 97 aa and a membrane-spanning domain (aa 221 to 236). These structural features are characteristic of pIs of several filamentous phages which are transmembrane proteins required for phage assembly. Thus far, nine phi Lf genes have been identified which are organized in the order GII-gX-gV-gVII-gIX-gVIII-gIII-gVI-gI, similar to the genome organization of E. coli filamentous phages.

Isolation and characterization of the Xanthomonas campestris rpoH gene coding for a 32-kDa heat shock sigma factor

Degenerate oligonucleotide primers corresponding to the conserved regions of bacterial heat shock sigma factor RpoH (sigma 32) were used to amplify a 190-bp fragment by PCR on the X. campestris pv. campestris strain 11 chromosome. Using this fragment as a probe, plasmid pXC57 carrying a 4.7-kb insert was isolated from a genomic library of Xc11. Sequence analysis of a stretch of 2,053 bp from the pXC57 insert revealed an ORF encoding a polypeptide of 291 aa (32,854 dal) which displays 59.6% and 57.3% identity to the rpoH gene products of E. coli and P. aeruginosa, respectively. The Xc11 rpoH gene was able to complement the RpoH deficient E. coli strain A7448. Both amino acid and mRNA sequences deduced from the Xc11 rpoH gene show structural features characteristics of the corresponding sequences from those of the gamma subgroup proteobacteria. The RpoH levels in Xc11 were demonstrated to increase transiently in response to heat shock treatment by immunoblot analysis using the polyclonal antibody raised against the purified Xc11 RpoH.

Purification and expression of the gene III protein from filamentous phage phi Lf

The gene III protein (pIII) from phi Lf, a filamentous phage of Xanthomonas campestris pv.campestris, was purified by gel filtration with FPLC. The gIII coding region was amplified by PCR, which was then cloned into pUC18 and expressed in Escherichia coli. The size of both pIII, purified from phage particle and expressed in E. coli, is similar to the value deduced from the nucleotide sequence as shown by Western blot analysis. This is different from the case in Ff phages (f1, fd, and M13), in which the size of pIII observed in SDS-polyacrylamide gel electrophoresis is substantially larger than the deduced value. Upon infection of X. c. pv. vesicatoria carrying cloned phi Lf gIII with phi Xv, a filamentous phage of pv. vesicatoria, the progeny particles in supernatant were able to infect both pv. campestris carrying cloned phi Lf gIII and pv. vesicatoria, indicating that a mixture of authentic phi Xv and chimeric phage consisting of phi Xv DNA and phi Lf pIII was produced. These results suggest pIII to be the adsorption protein required for host recognition.

Lacunar infarctions presenting as memory loss and mental changes: four cases report

Impairment of higher cortical functions is usually not considered as a typical presentation of lacunar infarction. However, a small discrete lesion at strategically important locations may produce memory loss and mental changes. We report 4 patients with lacunar infarctions manifested as acute amnesia and mental changes. One patient had left thalamic infarction, one had left capsular genu infarction, one had right capsular genu infarction, and one had left capsular genu infarction extending to the ipsilateral thalamus. The mental and memory impairment was transient in one patient but was persistent in the other 3 patients. Our report reconfirms that a lacunar infarction can cause impairment of higher cortical functions.

Hypovolemic shock induced by laparoscopic cholecystectomy--a case report

Since its introduction and development in the 1960s, laparoscopic cholecystectomy has become widely accepted by the medical community and the public as the treatment of choice for various gallbladder disorders. We present a 46-year-old male who underwent laparoscopic cholecystectomy, during which inadvertent penetration of the first trocar resulted in injury of the abdominal aorta and then hypovolemic shock ensured. The time from notification of shock by the anesthesiologist to switch of procedure to exploratory laparotomy for stanching hemorrhage was twenty minutes. During the intervention, blood loss was over 3,000 ml and despite rapid infusion of plasma expander, blood pressure could only be maintained between 40/18 to 60/20 mmHg. After the patient became stabilized and blood pressure was elevated to acceptable levels, conventional cholecystectomy was performed instead. Perioperative blood loss of 7,300 ml was estimated. In total, the patient received 24 units of packed red blood cells, 12 units of fresh frozen plasma, and 12 units of platelets. After the operation, the patient was transferred to the surgical ICU for further observation. For 24 h at the ICU, blood pressure remained unstable, urine output decreased gradually, and scrotal and leg edema developed. Forty-four h after admission to the surgical ICU, arrhythmia and profound hypotension were noted and cardiac arrest ensued. After resuscitation for 2 h, the patient could not be revived and succumbed to cardiovascular decompensation secondary to acute renal shutdown and continuous retroperitoneal hemorrhage.

Transcriptional analysis of the threonine dehydrogenase gene of Xanthomonas campestris

The nucleotide sequence has previously been determined for the Xanthomonas campestris pv. campestris gene coding for threonine dehydrogenase (tdh). Flanking this gene are the upstream region possessing promoter activity and the downstream perfect inverted repeat having potential to form a stem-loop structure which resembles a transcription terminator. In addition, Northern blot analysis suggested the transcript of this gene to be monocistronic. In the present study, the essential region for promoter activity was narrowed down to a stretch of 57 bp which still retained 84% of the promoter activity. The first nucleotide to be transcribed is the guanosine at 30 nt upstream from the proposed tdh start codon. The putative terminator exhibited transcriptional termination activity bidirectionally in both Escherichia coli and X. campestris. These observations indicate that the transcriptional structure of X. campestris tdh is different from that of E. coli where tdh and kbl are organized into the tdh operon. Furthermore, the expression of tdh in X. campestris is repressed by leucine, a situation different from that in E. coli where leucine induces the expression of tdh operon.

Identification of gene VI of filamentous phage phi Lf coding for a 10-kDa minor coat protein

ORF95 in the filamentous phage phi Lf genome, locating behind gIII, was identified to be the gene (gVI) coding for minor coat protein pVI (95 amino acids, 10,245 dal). It was shown to be virion associated by Western blot analysis of chloroform-treated phage particles. Computer analysis predicted two transmembrane regions for this protein. Since no signal peptide was suggested and the size estimated by SDS-polyacrylamide gel electrophoresis matches that deduced from nucleotide sequence, it appears to be incorporated into the phage particle as its primary translational product. After completion of this study, eight genes organizing into an order of gVII-gX-gV-gVII-gIX-gIII-gIII-gVI have been identified for phi Lf.

Sequence and copy number of the Xanthomonas campestris pv. campestris gene encoding 16S rRNA

A 6.7-kb Sau3A1 fragment containing ribosomal RNA genes was cloned from the chromosome of Xanthomonas campestris pv. campestris strain 17 by a PCR-based strategy. Nucleotide sequence was determined for the 16S rRNA gene (1,544 nt). This gene has a G+C content of 54.9% which is similar to the 16S rRNA genes of Escherichia coli and Pseudomonas aeruginosa but different from the value reported for the whole X. campestris chromosome (64%). Sequence alignment revealed that AGGAGG is consensus for ribosome binding, with the internal GGAG to be paired most frequently with the anti-Shine-Dalgarno sequence. This consensus sequence was found in the regions upstream from the initiation codon of 98 Xanthomonas genes among 116 aligned, but not in the remaining genes. This suggests that about 16% of the Xanthomonas genes do not possess typical ribosome binding sites and another mechanism may be required for recognition of correct translation initiation sites. Two rrn operons were detected in Xc17 chromosome by pulsed-field gel electrophoresis and Southern hybridization.

Molecular characterization of the gene coding for threonine dehydrogenase in Xanthomonas campestris

The Xanthomonas campestris pv. campestris 17 gene tdh, which codes for the threonine dehydrogenase (TDH), was cloned and sequenced. The deduced gene product, a polypeptide consisting of 340 amino acids (Mr = 37,048), has 63.5% identity to the E. coli TDH in amino acid sequence and shares residue conservation with the alcohol/polyol dehydrogenases from different organisms. TDH activity was not detectable in the tdh mutant constructed by gene replacement; however, the enzyme activity in the mutant complemented in trans by a plasmid containing the complete tdh sequence was increased by 15 folds over Xc17. Northern blot analysis detected an mRNA with a size similar to that of the Xc17 tdh coding region, suggesting that the tdh gene-containing transcript may be monocistronic.

The Xanthomonas campestris gumD gene required for synthesis of xanthan gum is involved in normal pigmentation and virulence in causing black rot

A cloned 4.1-kb EcoRI fragment from Xanthomonas campestris pv. campestris was previously shown to complement the non-mucoid mutant P22 and increase xanthan gum production after being transformed into the wild-type strain Xc17. The gene responsible for these effects was identified, sequenced, and shown to be the gumD gene which has previously been proposed to encode glucose transferase activity, an enzyme required for adding the first glucose residue to the isoprenoid glycosyl carrier lipid during xanthan synthesis. A gumD mutant, isolated from Xc17 by gene replacement, was shown to possess altered pigment xanthomonadin profiles and exhibit reduced virulence in causing black rot in broccoli. This study appears to be the first to demonstrate that interruption of a gene required for xanthan synthesis can lead to reduced virulence of X. campestris.

Regulation of interleukin (IL)-1alpha, IL-1beta, and IL-6 expression by growth hormone and prolactin in bovine thymic stromal cells

Growth hormone (GH) and prolactin (PRL) have been implicated in T-cell development, but relatively little is known about the mechanism(s) of their actions on the multiple cell types in this complex tissue. Here, we investigated the effects of GH and PRL on the expression of interleukin (IL)-1alpha, IL-1beta and IL-6 in thymic stromal cells (TSC). These cytokine mRNAs were increased by GH, PRL and placental lactogen (PL) in primary cultures prepared from mid-gestational fetuses in a dose-dependent manner. IL-1 receptor antagonist (IL-1ra) abolished the hormone-induced IL-6 expression, suggesting that the induction of IL-6 was secondary to IL-1 activity. To examine the effects of these hormones on an individual cell type and develop a system in which signalling mechanisms can be studied, we generated immortalized cell lines using a strategy of conditional transformation. In the cell line, TSC-936, which displayed vimentin-positive staining and morphological characteristics of mesenchymal cells, both GH and PRL increased levels of steady-state mRNAs for IL-1alpha and IL-1beta. Nuclear run-on analysis revealed that the transcription rate of the IL-1beta gene was significantly increased by GH and PRL at 30 and 60 min, respectively, but that for IL-1alpha was not significantly changed, suggesting the possibility of an alternative mechanism mediating this response. These data suggest that modulation of cytokine gene expression is one mechanism by which GH and PRL facilitate thymic development and T-cell maturation.

Cloning, sequencing, and expression of the rpoD gene encoding the primary sigma factor of Xanthomonas campestris

A DNA fragment encoding the primary sigma factor from Xanthomonas campestris pv. campestris was cloned and sequenced. The gene (rpoD) encodes a polypeptide of 622 amino acids with a calculated MW of 70,700. The deduced amino acid sequence exhibits extensive sequence homology to the conserved regions of the primary sigma factors from bacteria. The gene product expressed in Escherichia coli, detected by Western blot analysis, had a MW similar to that estimated for the purified protein in SDS-PAGE. The NH2-terminal amino acid sequence determined chemically matched with that deduced from the nucleotide sequence of the rpoD gene. The calculated pI value (9.31) for the X. campestris primary sigma factor is much higher than the values observed for the analogous proteins from other bacteria.

Sequence analysis of the small cryptic Xanthomonas campestris pv. vesicatoria plasmid pXV64 encoding a Rep protein similar to gene II protein of phage 12-2

The complete nucleotide sequence (1,851 bp) was determined for the Xanthomonas campestris pv. vesicatoria plasmid pXV64. Sequence analysis revealed an intergenic region (IG) of 355 bp and two oppositely running open reading frames, ORF1 and ORF2, encoding polypeptides of 39 and 16 kDa, respectively. While the function of ORF2 is not known, ORF1 is suggested to be the gene encoding Rep protein based on (i) similarity in amino acid sequence to that of the gene II protein (gIIP) of filamentous phage 12-2, (ii) presence of a sequence in the ori-containing region which is similar to the sequence around the Rep nicking site in some rolling circle-replicating replicons, and (iii) ability to support replication in trans of the region containing pXV64 ori (392 bp) which is located within the region including IG and a short stretch in the N-terminus of ORF2.

Three-dimensional object representation and invariant recognition using continuous distance transform neural networks

3D object recognition under partial object viewing is a difficult pattern recognition task. In this paper, we introduce a neural-network solution that is robust to partial viewing of objects and noise corruption. This method directly utilizes the acquired 3D data and requires no feature extraction. The object is first parametrically represented by a continuous distance transform neural network (CDTNN) trained by the surface points of the exemplar object. The CDTNN maps any 3D coordinate into a value that corresponds to the distance between the point and the nearest surface point of the object. Therefore, a mismatch between the exemplar object and an unknown object can be easily computed. When encountered with deformed objects, this mismatch information can be backpropagated through the CDTNN to iteratively determine the deformation in terms of affine transform. Application to 3D heart contour delineation and invariant recognition of 3D rigid-body objects is presented.

IS element ISXC6 of Xanthomonas campestris pv. campestris

An insertion sequence element, ISXC6, was isolated from Xanthomonas campestris pv. campestris 17 (Xc17). Sequence analysis showed that it is 1,500 bp long and has 20-bp perfect inverted repeat ends. Upon transposition, a direct repeat TAATTC was generated, flanking this IS. No significant homology was observed between this sequence and other sequences in database. Results of Southern hybridization showed that multiple copies of ISXC6 were present in 7 strains of Xanthomonas examined.

The ori of filamentous phage phi Lf is located within the gene encoding the replication initiation protein

phi Lf is a filamentous phage of Xanthomonas campestris pv. campestris. In this study, the origin for phi Lf replication was located in a 121-bp TaqI fragment within gII, the gene encoding the replication initiation protein. This fragment, ligating with a GmR catridge, was able to be maintained as a plasmid (pT2) in strain Xc17 with the gII being provided in trans. ssDNA of pT2 was detected in the cells, indicating that pT2 may replicate by a rolling circle replication mechanism. Upon superinfection of Xc17 containing pT2 with phi Lf, transducing particles containing ssDNA of pT2 were released, suggesting the presence of packaging signal in the 121-bp TaqI fragment. This fragment contains a sequence homologous to the nicking sites for superfamily I Rep proteins of the rolling circle-replicating replicons, in concert with the presence of conserved amino acid sequence motifs of the superfamily I Rep proteins in the phi Lf gIIP.

Construction of a broad-host-range promoter-probing vector and cloning of promoter fragments of Xanthomonas campestris

A broad-host-range promoter-probing vector, pMY3 (8.0 kb), was constructed for cloning of DNA fragments containing promoter sequences of Xanthomonas campestris pv. campestris. This vector (pMY3) consists of the RK2 replicon, promoterless luxAB genes, the thr attenuator to block the transcription of RNA into the luxAB region, and multiple cloning sites for cloning of the fragment carrying promoter sequences. The feasibility of using pMY3 as a promoter-probing vector in both E. coli and Xc17 was demonstrated by using the lac promoter of E. coli, and the amy promoter of X. campestris in Xc17. Among the 63 promoter-containing fragments cloned from Xc17, only 9 were able to express in E. coli. It appears that X. campestris can recognize most E. coli type promoters, but, E. coli can recognize only a small portion of the X. campestris type promoters.

Detection of congenital cytomegalovirus infection in Chinese newborn infants using polymerase chain reaction

Polymerase chain reaction (PCR) amplification was used to detect cytomegalovirus (CMV) in 1000 urine specimens from Chinese newborns for defining the incidence of congenital CMV infection in the Chinese population. The major immediate-early and the late antigen genes of CMV were amplified and detected by gel electrophoresis. There were 18 congenitally infected infants found when tests were performed with one or both primer pairs. Comparing with tissue culture, PCR of both primer sets provided a sensitivity of 94%, a specificity of 100% and a predictive value of positive result of 100%.

The gene encoding UDP-glucose pyrophosphorylase is required for the synthesis of xanthan gum in Xanthomonas campestris

Xanthomonas campestris pv. campestris produces a large quantity of exopolysaccharide, xanthan gum, rendering the colonies mucoid. G76E was a non-mucoid mutant isolated from Xc17 by Tn5 mutagenesis. A 3.0-kb KpnI-EcoRI fragment from the Xc17 chromosome was able to restore mucoid phenotype to G76E. Sequence analysis of the region responsible for the restoration revealed an open reading frame, ORF324, able to encode a polypeptide of 35,232 Da which shows striking similarity to the UDP-glucose pyrophosphorylases from bacteria. The activity of UDP-glucose pyrophosphorylase reduced drastically in G76E was found to be regained in the presence of the cloned 3.0-kb KpnI-EcoRI fragment. In vitro expression of the gene in the S30 transcription/translation system produced a protein of ca. 35 kDa.

Nucleotide sequence of the gene presumably encoding the adsorption protein of filamentous phage phi Lf

A 1170-nucleotide fragment of phi Lf DNA was sequenced. This fragment contains an open reading frame, ORF367, encoding a protein of 367 amino acids (aa) (36710 Da). ORF367 is located downstream from the gene encoding the major coat protein (gVIIIp) and a Rho-independent termination signal. Sequence analysis revealed that the gene product has a Gly-rich domain (70 aa) at the center and a hydrophobic region (26 aa) at the C terminus. These structural features suggest that ORF367 may encode the adsorption protein of phi Lf.

Isolation and characterization of the recA gene of Xanthomonas campestris pv. campestris

A 1.8-kb NsiI-StuI fragment containing the recA gene of Xanthomonas campestris pv. campestris was cloned by a PCR-based approach and complementation of Escherichia coli HB 101. Sequence analysis of this fragment revealed an ORF (orf343) of 1,032 bp able to encode a protein of 343 amino acids with a calculated MW of 37,021 Da, a size similar to the values detected by in vitro system and Western blotting. It showed 69.6% identity to the E. coli RecA in amino acid sequence. Amino acid residues of the E coli RecA associated with functional activities are conserved in this Xc17 RecA. The recA mutant, L1, constructed by gene replacement, was sensitive to ultraviolet irradiation and methyl methanesulfonate, and deficient in homologous recombination.

A region of the filamentous phage phi Lf genome that can support autonomous replication and miniphage production

A 2028-bp fragment from the RF DNA of phi Lf, a filamentous phage of Xanthomonas campestris pv. campestris, was maintained autonomously as a minireplicon. Upon superinfection of the cells harboring the minireplicon with phi Lf, transducing miniphage particles were released. The minireplicon contained an open reading frame (ORF346) able to encode a polypeptide of MW39144, which possessed consensus motifs found in the Rep proteins from various sources. These findings suggested ORF346 to be the gene encoding replication initiation protein, gene II (gII) of phi Lf. Upstream to ORF346 were sequences with potential to form hairpin structures and a sequence similar to the integration host factor (IHF) binding site, structures similar to the intergenic region (IR) of the Ff phages. A 15 bp AT-rich core for phi Lf integration was found 37 bp downstream to the IHF binding site.

Nucleotide sequence and expression of UDP-glucose dehydrogenase gene required for the synthesis of xanthan gum in Xanthomonas campestris

Xanthomonas campestris pv. campestris, producing large amounts of exopolysaccharide xanthan gum, has a mucoid phenotype. Strain SD7 was a non-mucoid mutant deficient in UDP-glucose dehydrogenase. A DNA fragment able to complement the mutation of SD7 was cloned from the parental wild-type strain Xc11. Sequence analysis of the region required for the complementation revealed an open reading frame which could encode a polypeptide of 445 amino acids with a calculated molecular weight of 48,432, a size similar to that of the product produced by maxicell. The amino acid sequence had significant homology to that of the GDP-mannose dehydrogenase from Pseudomonas aeruginosa.

MRI diagnosis of spinal cord infarction: report of a case

A 62-year-old diabetic women developed acute quadriparesis. Her first symptom was clumsiness of the right limbs, which was followed shortly after by quadriparesis with severe left-sided symptoms. Sensory examination showed pinprick and thermal sensation deficits below the left T6 and right T8 dermatomes. An intramedullary infarction in the cervical cord at C5 to C6 levels was demonstrated by serial magnetic resonance imaging (MRI) studies with Gadolinium-DTPA (Gd-DTPA) enhancement. Based on the findings from this patient and 20 patients with spinal cord infarction reported in the literature, it was concluded that spinal cord infarct lesions are characterized by negative Gd-DTPA enhancement at the acute and chronic stages and positive enhancement at the subacute stage, 1 to 4 weeks after the onset of infarction.

Characterization of two novel filamentous phages of Xanthomonas

Two filamentous phages of Xanthomonas campestris pv. vesicatoria and Xanthomonas oryzae pv. oryzae were isolated and designated phi Xv and phi Xo, respectively. They were similar to other filamentous phages of Xanthomonas in (i) shape, (ii) restrictive host specificity, (iii) high stability, (iv) an ssDNA genome, (v) a dsDNA as the replicative form (RF), (vi) propagation without lysis of host cells and (vii) ability to integrate into the host chromosome. These phages showed sequence homology to filamentous phage phi Lf of X. c. pv. campestris. phi Xv was inactivated by antisera against phi Xv, phi Xo and phi Lf, whereas phi Xo and phi Lf were inactivated only by their respective antisera and the anti-phi Xv serum. Both the single-stranded phage DNAs and the RF DNAs of phi Xv, phi Xo and phi Lf were able to transfect X. c. pv. vesicatoria, X. o. pv. oryzae and X. c. pv. campestris. Physical maps of phi Xv and phi Xo were constructed for the RF DNAs. Genome sizes were estimated, based on mapping data, to be 6.8 kb for phi Xv and 7.6 kb for phi Xo, larger than that of the phi Lf genome (6.0 kb). The difference in genome sizes appeared to result from insertions of large DNA fragments. These fragments and the regions mediating integration were localized in the physical maps.

Nucleotide sequence determination, characterization and purification of the single-stranded DNA-binding protein and major coat protein of filamentous phage phi Lf of Xanthomonas campestris pv. campestris

phi Lf is a filamentous bacteriophage of Xanthomonas campestris pv. campestris, which can integrate its genome into the host chromosome. The nucleotide sequence of an EcoRV-SphI fragment (1018 bp) from the phi Lf replicative form DNA was determined. Four contiguous open reading frames (ORFs), orf98-orf43-orf38-orf42, were revealed. ORFs 98 and 42 were identified as the genes encoding a single-stranded DNA-binding protein (Sbp) and a major coat protein, respectively. Sbp was purified and found to bind with a high affinity to ssDNA prepared from phi Lf phage particles. The major coat protein showed sequence features similar to those of the typical major coat proteins of other filamentous phages. However, it appears to be synthesized as a mature product, similar to the situation with Pf3 but different from that with other filamentous phage major coat proteins which are synthesized as pre-coats and are subject to post-translational processing. The M(r)s, estimated by SDS-PAGE, of both the Sbp (10.9K) and the major coat protein (4.1K) coincide with the values deduced from the nucleotide sequences. ORFs 43 and 38 are proposed to be the genes encoding two minor coat proteins. The order of these four genes is similar to that found in the Escherichia coli filamentous phages.