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PubMed1998

A virulence-associated, 6.4-kb, double-stranded RNA from Rhizoctonia solani is phylogenetically related to plant bromoviruses and electron transport enzymes.

We have recently shown that acquisition of a 6.4-kb, double-stranded (ds) RNA (M1) by hyphal anastomosis is associated with enhanced vigor and virulence, whereas its removal by hyphal tipping correlates with diminished virulence in the plant-pathogenic basidiomycete Rhizoctonia solani. The M1 dsRNA is not encapsidated by a typical nucleocapsid, has a circular and/or concatemeric form, and is associated with the mitochondrial and cytosolic fractions. M1 possesses six open reading frames (ORFs) the longest of which (ORF 2) is located on the (+) strand, and encodes a putative polypeptide consisting of 1,747 amino acids or 199.4 kDa. This polypeptide has a significant amino acid sequence similarity, including six conserved helicase domains and an ATP/GTP binding motif, with the 1A protein of broad bean mottle virus (BBMV) and other bromoviruses. ORF 5, which is located on the (-) strand of M1 and is complementary to a region of ORF 2, codes for a putative polypeptide that has a significant amino acid sequence similarity with the cytochrome c oxidase assembly factor. This complementarity provides direct evidence suggesting that the long-standing hypothesis of viruses evolving from cellular genes may be valid.

Amino Acid Sequence↗
PubMedDate not supplied

Dual modality of 18F-fluorodeoxyglucose-positron emission tomography/computed tomography in patients with cervical carcinoma of unknown primary.

OBJECTIVE: To evaluate an optimized F-18-flurodeoxyglucose-positron emission tomography/computed tomography (FDG-PET/CT) acquisition protocol for head and neck cancer and assess the usefulness of combined FDG-PET/CT in locating unknown primary tumors in patients with biopsy-proven cervical lymph node metastases. SUBJECTS AND METHODS: Twenty-one patients with cervical lymph node metastases of unknown primary tumors underwent staging with FDG-PET/CT. The images of FDG-PET alone, CT alone, FDG-PET/CT read side by side and fused and FDG-PET/CT were evaluated separately by 2 physicians. Imaging results were correlated with either histology (n = 14) or clinical follow-up (n = 7). RESULTS: On the fused FDG-PET/CT images, primary tumors were identified in 12 patients (57%); with FDG-PET alone and FDG-PET and CT read side by side 11 (52%) primary tumors were found while CT alone identified 5 (23%) primary tumors. CONCLUSION: Our data indicate that fused FDG-PET and CT images increased the sensitivity of detecting carcinoma of unknown primary (CUP) tumors compared to CT alone, but not to FDG-PET alone or FDG-PET and CT read side by side. Hence accurate fusion of functional and morphologic data by FDG-PET/CT is a promising imaging modality in the clinical workup of patients with cervical CUP tumors.

Aged↗
PubMedDate not supplied

Multiparametric quantitative evaluation of the speech production system: a study in normal subjects.

This paper describes a systems architecture developed for the study of the speech production system. The architecture utilizes two personal computers: the "Word-Image Presenter" (WIP) that presents a sequence of words to the subject under examination as visual stimulation, and the "Signal Acquisition System" that controls the WIP, acquires the acoustic signal, the oromandibular electromyographic signals, the kinematic lip and jaw signals and measures reaction times and durations. Thirty normal subjects divided into three age groups (18-44, 45-59, 60-80) underwent examination by means of the described system. During the test a random sequence of two words was presented to the subjects; the protocol consisted of an immediate reading task and two delayed reading tasks with variable foreperiods of 0.1 and 1.5 s for one task and 0.5 and 4 s for the other. The analysis of the resultant acoustic and electromyographic signals indicated that reaction times increased with age in both the immediate and delayed tasks. The analysis of variance showed that the difference between the young and elderly groups was statistically significant. The sample size of the groups, however, is too small to consider these results normative data.

Adolescent↗
PubMed2006

Evidence for transit peptide acquisition through duplication and subsequent frameshift mutation of a preexisting protein gene in rice.

Many proteins synthesized in the cytosol are delivered to their appropriate compartments in the cell by specific targeting signals. Here, we provide new insight into the generation of the chloroplast-targeting signal (called the transit peptide) in rice. First, we identified the mitochondrial ribosomal protein L13 (mt rpl13) gene on chromosome 5. Downstream of the gene, we identified a DNA fragment of 266 bp: a segment within a duplication of mt rpl13. The duplicated region was transcribed and found to encode an open reading frame (ORF) of 160 amino acids (aa) (orf160). The orf160 gene comprises C-terminal 60 aa derived from the mt rpl13 gene and N-terminal 100 aa derived from another duplicated fragment of a pentatricopeptide repeat (ppr)564 gene that encodes 564 aa with ppr motifs on chromosome 1. Examination of the localization of the ORF160 protein tagged with green fluorescent protein (GFP) showed that it is targeted to the chloroplasts. As such, ORF160 clearly contains a transit peptide. Interestingly, this was translated from the alternative reading frame of the duplicated fragment of ppr564. To confirm this, the reading frame of the ppr564 gene was shifted according to that of the orf160 gene, and the frameshifted ppr564 sequence was fused to the gene for GFP. The expressed GFP-fused protein was also located in the chloroplasts. These results provide clear evidence for the generation of the transit peptide through duplication and subsequent frameshifting of a reading frame of a preexisting protein gene. We also demonstrate the importance of sequence redundancy and frameshift mutation in this evolutionary process.

Amino Acid Sequence↗
PubMed2003

Monoterpene double-bond reductases of the (-)-menthol biosynthetic pathway: isolation and characterization of cDNAs encoding (-)-isopiperitenone reductase and (+)-pulegone reductase of peppermint.

Random sequencing of a peppermint essential oil gland secretory cell cDNA library revealed a large number of clones that specified redox-type enzymes. Full-length acquisitions of each type were screened by functional expression in Escherichia coli using a newly developed in situ assay. cDNA clones encoding the monoterpene double-bond reductases (-)-isopiperitenone reductase and (+)-pulegone reductase were isolated, representing two central steps in the biosynthesis of (-)-menthol, the principal component of peppermint essential oil, and the first reductase genes of terpenoid metabolism to be described. The (-)-isopiperitenone reductase cDNA has an open reading frame of 942 nucleotides that encodes a 314 residue protein with a calculated molecular weight of 34,409. The recombinant reductase has an optimum pH of 5.5, and K(m) values of 1.0 and 2.2 microM for (-)-isopiperitenone and NADPH, respectively, with k(cat) of 1.3s(-1) for the formation of the product (+)-cis-isopulegone. The (+)-pulegone reductase cDNA has an open reading frame of 1026 nucleotides and encodes a 342 residue protein with a calculated molecular weight of 37,914. This recombinant reductase catalyzes the reduction of the 4(8)-double bond of (+)-pulegone to produce both (-)-menthone and (+)-isomenthone in a 55:45 ratio, has an optimum pH of 5.0, and K(m) values of 2.3 and 6.9 microM for (+)-pulegone and NADPH, respectively, with k(cat) of 1.8s(-1). Deduced sequence comparison revealed that these two highly substrate specific double-bond reductases show less than 12% identity. (-)-Isopiperitenone reductase is a member of the short-chain dehydrogenase/reductase superfamily and (+)-pulegone reductase is a member of the medium-chain dehydrogenase/reductase superfamily, implying very different evolutionary origins in spite of the similarity in substrates utilized and reactions catalyzed.

Amino Acid Sequence↗
PubMed2001

Acquisition of skilled visual search performance following severe closed-head injury.

This study used a semantic-category visual search task to investigate skill acquisition and automatic process development in a severe closed-head injured (CHI) population. Eighteen severe CHI participants (> I year post injury) and 18 matched controls completed over 3600 trials of training in both consistent mapping (CM) and varied mapping (VM) training situations. Transfer conditions were also used to test for development of an automatic attention response (AAR) that was independent of general, task-related learning. For both the severe CHI and control group, CM training, where individuals always responded in the same way to a specific class of stimuli, resulted in dramatic performance improvements and the development of an AAR. In the VM training condition, where individuals could not respond in the same way to a class of stimuli from one stimulus exposure to the next, there was little performance improvement and continued reliance on controlled processes. The visual search rates of the CHI participants also remained slower than those of controls following extended VM but not extended CM practice. These results indicate that skill acquisition training guidelines can be used to teach severe CHI patients to develop a new automatic skill.

Adult↗
PubMed1998

Isolation and characterization of an extracellular haem-binding protein from Pseudomonas aeruginosa that shares function and sequence similarities with the Serratia marcescens HasA haemophore.

The major mechanism by which bacteria acquire free or haemoglobin-bound haem involves direct binding to specific outer membrane receptors. Serratia marcescens also secretes a haem-binding protein, HasA, which functions as a haemophore that catches haem and shuttles it to a cell surface specific outer membrane receptor, HasR. We report the isolation and characterization of hasAp, a gene from Pseudomonas aeruginosa. HasAp is an iron-regulated extracellular haem-binding protein that shares about 50% identity with HasA. HasAp is required for P. aeruginosa utilization of haemoglobin iron. It can replace HasA for HasR-dependent haemoblobin acquisition in a system reconstituted in Escherichia coli. HasAp, like HasA, lacks a signal peptide and is secreted by an ABC transporter. These findings show that haemophore-dependent haem acquisition is not unique to S. marcescens.

ATP-Binding Cassette Transporters↗
PubMed2006

Sonographic diagnosis of gestational trophoblastic disease and comparison with retained products of conception.

OBJECTIVE: Gestational trophoblastic disease (GTD) and retained products of conception (RPC) can be difficult to distinguish sonographically. The aim of this study was to determine whether there were any sonographic criteria that could prospectively distinguish one from the other. METHODS: Institutional ethics approval was obtained, and acquisition of consent was waived by the Institutional Review Board. A retrospective review of gynecologic oncology and pathology databases identified 17 cases of GTD and 14 cases of RPC. Findings from the pre-evacuation transvaginal sonographic examinations were analyzed. The scans were independently reviewed by 2 senior radiologists with specific expertise in pelvic sonography using several predetermined sonographic features. The reviewers were blinded to the diagnosis. A consensus reading was obtained. RESULTS: The sonographic features that predicted GTD were a myometrial epicenter (P = .0002; odds ratio [OR] = 28), depth of myometrial invasion of more than one third (P = .001; OR = 20), placental venous lakes (P = .04; OR = 9), maximum mass dimensions of more than 3.45 cm (P = .009), and maximum endometrial thickness of less than 12 mm (P = .02). The remaining criteria were not statistically significant and included the characteristics of the mass, ascites, a "snowstorm" appearance, mass vascularity (including resistive index and peak systolic velocity), and the presence of ovarian cysts. CONCLUSIONS: There are specific transvaginal sonographic features that can accurately differentiate GTD and RPC.

Abortion, Incomplete↗
PubMed2003

Involvement of the adc operon and manganese homeostasis in Streptococcus gordonii biofilm formation.

Pioneer oral bacteria, including Streptococcus gordonii, initiate the formation of oral biofilms on tooth surfaces, which requires differential expression of genes that recognize unique environmental cues. An S. gordonii::Tn917-lac biofilm-defective mutant was isolated by using an in vitro biofilm formation assay. Subsequent inverse PCR and sequence analyses identified the transposon insertion to be near the 3' end of an open reading frame (ORF) encoding a protein homologous to a Streptococcus pneumoniae repressor, AdcR. The S. gordonii adc operon, consisting of the four ORFs adcR, adcC, adcB, and adcA, is homologous to the adc operon of S. pneumoniae, which plays a role in zinc and/or manganese transport and genetic competence in S. pneumoniae. AdcR is a metal-dependent repressor protein containing a putative metal-binding site, AdcC contains a consensus-binding site for ATP, AdcB is a hydrophobic protein with seven hydrophobic membrane-spanning regions, and AdcA is a lipoprotein permease with a putative metal-binding site. The three proteins (AdcC through -A) are similar to those of the binding-lipoprotein-dependent transport system of gram-positive bacteria. Reverse transcriptase PCR confirmed that adcRCBA are cotranscribed as an operon in S. gordonii and that the transposon insertion in S. gordonii adcR::Tn917-lac had resulted in a polar mutation. Expression of adcR, measured by the beta-galactosidase activity of the adcR::Tn917-lac mutant, was growth phase dependent and increased when the mutant was grown in media with high levels of manganese (>1 mM) and to a lesser extent in media with zinc, indicating that AdcR may be a regulator at high levels of extracellular manganese. A nonpolar inactivation of adcR generated by allelic replacement resulted in a biofilm- and competence-defective phenotype. The biofilm-defective phenotype observed suggests that AdcR is an active repressor when synthesized and acts at a distant site(s) on the chromosome. Thus, the adc operon is involved in manganese acquisition in S. gordonii and manganese homeostasis and appears to modulate sessile growth in this bacterium.

ATP-Binding Cassette Transporters↗
PubMed2005

The goose reovirus genome segment encoding the minor outer capsid protein, sigma1/sigmaC, is bicistronic and shares structural similarities with its counterpart in Muscovy duck reovirus.

Reoviruses have recently been shown to be associated with disease in young geese and to be involved in epizooties of severe outcome in Hungary. To assess the genetic variability among these pathogenic goose reoviruses (GRVs), we sequenced the S4 genome segment of five GRV strains isolated from different diseased flocks. We found that the GRV S4 genome segment, consisting of two partially overlapping open reading frames (ORFs), shares substantial structural similarity with its counterpart in muscovy duck reoviruses (DRVs). ORF1 is predicted to encode a polypeptide highly similar to the p10 polypeptide of DRV, and ORF2 supposedly encodes the minor outer capsid protein, sigma1/sigmaC. In one of the five GRV strains examined, we identified a single uracil base insertion close to the middle of ORF2. This insertion resulted in a frameshift and in concomitant acquisition of a termination codon (UAA) a few codons downstream, apparently causing truncation of the C-terminal part of the protein. The functional consequences of this assumed mutation, which would result in loss of more than a half of the protein, have yet to be determined. Nonetheless, the sequence and structural similarities between the genome segment encoding sigmal/sigmaC in GRVs and DRVs suggest that these viruses belong to a species distinct from other established species within subgroup 2 of orthoreoviruses.

Amino Acid Sequence↗
PubMed2001

Investing in emergent literacy intervention: a key role for speech-language pathologists.

Emergent literacy is a developmental period that is receiving renewed and increased emphasis in the fields of education and speech-language pathology because of its influence on the later literacy development and achievement of students. With their strong background in language, language development, and language disorders, speech-language pathologists (SLPs) can make significant contributions to the acquisition of emergent literacy skills. This article focuses on SLP direct-service roles for students with identified communication impairments and on indirect roles of assisting teachers and others to promote the emergent literacy skills of all students. In addition to the acknowledged importance of general oral language, guidelines, suggestions, and resources are offered to foster emergent literacy skills in five specific areas: (1) early phonological awareness, (2) joint book reading and sense of story, (3) alphabetic letter knowledge, (4) adult modeling of literacy activities, and (5) experience with writing materials.

Awareness↗
PubMed1999

Salmonella typhimurium encodes a putative iron transport system within the centisome 63 pathogenicity island.

Upon entry into the host, Salmonella enterica strains are presumed to encounter an iron-restricted environment. Consequently, these bacteria have evolved a variety of often-redundant high-affinity acquisition systems to obtain iron in this restricted environment. We have identified an iron transport system that is encoded within the centisome 63 pathogenicity island of Salmonella typhimurium. The nucleotide composition of this locus is significantly different from that of the rest of this pathogenicity island, suggesting a different ancestry and a mosaic structure for this region of the S. typhimurium chromosome. This locus, designated sit, consists of four open reading frames which encode polypeptides with extensive homology to the yfe ABC iron transport system of Yersinia pestis, as well as other ABC transporters. The sitA gene encodes a putative periplasmic binding protein, sitB encodes an ATP-binding protein, and sitC and sitD encode two putative permeases (integral membrane proteins). This operon is capable of complementing the growth defect of the enterobactin-deficient Escherichia coli strain SAB11 in iron-restricted minimal medium. Transcription of the sit operon is repressed under iron-rich growth conditions in a fur-dependent manner. Introduction of a sitBCD deletion into wild-type S. typhimurium resulted in no apparent growth defect in either nutrient-rich or minimal medium and no measurable virulence phenotype. These results further support the existence of redundant iron uptake systems in S. enterica.

ATP-Binding Cassette Transporters↗
PubMed2001

Formal schooling influences two- but not three-dimensional naming skills.

The modulatory influence of literacy on the cognitive system of the human brain has been indicated in behavioral, neuroanatomic, and functional neuroimaging studies. In this study we explored the functional consequences of formal education and the acquisition of an alphabetic written language on two- and three-dimensional visual naming. The results show that illiterate subjects perform significantly worse on immediate naming of two-dimensional representations of common everyday objects compared to literate subjects, both in terms of accuracy and reaction times. In contrast, there was no significant difference when the subjects named the corresponding real objects. The results suggest that formal education and learning to read and to write modulate the cognitive process involved in processing two- but not three-dimensional representations of common everyday objects. Both the results of the reaction time and the error pattern analyses can be interpreted as indicating that the major influence of literacy affects the visual system or the interaction between the visual and the language systems. We suggest that the visual system in a wide sense and/or the interface between the visual and the language system are differently formatted in literate and illiterate subjects. In other words, we hypothesize that the pattern of interactions in the functional-anatomical networks subserving visual naming, that is, the interactions within and between the visual and language processing networks, differ in literate and illiterate subjects.

Aged↗
PubMed1999

A novel cytolysis assay using fluorescent labeling and quantitative fluorescent scanning technology.

A novel cellular cytotoxicity assay using Calcein acetoxymethyl (Calcein-AM), a cytoplasmic fluorescent label, has been developed as an alternative to the standard 51Chromium (Cr)-release. Target cells were loaded with Calcein-AM and then co-incubated with effector cells. An additional reagent, FluoroQuench, is added to extinguish fluorescence of dying target cells and of the culture media. Assay plates are read on a quantitative fluorescent scanner for determination of viable target cells. Percent lysis is calculated as one minus the percent viable cells as compared to fluorescent-labeled targets-only wells. The assay was tested to demonstrate the lytic activity of cytotoxic T lymphocyte (CTL) cultures, lymphokine-activated killer (LAK), and natural killer (NK) cell line effectors against peptide-pulsed and melanoma targets. In addition to the acquisition of results comparable to the 51Cr-release assay, the Calcein assay reliably measures cell-mediated cytotoxicity with little variance among replicates. The fluorescent assay represents a simple and useful alternative to the use of radioactive materials and adds the additional benefit of digital images and analysis.

Chromium↗
PubMed2001

99Tcm-dimercaptosuccinic acid renal scintigraphy for detection of renal cortical defects in acute pyelonephritis: posterior 180 degrees SPECT versus planar image and 360 degrees SPECT.

To evaluate the usefulness of the posterior 180 degrees acquisition technique for renal defects in acute pyelonephritis (APN), a prospective study was conducted using planar imaging, 360 degrees and posterior 180 degrees renal single photon emission computed tomography (SPECT) with 99Tcm-dimercaptosuccinic acid. Sixty subjects with the suspicion of APN were included. The kidneys were divided into three zones: each was graded as positive, equivocal or negative for renal defects. To evaluate inter-observer variation, each study was read in a double-blind fashion by two nuclear physicians. Renal defects were found in 24 patients (31 kidneys and 47 zones) with posterior 180 degrees SPECT, 23 patients (29 kidneys and 44 zones) with 360 degrees SPECT (McNemar's test, P = 0.375 for zones) and 15 patients (16 kidneys and 24 zones) with planar image (P = 0.001 for zones, vs 180 degrees and 360 degrees SPECT). The proportion of positive agreement for posterior 180 degrees and 360 degrees SPECT between readers for the presence of renal defects was 0.81 and 0.62, respectively, whereas the proportion of negative agreement was 0.92 and 0.87, respectively. Both posterior 180 degrees and 360 degrees SPECTs significantly detected more renal defects than planar imaging. The detectability of renal defects in APN by posterior 180 degrees renal SPECT was equal to 360 degrees SPECT but inter-observer agreement was better.

Adolescent↗
PubMed2001

The Bordetella bhu locus is required for heme iron utilization.

Bordetella pertussis and Bordetella bronchiseptica are capable of obtaining iron from hemin and hemoglobin. Genes encoding a putative bacterial heme iron acquisition system (bhu, for Bordetella heme utilization) were identified in a B. pertussis genomic sequence database, and the corresponding DNA was isolated from a virulent strain of B. pertussis. A B. pertussis bhuR mutant, predicted to lack the heme outer membrane receptor, was generated by allelic exchange. In contrast to the wild-type strain, bhuR mutant PM5 was incapable of acquiring iron from hemin and hemoglobin; genetic complementation of PM5 with the cloned bhuRSTUV genes restored heme utilization to wild-type levels. In parallel studies, B. bronchiseptica bhu sequences were also identified and a B. bronchiseptica bhuR mutant was constructed and confirmed to be defective in heme iron acquisition. The wild-type B. bronchiseptica parent strain grown under low-iron conditions produced the presumptive BhuR protein, which was absent in the bhuR mutant. Furthermore, production of BhuR by iron-starved B. bronchiseptica was markedly enhanced by culture in hemin-supplemented medium, suggesting that these organisms sense and respond to heme in the environment. Analysis of the genetic region upstream of the bhu cluster identified open reading frames predicted to encode homologs of the Escherichia coli ferric citrate uptake regulators FecI and FecR. These putative Bordetella regulators may mediate heme-responsive positive transcriptional control of the bhu genes.

Amino Acid Sequence↗
PubMed2004

Speech-language and educational consequences of unilateral hearing loss in children.

BACKGROUND: In the past, unilateral hearing loss (UHL) in children was thought to have little consequence because speech and language presumably developed appropriately with one normal-hearing ear. Some studies from the 1980s and 1990s have suggested that a significantly increased proportion of children with UHL may have educational and/or behavioral problems, compared with their normal-hearing peers. Limited data exist about the effect of UHL on acquisition of speech and language skills. OBJECTIVE: To review the current literature about the impact UHL has on the development of speech and language and educational achievement. DATA SOURCE: MEDLINE search between 1966 and June 1, 2003, using the medical subject heading "hearing loss," combined with the textword "unilateral." STUDY SELECTION: Studies were limited to those written in English, reporting speech-language and/or educational results in children. DATA EXTRACTION: Articles were read with attention to study design, population, recruitment of subjects, and outcomes measured. DATA SYNTHESIS: Problems in school included a 22% to 35% rate of repeating at least one grade, and 12% to 41% receiving additional educational assistance. Speech and language delays have been reported in some but not all studies. CONCLUSIONS: School-age children with UHL appear to have increased rates of grade failures, need for additional educational assistance, and perceived behavioral issues in the classroom. Speech and language delays may occur in some children with UHL, but it is unclear if children "catch up" as they grow older. Research into this area is necessary to clarify these issues and to determine whether interventions may prevent potential problems.

Child↗
PubMed1989

A selective excitation/B0 gradient technique for high-resolution 1H NMR studies of metabolites via zero-quantum coherence and polarization transfer.

A new method for selective observation of scalar coupled metabolites by either zero-quantum coherence transfer or polarization transfer with concurrent water suppression in a single acquisition was developed. Gaussian shaped RF pulses were used to selectively generate multiple-quantum and zero-quantum coherence in the metabolite of interest, single quantum (including water) and double quantum coherences were then dephased under the influence of a B0 field gradient and the surviving zero-quantum coherence was converted to observable metabolite signal. The duration of the gradient application and the frequency and angle of the final selective read pulse determined whether a polarization transfer or a coherence transfer signal was observed. Water suppression factors of around 8000 were achieved which allowed operation of the receiver at high gain levels resulting in greatly improved signal to noise in the metabolite spectra. The CH3 and CH resonances of lactate in a mouse brain homogenate were selectively edited and the method was also applied to selective editing of ethanol.

Animals↗