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PubMed1988

Structural conservation among three homologous introns of bacteriophage T4 and the group I introns of eukaryotes.

Three group I introns of bacteriophage T4 have been compared with respect to their sequence and structural properties. The introns include the td intervening sequence, as well as the two newly described introns in the nrdB and sunY genes of T4. The T4 introns are very closely related, containing phylogenetically conserved sequence elements that allow them to be folded into a core structure that is characteristic of eukaryotic group IA introns. Similarities extend outward to the exon sequences surrounding the three introns. All three introns contain open reading frames (ORFs). Although the intron ORFs are not homologous and occur at different positions, all three ORFs are looped-out of the structure models, with only the 3' ends of each of the ORFs extending into the secondary structure. This arrangement invites interesting speculations on the regulation of splicing by translation. The high degree of similarity between the T4 introns and the eukaryotic group I introns must reflect a common ancestry, resulting either from vertical acquisition of a primordial RNA element or from horizontal transfer.

Animals↗

PubMed1994

An intron in the thymidylate synthase gene of Bacillus bacteriophage beta 22: evidence for independent evolution of a gene, its group I intron, and the intron open reading frame.

The thymidylate synthase gene (thy) (EC 2.1.1.45) of Bacillus subtilis bacteriophage beta 22 has a self-splicing, group I intron inserted into a highly conserved region of the coding sequence. The intron is very similar to one that is inserted 21 bp further downstream in the homologous thymidylate synthase gene (td) of Escherichia coli bacteriophage T4. In contrast, the amino acid sequences of the bacteriophage thymidylate synthases are highly divergent. The beta 22 intron has a fragmentary open reading frame (ORF) that encodes a putative helix-turn-helix DNA-binding motif, similar to one at the carboxyl terminus of the homing endonuclease (I-TevI) encoded by the T4 td intron. The td ORF and the thy ORF fragments are inserted into different regions of their respective intron structures. These results suggest that the thymidylate synthase genes, their introns, and their respective intron-ORFs all have separate evolutionary histories and that the acquisition of the intron could not have occurred by a simple homing event.

Amino Acid Sequence↗

PubMed2026

VisPan: real-time visualisation of multiplex amplicon-based sequencing panels for rapid syndromic surveillance and pathogen detection.

MOTIVATION: Infectious diseases persist as a major global public health challenge. Diverse factors, including climate change, globalization, deforestation, human-animal interactions, lifestyle choices, and various biological factors, can contribute to their emergence and reemergence. Rapid detection and characterization of (re)emerging pathogens are therefore critical for effective outbreak management and for enhancing our understanding of epidemics by monitoring the transmission, spread, evolution, and genomics of pathogens. In this context, next-generation sequencing technologies (NGS), particularly long-read platforms such as Oxford Nanopore Technologies (ONT), have opened new avenues for real-time pathogen monitoring. However, the bioinformatics bottleneck remains a challenge, emphasizing the need for efficient, accessible, and user-friendly analysis tools. RESULTS: Here, we present a tool adapted from the RAMPART software that enables real-time data visualisation of multiplex PCR syndromic panels combined with Oxford Nanopore sequencing. This real-time analysis enables rapid pathogen detection, from raw data acquisition to taxonomic assignment, within minutes. The interface offers dynamic visual tracking of the sequencing run and amplicon coverage, facilitating immediate insights during diagnostic workflows. Validation experiments confirmed the system's reliability, accurately identifying all pathogens present in complex clinical or environmental samples. This tool provides an integrated, user-friendly solution for genomic pathogen surveillance in field or clinical settings.

Software↗

PubMed1999

MAD data collection - current trends.

The multiwavelength anomalous dispersion (MAD) method of protein structure determination is becoming a routine technique in protein crystallography. The increased number of wavelength-tuneable synchrotron beamlines capable of performing challenging MAD experiments, coupled with the widespread availability of charge-coupled device (CCD) based X-ray detectors with fast read-out times have brought MAD structure determination to a new exciting level. Ultrafast MAD data collection is now possible and, with the widespread use of selenium in the form of selenomethionine for phase determination, the method is growing in popularity. Recent developments in crystallographic software are complementing the above advances, paving the way for rapid protein structure determination. An overview of a typical MAD experiment is described, with emphasis on the rates and quality of data acquisition now achievable at third-generation synchrotron sources.

Chaperonins↗

PubMed2006

Three-dimensional US of the fetus: volume imaging.

PURPOSE: To retrospectively compare the rapidity, efficiency, and accuracy of three-dimensional (3D) and two-dimensional (2D) ultrasonography (US) for complete anatomic survey in fetuses at 17-21 weeks of gestation. MATERIALS AND METHODS: Institutional review board approval was obtained, informed consent was waived, and the study was HIPAA compliant. Fifty consecutive women undergoing fetal anatomic survey at 17-21 weeks of gestation formed the study cohort. After standard 2D US was performed by one of eight sonographers, the same sonographer also obtained five 3D volumes to encompass the entire fetal anatomy. Three physicians interpreting the scans independently evaluated the completeness of the examination and time needed to read the scans, comparing the standard 2D method with the 3D volume reconstruction technique. The paired t test was used to compare biparietal diameter (BPD), femur length, and performance times between the 3D measurements and the 2D measurement. The t test was used to compare fetal anatomy according to volume angle. Differences were significant when P < .05. RESULTS: Mean time to perform 2D US was 19.6 minutes per examination, whereas mean time to perform complete 3D volume acquisition was 1.8 minutes. Mean times needed to interpret 3D images and measure the BPD and femur were 5.53, 4.79, and 5.34 minutes for the three interpreting physicians. Compared with complete fetal surveys performed with 2D US, individual fetal anatomic landmarks (except for fetal arms and cavum septum pellucidum) were identified more than 94% of the time by using 3D US. Grouping anatomic views by region, the heart, head, extremities, and abdominal views were completely seen in 88%, 90%, 90%, and 95% of patients, respectively. No significant difference was seen between the three physicians regarding completeness of the 3D examinations (P = .7). One fetus had multiple anomalies, with 3D volumes identified as abnormal by all three physicians. Overall, 74% of 3D BPD measurements were within 1 mm of the 2D measurements, and 64% of 3D femur measurements were within 1 mm of the 2D measurements. CONCLUSION: The standard fetal anatomic survey can be performed in less than 2 minutes with 3D volume US, and the volumes can be interpreted in 6-7 minutes, compared with a mean of 19.6 minutes to perform standard 2D US.

Adult↗

PubMed2003

Age-of-acquisition effects in native speakers and second-language learners.

Two lexical decision experiments were conducted to study the locus of age-of-acquisition (AoA) effects in skilled readers with English or Dutch as their first language. AoA effects have generally been explained in terms of phonological processing. In Experiment 1, Dutch elementary school and secondary school students were presented with words factorially manipulated on surface frequency and AoA). Two main effects and an interaction were found, confirming findings reported for English speakers by Gerhand and Barry (1999). In addition, a language development effect was established: AoA effects decreased with reading age. Elementary school students showed the largest AoA effects. Experiment 2 used two groups of subjects. The first group consisted of Dutch students enrolled in a master's degree program in English. The second group consisted of native speakers of English. All subjects were presented with the experimental set of words used by Gerhand and Barry (1999). British subjects showed the same response pattern as reported by Gerhand and Barry (1999). The question of interest was whether Dutch subjects would show an AoA effect on the English set or not. The answer was affirmative. Dutch subjects produced identical response patterns as the British group, showing only an overall 94-msec latency delay. This result challenges predictions of the phonological completeness hypothesis. Alternative accounts in terms of semantic processing are discussed.

Adolescent↗

PubMed2002

Biliary stones and stenoses: diagnostic value of magnetic resonance cholangiography.

BACKGROUND/AIMS: To evaluate the accuracy of magnetic resonance cholangiography for detection of bile duct calculi and stenosis. METHODS: Half-Fourier single-shot rapid acquisition with relaxation enhancement sequence magnetic resonance cholangiography was performed prospectively in 68 patients who were suspected of having choledocholithiasis or biliary tree stenosis. On the basis of findings at ultrasound, computed tomography, endoscopic retrograde or percutaneous cholangiography, intraoperative cholangiography or choledocoscopy and exploration, final diagnoses were normal bile ducts (n=8), choledocholithiasis (n=28), benign or malignant stenosis (n=32). RESULTS: Choledocholithiasis was diagnosed with a sensitivity of 96% and a specificity of 98%. False negative readings occurred due to stones less than two mm at in size at the distal common bile duct. A false diagnosis of choledocholithiasis (single impacted stone) by magnetic resonance cholangiography occurred in only one case for whom the final diagnosis was main bile duct adenocarcinoma, suspected on endoscopic retrograde cholangiography and confirmed at surgery. Bile duct stenosis was diagnosed with a sensitivity of 97% and a specificity of 94%. CONCLUSIONS: With magnetic resonance cholangiography, bile duct calculi and stenosis can be diagnosed with high accuracy. It is a fast, accurate and noninvasive alternative to endoscopic retrograde cholangiography in the evaluation of biliary tract disease.

Journal Article↗

PubMed2002

The importance of head growth patterns in predicting the cognitive abilities and literacy skills of small-for-gestational-age children.

This study evaluated the effects of head growth compromise beginning in utero and continuing, in some cases, through the first 9 months of life on the cognitive and literacy skills of school-age small-for-gestational-age (SGA) children. Seventy-one SGA children, aged 7 to 9 years (gestational ages, 24-41 weeks) and 16 full-term appropriate-for-gestational-age control children of comparable socioeconomic backgrounds and age at testing completed tests assessing intelligence, receptive language, working memory, problem solving, visual-motor integration, phonological awareness, reading, and spelling. SGA children were subdivided into head-growth pattern groups based on their head circumference at birth and at 9 months postterm. Analyses showed that SGA children with poor prenatal and postnatal head growth had the worst outcomes, followed by those with prenatal brain compromise, but good postnatal head growth. SGA children with preserved head growth in utero as well as good head growth after birth demonstrated the best outcomes, although spelling skills were deficient relative to full-term peers. The Verbal and Full Scale IQ ratings of the SGA children who had experienced brain compromise in utero declined significantly from 5 to 8 years of age. We conclude that mild intrauterine growth retardation (IUGR) has a minimal effect on the development of cognitive or academic abilities, providing that brain growth in utero is not affected. IUGR that slows brain growth in utero impairs the acquisition of some cognitive and academic abilities, even when followed by good catch-up head growth after birth, whereas poor brain growth in utero followed by little or no catch-up head growth results in widespread impairments. Findings highlight the limits to brain plasticity and emphasize the importance of optimal prenatal and postnatal brain growth.

Birth Weight↗

PubMed1976

An off-line data processing system for biochemistry profiling based on a 2K programmable calculator.

An off-line data processing system based on a Hewlett Packard 2K programmable calculator to be used with a biochemistry profiling system is described. The program is in two sections. A Data Acquisition phase calculates results from Auto Analyser II peak heights after corrections for drift and stores them on magnetic tape cassettes. Quality control statistics are produced. A Reporting phase types the profile results on self-adhesive pre-printed labels to be attached to the test-request form and also prepares a laboratory record sheet. The system is routinely used to process up to 2000 peak heights per day. Non-profile heights may also be read using this program.

Autoanalysis↗

PubMed2003

dUTPase and nucleocapsid polypeptides of the Mason-Pfizer monkey virus form a fusion protein in the virion with homotrimeric organization and low catalytic efficiency.

Betaretroviruses encode dUTPase, an essential factor in DNA metabolism and repair, in the pro open reading frame located between gag and pol. Ribosomal frame-shifts during expression of retroviral proteins provide a unique possibility for covalent joining of nucleocapsid (NC) and dUTPase within Gag-Pro polyproteins. By developing an antibody against the prototype betaretrovirus Mason-Pfizer monkey virus dUTPase, we demonstrate that i) the NC-dUTPase fusion protein exists both within the virions and infected cells providing the only form of dUTPase, and ii) the retroviral protease does not cleave NC-dUTPase either in the virion or in vitro. We show that recombinant betaretroviral NC-dUTPase and dUTPase are both inefficient catalysts compared with all other dUTPases. Dynamic light scattering and gel filtration confirm that the homotrimeric organization, common among dUTPases, is retained in the NC-dUTPase fusion protein. The betaretroviral dUTPase has been crystallized and single crystals contain homotrimers. Oligonucleotide and Zn2+ binding is well retained in the fusion protein, which is the first example of acquisition of a functional nucleic acid binding module by the DNA repair factor dUTPase. Binding of the hexanucleotide ACTGCC or the octanucleotide (TG)4 to NC-dUTPase modulates enzymatic function, indicating that the low catalytic activity may be compensated by adequate localization.

Amino Acid Sequence↗

PubMed1993

Accelerating language acquisition.

How much can the development of language and other skills be accelerated in the general population? High correlations between early verbal and mental competencies and parent and teacher language socialization practices suggest enormous potential for widespread improvement. Here we report follow-up research in progress in studies of late adolescent children from diverse ethnic and educational backgrounds who participated in a language enrichment programme during infancy in the home or day-care. In 39 of 44 home-stimulated children located to date (nearly all from college-educated families) 62-93% were: in gifted or advanced programmes, obtaining high grades, avid readers and skilled in writing (over half read before school and wrote creative material independently) and generally highly skilled in verbal, mathematical and other academic domains. They also excelled socially and in sports, and showed intellectual independence. Additional subjects and data (on competence, later experiences and Scholastic Aptitude Test [SAT] scores) are currently being collected. Preliminary data analyses suggest that although early language enrichment can in the short term easily increase competence in all groups well beyond norms generated by current socialization practices, long-term outcomes are a complex function of developmental dynamics between the early, complex, foundation of high skills and motivation for learning, and the interaction with facilitative parental resources.

Adolescent↗

PubMedDate not supplied

Three-dimensional reconstruction of the flow in a human left heart by using magnetic resonance phase velocity encoding.

Intraventricular flows have been correlated with disease and are of interest to cardiologists as a possible means of diagnosis. This study extends a method that use magnetic resonance (MR) to measure the three-dimensional nature of these flows. Four coplanar, sagittal MR slices were located that spanned the left ventricle of a healthy human. All three velocity components were measured in each slice and 18 phases were obtained per beat. With use of the MR magnitude images, masks were created to isolate the velocity data within the heart. These data were read into the software package, Data Visualizer, and the data from the four slices were aligned so as to reconstruct the three-dimensional volume of the left ventricle and atrium. By representing the velocity in vectorial form, the three-dimensional intraventricular flow field was visualized. This revealed the presence of one large line vortex in the ventricle during late diastole but a more ordered flow during early diastole and systole. In conclusion, the use of MR velocity acquisition is a suitable method to obtain the complex intraventricular flow fields in humans and may lead to a better understanding of the importance of these flows.

Adult↗

PubMed2002

The effect of cognitive education on the performance of students with neurological developmental disabilities.

A cognitive education program was developed to facilitate acquisition of cognitive skills and address the learning deficits of adolescent students with neurological, developmental disabilities, and autism. This study examined the outcomes of incorporating mediated cognitive education into special education classrooms. Cognitive education provided cognitive training utilizing REHABIT materials through mediated teaching. Following a matched pair model, forty-six students were assigned to either a treatment or a control group. All students received weekly instruction in Individual Educational Program (IEP) goals. Curriculum areas included IEP objectives in reading, math, social skills, health, science and social studies. Students in the control group received regular classroom instruction. Students in the treatment group participated in cognitive educated one hour per week replacing thirty minutes of reading and thirty minutes of math. Pre and posttest comparisons on measures of intelligence, achievement and adaptive behavior showed those students in the treatment group attained higher scores across measures.

Adolescent↗

PubMed2001

A cascade of complex subtelomeric duplications during the evolution of the hominoid and Old World monkey genomes.

Subtelomeric duplications of an obscure tubulin "genic" segment located near the telomere of human chromosome 4q35 have occurred at different evolutionary time points within the last 25 million years of the catarrhine (i.e., hominoid and Old World monkey) evolution. The analyses of these segments reported here indicate an exceptional level of evolutionary instability. Substantial intra- and interspecific differences in copy number and distribution are observed among cercopithecoid (Old World monkey) and hominoid genomes. Characterization of the hominoid duplicated segments reveals a strong positional bias within pericentromeric and subtelomeric regions of the genome. On the basis of phylogenetic analysis from predicted proteins and comparisons of nucleotide-substitution rates, we present evidence of a conserved b-tubulin gene among the duplications. Remarkably, the evolutionary conservation has occurred in a nonorthologous fashion, such that the functional copy has shifted its positional context between hominoids and cercopithecoids. We propose that, in a chimpanzee-human common ancestor, one of the paralogous copies assumed the original function, whereas the ancestral copy acquired mutations and eventually became silenced. Our analysis emphasizes the dynamic nature of duplication-mediated genome evolution and the delicate balance between gene acquisition and silencing.

Animals↗

PubMed2000

Mutator-like elements in Arabidopsis thaliana. Structure, diversity and evolution.

While genome-wide surveys of abundance and diversity of mobile elements have been conducted for some class I transposable element families, little is known about the nature of class II transposable elements on this scale. In this report, we present the results from analysis of the sequence and structural diversity of Mutator-like elements (MULEs) in the genome of Arabidopsis thaliana (Columbia). Sequence similarity searches and subsequent characterization suggest that MULEs exhibit extreme structure, sequence, and size heterogeneity. Multiple alignments at the nucleotide and amino acid levels reveal conserved, potentially transposition-related sequence motifs. While many MULEs share common structural features to Mu elements in maize, some groups lack characteristic long terminal inverted repeats. High sequence similarity and phylogenetic analyses based on nucleotide sequence alignments indicate that many of these elements with diverse structural features may remain transpositionally competent and that multiple MULE lineages may have been evolving independently over long time scales. Finally, there is evidence that MULEs are capable of the acquisition of host DNA segments, which may have implications for adaptive evolution, both at the element and host levels.

Amino Acid Motifs↗

PubMed1988

Nucleotide sequence of the hemB gene of Escherichia coli K12.

The hemB gene of Escherichia coli K12, coding for porphobilinogen synthase (PBG-S; syn., 5-aminolevulinic acid dehydratase, ALA-D), was cloned following insertion of an EcoRI fragment of plasmid F'13 into the mobilizable vector pCR1. The hybrid plasmid carrying the hemB gene was able to complement a hemB mutant of E. coli K12: not only was the PBG-S activity of the mutant restored after the acquisition of the hemB gene, but it was about ten times higher than that of the wild type. Subcloning of the original EcoRI fragment (14.6 kb) enabled us to locate the hemB gene on an NruI-HpaI fragment of about 1.1 kb. The hemB promoter was located toward the NruI end of the fragment, as shown by the use of the pKO promoter-probe series of vectors. Sequencing of the hemB gene indicated the presence of an open reading frame (ORF) of 1051 nucleotides, which should correspond to the HemB protein. Primer extension experiments enabled us to identify the 5' end of the hemB mRNA, and to deduce the -10 and -35 regions of the hemB promoter. Protein synthesis performed by an in vitro coupled transcription-translation system, showed the presence of a protein of about 35 kDa. This is in agreement with the molecular weight of the HemB protein (35.6 kDa), as deduced from the nucleotide sequence of the gene. Comparison of the amino acid sequences of E. coli and human PBG-S allowed the detection of several regions of strong homology between the two proteins. Two of these regions correspond, as expected, to the putative zinc-binding and catalytic sites of the human PBG-S.

Amino Acid Sequence↗

PubMed2006

Interventional suite and equipment management: cradle to grave.

The acquisition process for interventional equipment and the care that this equipment receives constitute a comprehensive quality improvement program. This program strives to (a) achieve the production of good image quality that meets clinical needs, (b) reduce radiation doses to the patient and personnel to their lowest possible levels, and (c) provide overall good patient care at reduced cost. Interventional imaging equipment is only as effective and efficient as its supporting facility. The acquisition process of interventional equipment and the development of its environment demand a clinical project leader who can effectively coordinate the efforts of the many professionals who must communicate and work effectively on this type of project. The clinical project leader needs to understand (a) clinical needs of the end users, (b) how to justify the cost of the project, (c) the technical needs of the imaging and all associated equipment, (d) building and construction limitations, (e) how to effectively read construction drawings, and (f) how to negotiate and contract the imaging equipment from the appropriate vendor. After the initial commissioning of the equipment, it must not be forgotten. The capabilities designed into the imaging device can be properly utilized only by well-trained operators and staff who were initially properly trained and receive ongoing training concerning the latest clinical techniques throughout the equipment's lifetime. A comprehensive, ongoing maintenance and repair program is paramount to reducing costly downtime of the imaging device. A planned periodic maintenance program can identify and eliminate problems with the imaging device before these problems negatively impact patient care.

Body Burden↗

PubMed1999

Identification and characterization of two divergently transcribed iron regulated genes in Mycobacterium tuberculosis.

SETTING: Low iron availability in the host induces the expression of iron acquisition systems and virulence genes in many pathogens. IdeR is a mycobacterial iron dependent regulator that controls the iron starvation and oxidative stress responses in Mycobacterium smegmatis. It is important to determine the role of IdeR and its regulon in M. tuberculosis, as identification of iron regulated genes can aid in the design of new drugs and generation of attenuated strains. OBJECTIVE: A potential IdeR binding site was found in the M. tuberculosis genome flanked by two divergently oriented open reading frames, irg1 and irg2. The aim of this study was to determine whether irg1 and irg2 were iron and IdeR regulated genes. DESIGN: Interaction of IdeR with the putative binding sequence was examined by gel shift and footprinting assays. Transcriptional fusions of irg1 and irg2 to IacZ were used to study the effect of iron levels on the expression of these genes. RESULTS: IdeR binds to the predicted binding site, which overlaps with the irg1 promoter. irg1 and irg2 expression was decreased by iron in M. tuberculosis and in wild type M. smegmatis, but not in a M. smegmatis ideR mutant. CONCLUSION: Two M. tuberculosis iron/IdeR regulated genes were identified. irg1 is predicted to be the M. tuberculosis hisE gene, which is involved in histidine biosynthesis. It is directly upstream of the M. tuberculosis hisG. irg2 encodes a putative membrane protein that is a member of the PPE family.

Bacterial Proteins↗