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PubMed1986

Plasmid map: a microcomputer program for display and storage of plasmid data.

We describe a plasmid map program which runs on an IBM PC microcomputer and facilitates the drawing of circular plasmid maps. The user enters information from the keyboard in the form of restriction enzyme sites, genes and their locations, and other plasmid markers such as promoters, origins, or other sites. This information can then be stored in a file for future reference. The plasmid map can be displayed on the screen, printed on a dot-matrix printer, or plotted on a Hewlett Packard HP7475A plotter.

Base Sequence↗
PubMed1995

Three-dimensional demarcation of perfusion zones corresponding to specific coronary arteries: application for automated interpretation of myocardial SPECT.

UNLABELLED: In this study, three-dimensional maps of specific coronary artery territories were derived and combined with normal distribution maps as a reference for automated characterization of defects, including location and size. METHODS: One hundred sixty-eight 99mTc-sestamibi myocardial perfusion SPECT scans from normal patients and patients with single-vessel disease were selected according to angiographic data. Five separate groups were established for men and women: normal, proximal left anterior descending (PLAD), distal left anterior descending (DLAD), right coronary artery (RCA) and left circumflex (LCx). All myocardial perfusion studies were aligned and sized to the same three-dimensional orientation using a previously developed automated image registration technique. Mean and variation three-dimensional templates were constructed from stress images in each group. Normal templates were demarcated with hypoperfusion regions obtained from disease templates. The defects were detected in the individual patient's images by a region-growing algorithm which identified abnormal voxels by comparison to the corresponding voxels in the mean and variation templates. RESULTS: Defects were quantified with respect to volume, location relative to the expected hypoperfusion zones and severity index. Abnormal regions could be marked directly on tomographic slices and visualized in various orientations. Single defects greater than 2% of the myocardium positioned within demarcated perfusion territories were detected in 105/119 abnormal patients and in 3/49 normal patients. CONCLUSION: Maps of myocardial perfusion zones created from images of angiographically selected patients provide a reference for automated localization of myocardial perfusion defects. A template-based region-growing is a robust technique for volumetric quantification and localization of abnormal regions.

Algorithms↗
PubMed2026

Ambient temperature storage of individual parasitic nematode larvae for whole genome sequencing.

Soil-transmitted helminth (STH) infections are a major public health burden, and there are programmes of mass drug administration that attempt to ameliorate the harm that they cause. There has been increasing use of genomics to study STH infections and other parasitic nematodes, with particular interest in whole genome sequencing (WGS). For such studies, samples are commonly stored frozen, but in settings where these infections are endemic this can be difficult, and so there would be advantages to having ambient temperature storage methods. We investigated two ambient temperature storage methods - FTA cards and DESS buffer - for infective larvae of the rat parasites Nippostrongylus brasiliensis and Strongyloides ratti, prior to DNA extraction and then WGS. Our results showed that for individual larvae stored on FTA cards or in DESS buffer, this resulted in a lower proportion of sequence reads that mapped to the reference genomes, compared to the frozen control samples. Generally, for individual larvae, DESS-storage resulted in better sequencing results than FTA-storage. However, for pools of 10 or 50 larvae, then these ambient temperature storage methods generally resulted in comparable sequence read mapping to the frozen control samples.

Animals↗
PubMed2026

Comparison of paralog identification methods and their impact on species tree topologies in target capture phylogenomics within the Sindora clade (Detarioideae: Leguminosae).

Target capture is a common method of generating high throughput DNA sequencing data for phylogenetic reconstruction of species relationships, for which single copy genes are usually most informative. However, a pervasive problem with target capture is that putatively single copy genes may in fact be paralogs resulting from gene duplication, which are problematic for phylogenetic inference because their evolutionary history may differ from the divergence history of species. Here, we use as a case study a target enrichment dataset of 88 species of Detarioideae (Leguminosae) with a focus on the Sindora clade to examine approaches for handling paralogs, including the built-in paralog handling functions in HybPiper and CAPTUS, plus subsequent steps using Putative Paralog Detection and the tree-based Yang & Smith orthology inference approach. We compare the paralogs flagged using these methods and verify their performance with BLAST mapping against a reference genome sequence of Sindora glabra, and then subsequently compare the species tree topologies produced across these methods. Our comparisons of paralogs flagged across the Sindora clade show that the Putative Paralog Detection pipeline was the most accurate in identifying paralogs in terms of its similarity to the BLAST mapping, followed by the built-in paralog identification function of CAPTUS. However, the results we recovered for the Detarioideae subfamily suggest that the largest differences in species tree topology resulted from the use of paralog-filtered alignments (such as with the Putative Paralog Detection pipeline and the Yang & Smith orthology inference approaches) rather than just by removing the sequences of identified paralogous genes. This was the true for HybPiper-assembled datasets but was not seen in CAPTUS-assembled datasets. In all comparisons, the topological differences caused by different paralog handling methods tended to be confined to clades where processes such as hybridisation and introgression are prevalent. Our study provides a roadmap to establish the best approach to identify, eliminate or separate paralogs in the absence of a chromosomally contiguous reference genome for a study group, and highlights the importance of careful data inspection and processing in addition to understanding the extent of paralogy and paralog characteristics (e.g. sequence divergence between copies) for their study group.

Phylogeny↗
PubMed2006

PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data.

BACKGROUND: We recently developed the Paired End diTag (PET) strategy for efficient characterization of mammalian transcriptomes and genomes. The paired end nature of short PET sequences derived from long DNA fragments raised a new set of bioinformatics challenges, including how to extract PETs from raw sequence reads, and correctly yet efficiently map PETs to reference genome sequences. To accommodate and streamline data analysis of the large volume PET sequences generated from each PET experiment, an automated PET data process pipeline is desirable. RESULTS: We designed an integrated computation program package, PET-Tool, to automatically process PET sequences and map them to the genome sequences. The Tool was implemented as a web-based application composed of four modules: the Extractor module for PET extraction; the Examiner module for analytic evaluation of PET sequence quality; the Mapper module for locating PET sequences in the genome sequences; and the Project Manager module for data organization. The performance of PET-Tool was evaluated through the analyses of 2.7 million PET sequences. It was demonstrated that PET-Tool is accurate and efficient in extracting PET sequences and removing artifacts from large volume dataset. Using optimized mapping criteria, over 70% of quality PET sequences were mapped specifically to the genome sequences. With a 2.4 GHz LINUX machine, it takes approximately six hours to process one million PETs from extraction to mapping. CONCLUSION: The speed, accuracy, and comprehensiveness have proved that PET-Tool is an important and useful component in PET experiments, and can be extended to accommodate other related analyses of paired-end sequences. The Tool also provides user-friendly functions for data quality check and system for multi-layer data management.

Animals↗
PubMed1991

Deletion of 20p 11.23----pter with normal growth hormone-releasing hormone genes.

Using a molecular analysis of the DNA from a patient with a deletion of chromosome 20 [46,XX,del(20)(p 11.23)], we have excluded the growth hormone-releasing hormone (GHRH) gene from the region 20p11.23----pter. The patient had minor facial anomalies. Rieger eye anomaly, a congenital heart defect, severe failure to thrive, and a neurosecretory problem in growth hormone (GH) secretion. Since the GHRH gene was previously mapped to chromosome 20, we used molecular genetic methods to determine whether the growth abnormalities were due to the deletion of this gene. DNAs of the patient and 2 normal control subjects were analyzed by quantitative Southern blotting using a DNA probe for the GHRH gene and 2 reference DNA probes mapping to chromosome 21. The GHRH gene was found to be present in 2 copies in the patient. This indicates that the gene for GHRH maps to the region outside the patient's deletion, in 20p11.23----qter. Furthermore, our results suggest that genes other than GHRH on 20p are important for developmental steps leading to normal neurosecretory function of GH and may also be involved in generating Rieger eye anomaly. Finally, GH deficiency and Rieger eye anomaly should be sought in other patients with deletions of 20p.

Child↗
PubMedDate not supplied

Generalization of map estimation in SAAM II: validation against ADAPT II in a glucose model case study.

Bayesian approaches to model identification [e.g., maximum a posteriori (MAP) estimation] are receiving increasing attention in metabolism since important quantitative knowledge has become available in the last decades, e.g., from tracer experiments. By suitably exploiting this knowledge, more complex physiological models than those solely based on experimental data (Fisherian approach) become resolvable. While ADAPT II is the reference software for MAP estimation in pharmacokinetic/pharmacodynamic/metabolic system analysis, another popular, user-friendly and state-of-the-art software is SAAM II. However, SAAM II does not handle a priori information on correlation among parameters, thus allowing a limited version of MAP estimation to be performed. The aim here is twofold. First, we show that this limitation of SAAM II can be easily overcome by resorting to a probability theory result. Second, we test SAAM II vs ADAPT II implementation of MAP estimation in a real case study: the Bayesian identification of a recently proposed two-compartment minimal model of glucose kinetics during an intravenous glucose tolerance test. SAAM II MAP estimates of glucose effectiveness (SG) and insulin sensitivity (S(I)) obtained in a group of 22 healthy humans are in excellent agreement with those of ADAPT II: S(G) = 2.84 +/- 0.27 vs. 2.84 +/- 0.27 (mlmin(-1) kg(-1), mean +/- SD) and S(I) = 11.46 +/- 1.69 vs. 11.47 +/- 1.69 [10(-2) ml kg(-1) min(-1)/ (microU ml(-1))]. The SAAM II vs. ADAPT II estimates are virtually identical (P > 0.44 and 0.68 for S(G) and S(I), respectively) and also closely correlated (p = 0.9998 and 0.9999).

Algorithms↗
PubMed2003

Mean arterial pressure in very low birth weight (801 to 1500 g) concordant and discordant twins during the first day of life.

OBJECTIVE: To determine retrospectively mean arterial pressure (MAP) for stable and unstable concordant and discordant very low birth weight (VLBW: 801 to 1500 g) twins during the first 24 hours of life. BACKGROUND: Morbidity and mortality are much higher for extremely low birth weight (ELBW < or =800 g) than for VLBW twins. Recently, we reported MAP trends and reference values in concordant and discordant ELBW twins. No comparable information is available for VLBW infants. DESIGN: Retrospective cohort study. METHODS: We studied 48 sets of concordant and 40 sets of discordant (birth weight difference > or =20%) consecutively born VLBW twins. Stable patients were defined as having umbilical cord hemoglobin > or =14 g/dl, nonacidotic blood gases, never treated for hypotension and survived at least 7 days. MAPs (Torr) were measured by oscillometry in 3163 and by transducer via umbilical artery in 2028 instances. RESULTS: Concordant and discordant twins were similar in demographics, history of twin-twin transfusion (TTTX), antenatal steroids, chorioamnionitis, pre-eclampsia, cesarean delivery, cord hemoglobin, normal head ultrasounds or I to II intracranial hemorrhage (97 and 99%) and neonatal mortality (4 and 5%), but were different in incidence of preterm labor (83 and 58%), birth weight (1227 and 1509 g) and gestational age (GA) (30 and 32 weeks). In all, 66 (69%) concordant twins and 61 (76%) discordant twins were stable. Stable concordant twins, whether small or large, had comparable MAP on admission that increased to 24 hours. Twins of < or =32 weeks GA had lower MAP throughout than those of > or =33 weeks GA. Although their mean birth weights were similar (1262 and 1274 g), 23 stable concordant males had significantly higher MAP than 43 concordant females. Stable discordant twins were divided into 31 small (1241 g) and 30 large (1845 g); their MAPs were different (p<0.05): 35 and 39 (admission), 35 and 39 (1 hour), 36 and 46 (6 hours), 38 and 41 (12 hours), 40 and 41 (18 hours) and 42 and 42 (24 hours) Torr. In all, 88% of small discordant twins were IUGR and 91% of large discordant twins had normal growth. TTTX syndrome occurred in 12 monochorionic sets. Nine of 12 donors were IUGR while 10 of 12 recipients had normal growth. Four of 12 donors had grades III to IV intracranial hemorrhage, eight donors and all 12 recipients had normal ultrasounds. Although their cord hemoglobin levels were similar, donor and recipient MAPs were higher than in any other group and, opposite to concordant and discordant twins, their values decreased from birth to 24 hours. CONCLUSION: In stable concordant, stable discordant, and small and large discordant twins, MAP correlates with birth weight, GA and postnatal age, and increases during the first 24 hours. In recipient and donor twin-twin transfusion infants, MAP is higher throughout and declines over time.

Birth Weight↗
PubMed2002

A sequence-based map of the nine genes of the human interleukin-1 cluster.

Six novel genes encoding proteins with the interleukin (IL)-1 fold have been identified recently. The classical family members are involved in inflammatory signaling. Previous work has placed the novel genes close to or within the same cluster as IL1A, IL1B, and IL1RN, which occupy an approximately 400-kb interval on chromosome 2. We have combined the incomplete public database sequence with our own sequence to generate a reference sequence and map that encompass all of the novel genes, allowing determination of the gene structures, precise localization of exons, and determination of distances between conventional SNP and microsatellite markers. Gene order from centromere to telomere is IL1A-IL1B-IL1F7-IL1F9-IL1F6-IL1F8-IL1F5-IL1F10-IL1RN, of which only IL1A, IL1B, and IL1F8 are transcribed towards the centromere. The gene order relates to the evolutionary relationship between the genes. Key features of exon boundaries are conserved. There is no evidence for other IL-1 family members within the cluster.

Amino Acid Sequence↗
PubMed2005

International Equine Gene Mapping Workshop Report: a comprehensive linkage map constructed with data from new markers and by merging four mapping resources.

A comprehensive male linkage map was generated by adding 359 new, informative microsatellites to the International Equine Gene Map half-sibling reference families and by combining genotype data from three independent mapping resources: a full sibling family created at the Animal Health Trust in Newmarket, United Kingdom, eight half-sibling families from Sweden and two half-sibling families from the University of California, Davis. Because the combined data were derived primarily from half-sibling families, only autosomal markers were analyzed. The map was constructed from a total of 766 markers distributed on the 31 equine chromosomes. It has a higher marker density than that of previously reported maps, with 626 markers linearly ordered and 140 other markers assigned to a chromosomal region. Fifty-nine markers (7%) failed to meet the criteria for statistical evidence of linkage and remain unassigned. The map spans 3,740 cM with an average distance of 6.3 cM between markers. Fifty-five percent of the intervals are < or = 5 cM and only 3% > or = 20 cM. The present map demonstrates the cohesiveness of the different data sets and provides a single resource for genome scan analyses and integration with the radiation hybrid map.

Animals↗
PubMed2003

Characterization of human cervical precancerous tissue through the fourier transform infrared microscopy with mapping method.

OBJECTIVE: The aim of this study was to evaluate directly the utility of Fourier transform infrared microscopy (FTIR-MC) in detecting cervical precancer by comparison with the pathological examination of biopsy tissue. METHODS: Cervical biopsy specimens were obtained from the outpatient department at Kaohsiung Municipal Ta-Tung Hospital. Freshly isolated tissue was washed in isotonic saline and then frozen for use. Two successive slices were cut with a microtome. One unstained slice was used for reflectance FTIR-MC analysis; the other slice was stained with hematoxylin and eosin and used for position reference by microscopic mapping. RESULTS: The spectral region from 950 to 1500 cm(-1) is the most critical region in the IR spectrum of the tissue. There were two special peaks that had growth and decline in the IR spectra. The one at 1150 cm(-1) disappeared and the other at 1240 cm(-1) broadened when the tissue had pathological changes. From the results, we found that the ratio of the areas of the two regions between 1130 to 1180 cm(-1) and 1180 to 1260 cm(-1) was an exceptionally useful factor in discriminating precancerous tissues from normal tissues. CONCLUSION: We carried out microscopic mapping of the tissues and demonstrated that the color map reflects pathological changes in the cervical tissues.

Biopsy↗
PubMed1973

Genetic analysis of bacteriophage Mu-induced flagellar mutants in Escherichia coli.

In previous work, at least 10 discrete cistrons involved in the synthesis of flagella in Escherichia coli were described. Six cistrons were located between his and uvrC on the genetic map. These were referred to as hag, flaA, flaB, flaC, flaD, and flaE. Four cistrons referred to as mot, flaG, flaH, and flaI were located between uvrC and aroD. In order to determine whether these genes are organized into transcriptional units, a series of Mu phage-induced flagellar mutants was studied. The mutant strains behaved as if they were carrying strong polar mutations. Of 228 independent Mu-induced mutants, 114 with mutations in the his-aroD region of the genetic map were tested by preparing partial diploid strains with episomes carrying a variety of previously defined mutations. The pattern of complementation that emerged indicated that cistrons flaB, flaC, and flaE form a transcriptional unit. Cistron flaO, defined in the course of this study, is also a member of this transcriptional unit. The order of transcription is B-C-O-E. flaA was found to be complex, and it included four cistrons, flaA, flaP, flaQ, and flaR, with the transcriptional order A-P-Q-R. Cistrons flaG and flaH are cotranscribed with the transcriptional order G-H. The remaining genes, flaD, flaI, hag, and mot do not belong to multicistronic transcriptional units. Complementation analysis suggested that the cheC locus is the same as cistron flaA.

Chromosome Mapping↗
PubMed1990

Mean arterial blood pressure changes in premature infants and those at risk for intraventricular hemorrhage.

Bedside microcomputer-derived, minute-to-minute mean arterial pressure (MAP) values during the first 48 hours of life were studied in 100 preterm babies with birth weight less than or equal to 1500 gm. In those babies (n = 72) with no periventricular-intraventricular hemorrhage (PV-IVH) or with grade 1 PV-IVH, the MAP values increased during the study period, with minute-to-minute variation and interval undulation. The MAP values in those with birth weight greater than 1000 gm were higher than in those of lower birth weight. Infants in whom grades 2 to 4 PV-IVH developed (n = 28) had consistently lower MAP values during the study period. Minute-to-minute variability, expressed as the average of the coefficients of variation at 15-minute intervals, did not differ between birth weight groups, nor did they differ between the PV-IVH group and their matched control subjects. However, those with PV-IVH spent a greater percentage of time, with a coefficient of variation greater than or equal to 13% or less than 3%, than their matched control subjects spent (p less than 0.005). This study provides reference data for MAP changes in premature babies. The observed MAP changes in those with PV-IVH lend support to a significant role for MAP alterations in the pathogenesis of PV-IVH.

Blood Pressure↗
PubMed1993

Plasma and red blood cell protein maps: update 1993.

This publication updates the reference plasma and red blood cell protein maps obtained with immobilized pH gradients. Seventeen polypeptide spots or chains were partially characterized by direct N-terminal sequencing or by sequencing of peptides obtained from enzymatic digestion. Additional new polypeptides and previously known proteins are listed in a table and/or labeled on the protein maps, thus providing the 1993 update of the human plasma and red blood cell two-dimensional gel SWISS-2DPAGE database. SWISS-2DPAGE and the SWISS-PROT protein sequence databases are closely linked together through the use of common accession numbers.

Amino Acid Sequence↗
PubMed2006

[Establishment of the 2-D synthetic map of total protein of normal human spermatozoa enriched with low abundance protein].

OBJECTIVE: To separate the low abundance protein and establish the 2-DE synthetic map of total protein of human normal spermatozoa by using the 2-DE technology. METHODS: All the needed human spermatozoa were collected and mixed, and proteins were extracted at one time with the method of urea/thiourea and ultra-sound. 0.8 mg, 0.6 mg, 0.5 mg, 0.3 mg sperm protein extracts were separated with 2-DE. Analyzed with MALDI-TOF-MS, PI and MW of 2 spots were obtained. Then set the 2 spots as the referent spots, different maps were compared and analyzed. At last, a synthetic map enriched with low abundance protein was obtained. RESULTS: 1,080 +/- 23 protein spots have been separated on the 2-DE map with standard 0.5 mg loading amount and a synthetic map A was constructed which consist of 889 matched protein spots on the all maps with 0.5 mg loading amount. 381, 50 and 32 new spots were detected individually on the maps with 0.8 mg, 0.6 mg and 0.3 mg protein loading amount. A synthetic map with 1,352 protein spots was obtained. CONCLUSION: Low abundance protein was separated and a synthetic map enriched with low abundant protein was obtained by changing the protein loading amount.

Electrophoresis, Gel, Two-Dimensional↗