scholarly journals Comparative Analyses of Base Compositions, DNA Sizes, and Dinucleotide Frequency Profiles in Archaeal and Bacterial Chromosomes and Plasmids

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Hiromi Nishida
Keyword(s):  
Correlation Coefficient ◽  
Gc Content ◽  
Chromosome Size ◽  
Dinucleotide Frequency ◽  
Host Chromosome ◽  
Frequency Profile ◽  
Bacterial Plasmids ◽  
Bacterial Chromosomes ◽  
Highly Correlated ◽  
Gc Contents

In the present paper, I compared guanine-cytosine (GC) contents, DNA sizes, and dinucleotide frequency profiles in 109 archaeal chromosomes, 59 archaeal plasmids, 1379 bacterial chromosomes, and 854 bacterial plasmids. In more than 80% of archaeal and bacterial plasmids, the GC content was lower than that of the host chromosome. Furthermore, most of the differences in GC content found between a plasmid and its host chromosome were less than 10%, and the GC content in plasmids and host chromosomes was highly correlated (Pearson’s correlation coefficient in bacteria and 0.917 in archaea). These results support the hypothesis that horizontal gene transfers have occurred frequently via plasmid distribution during evolution. GC content and chromosome size were more highly correlated in bacteria () than in archaea (). Interestingly, there was a tendency for archaea with plasmids to have higher GC content in the chromosome and plasmid than those without plasmids. Thus, the dinucleotide frequency profile of the archaeal plasmids has a bias toward high GC content.

scholarly journals OP0178 IMAGING NEOANGIOGENESIS IN RHEUMATOID ARTHRITIS (INIRA): WHOLE-BODY SYNOVIAL UPTAKE OF A 99MTC-LABELLED RGD PEPTIDE IS HIGHLY CORRELATED WITH POWER DOPPLER ULTRASOUND

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 110.2-111
Author(s):  
L. Attipoe ◽  
S. Subesinghe ◽  
C. Blanco-Gil ◽  
M. Opena ◽  
M. Rosser ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Correlation Coefficient ◽  
Doppler Ultrasound ◽  
Imaging Modality ◽  
Power Doppler ◽  
Whole Body ◽  
Total Power ◽  
Acquisition Time ◽  
Power Doppler Ultrasound ◽  
Highly Correlated

Background:Power Doppler ultrasound (PDUS) is superior to clinical examination in detecting synovitis in patients with rheumatoid arthritis (RA). Although dynamic and cheap it is impractical to scan large numbers of joints in routine clinical settings. MRI, whilst sensitive for synovitis, is expensive and routine use is limited to targeted joints. Bone scintigraphy produces whole body images but due to limited specificity is not routinely used.99mTc-maraciclatide (Serac Healthcare) is a radiolabelled tracer which binds with high affinity to integrin αvβ3, a cell-adhesion molecule up-regulated on neoangiogenic blood vessels. It therefore has the potential to image synovial inflammation at the whole-body level. We previously showed in a pilot study that uptake was seen in the inflamed joints of five RA patients and that this correlated with PDUS. This study explores correlation with PDUS in a larger groups of patients with varied disease activity.Objectives:To determine the correlation between ultrasound and99mTc-maraciclatide imaging in patients with rheumatoid arthritis.Methods:50 patients with RA fulfilling ACR 2010 classification criteria were recruited. Patients underwent an ultrasound scan of 40 joints with grey scale (GS) and PD quantification. Each joint was scored on a scale of 0-3 for GS and PD with a total score calculated for each patient. Within 3 hours of the ultrasound patients were injected with 740 MBq of99mTc-maraciclatide. Using a gamma camera, whole body planar views and dedicated hand and foot views were taken 2 hours after injection (Figure 1). Acquisition time was 20 minutes for whole body and 20 minutes for hand and foot views.99mTc-maraciclatide images were scored as positive or negative uptake for each joint (binary score). A quantitative score was also calculated for each joint where there was uptake with this corrected for background uptake. Total binary and quantitative scores per patient were calculated.Ultrasound and99mTc-maraciclatide scores were tested for correlation with Pearson’s correlation coefficient (r). Interrater agreement for 2 scorers was calculated using kappa (ĸ) and concordance correlation coefficient (Pc).Results:Strong correlation was seen when total PDUS was compared to binary scores (r=0.92, r2=0.85) (Figure 2) and quantitative scores (r=0.85, r2=0.72). ĸ was 0.82 and 0.79 for binary and ultrasound scores respectively.Pcwas 0.82 for quantitative scores. p was <0.0005 for all results.99mTc-maraciclatide uptake was also seen in inflamed tendons/tendon sheaths. The imaging procedure was well-tolerated. There were no tracer-related adverse events.Figure 1.99mTc-maraciclatide imaging with dedicated hand and foot viewsConclusion:99mTc-maraciclatide uptake was highly correlated with PDUS highlighting its potential as an alternative imaging modality.99mTc-based planar imaging has the unique capacity to image the whole body and hence the total synovial inflammatory load in a quick acquisition. The imaging equipment to perform these scans is already widely available in radiology departments. Interpretation of scans is also much simpler compared to US/MRI. It could therefore have a role in key decision-making points in pathways for diagnosis, treatment failure, and remission prior to dose tapering.Figure 2.Correlation between total power doppler and99mTc-maraciclatide binary scoresDisclosure of Interests:None declared

scholarly journals Evolution of Nucleotide Composition in the SARS-CoV-2 Lineage: Implications for Vaccine Design

2020 ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Base Composition ◽  
Scientific Community ◽  
Significant Positive Correlation ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Reverse Direction ◽  
Novel Coronavirus ◽  
Near Future ◽  
Systematic Reduction ◽  
Gc Contents

The worldwide outbreak of a novel coronavirus, SARS-CoV-2 has caused a pandemic of respiratory disease. Due to this emergency, researchers around the globe have been investigating the evolution of the genome of SARS-CoV-2 in order to design vaccines. Here I examined the evolution of GC content of SARS-CoV-2 by comparing the genomes of the members of the group Betacoronavirus. The results of this investigation revealed a highly significant positive correlation between the GC contents of betacoronaviruses and their divergence from SARS-CoV-2. The betacoronaviruses that are distantly related to SARS-CoV-2 have much higher GC contents than the latter. Conversely, the closely related ones have low GC contents, which are only slightly higher than that of SARS-CoV-2. This suggests a systematic reduction in the GC content in the SARS-CoV-2 lineage over time. The declining trend in this lineage predicts a much-reduced GC content in the coronaviruses that will descend/evolve from SARS-CoV-2 in the future. Due to the three consecutive outbreaks (MERS-CoV, SARS-CoV and SARS-CoV-2) caused by the members of the SARS-CoV-2, the scientific community is emphasizing the need for universal vaccines that are effective across many strains including those, that will inevitably emerge in the near future. The reduction in GC contents implies an increase in the rate of GC&rarr;AT mutations than that the mutational changes in the reverse direction. Therefore, understanding the evolution of base composition and mutational patterns of SARS-CoV-2 could be useful in designing broad-spectrum vaccines that could identify and neutralize the present and future strains of this virus.

scholarly journals GPRED-GC: a Gene PREDiction model accounting for 5 ′- 3′ GC gradient

2019 ◽  
Vol 20 (S15) ◽  
Author(s):  
Prapaporn Techa-Angkoon ◽  
Kevin L. Childs ◽  
Yanni Sun
Keyword(s):  
Ab Initio ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Source Code ◽  
Gc Content ◽  
Prediction Tools ◽  
Homologous Sequences ◽  
Manual Intervention ◽  
Grass Genomes ◽  
Gc Contents

Abstract Background Gene is a key step in genome annotation. Ab initio gene prediction enables gene annotation of new genomes regardless of availability of homologous sequences. There exist a number of ab initio gene prediction tools and they have been widely used for gene annotation for various species. However, existing tools are not optimized for identifying genes with highly variable GC content. In addition, some genes in grass genomes exhibit a sharp 5 ′- 3′ decreasing GC content gradient, which is not carefully modeled by available gene prediction tools. Thus, there is still room to improve the sensitivity and accuracy for predicting genes with GC gradients. Results In this work, we designed and implemented a new hidden Markov model (HMM)-based ab initio gene prediction tool, which is optimized for finding genes with highly variable GC contents, such as the genes with negative GC gradients in grass genomes. We tested the tool on three datasets from Arabidopsis thaliana and Oryza sativa. The results showed that our tool can identify genes missed by existing tools due to the highly variable GC contents. Conclusions GPRED-GC can effectively predict genes with highly variable GC contents without manual intervention. It provides a useful complementary tool to existing ones such as Augustus for more sensitive gene discovery. The source code is freely available at https://sourceforge.net/projects/gpred-gc/.

Relationships between body weight and some follicle and fleece characters in an Australian fine-wool Merino flock

1969 ◽  
Vol 20 (6) ◽  
pp. 1177 ◽  
Author(s):  
T Nay ◽  
RH Hayman
Keyword(s):  
Body Weight ◽  
Correlation Coefficient ◽  
Unit Area ◽  
Additive Effect ◽  
Phenotypic Correlations ◽  
Close Relationship ◽  
Simultaneous Selection ◽  
Selection For ◽  
Fleece Weight ◽  
Highly Correlated

Phenotypic correlations between body weight, follicle characters, and fleece characters have been investigated in a flock of 95 fine-wool non-Peppin Merino wethers, reared in the same locality under the same conditions. The results indicated that three follicle characters, follicle chord, follicle depth, and the index of follicle bending, were independent of body weight. It was found, in agreement with the results of other workers, that body weight was highly correlated with both greasy and clean wool weights (r = 0.53 and 0.51 respectively). It was also found that follicle characters were significantly correlated with most of the fleece characters which contribute to the clean fleece weight per unit area of skin. The correlation coefficient of wool weight per unit area of skin with follicle chord was 0.33, with follicle depth 0.28, and with follicle bending index –0.35. The follicle characters were also correlated with greasy and clean fleece weights. Crimp number per inch was predicted for individual animals by using as criterion the length of the follicle chord. A highly significant correlation coefficient of 0.67 was obtained between predicted and observed crimp number. The close relationship between crimp chord and follicle chord reported in previous work was confirmed. It is suggested that simultaneous selection for body weight and certain follicle characters may have an additive effect on the production of clean wool. It is also suggested that the genetic antagonism between clean wool weight and number of crimps per inch can be explained in anatomical terms.

scholarly journals Phylogenetic and Guanine-Cytosine Content Analysis of Symbiobacterium thermophilum Genes

2011 ◽  
Vol 2011 ◽  
pp. 1-5 ◽  
Author(s):  
Hiromi Nishida ◽  
Choong-Soo Yun
Keyword(s):  
Content Analysis ◽  
Gene Silencing ◽  
Early Stage ◽  
Gc Content ◽  
Dna Fragments ◽  
Bacterial Group ◽  
A Genome ◽  
Transposable Genetic Elements ◽  
Similar Gene ◽  
Gc Contents

Although the bacterium Symbiobacterium thermophilum has a genome with a high guanine-cytosine (GC) content (69%), it belongs to a low GC content bacterial group. We detected only 18 low GC content regions with 5 or more consecutive genes whose GC contents were below 65% in the genome of this organism. S. thermophilum has 66 transposase genes, which are markers of transposable genetic elements, and 38 (58%) of them were located in the low GC content regions, suggesting that Symbiobacterium has a similar gene silencing system as Salmonella. The top hit (best match) analyses for each Symbiobacterium protein showed that putative horizontally transferred genes and vertically inherited genes are scattered across the genome. Approximately 25% of the 3338 Symbiobacterium proteins have the highest similarity with the protein of a phylogenetically distant organism. The putative horizontally transferred genes also have a high GC content, suggesting that Symbiobacterium has gained many DNA fragments from phylogenetically distant organisms during the early stage of Firmicutes evolution. After acquiring genes, Symbiobacterium increased the GC content of the horizontally transferred genes and thereby maintained a genome with a high GC content.

Breed and environmental effects on lamb production in Nigeria

1981 ◽  
Vol 96 (1) ◽  
pp. 9-15 ◽  
Author(s):  
V. Buvanendran ◽  
I. F. Adu ◽  
B. A. Oyejola
Keyword(s):  
Body Weight ◽  
Environmental Factors ◽  
Least Squares ◽  
Correlation Coefficient ◽  
Environmental Effects ◽  
Correlation Coefficients ◽  
Correction Factors ◽  
The Cross ◽  
Highly Correlated ◽  
Least Squares Estimates

SUMMARYTwo indigenous breeds of sheep in Nigeria, the Yankasa and Uda and crosses of these with exotic breeds, were evaluated for lamb weights at birth, 3 months and 6 months of age and for adult ewe weight. The cross-bred lambs were significantly (P < 0·05) heavier than the indigenous breeds at all ages. Differences among the indigenous breeds were not significant. Mature ewe weight was 40·8 kg in the cross-bred and 36·0 and 31·1 kg in the Uda and Yankasa respectively, differences between all breeds being significant (P <0·05). Lamb productivity (lamb weight per kg of ewe metabolic body weight) estimates demonstrated that the differences between breeds were small.Least-squares estimates of effects of environmental factors on lamb performance showed that type of birth and age of dam were important for lamb weights at the three ages. Season and sex also had significant effects on birth and 6-month weights respectively. Correction factors for lamb weights were derived from least-squares estimates.The correlation coefficient between birth and 3-month weight was significant in all breeds and ranged from 0·39 to 0·55. Three-month and 6-month weights were highly correlated with estimates of correlation coefficients ranging from 0·71 to 0·74. Repeatability estimates of birth, 3·month, 6·month and ewe weights, all as traits of the ewe in the Yankasa, were 0·25, 0·21, 0·09 and 0·48, respectively.

scholarly journals Distinct nucleosome distribution patterns in two structurally and functionally differentiated nuclei of a unicellular eukaryote

2015 ◽  
Author(s):  
Jie Xiong ◽  
Shan Gao ◽  
Wen Dui ◽  
Wentao Yang ◽  
Xiao Chen ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Dna Sequences ◽  
Germ Line ◽  
Nucleosome Occupancy ◽  
Gc Content ◽  
Distribution Patterns ◽  
Unicellular Eukaryote ◽  
Transcription Start Sites ◽  
Highly Correlated ◽  
Cis And Trans

The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: the transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites (TSS) likely connected with promoter proximal pausing of RNA polymerase II, as well as in exonic regions flanking both the 5′ and 3′ splice sites. In contrast, nucleosomes in MIC are more delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other and with predictions based upon DNA sequence features. Arrays of well-positioned nucleosomes are often correlated with GC content oscillations, suggesting significant contributions from cis-determinants. We propose that cis- and trans-determinants may coordinately accommodate some well-positioned nucleosomes with important functions, driven by a process in which positioned nucleosomes shape the mutational landscape of associated DNA sequences, while the DNA sequences in turn reinforce nucleosome positioning.

scholarly journals High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing

2019 ◽  
Author(s):  
Devika Ganesamoorthy ◽  
Mengjia Yan ◽  
Valentine Murigneux ◽  
Chenxi Zhou ◽  
Minh Duc Cao ◽  
...  
Keyword(s):  
Large Scale ◽  
Tandem Repeats ◽  
Gc Content ◽  
Genomic Variation ◽  
Population Variation ◽  
Small Subset ◽  
Sequence Coverage ◽  
Copy Numbers ◽  
Long Read ◽  
Highly Correlated

ABSTRACTTandem repeats (TRs) are highly prone to variation in copy numbers due to their repetitive and unstable nature, which makes them a major source of genomic variation between individuals. However, population variation of TRs have not been widely explored due to the limitations of existing tools, which are either low-throughput or restricted to a small subset of TRs. Here, we used SureSelect targeted sequencing approach combined with Nanopore sequencing to overcome these limitations. We achieved an average of 3062-fold target enrichment on a panel of 142 TR loci, generating an average of 97X sequence coverage on 7 samples utilizing 2 MinION flow-cells with 200ng of input DNA per sample. We identified a subset of 110 TR loci with length less than 2kb, and GC content greater than 25% for which we achieved an average genotyping rate of 75% and increasing to 91% for the highest-coverage sample. Alleles estimated from targeted long-read sequencing were concordant with gold standard PCR sizing analysis and moreover highly correlated with alleles estimated from whole genome long-read sequencing. We demonstrate a targeted long-read sequencing approach that enables simultaneous analysis of hundreds of TRs and accuracy is comparable to PCR sizing analysis. Our approach is feasible to scale for more targets and more samples facilitating large-scale analysis of TRs.

scholarly journals Electrocardiographic Imaging of Repolarization Abnormalities

2021 ◽  
Vol 10 (9) ◽  
Author(s):  
Laura R. Bear ◽  
Matthijs Cluitmans ◽  
Emma Abell ◽  
Julien Rogier ◽  
Louis Labrousse ◽  
...  
Keyword(s):  
Sinus Rhythm ◽  
Correlation Coefficient ◽  
Ex Vivo ◽  
Data Sets ◽  
Human Donor ◽  
Electrocardiographic Imaging ◽  
Significant Difference ◽  
Highly Correlated ◽  
Repolarization Abnormalities

Background Dispersion and gradients in repolarization have been associated with life‐threatening arrhythmias, but are difficult to quantify precisely from surface electrocardiography. The objective of this study was to evaluate electrocardiographic imaging (ECGI) to noninvasively detect repolarization‐based abnormalities. Methods and Results Ex vivo data were obtained from Langendorff‐perfused pig hearts (n=8) and a human donor heart. Unipolar electrograms were recorded simultaneously during sinus rhythm from an epicardial sock and the torso‐shaped tank within which the heart was suspended. Regional repolarization heterogeneities were introduced through perfusion of dofetilide and pinacidil into separate perfusion beds. In vivo data included torso and epicardial potentials recorded simultaneously in anesthetized, closed‐chest pigs (n=5), during sinus rhythm, and ventricular pacing. For both data sets, ECGI accurately reconstructed T‐wave electrogram morphologies when compared with those recorded by the sock (ex vivo: correlation coefficient, 0.85 [0.52–0.96], in vivo: correlation coefficient, 0.86 [0.52–0.96]) and repolarization time maps (ex‐vivo: correlation coefficient, 0.73 [0.63–0.83], in vivo: correlation coefficient, 0.76 [0.67–0.82]). ECGI‐reconstructed repolarization time distributions were strongly correlated to those measured by the sock (both data sets, R 2 ≥0.92). Although the position of the gradient was slightly shifted by 8.3 (0–13.9) mm, the mean, max, and SD between ECGI and recorded gradient values were highly correlated ( R 2 =0.87, 0.75, and 0.86 respectively). There was no significant difference in ECGI accuracy between ex vivo and in vivo data. Conclusions ECGI reliably and accurately maps potentially critical repolarization abnormalities. This noninvasive approach allows imaging and quantifying individual parameters of abnormal repolarization‐based substrates in patients with arrhythmogenesis, to improve diagnosis and risk stratification.

scholarly journals The statistical studies of the inner boundary of plasma sheet

2011 ◽  
Vol 29 (2) ◽  
pp. 289-298 ◽  
Author(s):  
J. B. Cao ◽  
W. Z. Ding ◽  
H. Reme ◽  
I. Dandouras ◽  
M. Dunlop ◽  
...  
Keyword(s):  
Correlation Coefficient ◽  
Plasma Sheet ◽  
Radial Distance ◽  
Correlation Coefficients ◽  
Geosynchronous Orbit ◽  
Direct Observations ◽  
The Earth ◽  
Night Side ◽  
Statistical Studies ◽  
Highly Correlated

Abstract. The penetration of plasma sheet ions into the inner magnetosphere is very important to the inner magnetospheric dynamics since plasma sheet ions are one of the major particle sources of ring current during storm times. However, the direct observations of the inner boundary of the plasma sheet are fairly rare due to the limited number of satellites in near equatorial orbits outside 6.6 RE. In this paper, we used the ion data recorded by TC-1 from 2004 to 2006 to study the distribution of inner boundary of ion plasma sheet (IBIPS) and for the first time show the observational distribution of IBIPS in the equatorial plane. The IBIPS has a dawn-dusk asymmetry, being farthest to the Earth in the 06:00 08:00 LT bin and closest to the Earth in the 18:00–20:00 LT bin. Besides, the IBIPS has also a day-night asymmetry, which may be due to the fact that the ions on the dayside are exposed more time to loss mechanisms on their drift paths. The radial distance of IBIPS decrease generally with the increase of Kp index. The mean radial distance of IBIPS is basically larger than 6.6 RE during quiet times and smaller than 6.6 RE during active times. When the strength of convection electric field increases, the inward shift of IBIPS is most significant on the night side (22:00–02:00 LT). For Kp ≤ 0+, only 16% of IBIPSs penetrate inside the geosynchronous orbit. For 2 ≤ Kp < 3+, however, 70% of IBIPSs penetrate inside the geosynchronous orbit. The IBIPS has weak correlations with the AE and Dst indexes. The average correlation coefficient between Ri and Kp is −0.58 while the correlation coefficient between Ri and AE/Dst is only −0.29/0.17. The correlation coefficients are local time dependent. Particularly, Ri and Kp are highly correlated (r=−0.72) in the night sector, meaning that the radial distance of IBIPS Ri in the night sector has the good response to the Kp index These observations indicate that Kp plays a key role in determining the position of IBIPS.

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