Analysis Of Genetic Sequences Research Articles

Recognition of dual targets by a molecular beacon-based sensor: subtyping of influenza A virus.

A molecular beacon (MB)-based sensor to offer a decisive answer in combination with information originated from dual-target inputs is designed. The system harnesses an assistant strand and thermodynamically favored designation of unpaired nucleotides (UNs) to process the binary targets in "AND-gate" format and report fluorescence in "off-on" mechanism via a formation of a DNA four-way junction (4WJ). By manipulating composition of the UNs, the dynamic fluorescence difference between the binary targets-coexisting circumstance and any other scenario was maximized. Characteristic equilibrium constant (K), change of entropy (ΔS), and association rate constant (k) between the association ("on") and dissociation ("off") states of the 4WJ were evaluated to understand unfolding behavior of MB in connection to its sensing capability. Favorable MB and UNs were furthermore designed toward analysis of genuine genetic sequences of hemagglutinin (HA) and neuraminidase (NA) in an influenza A H5N2 isolate. The MB-based sensor was demonstrated to yield a linear calibration range from 1.2 to 240 nM and detection limit of 120 pM. Furthermore, high-fidelity subtyping of influenza virus was implemented in a sample of unpurified amplicons. The strategy opens an alternative avenue of MB-based sensors for dual targets toward applications in clinical diagnosis.

Closed form modeling of evolutionary rates by exponential Brownian functionals.

Accurate estimation of species divergence times from the analysis of genetic sequences relies on probabilistic models of evolution of the rate of molecular evolution. Importantly, while these models describe the sample paths of the substitution rates along a phylogenetic tree, only the (random) average rate can be estimated on each edge. For mathematical convenience, the stochastic nature of these averages is generally ignored. In this article we derive the probabilistic distribution of the average substitution rate assuming a geometric Brownian motion for the sample paths, and we investigate the corresponding error bounds via numerical simulations. In particular we confirm the validity of the gamma approximation proposed in Guindon (Syst Biol 62(1):22-34, 2013) for "small" values of the autocorrelation parameter.

K-mer natural vector and its application to the phylogenetic analysis of genetic sequences.

Based on the well-known k-mer model, we propose a k-mer natural vector model for representing a genetic sequence based on the numbers and distributions of k-mers in the sequence. We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency.

Genetic Diversity of Rotavirus Strains Circulating in Environmental Water and Bivalve Shellfish in Thailand

Rotavirus is a common cause of acute diarrhea in young children worldwide. This study investigated the prevalence and molecular characterization of rotavirus in environmental water and oyster samples in Thailand. A total of 114 water samples and 110 oyster samples were collected and tested for group A rotavirus using RT-nested PCR. Rotavirus genotype was identified by phylogenetic analysis of the VP7 genetic sequences. Group A rotavirus was detected in 21 water samples (18.4%) and six oyster samples (5.4%). Twenty five rotavirus strains were successfully sequenced and classified into four genotypes; G1, G2, G3, and G9. Rotavirus G1 (three strains), G2 (three strains), and G9 (two strains) demonstrated the genetic sequences similar to human strains (90%–99% nucleotide identity), whereas G3 (17 strains) was closely related to animal strains (84%–98% nucleotide identity). G1 strains belonged to lineages I (sub-lineage c) and II. G2 strains belonged to lineage II. G9 strains belonged to lineages III (sub-lineage b) and IV. G3 strains belonged to lineages I, III (sub-lineage c), and IV with a predominance of lineage I. The present study provides important information on the rotavirus strains circulating in the environment.

A Short Survey on Genetic Sequences, Chou’s Pseudo Amino Acid Composition and its Combination with Fuzzy Set Theory

The study of genetic sequences is of great importance in biology and medicine. Sequence analysis and taxonomy are two major fields of application of bioinformatics. In this survey, we present results concerning genetic sequences and Chou's pseudo amino acid composition as well as methodologies developed based on this concept along with elements of fuzzy set theory, and emphasize on fuzzy clustering and its application in analysis of genetic sequences.

Evolutionary analysis of hepatitis C virus gene sequences from 1953

Reconstructing the transmission history of infectious diseases in the absence of medical or epidemiological records often relies on the evolutionary analysis of pathogen genetic sequences. The precision of evolutionary estimates of epidemic history can be increased by the inclusion of sequences derived from 'archived' samples that are genetically distinct from contemporary strains. Historical sequences are especially valuable for viral pathogens that circulated for many years before being formally identified, including HIV and the hepatitis C virus (HCV). However, surprisingly few HCV isolates sampled before discovery of the virus in 1989 are currently available. Here, we report and analyse two HCV subgenomic sequences obtained from infected individuals in 1953, which represent the oldest genetic evidence of HCV infection. The pairwise genetic diversity between the two sequences indicates a substantial period of HCV transmission prior to the 1950s, and their inclusion in evolutionary analyses provides new estimates of the common ancestor of HCV in the USA. To explore and validate the evolutionary information provided by these sequences, we used a new phylogenetic molecular clock method to estimate the date of sampling of the archived strains, plus the dates of four more contemporary reference genomes. Despite the short fragments available, we conclude that the archived sequences are consistent with a proposed sampling date of 1953, although statistical uncertainty is large. Our cross-validation analyses suggest that the bias and low statistical power observed here likely arise from a combination of high evolutionary rate heterogeneity and an unstructured, star-like phylogeny. We expect that attempts to date other historical viruses under similar circumstances will meet similar problems.

Origin of the viruses and their evolutionary history

The human immunodeficiency virus (HIV) originated via a process of natural evolution, probably emerging from the primate SIV reservoir into the human population via hunting or other behavior involving contact with the blood of these animals. A particular subspecies of chimpanzee, the Pantroglodytes troglodytes, has been recognized as the most probable original source of human infection. Analysis of viral genetic sequences has allowed researchers to estimate that the native strain of HIV originated in 1931. In the West, sexual behavior patterns and injecting drug use subsequently began the epidemic. Polymerase Chain reaction (PCR), is a technique in molecular biology that amplifies a specific region of deoxyribonucleic acid (DNA), and has been useful in the molecular characterization of viruses. The Variola major, the virus that causes the smallpox, lethal virus in the 30% of the cases, was eradicated in 1979 in the human species, thanks to a capillary vaccination on global scale. It has now become a historical footprint in two known laboratories, one in the USA and another in Russia, leaving no obvious source for its often-theorized use as a bioterrorist weapon. Nevertheless, mass vaccination against smallpox continues to be a leading initiative in Western countries to guard against bioterrorist attack.

GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update

Summary: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G′ST, G′′ST, Jost’s Dest and F′ST through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised.Availability and implementation: GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx.Contact: rod.peakall@anu.edu.au

Comparison of the efficacies of amantadine treatment of swine-origin influenza virus A H1N1 and seasonal influenza H1N1 and H3N2 in Japan (2008–2009)

Amantadine is not thought to be effective for the treatment of swine-origin influenza virus (S-OIV) based on an analysis of genetic sequences of the M2 protein. However, the actual clinical efficacy of amantadine has not been well documented. Here, we were able to compare the efficacies of amantadine and neuraminidase inhibitors. Subjects consisted of 428 patients, including 144 with seasonal influenza (flu) identified between 2008 and 2009, and 284 with S-OIV identified between July 1 and November 30, 2009. Diagnosis of flu was established using a rapid diagnostic kit obtained commercially in Japan. Body temperature sheets were obtained from 95% of the S-OIV patients. Times required to recover normal body temperature were compared among subjects using different antiviral drugs. Genetic abnormalities in the M2 protein were also investigated in 66 randomly selected subjects from within the patient pool. Overall, the average hours required to recover normal body temperature in S-OIV patients treated with amantadine (160 cases), with oseltamivir (59 cases), or with zanamivir (65 cases) were 33.9±20.7, 31.7±16.0, or 36.3±21.6, respectively. These differences were not statistically significant. The N31S abnormality was found in all 14 samples taken from the H3N2 patients and in all of the 23 samples taken from in S-OIV patients. However, this abnormality was not found in any of the 30 samples taken from seasonal H1N1 patients. Amantadine was found to be equally effective in treating S-OIV patients as neuraminidase inhibitors. The genetic abnormality resulting in S31N amino acid conversion identified in some of the H3N2 and S-OIV patients is thought to alter the function of M2 protein only mildly.

Seroprevalence and genetic characteristics of five subtypes of influenza A viruses in the Chinese pig population: A pooled data analysis

A literature review and pooled data analysis were carried out to examine the prevalence of antibodies against five influenza virus subtypes in pigs in China over a 10-year period (1999-2009). The average seropositive frequencies of subtypes H1, H3, H5, H7 and H9 were 3478/11,168 (31.1%), 2900/10,139 (28.6%), 77/5945 (1.3%), 0/1440 (0%) and 86/3619 (2.4%), respectively. There was a geographical variation in the seroprevalence of subtype H1, with the highest seroprevalence in pigs in South and East China. BLAST analysis of genetic sequences revealed that genome segments with moderate homology to the 2009 pandemic influenza A (H1N1) virus were present among swine influenza viruses isolated in China, especially in South and East China. It was concluded from both serological and genetic studies that subtypes H1, H3, H5 and H9 are currently co-circulating in pigs in China, with the H1 subtype most commonly detected, followed by H3.

Interoperability of GADU in Using Heterogeneous Grid Resources for Bioinformatics Applications

Bioinformatics tools used for efficient and computationally intensive analysis of genetic sequences require large-scale computational resources to accommodate the growing data. Grid computational resources such as the Open Science Grid and TeraGrid have proved useful for scientific discovery. The genome analysis and database update system (GADU) is a high-throughput computational system developed to automate the steps involved in accessing the Grid resources for running bioinformatics applications. This paper describes the requirements for building an automated scalable system such as GADU that can run jobs on different Grids. The paper describes the resource-independent configuration of GADU using the Pegasus-based virtual data system that makes high-throughput computational tools interoperable on heterogeneous Grid resources. The paper also highlights the features implemented to make GADU a gateway to computationally intensive bioinformatics applications on the Grid. The paper will not go into the details of problems involved or the lessons learned in using individual Grid resources as it has already been published in our paper on genome analysis research environment (GNARE) and will focus primarily on the architecture that makes GADU resource independent and interoperable across heterogeneous Grid resources.

Hantavirus host/virus interactions within Southeast Europe

Viral studies have historically approached their phylogenetic analysis without consideration of the impact of the role the host plays in evolution. Our study examines host/viral interactions through analysis of the phylogenetic relationship between hantavirus genetic sequences and host cytochrome B sequences. Phylogenetic analysis of known Hantavirus genetic sequences were performed using PAUP 3.1.1 (vers. 4.0.0d64). Only sequences available through GENBANK were analyzed. Phylogenetic analysis of hantavirus sequences revealed distinct patterns based upon geographic area. These patterns coincided with the known ranges of reservoir hosts. Multiple hosts for individual viruses and multiple viruses in a single host species for hantaviruses have been described. This may be due to accidental exposure, host-switching, co-speciation, or broad co-accommodation. Since the host is the actual environment that the virus survives in, changes in the host over time could potentially directly influence changes in the virus. Multiple viruses and hosts collide in Southeastern Europe increasing the prospect of finding distinct viral/host relationships. Rodent Cytochrome B is very well conserved and can be used to tract host lineage. By tracking the relationship of infected hosts, we theorize that patterns in host DNA will emerge that will mirror patterns in viral sequences. This analysis of the host DNA could provide an understanding into the causes of variation in hantaviral sequences, pathogenicity, transmissibility, infectivity, viral range and expand our knowledge of viral/host interactions. Surveillance for viruses in the field should include analysis of the host DNA in combination with the viral analysis.

Label-free THz sensing of genetic sequences: towards 'THz biochips'.

THz-wave-based approaches for the label-free characterization of genetic material are described. Time-resolved THz spectroscopic analysis of genetic sequences (polynucleotides) demonstrate a distinct complex refractive index in the THz frequency range as a function of the binding state of the analysed DNA sequences. By monitoring THz signals, one can thus infer the binding state of oligo- and polynucleotides, enabling the label-free determination of the genetic composition of target polynucleotides by sensing their binding to known probe molecules. Here we review integrated THz sensing array developments exhibiting high sensitivity and single-base mutation detection capabilities. Recent achievements using functionalized biosensing arrays of high-Q resonators are illustrated.

Molecular systematics of the old world monkey tribe papionini: analysis of the total available genetic sequences.

The phylogenetic relationships among the genera of the tribe Papionini are inferred using a taxonomic congruence approach in which gene trees derived for eight unlinked genetic sequence datasets are compared. Population genetics theory predicts that species relationships will be revealed with greater probability when the topology of gene trees from many unlinked loci are found to be congruent. The theory underlying this approach is described. Monophyly of the mangabeys is not supported by any of the gene trees; instead, they are polyphyletic with Cercocebus found to be the sister taxon to Mandrillus in five gene trees (with no conflicting trees), and Lophocebus found to be closely related to Papio and/or Theropithecus in all trees. Theropithecus and Papio are not strongly supported as sister taxa (present in one or two trees only);Lophocebus and Papio are supported as sister taxa in the majority of trees. A close relationship between Mandrillus and Papio is not supported in any of the trees.The relationships among Papio, Lophocebus, and Theropithecus cannot be resolved by congruence, probably due to the short time interval estimated between their divergences. The mtDNA COII sequences are used to estimate divergence dates within the papionins. The internode between the divergences of these species is estimated to be between 290 ka and 370 ka. Lastly, the evolution of morphological features such as long faces, suborbital facial fossae, and terrestrial skeletal adaptations is discussed.

On: “3-D seismic imaging and seismic attribute analysis of genetic sequences deposited in low‐ accommodation conditions” (B. A. Hardage, D. L. Carr, D.E. Lancaster, J. L. Simmons Jr., D. S. Hamilton, R. Y. Elphick, K. L. Oliver, and R. A. Johns, GEOPHYSICS, 61, 1351–1362)

The paper deals with the results of a multidisciplinary study of the Bend Conglomerate (Middle Pennsylvanian fluvio‐deltaic clastics) in a portion of Boonsville gas field in the Fort Worth Basin of North‐Central Texas, especially with those related to the Caddo sequence, at the top of the Bend Conglomerate. The purpose of the study was “to determine how modern geophysical, geological, and engineering techniques could be combined to understand the mechanisms by which fluvio‐deltaic depositional processes create reservoir compartmentalization in a low‐ to moderate‐accommodation basin.” According to Hardage et al. (1996), complexly arranged key chronostratigraphic surfaces are major controls on compartmentalization and architecture of reservoirs. These key chronostratigraphic surfaces are flooding surfaces, maximum flooding surfaces, and erosion surfaces.

3-D seismic imaging and seismic attribute analysis of genetic sequences deposited in low‐accommodation conditions

A multidisciplinary team, composed of stratigraphers, petrophysicists, reservoir engineers, and geophysicists, studied a portion of Boonsville gas field in the Fort Worth Basin of North‐Central Texas to determine how modern geophysical, geological, and engineering techniques could be combined to understand the mechanisms by which fluvio‐deltaic depositional processes create reservoir compartmentalization in a low‐ to moderate‐accommodation basin. An extensive database involving well logs, cores, production, and pressure data from 200‐plus wells, [Formula: see text] [Formula: see text] of 3-D seismic data, vertical seismic profiles (VSPs), and checkshots was assembled to support this investigation. The reservoir system we studied was the Bend Conglomerate, a productive series of gas reservoirs composed of Middle Pennsylvanian fluvio‐deltaic clastics 900 to 1300 ft (275 to 400 m) thick in our project area. We were particularly interested in this reservoir system because evidence suggested that many of the sequences in this stratigraphic interval were deposited in low‐accommodation conditions (that is, in an environment where there was limited vertical space available for sediment accumulation), and our objective was to investigate how fluvio‐deltaic reservoirs were compartmentalized by low‐accommodation depositional processes. Using an extensive well log database (200 plus wells) and a core‐calibrated calculation of rock facies derived from these logs, we divided the Bend Conglomerate interval into ten genetic sequences, with each sequence being approximately 100 ft (30 m) thick. We then used local VSP and checkshot control to transform log‐measured depths of each sequence boundary to seismic two‐way time coordinates and identified narrow seismic data windows encompassing each sequence across the [Formula: see text] [Formula: see text] 3-D seismic grid. A series of seismic attributes was calculated in these carefully defined data windows to determine which attributes were reliable indicators of the presence of productive reservoir facies and which attributes could, therefore, reveal distinct reservoir compartments and potentially show where infield wells should be drilled to reach previously uncontacted gas reservoirs. Our best success was the seismic attribute correlations we found in the Upper and Lower Caddo sequences, at the top of the Bend Conglomerate. These sequences were deposited in a low‐accommodation setting, relative to other Boonsville sequences, and we found that reflection amplitude and instantaneous frequency, respectively, were reliable indicators of the areal distribution of reservoir facies in these low‐accommodation sequences.

Lack of HIV Transmission in the Practice of a Dentist with AIDS

To determine whether dentist-to-patient or patient-to-patient transmission of human immunodeficiency virus (HIV) occurred in the practice of a dentist who had the acquired immunodeficiency syndrome (AIDS). Retrospective epidemiologic investigation supported by molecular virology studies. The practice of a dentist with AIDS in an area with a high AIDS prevalence. A dentist with AIDS, his former employees, and his former patients, including 28 patients with HIV infection. Identification of potential risks for acquisition of HIV infection, genetic relatedness among HIV strains, and infection-control practices. A dentist with known behavioral risks for HIV infection, who was practicing in an area of Miami, Florida, that had a high rate of reported AIDS cases, disclosed that he frequently did invasive procedures and did not always follow recommended infection-control procedures. Of 6474 patients who had records of receiving care from the dentist during his last 5 years of practice, 1279 (19.8%) were known to have been tested for HIV infection and 24 of those (1.9%) were seropositive. Four other patients with HIV infection were identified through additional case-finding activities. Of these 28 patients with HIV infection, all but 4 had potential behavioral risk factors for infection. Phylogenetic tree analysis of HIV genetic sequences from the dentist and 24 of the patients with HIV infection showed an absence of strong bootstrap support for any grouping and therefore did not indicate that the virus strains were linked. Despite identifying numerous patients with HIV infection, we found no evidence of dentist-to-patient or patient-to-patient transmission of HIV during dental care. Our findings are consistent with those of all previous studies in this area, with the exception of one that did identify such transmission.

Computational Analysis of Genetic Sequences

Computational Analysis of Genetic Sequences

Increasing Our Capacities

Increasing Our Capacities