High Variation Rate Research Articles

Identifying Overlapping Phylogenetic and Geographic Roots of HIV – 1 Evolution through Computational Analyses

HIV-1 or Human Immuno Deficiency Virus-1 is the main causative agent of Acquired Immuno Deficiency Syndrome (AIDS). Human host infected with HIV - 1 extensively harbours many viral variants but very little is known about the difference in pattern[17] of evolution of phylogenetic lineages of HIV-1 non recombinant, normal inter subtype recombinant and main two specific recombinant forms of HIV-1 i.e., Circulating Recombinant Forms (CRFs) and Unique Recombinant Forms (URFs). This study is mainly concerned with study of the difference in evolutionary lineages of non-recombinant and recombinant sequences of HIV-1 genome sequences and identification of geographically rich areas which has reported high degree of HIV-1 occurrence and variety. Total 1550 HIV-1 genome sequences were obtained from HIV Los Alamos Database. The sequences were aligned using MAFFT (Multiple Alignment using Fast Fourier Transform) web server tool. Alignment was carried out using 10 different set of alignment parameter values. After alignment the aligned file was used for constructing N-J phylogenetic tree using Clustal X2 tool. Phylogenetic analysis was performed keeping in mind the category to which the sequence belongs. Upon analysis it was observed that the clade containing the probable ancestor belongs remained constant in all cases of different alignment values. Non recombinant isolates, inter subtype recombinants, CRFs, URFs all followed different patterns of evolution. Non recombinant sequences were found geographically specific and subtype specific to some extent whereas, normal recombinants were subtype specific and less geographically specific. CRFs showed variation among the pattern of their evolution. At some instances the sequences occurred as sister taxa of non-recombinant or normal inter subtype recombinant sequences, while at some instances as sister taxa of other CRFs where they were geographically specific. Three CRFs existed as completely diverged sequences. URFs were four in number; two of them were Indian isolates of while other two were Japanese isolates. URFs were found to be totally geographically specific. Geography wise high rate of variation was observed in India and Japan as these two countries had sequences belonging to all of the above categories. Cameroon and South Africa have very large number isolates and a considerable amount of genetic variation among isolates but they lack URFs.

Finish machining of mirror-like diamond surfaces using a composite electroplating in-process sharpening method

Finishing mirror-like surfaces on chemically vapor-deposited diamond film using an in-process composite electroplating of diamond grains onto the tool surface, the tool can maintain its sharpness in a grinding process. The effect of diamond grit size of the tool on the grinding characteristics of diamond film is investigated. To promote optimum grinding efficiency, a high variation rate in the surface roughness of diamond film and a small growth rate in the coating thickness are desired. A distribution model of the diamond grits in the coating layer is deduced, and a composite electroplating in-process sharpening grinding mechanism is developed using a body-centered tetragonal structure. A two-stage composite electroplating in-process sharpening grinding procedure is used to grind the diamond film. A grit size of 25 µm is selected to conduct the composite electroplating in-process sharpening grinding for 30 min at an initial surface roughness of 1.1 µm. Then, the operating conditions are switched to a grit size of 3 µm and a grinding time of 180 min, and a mirror-like surface on the diamond film with an average surface roughness of 0.03 µm is obtained.

Research and Application of Dynamic Secondary Cooling Control Method for Slab Caster of CISDI

After analyzing the characteristics of each type of dynamic secondary cooling control methods, the combination use of on-line thermal model control and effective casting speed computer dynamic control method was adopted in CISDI dynamic secondary cooling control. On the basis, the transient heat-transfer mathematic model was developed, the determination methods of strand target surface temperature and real time cooling water were proposed, and the design idea of effective casting speed computer dynamic control method was introduced. Considering the probably unreliability of heat transfer difference calculation and inadaptability of heat transfer boundary conditions when too low, too high casting speed or speed variation rate, the on-line thermal model control method was used when the casting speed between 0.8m/min and 1.4 m/min and casting speed variation rate within 0.1m/(min·s), in other cases, effective casting speed computer dynamic control method was adopted.

Fluctuation of farming-pastoral ecotone in association with changing East Asia monsoon climate

As a monsoon climate dominated region, East Asia has a high rate of climate variation. Previous studies demonstrated that the East Asian monsoon had weakened since the end of 1970's; however, contrary to the climatic trend, a common scenario of advancing farming-pastoral ecotone (FPE) has been proposed. The objective of this study is to analyze land surface changes in association with monsoon climate variability over past 25 years in East Asia. A combination of intensive ground survey of vegetation and land use, meteoro- logical data, and remote sensing are used to quantify the relationship between vegetation and climate and to analyze the FPE fluctuations associated with changing climate. Field precip- itation data from 1981 to 2005, are used to represent climate variations and to delineate the FPE boundary. NDVI data are used to evaluate greenness-precipitation linkages by vegeta- tion type and to create land cover maps depicting spatial pattern fluctuations of the FPE. This study demonstrates that: (1) There was no persistent northwest shifting trend of either the FPE boundary or vegetation cover during last 25 years. (2) Time integrated NDVI (TI- NDVI) varies with precipitation, and the maximum or minimum NDVI may be only sensitive to precipitation for areas with mean annual precipitation lower than approximately 200 mm. (3) A significant relationship exists between NDVI and precipitation variations for areas with mean annual precipitation greater than approximately 300 mm, especially the ecotone with a ΔNDVI of 0.122±0.032. (4) The "advances" of FPE closely mimic fluctu- ations of precipitation in East Asia.

Analysis of genomic DNA methylation patterns in regenerated and control plants of rye (Secale cereale L.)

Rye (Secale cereale L.) is a species that has shown high rates of somaclonal variation when plants obtained by in vitro culture were analysed using different techniques. In this study, using methylation-sensitive amplified polymorphism (MSAP) markers, we analysed the cytosine methylation status at genomic level of regenerated plants of rye that were obtained by somatic embryogenesis. Such plants were originated from three different cell lines and the results were compared with the data obtained from the control plants grown from seeds of the same cultivar and lot. A similar total number of MSAP markers was observed in the regenerated (937) and control plants (1,022), while the mean number detected per plant was significantly higher in regenerated (554.43) than in control plants (356.00). The analysis indicated conservation of the number of partially-methylated CCGG/GGCC sites for all type of plants. However the mean number of non-methylated sites was near twofold in the regenerated plants (442.48) than in control plants (248.19). Methylation changes have been detected in all the regenerated plants when compared within cell lines, with an average frequency of 9.01 % of the detected markers. We also observed that regenerated plants from one or several cell lines shared methylation changes at the same locus pointing to a non-random behaviour of the changes in genomic methylation.

Rapid deposition process for zinc oxide film applications in pyroelectric devices

Aerosol deposition (AD) is a rapid process for the deposition of films. Zinc oxide is a low toxicity and environmentally friendly material, and it possesses properties such as semiconductivity, pyroelectricity and piezoelectricity without the poling process. Therefore, AD is used to accelerate the manufacturing process for applications of ZnO films in pyroelectric devices. Increasing the temperature variation rate in pyroelectric films is a useful method for enhancing the responsivity of pyroelectric devices. In the present study, a porous ZnO film possessing the properties of large heat absorption and high temperature variation rate is successfully produced by the AD rapid process and laser annealing for application in pyroelectric devices.

Tracking control of variable stiffness hysteretic-systems using linear-parameter-varying gain-scheduled controller

Tracking control of systems with variable stiffness hysteresis using a gain-scheduled (GS) controller is developed in this paper. Variable stiffness hysteretic system is represented as quasi linear parameter dependent system with known bounds on parameters. Assuming that the parameters can be measured or estimated in real-time, a GS controller that ensures the performance and the stability of the closed-loop system over the entire range of parameter variation is designed. The proposed method is implemented on a spring-mass system which consists of a semi-active independently variable stiffness (SAIVS) device that exhibits hysteresis and precisely controllable stiffness change in real-time. The SAIVS system with variable stiffness hysteresis is represented as quasi linear parameter varying (LPV) system with two parameters: linear time-varying stiffness (parameter with slow variation rate) and stiffness of the friction-hysteresis (parameter with high variation rate). The proposed LPV-GS controller can accommodate both slow and fast varying parameter, which was not possible with the controllers proposed in the prior studies. Effectiveness of the proposed controller is demonstrated by comparing the results with a fixed robust <TEX>$\mathcal{H}_{\infty}$</TEX> controller that assumes the parameter variation as an uncertainty. Superior performance of the LPV-GS over the robust <TEX>$\mathcal{H}_{\infty}$</TEX> controller is demonstrated for varying stiffness hysteresis of SAIVS device and for different ranges of tracking displacements. The LPV-GS controller is capable of adapting to any parameter changes whereas the <TEX>$\mathcal{H}_{\infty}$</TEX> controller is effective only when the system parameters are in the vicinity of the nominal plant parameters for which the controller is designed. The robust <TEX>$\mathcal{H}_{\infty}$</TEX> controller becomes unstable under large parameter variations but the LPV-GS will ensure stability and guarantee the desired closed-loop performance.

Comparative Analysis of Mycobacterium tuberculosis pe and ppe Genes Reveals High Sequence Variation and an Apparent Absence of Selective Constraints

Mycobacterium tuberculosis complex (MTBC) genomes contain 2 large gene families termed pe and ppe. The function of pe/ppe proteins remains enigmatic but studies suggest that they are secreted or cell surface associated and are involved in bacterial virulence. Previous studies have also shown that some pe/ppe genes are polymorphic, a finding that suggests involvement in antigenic variation. Using comparative sequence analysis of 18 publicly available MTBC whole genome sequences, we have performed alignments of 33 pe (excluding pe_pgrs) and 66 ppe genes in order to detect the frequency and nature of genetic variation. This work has been supplemented by whole gene sequencing of 14 pe/ppe (including 5 pe_pgrs) genes in a cohort of 40 diverse and well defined clinical isolates covering all the main lineages of the M. tuberculosis phylogenetic tree. We show that nsSNP's in pe (excluding pgrs) and ppe genes are 3.0 and 3.3 times higher than in non-pe/ppe genes respectively and that numerous other mutation types are also present at a high frequency. It has previously been shown that non-pe/ppe M. tuberculosis genes display a remarkably low level of purifying selection. Here, we also show that compared to these genes those of the pe/ppe families show a further reduction of selection pressure that suggests neutral evolution. This is inconsistent with the positive selection pressure of “classical” antigenic variation. Finally, by analyzing such a large number of genes we were able to detect large differences in mutation type and frequency between both individual genes and gene sub-families. The high variation rates and absence of selective constraints provides valuable insights into potential pe/ppe function. Since pe/ppe proteins are highly antigenic and have been studied as potential vaccine components these results should also prove informative for aspects of M. tuberculosis vaccine design.

Molecular phylogeny and evolution of the Perissodactyla

The evolution of perissodactyls (rhinoceroses, tapirs, and horses) has been well studied primarily because of their extensive fossil record. Nevertheless, controversy persists regarding relationships of some of the extant taxa, reflecting inconsistencies between molecular and morphological studies. Here we examine the phylogenetic relationships of 16 living perissodactyl species by concatenating two mitochondrial and nine nuclear genes, and we estimate their divergence times using a relaxed Bayesian molecular clock approach. Our analyses recovered the monophyly of the suborders Ceratomorpha and Hippomorpha, and the families Rhinoceratidae, Tapiridae, and Equidae. We supported the early divergence of the Indian rhinoceros in the late Oligocene (26 Mya) relative to the Sumatran and African rhinoceroses, and the split of caballine (domestic horse and Przewalski's wild horse) and noncaballine equids (zebras and African and Asiatic asses) in the Pliocene (4 Mya). An important implication of this study is that Equus asinus, the African wild ass was found to be the sister taxon of Asiatic asses and zebras, diverging from the common ancestor with caballine horses 2 Mya. Rates of chromosome rearrangements were also evaluated in perissodactyls, placing a notably high rate of variation amongst equids, particularly within the zebra clade. The robust phylogenetic results presented here are relevant in terms of understanding the evolutionary history of this highly threatened group of mammals. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163, 1289–1303.

Detection and characterization of canine astroviruses

Astroviruses (AstVs) have been identified only occasionally in dogs. A canine AstV, strain Bari/08/ITA, was detected from a pup with gastroenteric signs and the virus was isolated in cell culture and characterized molecularly. In the full-length capsid protein, the virus displayed genetic similarities (83.5 % aa identity) to another canine AstV strain, although a high rate of variation occurred in the hypervariable domain, which is related to AstV antigenic specificity. Specific antibodies were detected in the convalescent dog, indicating seroconversion, and in 59 % of a collection of dog serum samples. Using primers specific for canine AstV, designed to detect a conserved region of ORF1b, canine AstVs were detected in 24.5 % of young pups with gastroenteritis, either alone or in mixed infections with other canine pathogens. In contrast, AstVs were detected in only 9.3 % of asymptomatic pups. These findings indicate that canine AstVs are common in dogs and may suggest a possible role as canine enteric pathogens.

Thermal Fatigue Study of Hardfaced Hot Forging Tool Using Numerical Analysis and Residual Stress Evaluation

Hot forging tools are exposed to severe thermo-mechanical load which cause their failure. The main failure mechanisms are mechanical fatigue, thermal fatigue, plastic deformation and abrasive wear. The use of hardfacing is an effective solution to increase tool life and consequently reducing the cost of forged part. In this work the use of a cobalt-base hard-facing obtained by Plasma Transferred Arc process is studied. The hardfacing is used for tool failed by thermal cracking. The high rate of temperature variation and high temperature gradient at the tool surface induce material softening and surface plastic deformation. These plastic deformations are accumulated during each cycle and eventually cause cracks in the most exposed zones and then tool failure after a few thousand cycles. Microstructure characterization and mechanical behavior analyses are required to prove the quality of coating. Finite element method is used to calculate stress distribution in tool resulting from external loading in order to optimize the thickness and the choice of coating used. Evaluation of residual stresses by ultrasonic technique is used to validate the finite element results and analyze the stress state by non destructive method.

Sagnac interferometer with adaptive nonlinear detection

We present a Sagnac interferometer that uses a nonlinear adaptive medium for detection. The nonlinearity of the medium being characterized by a finite response time, the detection has a finite frequency bandwidth determining two operational regimes: at low variation rate of the rotation speed the interferometer operates in the slow-light regime, providing a direct measurement of the angular acceleration. For high variation rate of the rotation speed the amplitude of the alternating component of the Sagnac phase shift is instead detected, with the continuous and low-frequency components filtered out by the adaptive nonlinear process in the medium.

Rev variation during persistent lentivirus infection.

The ability of lentiviruses to continually evolve and escape immune control is the central impediment in developing an effective vaccine for HIV-1 and other lentiviruses. Equine infectious anemia virus (EIAV) is considered a useful model for immune control of lentivirus infection. Virus-specific cytotoxic T lymphocytes (CTL) and broadly neutralizing antibody effectively control EIAV replication during inapparent stages of disease, but after years of low-level replication, the virus is still able to produce evasion genotypes that lead to late re-emergence of disease. There is a high rate of genetic variation in the EIAV surface envelope glycoprotein (SU) and in the region of the transmembrane protein (TM) overlapped by the major exon of Rev. This review examines genetic and phenotypic variation in Rev during EIAV disease and a possible role for Rev in immune evasion and virus persistence.

The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82

Soybean (Glycine max) is a self-pollinating species that has relatively low nucleotide polymorphism rates compared with other crop species. Despite the low rate of nucleotide polymorphisms, a wide range of heritable phenotypic variation exists. There is even evidence for heritable phenotypic variation among individuals within some cultivars. Williams 82, the soybean cultivar used to produce the reference genome sequence, was derived from backcrossing a Phytophthora root rot resistance locus from the donor parent Kingwa into the recurrent parent Williams. To explore the genetic basis of intracultivar variation, we investigated the nucleotide, structural, and gene content variation of different Williams 82 individuals. Williams 82 individuals exhibited variation in the number and size of introgressed Kingwa loci. In these regions of genomic heterogeneity, the reference Williams 82 genome sequence consists of a mosaic of Williams and Kingwa haplotypes. Genomic structural variation between Williams and Kingwa was maintained between the Williams 82 individuals within the regions of heterogeneity. Additionally, the regions of heterogeneity exhibited gene content differences between Williams 82 individuals. These findings show that genetic heterogeneity in Williams 82 primarily originated from the differential segregation of polymorphic chromosomal regions following the backcross and single-seed descent generations of the breeding process. We conclude that soybean haplotypes can possess a high rate of structural and gene content variation, and the impact of intracultivar genetic heterogeneity may be significant. This detailed characterization will be useful for interpreting soybean genomic data sets and highlights important considerations for research communities that are developing or utilizing a reference genome sequence.

Y chromosome variations and male infertility

Male infertility is a common complex disease. Y-linked spermatogenic failure is an important cause for this disorder. Due to the presence of many repeat sequences and the frequent occurrence of non-allelic homologous recombination between the sequences in the male-specific region of the Y (MSY) region of the chromosome, Y chromosome possesses high variation rate. The variations may result in the dosage changes of spermatogenesis-related gene families and lead to male infertility. The present article reviews the recent progress of the study on Y chromosome variations, and its possible effect on spermatogenic function, in DNA level.

Genetic diversity and population structure in Meconopsis quintuplinervia (Papaveraceae)

Meconopsis quintuplinervia is regarded as a valuable medicinal plant in Tibetan medicinal system. This species is distributed in Qinghai, Xizang, Sichuan, Shanxi ,Gansu and Hubei provinces of the People's Republic of China. Genetic variation of 16 M. quintuplinervia populations sampled from Qinghai and Gansu of China was examined by random amplified polymorphic DNA markers (RAPDs). In total, 225 scored DNA bands were amplified from the 17 primers used. Of the 225 loci, 192(85.33%) were polymorphic, and total genetic diversity (Ht) was 0.2954 and Shannon’s information index (I) was0.4371, suggesting a relatively high rate of genetic variation at the species level. The average within-population diversity also appeared to be high, with PPB, He and I values of 70.50%, 0.2408 and 0.3347, respectively. Analysis of molecular variance (AMOVA) revealed 78.3% of variation within populations and only 21.7% between populations. Nei’s coefficient of differentiation (GST) was found to be high (0.2320), also confirming the relatively high level of genetic differentiation within populations. By UPGMA cluster analysis, based on Nei’s standard genetic distance, the populations were divided into three groups including the populations distributed in same location together in every group. The results exhibit a strong genetic differentiation which is obviously due to genetic drift in the isolated populations. The genetic structure of M. quintuplinervia has probably been shaped by its breeding modes, biogeographic history and human impact (both grazing and collection for medicinal purposes). This research might be an efficient way to conserve genetic resources of the medicinal plant, in addition to its effective uses.

The development of entrepreneurship in Chinese communities: An organizational symbiosis perspective

Why has the rate of entrepreneurship recently gone down in Singapore? Why is entrepreneurship in Southern China (e.g., Guangdong or Fujian provinces) relatively higher than in the rest of China? Why is corruption rampant in some Chinese business communities but virtually nonexistent in others? Although we often speak of “Chinese entrepreneurship” as a monolithic entity, the fact is that there are many variants of Chinese entrepreneurship and these variants continue to rapidly evolve and take on new forms. Yet mainstream management or organizational theories have been at a loss to explain these high rates of variation and evolution. To shed light on these issues, we introduce the idea of symbiosis from biology and adapt it to the development of entrepreneurship in Chinese ethnic communities. Symbiosis is the science of how different organisms coexist with each other in a self-sustaining system. Using this approach, we develop six propositions to explain what types of entrepreneurship are likely to evolve in different Chinese ethnic communities and how this process of evolution is likely to proceed. The implications for researchers and practitioners are discussed.

Classification and Seed Set of Varied Embryo Sacs of Autotetraploid Rice*

Autotetraploid strains which are developed from diploid individuals by colchicine treatments exhibit high variation rates of embryo sacs. Abnormal embryo sacs frequently occur in the spikelets of main panicles and the first tillers 1~2 d before heading, leading to obvious decreases in the degrees of normal embryo sacs among the strains. The varied embryo sacs are classified into four types according to their different structures and origins: Degenerated embryo sac (DES), structure variation (SV), apomixis (Apo) and antipodal cell proliferation (ACP). The DES exhibits small embryo sac or no embryo sac, with the former showing a small sac and the latter showing no sac. The SV includes deletion, duplication and location variation, which suggests the occurrence of the variations of the eight nuclei, seven celled embryo sacs of the Polygonum type. The Apo occurs at very low frequency and includes antipodal embryo and egg embryo. The ACP frequently occurs in autotetraploid rice that leads to the increase in diversity of the embryo sacs and simultaneously influences seed germination. The Pearson’s correlation analysis shows that seed set is contributed by three main parts: normal embryo sac, small embryo sac with normal pattern and embryo sac with antipodal proliferation. These embryo sacs may be highly fertile and account for 72.44%, 15.12%, 12.44% of seed set, respectively. The NES is negatively related to seed set at the P0.01 level and the LV negatively related to seed set at the P0.05 level, which suggests strong stress on seed set by the two types.

Sensitive population profiling and genome assembly of HIV and Flaviviruses using ultra-deep sequencing technologies

Viral diseases such as HIV/AIDS and Dengue have an enormous impact on human health worldwide. Despite this, application of new sequencing technologies to viral genomics has lagged. We are using genome sequence data to study how populations of single stranded RNA viruses, including HIV, Dengue, West Nile and Hepatitis C, evolve within infected individuals in response to host immune, therapeutic and vaccine pressures. To support this, we have developed high-throughput sequencing, assembly and population profiling pipelines based on 454 and Illumina technology that are tuned to the specific needs of viral sequencing. These strategies can capture full genome sequences and can profile sequence diversity at each residue in the genome with unprecedented sensitivity. Our analytical pipeline for 454 and Illumina data (i) generates complete genome assemblies from short sequencing reads derived from populations with high rates of variation; and (ii) detects and quantifies variants in these populations with high sensitivity, while differentiating true variants from process errors. Initial results with our viral sequencing and analysis pipeline are extremely promising. We detected rare variants to below 1% frequency, revolutionizing our ability to accurately assess the earliest events in viral evolution. We have demonstrated effective assessment of genome-wide diversity during acute HIV infection, enabling rapid, affordable, and highly sensitive identification of the earliest cellular immune responses to HIV. This has allowed us to detect earlier evolutionary events, demonstrating, for example, that HIV cytotoxic T-lymphocyte (CTL) escape can occur much faster than previously known. In addition, we have shown that the extent of intra-host diversity in Flaviviruses such as DENV and WNV is different between these closely related viruses with the latter exhibiting greater genetic diversity. The results presented here demonstrate the power of scalable, next generation sequencing-based methodologies as a genome-wide and unbiased global approach to profiling genomic diversity in intra-host populations of single stranded RNA viruses.

GP practice variation in hospitalisation rates: a study of Partnership Health–enrolled patients

This project aims to provide information to support the planning and implementation of strategies to reduce hospitalisation. It examines variations in hospital discharge rates between practice populations and the use of special general practice access funding. Practice enrolment data for 345 254 patients enrolled with 102 Partnership Health Primary Health Organisation (PHO) general practices were sent to New Zealand Health Information Service. Data linked to the patient National Health Index (NHI) relating to hospital discharges were attached to the practice enrolment data for the two years ending June 2007 and returned to the researchers with the NHI numbers encrypted. Total discharges were 127426. The data were analysed for rates of hospital discharges for different population groups and by general practice. There is a substantial variation in hospital discharge rates between general practices, but this is only partly accounted for by practice population characteristics. Furthermore while there is a strong social gradient in European admissions, this is much less true for Maori. There was also a wide variation between practices in the uptake of High Use Health Cards, special funding for frequent attenders at general practices and 'Care Plus' funding for patients with chronic conditions. Practice deprivation, ethnicity and age only explained a minor part of this variation. The high rate of unexplained practice variation in chronic care management and hospitalisation rates, especially for Maori, is of concern. Further investigation of the causes of such variability is needed as afirst step in reducing hospitalisation.