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The entire transcribed sequences (from the 5' terminus of 18S to the 3′ terminus of 28S rRNA genes) of the ribosomal transcription units (rTU*) of five Asian Paragonimus species were obtained and characterized. The rTU* length was 7661 bp for P. heterotremus (LC strain, Vietnam), 7422 bp for P. iloktsuenensis (Amami strain, Japan), 6932 bp for P. skrjabini miyazakii (OkuST1 strain, Japan), 7422 bp for P. ohirai (Kino strain, Japan), and three strains of P. westermani: 8616 bp (Megha strain, India), 7292 bp (Bogil strain, South Korea), and 7052 bp (QT2 strain, Vietnam) without intergenic spacer region (IGS). All seven Asian Paragonimus strains’ genetic characteristics were described, including the length of individual genes/regions, repeat polymorphism, base composition, and skewness. To investigate the superfamilial relationships in the Xiphidiata, with a focus on the Troglotrematoidea and its associated superfamilies, we used the PhyML software package to create three comprehensive maximum-likelihood phylogenies. The datasets used were 83 concatenated 28S + 18S, 83 single complete 18S, and 157 single, partial 28S rDNA sequences, respectively, from entire rTUs and/or accessible ribosomal sequences of the same species from the suborders Xiphidiata, Echinostomata, and Haplosplanchnata, with a Schistosoma sequence as an outgroup. Three phylogenetic trees revealed that Echinostomata and Haplosplanchnata are monophyletic, while Xiphidiata is polyphyletic and contains the monophyletic Troglotrematoidea. The concatenated 18S + 28S and single 18S phylogenies revealed well-bootstrap supported seven superfamilies (Troglotrematoidea, Haploporoidea, Gorgoderoidea, Brachycladioidea, Microphalloidea, Plagiorchioidea, and Opecoeloidea) that are monophyletic in the Xiphidiata. The Haploporoidea was a basal superfamily nested close to the Gorgoderoidea and Troglotrematoidea and was not supported as a distinct suborder Haploporata. Six of seven xiphidiatan superfamilies were monophyletic in the partial 28S phylogeny, with the exception of Opecoeloidea, which was separated into two different subclades: Opecoelidae and Stenakridae/Zdzitowieckitrematidae. The monophyletic Haploporoidea/Haploporata was separated from the Gorgoderoidea associates and placed in a marginal group in Xiphidiata. There were two notable clusters in the Paragonimidae: mixed-Paragonimus, which included a fairly compact group of P. heterotremus strains, and P. westermani/siamensis, which was divided into geographical/country strain groups. In conclusion, combined ribosomal rDNA sequences were more effective than single rDNA markers in resolving interfamilial and familial relationships. The ribosomal datasets presented here will be useful for taxonomic reassessment, as well as evolutionary and population genetics research in the Troglotrematoidea and other superfamilies in the Xiphidiata and the class Trematoda. [ABSTRACT FROM AUTHOR]

Ticks are specialized ectoparasites that feed on blood, causing physical harm to the host and facilitating pathogen transmission. The genus Haemaphysalis contains vectors for numerous infectious agents. These agents cause various diseases in humans and animals. Mitochondrial genome sequences serve as reliable molecular markers, forming a crucial basis for evolutionary analyses, studying species origins, and exploring molecular phylogeny. We extracted mitochondrial genome from the enriched mitochondria of Haemaphysalis tibetensis and obtained a 14,714-bp sequence. The mitochondrial genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNAs (tRNAs), and two control regions. The nucleotide composition of H. tibetensis mitochondrial genome was 38.38 % for A, 9.61 % for G, 39.32 % for T, and 12.69 % for C. The A + T content of H. tibetensis mitochondrial genome was 77.7 %, significantly higher than the G + C content. The repeat units of H. tibetensis exhibited two identical repeat units of 33 bp in length, positioned downstream of nad1 and rrnL genes. Furthermore, phylogenetic analyses based on the 13 PCGs indicated that Haemaphysalis tibetensis (subgenus Allophysalis) formed a monophyletic clade with Haemaphysalis nepalensis (subgenus Herpetobia) and Haemaphysalis danieli (subgenus Allophysalis). Although the species Haemaphysalis inermis, Haemaphysalis kitaokai, Haemaphysalis kolonini, and Haemaphysalis colasbelcouri belong to the subgenus Alloceraea, which were morphologically primitive hemaphysalines just like H. tibetensis, these four tick species cannot form a single clade with H. tibetensis. In this study, the whole mitochondrial genome sequence of H. tibetensis from Tibet was obtained, which enriched the mitochondrial genome data of ticks and provided genetic markers to study the population heredity and molecular evolution of the genus Haemaphysalis.

Ticks are specialized ectoparasites that feed on blood, causing physical harm to the host and facilitating pathogen transmission. The genus Haemaphysalis contains vectors for numerous infectious agents. These agents cause various diseases in humans and animals. Mitochondrial genome sequences serve as reliable molecular markers, forming a crucial basis for evolutionary analyses, studying species origins, and exploring molecular phylogeny. We extracted mitochondrial genome from the enriched mitochondria of Haemaphysalis tibetensis and obtained a 14,714-bp sequence. The mitochondrial genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNAs (tRNAs), and two control regions. The nucleotide composition of H. tibetensis mitochondrial genome was 38.38 % for A, 9.61 % for G, 39.32 % for T, and 12.69 % for C. The A + T content of H. tibetensis mitochondrial genome was 77.7 %, significantly higher than the G + C content. The repeat units of H. tibetensis exhibited two identical repeat units of 33 bp in length, positioned downstream of nad1 and rrnL genes. Furthermore, phylogenetic analyses based on the 13 PCGs indicated that Haemaphysalis tibetensis (subgenus Allophysalis) formed a monophyletic clade with Haemaphysalis nepalensis (subgenus Herpetobia) and Haemaphysalis danieli (subgenus Allophysalis). Although the species Haemaphysalis inermis, Haemaphysalis kitaokai, Haemaphysalis kolonini , and Haemaphysalis colasbelcouri belong to the subgenus Alloceraea , which were morphologically primitive hemaphysalines just like H. tibetensis , these four tick species cannot form a single clade with H. tibetensis. In this study, the whole mitochondrial genome sequence of H. tibetensis from Tibet was obtained, which enriched the mitochondrial genome data of ticks and provided genetic markers to study the population heredity and molecular evolution of the genus Haemaphysalis. [ABSTRACT FROM AUTHOR]

Internal Transcribed Spacer structures are important in preserving accessibility to specific enzymes for the maturation of rRNAs. ITS1 sequences reported in the literature in Crustaceans range between 182 and 820 bp and are characterized by the absence of repeats or the presence of only a limited number of microsatellites. Here, we sequenced ITS1 for a range of shrimp families (infraorder Caridea) and show that most taxa have much larger ITS1 sequences. We find a high number of microsatellites in Alpheus hebes and Crangon crangon and we report repeat units in Pandalidae, Palaemonidae and mainly in Alpheidae species. Up to four repeats were found in A. vanderbilti (1915 bp), A. rostratus (1635 bp) and A. lottini (1625 bp). In general, four helices were found in ITS1. Repeat units led to extra hairpins and loops. No conserved positions occurred except in helix 4. Three clades were defined in A. lottini for the first time. We estimated the ITS1 divergence rate for the three clades of A. lottini collected in French Polynesia using existing calibrations of substitution rates. Rates of sequence evolution are largely influenced by repeat units, which likely evolve separately. By comparison with COI marker, we estimated the divergence rate of the whole ITS1 sequence to range from 0.5 to 1.4% Pmy and between 0.12 and 0.5% for the 3′ end of ITS1 located outside the repeat units. Given the degree of identity between repeats, we suggest that a duplication event recently occurred in A. floridanus (98% identity) whereas an ancient duplication happened in A. sulcatus (50% identity) early at the origination of the group Alpheidae, approximately 50 mya ago. In conclusion, our results highlight an over representation of shorter ITS1 sequences in public repositories, and underlines the importance to further understand patterns of molecular evolution of this functionally important gene. [ABSTRACT FROM AUTHOR]

BackgroundRecently, Mycobacterial Interspersed Repetitive Unit (MIRU) was supposed to be associated with drug resistance in M.tuberculosis (MTB). However, whether the MIRU was related to drug resistance actually was still unknown. This research was conducted to explore that association.MethodsDrug susceptibility testing was used to evaluate the drug resistance of five anti-tuberculosis drug (isoniazid, INH; rifampicin, RFP; streptomycin, SM; ethambutol, EMB; and Paminosalicylicacid, PAS.). We tested the number of the repeat unite of MIRU (Mycobacterial Interspersed Repetitive Unit) locus based on PCR of miru-vntr genotyping. Then, through logistic regression, we evaluated the association between fifteen MIRU and the resistance. In addition, we explored the most suitable MIRU locus of identified MIRU loci for drug resistance through multivariate logistic regression.ResultsAmong these fifteen MIRU, we found several MIRU loci could predict the drug resistance well. For example ,ETRB and ETRC could predict INH resistance; MIRU20 was associated with EMB resistance; and QUB11a was a predictive factor of PSA. ConclusionOur results may provide candidate regions for future genetic studies and aid in the prediction for drug resistance of MTB.

Background: Recently, Mycobacterial Interspersed Repetitive Unit (MIRU) was supposed to be associated with drug resistance in Mycobacterium tuberculosis (M. tuberculosis), but whether the association exists actually in local strains in China was still unknown. This research was conducted to explore that association and the predictability of MIRU to drug resistance of Tuberculosis (TB). Methods: The clinical isolates were collected and the susceptibility test were conducted with Lowenstein-Jensen (LJ) medium for five anti-TB drug. Based on PCR of MIRU- VNTR (Variable Number of Tandem Repeat) genotyping, we tested the number of the repeat unite of MIRU. Then, we used logistic regression to evaluate the association between 15 MIRU and drug resistance. In addition, we explored the most suitable MIRU locus of identified MIRU loci for drug resistance by multivariate logistic regression. Results: Of the 102 strains, one isolate was resistant to rifampicin and one isolate was resistant to streptomycin. Among these fifteen MIRU, there was a association between MIRU loci polymorphism and anti-tuberculosis drug resistance, ETRB (P = 0.03, OR = 0.19, 95% CI 0.05-0.81) and ETRC (P = 0.01, OR = 0.14, 95% CI 0.03-0.64) were negatively related to isoniazid resistance; MIRU20 (P = 0.05, OR = 2.87, 95% CI 1.01-8.12) was positively associated with ethambutol resistance; and QUB11a (P = 0.02, OR = 0.79, 95% CI 0.65-0.96) was a negative association factor of p-aminosalicylic acid resistance. Conclusion: Our research showed that MIRU loci may predict drug resistance of tuberculosis in China. However, the mechanism still needs further exploration. [ABSTRACT FROM AUTHOR]

This article continues modeling of the polaron conductance of polymer films in the general case of an arbitrary number of polymer repeat units included into the polaron structure. The main feature of the proposed approach is stipulated by the introduced definition of reduced quasi-particles as species that contain only one repeat unit of polymer chains, but not the same their quantity (usually, 3-6 units) included into polaron species according to the previously accepted description of polaron-containing polymer films. For a homogeneous population of polarons, every one of which contains the same number of repeat units, the analytical dependence of CV shape on such number m has been derived with a use of the proposed approach. The case of the simultaneous existence of two polaron kinds including different numbers of repeat units is also considered in scope of the applied method. The performed consideration leads to the following results. The quasi-equilibrium voltammetric curves derived with this approach are in a better agreement with experimental CV of conducting polymers than those calculated according to the approach accepted previously. In particular, the mid-widths of CV peaks calculated even without accounting for the so-called short-range interactions result in proximity to the actual values observed for various conducting polymers. In addition, such peculiarities of the real voltammetric curves, as the existence of several peaks or shoulders in their shape and the appearance of a plateau-like tail at high positive electrode potentials can be obtained with using simple assumptions. [ABSTRACT FROM AUTHOR]

Well-defined conjugated oligomers ( Sn) containing from 1 to 8 units of a tricyclic building block involving a dioctyloxybenzothiadiazole unit with two thienyl side rings ( S1) are synthesized by a bottom-up approach. UV-Vis absorption data of solutions show that chain extension produces a narrowing of the HOMO-LUMO gap (Δ E) to values slightly smaller than that of the parent polymer ( P1). Plots of Δ E and of the band gap of films ( Eg) versus the reciprocal chain length show that Δ E and Eg converge towards a limit corresponding to an effective conjugation length (ECL) of 7-8 S1 units. UV-Vis absorption and photoluminescence data of solutions and solid films show that chain extension enhances the propensity to inter-chain aggregation. This conclusion is confirmed by GIXD analyses which reveal that the edge-on orientation of short-chain systems evolves toward a face-on orientation as chain length increases while the π-stacking distance decreases beyond 7 units. The results obtained on solution-processed BHJ solar cells show a progressive improvement of power conversion efficiency (PCE) with chain extension; however, the convergence limit of PCE remains inferior to that obtained with the polymer. These results are discussed with regard to the role of mono/polydispersity and chain aggregation. [ABSTRACT FROM AUTHOR]

Background: Structural variants (SVs) are less common than single nucleotide polymorphisms and indels in the population, but collectively account for a significant fraction of genetic polymorphism and diseases. Base pair differences arising from SVs are on a much higher order (>100 fold) than point mutations; however, none of the current detection methods are comprehensive, and currently available methodologies are incapable of providing sufficient resolution and unambiguous information across complex regions in the human genome. To address these challenges, we applied a high-throughput, cost-effective genome mapping technology to comprehensively discover genome-wide SVs and characterize complex regions of the YH genome using long single molecules (>150 kb) in a global fashion. Results: Utilizing nanochannel-based genome mapping technology, we obtained 708 insertions/deletions and 17 inversions larger than 1 kb. Excluding the 59 SVs (54 insertions/deletions, 5 inversions) that overlap with N-base gaps in the reference assembly hg19, 666 non-gap SVs remained, and 396 of them (60%) were verified by paired-end data from whole-genome sequencing-based re-sequencing or de novo assembly sequence from fosmid data. Of the remaining 270 SVs, 260 are insertions and 213 overlap known SVs in the Database of Genomic Variants. Overall, 609 out of 666 (90%) variants were supported by experimental orthogonal methods or historical evidence in public databases. At the same time, genome mapping also provides valuable information for complex regions with haplotypes in a straightforward fashion. In addition, with long single-molecule labeling patterns, exogenous viral sequences were mapped on a whole-genome scale, and sample heterogeneity was analyzed at a new level. Conclusion: Our study highlights genome mapping technology as a comprehensive and cost-effective method for detecting structural variation and studying complex regions in the human genome, as well as deciphering viral integration into the host genome. [ABSTRACT FROM AUTHOR]

Abstract: Microsatellite (MS) markers in the SLA-1 region were characterized via sequencing analysis with BAC clones generated from the National Institute of Health miniature pigs (MIPs). A total of 16 BAC clones were sequenced producing 15,228 shotgun reads, corresponding to 11.2 X sequencing coverage, that were used to construct a contig of 12.18Mb in length. MS markers were compared with previously deposited GenBank sequences to verify the existence of 423 potential MS candidate markers in the SLA-1 region. Evaluation of these polymorphisms confirmed 59 markers in MIPs, and the combined data including sequences from GenBank revealed 155 polymorphic MS markers. MS markers identified from this analysis can be used to provide an alternative method to direct typing for determining an individual''s SLA-1 haplotype. [Copyright &y& Elsevier]

Telomere-associated DNA in Chironomus pallidivittatus contains tandemly repeated 340-bp units. We show that they are distributed among several subtypes of which we have characterized two, M1 and D1, with regard to base sequence, homogeneity, and intertelomeric distribution. Each subpopulation is highly homogeneous and the two subtypes have identical consensus sequences throughout 90% of their lengths. In the remaining part the homology is only about 60%. Each subpopulation has its specific intertelomeric distribution and there is no difference in the degree of homogenization within and between telomeres. The repeat unit contains two pairs of subrepeats embedded in linker DNA. This provides a model that makes it possible to relate the two subtypes to each other with regard to evolutionary history. The difference between the two subtypes is due to mutations that have occurred in only one of them, D1, resulting in a decreased similarity between one of its pairs of subrepeats. This type of repeat unit is therefore believed to be derived from the other, M1. The local decrease in similarity between M1 and D1 suggests that homogenization between them occurs by gene conversion. [ABSTRACT FROM AUTHOR]

An interspecies comparison was made between the 3′ ends of Balbiani ring genes from Chironomus. The comparison was focused on the BR2.2 gene, and a part at the 3′ end from Chironomus pallidivittatus (which included also a segment of the gene core) was cloned. Its sequence, and other previously published BR sequences from this species and from Chironomus tentans were used in the analysis. The 3′ parts of these repetitive genes can be divided into a region belonging to the core of the genes followed by a terminal region. In the core region the repeats (each of which consists of a constant part and a subrepeated part) are highly similar and the constant parts show little interspecies differentiation. Furthermore, the two parts of the repeats are units in an evolutionary and probably also functional sense. The terminal region contains modified constant units, usually isolated betwen acidic so-called cys regions, the whole arrangement lying upstream of an intron toward a 3′-terminal exon. Most of the modified constant units are mosaics in rates of evolution with stable outer quarters bordering to equally stable cys regions and a central half with a very high rate of evolution. One of the terminal units, present only in the BR2.2 gene and second from the end, differs distinctly not only from corresponding core units but also from other terminal units in the three normally active BR genes. It lies upstream of all cys regions and is evolutionarily conserved over most of its length. Furthermore, two-dimensional protein structure prediction does not exclude an endoproteolytic cleavage site in this unit. Such a site appears unlikely in other terminal or core regions. This is of interest in view of evidence for intracellular cleavage of the BR2.2 terminal region with liberation of a part containing a DNA-binding domain (Botella et al. 1988). All in all the fine anatomy of evolutionary changes at the BR gene termini shows interesting correlations with postulated functional relations and may have predictive value in the further functional analysis of this part of the gene. [ABSTRACT FROM AUTHOR]

A new type of repeat unit was isolated from Balbiani ring 1 of Chironomus pallidivittatus and designated, BR1β repeat. It consists of a constant and a subrepeated part, like previously described units belonging to the core blocks of the BR genes. The subrepeated part contains 10-codon subrepeats with an arrangement similar to the subrepeats of the previously described BR2β gene. The present unit differs from earlier reported core units firstly in a much lower number of copies (about 15) per genome, which are tandemly arranged. Secondly, the number of subrepeats per BR1β repeat unit can show great variations. On the basis of the pattern of codon usage, three types of subrepeats can be distinguished. One type lies 5′-proximal in the subrepeat array and consists of variable numbers of subrepeats almost identical at the nucleotide level. The last complete subrepeat represents another type, with consistent differences in codon usage as compared to subrepeats of the proximal type. Finally, there is an intermediate type represented by the subrepeat preceding the distal one. Here, codon characteristics from proximal and distal subrepeats are mixed in a patchy and irregular way. The evolution of the arrays can be understood either as being the result of subrepeat formation in two steps (occurring before and after amplification of whole repeat units) or as the result of a continuous process in which there is evidence for participation of gene conversion. [ABSTRACT FROM AUTHOR]

Background: Recently, Mycobacterial Interspersed Repetitive Unit (MIRU) was supposed to be associated with drug resistance in Mycobacterium tuberculosis (M. tuberculosis), but whether the association exists actually in local strains in China was still unknown. This research was conducted to explore that association and the predictability of MIRU to drug resistance of Tuberculosis (TB)., Methods: The clinical isolates were collected and the susceptibility test were conducted with Lowenstein-Jensen (LJ) medium for five anti-TB drug. Based on PCR of MIRU-VNTR (Variable Number of Tandem Repeat) genotyping, we tested the number of the repeat unite of MIRU. Then, we used logistic regression to evaluate the association between 15 MIRU and drug resistance. In addition, we explored the most suitable MIRU locus of identified MIRU loci for drug resistance by multivariate logistic regression., Results: Of the 102 strains, one isolate was resistant to rifampicin and one isolate was resistant to streptomycin. Among these fifteen MIRU, there was a association between MIRU loci polymorphism and anti-tuberculosis drug resistance, ETRB (P = 0.03, OR = 0.19, 95% CI 0.05-0.81) and ETRC (P = 0.01, OR = 0.14, 95% CI 0.03-0.64) were negatively related to isoniazid resistance; MIRU20 (P = 0.05, OR = 2.87, 95% CI 1.01-8.12) was positively associated with ethambutol resistance; and QUB11a (P = 0.02, OR = 0.79, 95% CI 0.65-0.96) was a negative association factor of p-aminosalicylic acid resistance., Conclusion: Our research showed that MIRU loci may predict drug resistance of tuberculosis in China. However, the mechanism still needs further exploration.

Background: Structural variants (SVs) are less common than single nucleotide polymorphisms and indels in the population, but collectively account for a significant fraction of genetic polymorphism and diseases. Base pair differences arising from SVs are on a much higher order (>100 fold) than point mutations; however, none of the current detection methods are comprehensive, and currently available methodologies are incapable of providing sufficient resolution and unambiguous information across complex regions in the human genome. To address these challenges, we applied a high-throughput, cost-effective genome mapping technology to comprehensively discover genome-wide SVs and characterize complex regions of the YH genome using long single molecules (>150 kb) in a global fashion., Results: Utilizing nanochannel-based genome mapping technology, we obtained 708 insertions/deletions and 17 inversions larger than 1 kb. Excluding the 59 SVs (54 insertions/deletions, 5 inversions) that overlap with N-base gaps in the reference assembly hg19, 666 non-gap SVs remained, and 396 of them (60%) were verified by paired-end data from whole-genome sequencing-based re-sequencing or de novo assembly sequence from fosmid data. Of the remaining 270 SVs, 260 are insertions and 213 overlap known SVs in the Database of Genomic Variants. Overall, 609 out of 666 (90%) variants were supported by experimental orthogonal methods or historical evidence in public databases. At the same time, genome mapping also provides valuable information for complex regions with haplotypes in a straightforward fashion. In addition, with long single-molecule labeling patterns, exogenous viral sequences were mapped on a whole-genome scale, and sample heterogeneity was analyzed at a new level., Conclusion: Our study highlights genome mapping technology as a comprehensive and cost-effective method for detecting structural variation and studying complex regions in the human genome, as well as deciphering viral integration into the host genome.