Graphical Representation and Similarity Analysis of Protein Sequences Based on Fractal Interpolation.

A new graphical representation of protein sequences is introduced in this paper. Nine main physicochemical properties of amino acids were used to obtain a 2D discrete point set for protein sequences by applying principal component analysis. The fractal method was then employed to interpolate discrete points in constructing a graphical representation of protein sequences. Fractal dimension of the protein curve was used to analyze the similarity of protein sequences by comparing the distance of vectors representing segments of protein sequences. The Jeffrey's and Matusita distance was modified in the similarity comparison of protein sequences with different lengths. Nine different species from Nicotinamide adenine dinucleotide (NADH) dehydrogenase 5 (ND5) protein sequences were tested as an example to demonstrate our method. Finally, a linear correlation and significance analysis was used to compare our results with other graphical representations referring to the ClustalW result. To confirm the validity of our method, eight species in NADH dehydrogenase 6 (ND6) protein families and twenty-seven species in beta-globin protein families were also analyzed. Experimental results show that the proposed method is effective for the similarity analysis of proteins.

The complete mitochondrial genome of Phrynocephalus forsythii (Reptilia, Squamata, Agamidae), a toad-headed agama endemic to the Taklamakan Desert.

The complete mitochondrial genome was sequenced from a viviparous toad-headed agama, Phrynocephalus forsythii, which is endemic to the Taklamakan Desert. The mitogenome sequence was 17,542 bp in size, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a control region (D-loop). The gene arrangement and composition of P. forsythii is identical to the mitogenome of P. theobaldi in that tRNA-Pro was translocated immediately downstream of tRNA-Phe. The D-loop comprised two parts, one existing between tRNA-Thr and tRNA-Phe, and another containing 12 copies of 36-bp tandem repeats inserting between tRNA-Pro and 12S rRNA. The complete mitogenome sequence of P. forsythii may provide fundamental data for unveiling the phylogenetic origin and adaptive evolution related to Phrynocephalus viviparity.

Sequencing and analysis of the whole mitochondrial genome of a variegated racerunner from Taklamakan Desert.

The whole mitochondrial genome of a variegated racerunner (Eremias vermiculata) from the Taklamakan Desert was determined using polymerase chain reaction and directly sequenced with a primer walking method. The mitogenome sequence was 19 796 bp in size, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop), which is similar to the typical mtDNA of vertebrates. Mitochondrial genomes analyses using maximum parsimony and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the seven Eremias species. Monophyly of the genus Eremias and E. vermiculata was recovered. The mitogenome presented here will contribute to the examination of genetic differentiation for E. vermiculata and understanding of the mitochondrial DNA evolution in Eremias.

Complete mitogenome of a variegated racerunner, Eremias vermiculata, from north of Tianshan Mountains, Xinjiang, China.

The complete mitochondrial genome was determined from a variegated racerunner, Eremias vermiculata, which was collected from north of Tianshan Mountains, Xinjiang, China. The mitogenome sequence was 19,494 bp in size, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop), which is similar to the typical mtDNA of vertebrates. All the protein-coding genes in E. vermiculata were distributed on the H-strand, except the ND6 gene and eight tRNA genes, which were encoded on the L-strand. The mitogenome sequence herein will provide fundamental data for further investigating the phylogeographical pattern of E. vermiculata, along with testing the barrier effect of the Tianshan Mountains to gene flow. A preliminary phylogenetic inference has been implemented with five racerunner species and several other related lacertid species.

Complete mitochondrial genome of Stummer's Racerunner (Eremias stummeri) from Kazakhstan.

The whole mitochondrial genome was determined from a viviparous racerunner, Eremias stummeri, which was collected from southeast Kazakhstan. The mitogenome sequence was 19 602 bp in size, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region, which is similar to the typical mtDNA of vertebrates. Mitochondrial genomes analyses using maximum parsimony and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the sampled taxa in genus Eremias. Monophyly of both Eremias and its viviparous group is recovered. The complete mitogenome sequence of E. stummeri provides fundamental data for resolving phylogeneitc and genetic problems related to Eremias viviparity.

Molecular detection, identification and phylogenetic inference of Leishmania spp. in some desert lizards from Northwest China by using internal transcribed spacer 1 (ITS1) sequences.

Leishmaniasis caused by Leishmania is still endemic in Northwest China. It has been thought that reptiles could be a reservoir for mammalian leishmaniasis. However, data are still scarce on natural infection of lizards with Leishmania spp. in China. The present study deals with detection, identification and phylogenetic inference of Leishmania parasites at species and intraspecies levels isolated from six desert lizard species from 10 geographical locations in Northwest China using amplification and sequencing of ITS-rDNA. In total, 83 haplotypes were found among 137 ITS1 sequences obtained from up to 64.6% of all captured lizards. Representative sequences of Leishmania available in GenBank were compiled for comparison with the obtained haplotypes. Tree-based species delimitation was achieved by using Bayesian phylogenitc analyses and maximum parsimony approach. Phylogenetic trees congruently supported that the haplotypes were found to belong to three Leishmania species including L. (sauroleishmania) sp., Leishmania tropica and Leishmania donovani complex. A network approach revealed paraphyletic populations of L. (sauroleishmania) sp. and L. tropica at intraspecies level regarding geographical origin and low host specificity. Chinese L. tropica from lizards showed significant heterogeneity as the obtained haplotypes were distributed in different clusters from other countries. Common ancestry was observed between some sequences of L. tropica from lizards and other sequence types from clinical samples from other countries. This may lend support to the potential reservoir role of lizards for human leishmaniasis. Our results appear to be the first molecular evidence for natural infection of lizards in Northwest China with reptilian Leishmania and mammalian Leishmania species. Desert lizards may be considered as putative reservoir hosts for Leishmania in China. Further studies on persistence of the Leishmania parasites in lizards and sandflies are recommended for the better understanding of their epidemiological involvement.

[Effects of plastic film mulching on soil CO2 efflux and CO2 concentration in an oasis cotton field].

A field study was conducted to compare soil CO2 efflux and CO2 concentration between mulched and non-mulched cotton fields by using closed chamber method and diffusion chamber technique. Soil CO2 efflux and CO2 concentration exhibited a similar seasonal pattern, decreasing from July to October. Mulched field had a lower soil CO2 efflux but a higher CO2 concentration, compared to those of non-mulched fields. Over the measurement period, cumulative CO2 efflux was 1871.95 kg C . hm-2 for mulched field and 2032.81 kg C . hm-2 for non-mulched field. Soil CO2 concentration was higher in mulched field (ranging from 5137 to 25945 µL . L-1) than in non- mulched field (ranging from 2165 to 23986 µL . L-1). The correlation coefficients between soil CO2 concentrations at different depths and soil CO2 effluxes were 0.60 to 0.73 and 0.57 to 0.75 for the mulched and non-mulched fields, indicating that soil CO2 concentration played a crucial role in soil CO2 emission. The Q10 values were 2.77 and 2.48 for the mulched and non-mulched fields, respectively, suggesting that CO2 efflux in mulched field was more sensitive to the temperature.