Phylogenetic Relationships and Status Quo of Colonies for Gayal Based on Analysis of Cytochrome b Gene Partial Sequences

Thirty-three mutations and four different haplotypes were found when cytochrome b（Cytb） gene partial sequences of 12 gayals were analyzed. Together with sequences of Bos indicus, Bos taurus, Bos grunniens, and Bos gaurus with Bubalus bubalis as the out group, the partial sequences of Cytb gene of gayals were aligned and base composition and nucleotide variation of Cytb gene were analyzed. The phylogenetic trees were constructed by the NJ method and the MP method respectively, both supporting almost the same topology. Gayal is an independent species of Bos from Bos indicus, Bos taurus, and Bos gaurus. The results also indicate that a great proportion of gayal bloodline was invaded by other species, and the protection of gayal is facing a formidable situation.

Identification of sika deer and red deer using partial cytochrome b and 12s ribosomal RNA genes

A study was conducted on the identifications of the degraded samples of sika deer （Cervus nippon） and red deer （Cervus elaphus） by phylogenetic and nucleotide distance analysis of partial Cytb and 12s rRNA genes sequences. 402 bp Cytb genes were achieved by PCR-sequencing using DNA extracted from 8 case samples, and contrasted with 27 sequences of Cytb gene downloaded from GenBank database. The values of three nucleotide distance between three suspected samples and sika deer were identical （0.026±0.006）, which was smaller than the smallest nucleotide distance between eastern red deer and sika deer （0.036）. Furthermore, phylogenetic analysis of sika deer and red deer indicated that the evidences located within the same cluster as sika deer. The evidences were sika deer materials. As the same way, other three suspected samples were derived from red deer. The results were further confirmed by phylogenetic and nucleotide distance analysis of 387 bp 12s rRNA gene. The method was powerful and less time-consuming and helpful to reduce the related cases with wildlife.

Phylogenetic Relationships of 11 Bumblebee Species (Hymenoptera:Apidae) Based on Mitochondrial Cytochrome b Gene Sequences

Phylogenetic relationships of 11 bumblebee species,including 5 subgenera:Bombus (5 species),Thoracobombus (3 species),Mendacibombus (1 species),Fervidobombus (1 species) and Pyrobombus (1 species),were analyzed based on the 357?bp mitochondrial cytochrome b gene sequences.There are 65 singleton polymorphic sites and 71 parsimony informative polymorphic sites in this DNA segment,and 45 polymorphic sites within the total 119 translated amino acids segment.Both NJ tree and MP tree show that Mendacibombus (B.avinovielllus) is basal to others,followed by Fervidobombus (B.pensylvanicus);Pyrobombus (B.impatiens) and Bombus are sister subgenera;the subgenus of Bombus is monophyletic,in which B.ignitus diverged first.

Sequence Comparison of Partial Cytochrome b Genes of Two Coilia species

Sequence variation of partial cytochrome b genes between two Coilia species, C. ectenes and C. mystus, was in- vestigated. Of the 402 nucleotides, twenty-seven (6.72%) are polymorphic and all are synonymous substitutions. At the third positions of genetic condon of cytochrome b gene, the two species show an extreme anti-G bias (<4%) and a pronounced bias towards A and C (>68%). There is no amino acid sequence divergence between the partial cytochrome b genes of the two species, indicating a close genetic relationship between them. The k-2p genetic distance of partial cytochrome b segment of the two species is 0.072, suggesting that the species were separated 3.6 Ma ago, in the middle Pliocene. Our result reveals that the cytochrome b gene is an appropriate marker for studies of population genetic structures and phylogeographic pat- terns of the two species.

Molecular Phylogeny of Slow Lorises (Nycticebus) Revealed by D-loop Sequences and Complete Cytochrome b Gene Sequences of Mitochondrial DNA

Partial sequences of the D-loop and the complete sequences of cytochrome b gene (1 140 bp) of the slow lorises (genus Nycticebus) were undertaken to investigate evolutionary relationships among species of Nycticebus.Sequence analysis results consistently provide new taxonomy evidence at the DNA level for supporting Ratajszczak and Groves’ viewpoint that N.intermedus is merely the adult of N.pygmaeus (Ratajszczak,1998;Groves,1971).Phylogenetic analysis was performed by means of the combined data and these two separate sequences data,respectively,by using various methods,supporting the same topology,in which genus Nycticebus was formed of two clusters.The first cluster was composed of N.pygmaeus,and the second cluster of N.coucang.It also could provide a new molecular genetic evidence to support the view that the genus comprises two species:N.coucang and N.pygmaeus.

Cloning, characterization, and expression of Cytochrome b (Cytb)——a key mitochondrial gene from Prorocentrum donghaiense

Mitochondrial cytochrome b （Cytb）, one of the few proteins encoded by the mitochondrial DNA, plays an important role in transferring electrons. As a mitochondrial gene, it has been widely used for phylogenetic analysis. Previously, a 949-bp fragment of the coding gene and mRNA editing were characterized from Prorocentrum donghaiense, which might prove useful for resolving P. donghaiense from closely related species. However, the full-length coding region has not been characterized. Ih this study, we used rapid amplification of cDNA ends （RACE） to obtain full-length, 1 124 bp cDNA. Cytb transcript contained a standard initiation codon ATG, but did not have a recognizable stop codon. Homology comparison showed that the P. donghaiense Cytb had a high sequence identity to Cytb sequences from other dinoflagellate species. Phylogenetic analysis placed Cytb from P. donghaiense in the clade of dinoflagellates and it clustered together strongly with that from P. minimum. Based on the full-length sequence, we inferred 32 editing events at different positions, accounting for 2.93% of the Cytb gene. 34.4% （11） of the changes were A to G, 25% （8） were T to C, and 25% （8） were C to U, with smaller proportions of G to C and G to A edits （9.4% （3） and 6.2% （2）, respectively）. The expression level of the Cytb transcript was quantified by real-time PCR with a TaqMan probe at different times during the whole growth phase. The average Cytb transcript was present at 39.277.46 copies of cDNA per cell during the whole growth cycle, and the expression of Cytb was relatively stable over the different phases. These results deepen our understanding of the structure and characteristics of Cytb in P. donghaiense, and confirmed that Cytb in P. donghaiense is a candidate reference gene for studying the expression of other genes.

Preliminary Study on Geographical Variation of Cytochrome b gene and ITS2-rDNA among Populations of Rhynchophorus ferrugineus

The Red Palm Weevil （RPW）, Rhynchophorus ferrugineus （Olivier）, （Coleoptera, Curculionidae, Rhynchophorinae）, is an invasive species that is originated from Southeast Asia. It has invaded Middle East, several countries of the Mediterranean Basin, Caribbean （Island of Curacao, Netherland Antilles）, Lebanon and United States of America （Laguna Beach, Orange County, California） during the last three decades where it attacks palm trees. This study investigated the geographical variation among geographic populations of RPW collected from twelve invaded countries using cytochrome b （Cytb） and ITS2 partial sequences. The comparison among the Cytb sequences resulted in three different haplotypes designated as HB 1 to HB3. The three haplotypes were subdivided into two phylogenetic groups according to their geographic positions： （1） the ＂Multi-Continent＂ group containing HB 1 haplotype detected in eight populations belonging to three different Continents such as Africa-Egypt, Asia-Kingdom of Saudi Arabia and Turkey and Europe-Spain, Italy, Greece, Cyprus and France, and （2） the ＂Asian＂ group includes four populations from Iran （harboring HB2 haplotype）, Pakistan, UAE, and Oman （harboring HB3 haplotype）. This mitochondrial pattern of genetic diversity suggests that the tested RPW populations subdivided genetically into different sub-populations under the influence of genetic drift. According to these results we concluded that the twelve studied RPW populations are originating from different source populations in the RPW area of origin.

4-Hydroxycinnamic acid attenuates neuronal cell death by inducing expression of plasma membrane redox enzymes and improving mitochondrial functions

Many approaches to neurodegenerative diseases that focus on amyloid-βclearance and gene therapy have not been successful.Some therapeutic applications focus on enhancing neuronal cell survival during the pathogenesis of neurodegenerative diseases,including mitochondrial dysfunction.Plasma membrane(PM)redox enzymes are crucial in maintaining cellular physiology and redox homeostasis in response to mitochondrial dysfunction.Neurohormetic phytochemicals are known to induce the expression of detoxifying enzymes under stress conditions.In this study,mechanisms of neuroprotective effects of 4-hydroxycinnamic acid(HCA)were examined by analyzing cell survival,levels of abnormal proteins,and mitochondrial functions in two different neuronal cells.HCA protected two neuronal cells exhibited high expression of PM redox enzymes and the consequent increase in the NAD^(+)/NADH ratio.Cells cultured with HCA showed delayed apoptosis and decreased oxidative/nitrative damage accompanied by decreased ROS production in the mitochondria.HCA increased the mitochondrial complexes I and II activities and ATP production.Also,HCA increased mitochondrial fusion and decreased mitochondrial fission.Overall,HCA maintains redox homeostasis and energy metabolism under oxidative/metabolic stress conditions.These findings suggest that HCA could be a promising therapeutic approach for neurodegenerative diseases.

Intraspecific Relationship of Sheep Based on Mitochondrial Cytochrome b Gene

[ Objective] To preliminarily explore the intraspecific relationship of sheep based on cytochrome b （ Cyt b） gene of mitochondrial DNA （mtDNA）. [Method] The Cyt b gene sequences in 112 sheep individuals of two local sheep breeds were amplified by PCR. Then the amplified products were digested with EcoR I and analyzed by restriction fragment length polymorphism （RFLP）. [ Result] As many as 56 samples from Tan sheep and 56 samples from Wadi sheep were detected. The results showed that the amplified Cyt b gene in 51 individuals of Tan sheep had one EcoR I restriction site and no EcoR I restriction site in other five individuals, thus the Cyt b gene in Tan sheep showed two restriction morphs; the Cyt b gene in all 56 individuals of Wadi sheep had one EcoR I restriction site and showed one restriction morph. [ Conclusion] The polymorphism of mitochondrial Cyt b gene in Tan sheep and Wadi sheep is poor, and the Cyt b gene in sheep breeds is very conservative. Therefore, using Cyt b gene as gene marker to study the intraspecific relationship of sheep has some limitations.

Molecular Evolution of the Cytochrome b Gene in Geographically Isolated Populations of Oryzias Latipes

The mitochondrial cytochrome b gene was isolated from the caudal fin of Oryzias latipes and PCR was undertaken to determine phylogeny. The nucleotide sequence of the complete cytochrome b gene including the 5＇ and 3＇ ends was 1,143 base pairs （bp） and 1,137 bp encoding 380 and 378 amino acids in the K-11 strain and HS strain, respectively. In addition, higher substitutions both in base and amino acid residues occurred more frequently between the former control （Hd-rR strain） and HS strains than the K-I 1 strain. Approximately similar values in polymorphism, as assessed by restriction endonuclease digestion, were detected when utilizing 20 different enzymes. Therefore, the evolutionary processes were unlikely to involve common ancestors, especially between the K-11 strain and HS strains, in O. latipes populations in Japan. The sequence had been deposited in GenBank Data Base under accession number AB480878 （K-I I strain） and AB480879 （HS strain）.

The Cytochrome b Polymorphism of Meat Lines Rabbits

The cytochrome b mtDNA was analysed from peripheral whole blood samples of meat lines rabbits. The PCR product--692 bp long fragment of Oryctolagus cuniculus_cytochrome b （0CU07566 GenBank, NCB1, USA） was amplified. Synthetically produced oligonucleotides for the detection ofcyt b were designed by own algorithm： ORYCTO-cyt b-FOR 5＇- CTA TCA GCA ATC CCA TAT ATC -3＇ and ORYCTO-cyt b-REV 5＇- CTT CAT TTG AGG ATT TTG TT -3＇. Based on AluI-RFLP were described two cytochrome b haplotypes--cyt b 430 and cyt b 306. Haplotype cyt b 430 is 571A （190Threonine-T） ＋ 877G （292Alanine-A）. The new haplotype cyt b 306 is presented A571G nucleotide substitution, i.e, 571G （190Alanine-A） ＋ 877G （292Alanine-A）.

Phylogenetic relationships of some Sylviidae species based on complete mtDNA cyt b and partial COI sequence data

Members of the passerine family Sylviidae are distributed widely around the Old World and the phylogenetic relationships of many species still remain controversial.In this study,we investigated the phylogeny and relationships among 37 species of 11 genera by analyzing DNA sequences obtained from the complete mitochondrial cytochrome b (cyt b) and partial cytochrome oxidase I (COI) genes.The data were analyzed by maximum-likelihood analysis and Bayesian inference.The results demonstrate that the current genus Phylloscopus is non-monophyletic,while Seicercus is synonymized with Phylloscopus or is a group within the genus Phylloscopus.We may conclude that within Phylloscopus there are close relations between P.magnirostris and P.borealis;among P.proregulus,P.yunnanensis,P.pulcher and P.maculipennis,as well as among P.occisinensis,P.schwarzi,P.armandii,P.collybita and P.fuscatus.Monophyly of the genus Cettia could not be corroborated;it is closely related to the genera Abroscopus and Tesia.However monophyly of Acrocephalus is supported.Furthermore,the close relationships between Sylvia and Zosterops and among Prinia,Orthotomus and Cisticola are also supported.

红鮊属三种鱼类线粒体细胞色素b基因片段序列分析

本文测定了红珀属的翘嘴红约、青梢红铂和蒙古红铂细胞色素b基因片段序列（1091bp），对其碱基组成变异情况及核苷酸序列差异进行了分析。并以红鳍珀为外类群，用NJ法和UPGMA法构建系统关系树。结果表明：（1）四种鱼（包括外类群）Cytb基因片段序列碱基平均差异为6．2％，变异位点184个，具有简约性信息位点141个，平均转换颠换比为7．4；（2）本文测定的红鲐属三种鱼形成一个单系群，其中翘嘴红珀与青梢红珀亲缘关系较近。

Molecular evidence suggests that the enigmatic Sulawesi endemic Geomalia heinrichi belongs in the genus Zoothera (Turdidae, Aves)

The taxonomic status of the Sulawesi endemic Geomalia heinrichi has long been debated, and it has variously been treated as a babbler (Timaliidae) or a turdid (Turdidae). We estimated the phylogeny of 43 taxa in the family Turdidae based on the mitochondrial cytochrome b gene and the nuclear myoglobin intron 2 and ornithine decarboxylase introns 6–7. Geomalia heinrichi was shown to be part of the Zoothera clade with high support. We propose that Geomalia is transferred to Zoothera under the name Zoothera heinrichi.

Effects of Hyperoxia on Mitochondrial Multienzyme Complex Ⅲ and Ⅴ in Premature Newborn Rat Lung

To investigate the effects of hyperoxia on mitochondrial multienzyme complex Ⅲ （cytochrome, Cytb） and Ⅴ （ATPase6, 8） in premature newborn rat lung, the 1-day-old preterm SD rats were randomly assigned to hyperoxia group and air group, The rats in hyperoxia group were continuously exposed to 85% oxygen and those in air group to room air. After 1, 4, 7, 10, 14 day（s） of exposure, these rats were killed, total lung RNA was extracted and Cytb, ATPase6, 8 mRNA were detected by reverse transcription polymerase chain reaction （RT-PCR）. Western blotting was used to detect the expression of Cytb protein in lung tissue. The results showed that compared with air group, Cytb mRNA expression was significantly increased （P〉0,05） after 1, 4 day（s） of exposure. The general tendency decreased after 7 days, and its expression became weak but difference in mRNA expression between the two groups was not significant （P〉0.05）. ATPase6 mRNA expression was significantly increased 1 day after the exposure （P〈0.05） and did not show any significant change 4, 7, 10 days after the exposure （P〉0.05）. At the 14th day, ATPase6 mRNA expression was significantly increased （P〈0.05）, ATPase8 mRNA expression did not show any significant change 1, 4, 10 day（s） after the exposure （P〉0.05）, At the 7th and 14th day, ATPase8 mRNA expression was significantly increased （P〈0.05）. Western blotting showed that Cytb protein expression was increased 1,4 day（s） after the exposure, but the difference between the two groups was not significant （P〉0.05）. The general tendency was decreased after 7 days, and its expression became weak but difference was not significant 7, 10 days after the exposure （P〉0.05）. At day 14 its expression became significantly weak （P〈0.05）. We are led to conclude that exposure to high concentrations of oxygen can significantly change the expression of Cytb and ATPase6, 8, which results in uncoupling of oxidative phosphorylation in mitochondrial respiration chain, and plays an important role in the mechanism of hyperoxia-induced lung injury.

Phlebotomus(Adlerius) kabulensis(Diptera: Psychodidae) a new record sand fly species from Iran: Morphological and molecular aspects

Objective: To represent a new geographical record, Phlebotomus(Adlerius) kabulensis(P.kabulensis), which is suspected to be a potential vector of visceral leishmaniasis.Methods: For the first time, P.kabulensis specimens were collected using the sticky paper traps method in outdoor places in mountainous areas with vegetation coverage of three provinces in Iran.Identification of males was based on ecological, morphological, morphometric and molecular(mtDNA cytochrome b gene sequences) criteria.Generally, males have two ascoids on the 8^(th)antennal segment and one ascoid on segments 9^(th)to 15^(th), aedeagus with normal obtuseangled sub-terminal notch and coxite with 27–50 groups of hairs on the distal half of its body.Results: Morphometric measurement revealed that P.kabulensis specimens were the same as compared with seven other morphological characters in three provinces of the country but lengths of the coxite were significantly different.The PCR result of the cytochrome b(Cyt b)-mtDNA fragment shows 550-bp length, with its special nucleotide arrangement.The male and female of P.kabulensis were newly discovered members of the subgenus Adlerius from Iran.Initial DNA analysis indicated how distinct this species is.Conclusions: The results show that the P.kabulensis female will be identified by comparing with other Adlerius female groups regarding its morphometric characters and molecular sequencing.

Availability of Myoglobin as a Molecular Marker for Phylogenetic Relationships of Fish

In order to elucidate the phylogenetic relationship of fish, DNA and deduced amino acid sequences of myoglobin （Mb） were used for the phylogenetic analyses based on different approaches, namely, maximum likelihood （ML）, neighbor joining （NJ）, unweighted pair group method with arithmetic means （UPGMA） and maximum parsimony （MP） methods in comparison with the conventional molecular markers, mitochondrial cytochrome b （cyt-b） and cytochrome c oxidase subunit I （COI）. The phylogenetic trees drawn based on Mb sequences were similar to those by the traditional classification based on the other molecular markers. The primary and secondary structures, as well as the modeled tertiary structures of Mbs were similar to each other, but were clearly distinguishable among those species. Such differences in structure would be associated with adaptation of Mb molecule to the physiological conditions of each species. These results suggest that Mb can be a molecular marker for the phylogenetic relationship of fish.

Genetic Diversity and Structure in Japanese Populations of the Osprey (<i>Pandion haliaetus</i>), Based on mtDNA

Osprey is a type of bird of prey that lives almost all over the world. In Japan, it is designated as a near-threatened species because it has less than 1000 individuals. In recent years, it inhabits more inland than in coastal areas. In this study, we conducted a population genetic analysis focusing on what kind of genetic structure Japanese Osprey retains and whether there are differences between coastal and inland populations. We also performed genetic diversity assessments. We sequenced about 2.3 kb of mtDNA for 27 individuals in Japan, and phylogenetic analysis, network analysis, neutrality test and mismatch distribution analysis were performed. Eighteen haplotypes were detected in 27 individuals, indicating that genetic diversity was sufficiently high. Both unique and common haplotypes were detected between inland and coastal populations, suggesting gene flow between the two populations. Phylogenetic analysis results show no genetic differentiation in the Japanese Osprey population. From the results of network analysis, neutrality test and mismatch distribution analysis, it was inferred that the Japanese Osprey had a population expansion in the past. This study indicated that the dispersion of Japanese Osprey was random and there were no restrictions on the breeding area. The information presented here can be used towards implementing future conservation actions.

The thylakoid membrane protein NTA1 is an assembly factor of the cytochrome b6f complex essential for chloroplast development in Arabidopsis

The cytochrome b_(6f)(Cyt b_(6f))complex is a multisubunit protein complex in chloroplast thylakoid membranes required for photosynthetic electron transport.Here we report the isolation and characterization of the new tiny albino 1(nta1)mutant in Arabidopsis,which has severe defects in Cyt b_(6f) accumulation and chloroplast development.Gene cloning revealed that the nta1 phenotype was caused by disruption of a single nuclear gene,NTA1,which encodes an integral thylakoid membrane protein conserved across green algae and plants.Overexpression of NTA1 completely rescued the nta1 phenotype,and knockout of NTA1 in wild-type plants recapitulated the mutant phenotype.Loss of NTA1 function severely impaired the accumulation of multiprotein complexes related to photosynthesis in thylakoid membranes,particularly the components of Cyt b_(6f).NTA1 was shown to directly interact with four subunits(Cyt b6/PetB,PetD,PetG,and PetN)of Cyt b_(6f) through the DUF1279 domain and C-terminal sequence to mediate their assembly.Taken together,our results identify NTA1 as a new and key regulator of chloroplast development that plays essential roles in assembly of the Cyt b_(6f) complex by interacting with multiple Cyt b_(6f) subunits.

Mitochondrial DNA Sequences Imply Anhui Musk Deer a Valid Species in Genus Moschus

Anhui musk deer [ Moschus ( moschiferus/berezovskii ) anhuiensis ] has been a taxonomic mystery since its discovery in early 80's.In this paper,with museum samples,we sequenced the complete cytochrome b gene of five Anhui musk deer.When compared with other species in Genus Moschus ,Anhui musk deer showed a rather level of sequence divergence from all the other species in this genus.The phylogenetic trees constructed by multiple methods supported the same topology,in which the monophyly of Anhui musk deer was clearly demonstrated.Therefore,our molecular data suggest a full species status for Anhui musk deer ( Moschus anhuiensis ),rather than a subspecies of either M moschiferus or M berezovskii previously suggested by morphological studies.