Sequence Difference of Mitochondrial DNA Control Region and Genetic Differentiation of Cervinae in China

[Objective] The study aimed at analyzing Genetic Differentiation of Cervinae. [Method] The complete mitochondrial DNA control region of five species of Cervinae was determined by direct DNA sequencing. Homologous sequences of others Cervinae were gained from GenBank, and then analyzed through biology software. [Result] The lengths of their control region were 921-1 072 bp, the nucleotide content of T, A, C, and G was 32.1%, 30.2%, 22.7% and 15.0% separately. Genetic distance of each species ranged from 0.062-0.106, which belonged to level of inter-genus. The molecular phylogenetic tree indicated that red deer, skia deer and White-lipped Deer had close relationship, and they constituted one branch with sambar deer. Eld＇s deer and elk deer constituted the second branch, and hog deer constituted the third branch alone. [Conclusion] Hog deer and fallow deer should be incorporated in Cervus, divergence time is about 1.55-2.60 million years among Cervinae in China.

A Molecular Phylogeny of Macaca Based on Mitochondrial Control Region Sequences

Nucleotide sequences of segments of the mitochondrial control regions were analyzed to infer the phylogenetic relationships among 7 macaques.High nucleotide diversity in Macaca assamensis and relatively low diversity in M.thibetana were found.Based on the ML tree from control regions,species in our study can roughly be sorted into three species groups except for the phylogenetic position of M.fascicularis,i.e.,silenus group,including M.leonina;sinica group,including M.arctoides,M.assamensis,and M.thibetana;and fascicularis group,including M.mulatta and M.cyclopis.A discrepancy between earlier studies (Fooden & Lanyon,1989;Tosi et al,2003a;Deinard & Smith,2001;Evans et al,1999;Hayasaka et al,1996;Morales & Melnick,1998),our result supported the hypothesis that M.fascicularis diverged earlier than M.leonina.Mitochondrial paraphyly in eastern M.mulatta (with respect to M.cyclopis) and eastern M.assamensis (with respect to M.thibetana) were clearly observed in our study.In accordance with the results of Y chromosome,allozyme,nuclear genes and some morphological data (Delson,1980;Fooden & Lanyon,1989;Fooden,1990;Tosi et al,2000,2003a,b;Deinard & Smith,2001),our study on control region sequences supported M.arctoides to be classified into the sinica group.However,this result disagreed with the previous mtDNA studies (Hayasaka et al,1996;Morales & Melnick,1998;Tosi et al,2003a).

Broader pattern of tandem repeats in the mitochondrial control region of Perciformes

Perciformes,the largest order of vertebrates with 20 suborders,is the most diverse fish order that dominates vertebrate ocean life.The complete mitochondrial control region(CR) of Trichiurus japonicus(Trichiuridae,Scombroidei) and Pampus sp.(Stromateidae,Stromateoidei) were amplified and sequenced.Together with data from GenBank,the tandem repeats in the mitochondrial CR from 48 species,which covered nine suborders of Perciformes,are reported in this study.The tandem repeats tend to be long in the suborder Percoidei and Stromateoidei.The identical repeats in 21 species of Cichlidae suggest a common origin and have existed before species divergence.Larimichthys crocea shows tandem repeats instead of the typical structure of the central conserved sequence blocks,which was first reported in Perciformes and vertebrates.This might have resulted from interruption of the polymerase activity during the H-strand synthesis.The four broader patterns presented here for the tandem repeats,including those in both the 5' and 3' ends,only in the either 5' or 3' end,and in the central conserved domain of the control region,will be useful for understanding the evolution of species.

Structure of Mitochondrial DNA Control Region of Pholis fangi and Its Phylogenetic Implication

In this study, the entire mitochondrial DNA(mtDNA) control region(CR) of Pholis fangi was amplified via polymerase chain reaction followed by direct sequencing. The length of the mtDNA CR consensus sequence of P. fangi was 853 bp in length. In accordance with the recognition sites as were previously reported in fish species, the mtDNA CR sequence of P. fangi can be divided into 3 domains, i.e., the extended terminal associated sequence(ETAS), the central conserved sequence block(CSB), and the CSB domain. In addition, the following structures were identified in the mtDNA CR sequence of P. fangi: 2 ETASs in the ETAS domain(TAS and cTAS), 6 CSBs in the central CSB domain(CSB-F to CSB-A), and 3 CSBs in the CSB domain(CSB-1 to CSB-3). These demonstrated that the structure of the mtDNA CR of P. fangi was substantially different from those of most other fish species. The mtDNA CR sequence of P. fangi contained one conserved region from 656 bp to 815 bp. Similar to most other fish species, P. fangi has no tandem repeat sequences in its mtDNA CR sequence. Phylogenetic analysis based on the complete mtDNA CR sequences showed that there were no genetic differences within P. fangi populations of the same geographical origin and between P. fangi populations of different geographical origins.

Mitochondrial DNA control region diversity and population structure of Pacific herring(Clupea pallasii)in the Yellow Sea and the Sea of Japan

To investigate the genetic variation and population structure of Pacific herring in the Yellow Sea and the genetic differentiation between the Yellow Sea and the Sea of Japan, fragments of 479-bp mitochondrial DNA control region were sequenced for 110 individuals collected from three different periods in the Yellow Sea and one locality in the Sea of Japan. High haplotype diversity and moderate nucleotide diversity were observed in Pacific herring. AMOVA and exact test of population differentiation showed no significant genetic differentiations among the three populations of the Yellow Sea and suggested the populations can be treated as a single panmictic stock in the Yellow Sea. However, a large and significant genetic differentiation （ФST=0.11; P=0.00） was detected between the populations in the Yellow Sea and the Sea of Japan. The high sea water temperature in the Tsushima Strait was thought a barrier to block the gene exchange between populations of the two sea areas. The neutrality tests and mismatch distribution indicated recent population expansion in Pacific herring.

Comparative Analysis of Mitochondrial Control Region Sequence from Three Flatfish Species(Pleuronectidae)

The 5’-end of the mitochondrial control region sequences of three flatfishes (Pleuronectiformes: Pleuronectidae) were amplified and sequenced. These sequences were compared with those of other three Pleuronectids species retrieved from GenBank. A phylogenetic tree was constructed based on the partial control region sequences. The results of phyloge- netic analysis are consistent with those of conventional systematics. Compared to previous studies, the structure of the 5’-end of mitochondrial control region was analyzed. The terminal associated sequence motif and its complementary motif were i- dentified at the 5’-end of the sequences. A conserved sequence block, named as CM5’d, was identified in the 5’-end of con- trol region sequences in all Pleuronectids. Another central conserved sequence block, named as CSB-F, was detected in the central conserved blocks.

Population Genetic Analysis of Sillago nigrofasciata (Perciformes:Sillaginidae) Along the Coast of China by Sequencing Mitochondrial DNA Control Region

Sillago nigrofasciata, a small to moderate size nearshore species, is newly found along the eastern and southern coasts of China. The present study is carried out in order to analyze the population genetics of the S. nigrofasciata. The control region sequence of mitochondrial DNA revealing 73 haplotypes were obtained from 162 individuals collected at 8 locations along the coast of China. The whole S. nigrofasciata population along the coast of China showed a low nucleotide diversity(0.012) and a high population diversity(haplotype diversity)(0.943), and all the 8 local populations showed low nucleotide diversities(0.014 – 0.001), suggesting the protective measures are effective. The haplotypes of the 8 local populations were widely distributed in haplotype network diagram and neighbor-joining phylogenetic tree, while no branch associating with sampling locations was detected. Recent gene flow analysis showed asymmetric gene exchanges among local populations. The pairwise FST values and unweighted pair-group method with arithmetic mean(UPGMA) tree revealed a certain amount of genetic difference among local populations. Moreover, analysis of molecular variance(AMOVA) reflected genetic differences between hypothetical subdivision groups. Neutral test and mismatch distribution of pairwise nucleotide suggested S. nigrofasciata may have experienced recent population expansion events. The historical geographic events associating with ice age may be the main explanation to the heterogeneity among local populations with short geographic distances, and the homogeneity among local populations with long geographic distances.

MITOCHONDRIAL DNA POLYMORPHISM IN CONTROL REGION FROM CHINESE YUGU POPULATION

Objective To investigate the mitochondrial DN A sequence polymorphism sites in Chinese YUGU ethnic group and to provide basic da ta used in forensic purpose. Methods Genomic DNA was extracted from the hole blood of 100 unrelated individuals of Chinese YUGU ethnic group by standard chelex-100 method. The sequence polymorphism sites was determined by PCR amplification and direct sequencing. Results 54 polymorphic sites were noted in mtDNA np16091-16418 region, and 46 haplotypes were identifi ed. The genetic diversity was calculated to be 0.9691, and the genetic identity was calculated to be 0.0406. Conclusion There are some particul ar polymorphism sites in Chinese YUGU ethnic group. The results suggest that seq uence polymorphism from np16091-16418 in human mitochondrial DNA can be used as a biological marker for forensic identity.

A DNA-binding protein factor in K562 nuclear extract interacts with positive control region (PCR) in the 5'flanking sequence of human β-globin gene

It has been known that there are at least three regulatory regions (NCR1, NCR2 and PCR) in the 5'-flanking sequence (from -610 bp to +1bp) of human β-globin gene and that the function of PCR is unique to the human erythroleukemia (K562) cells. Here we have detected a DNA-binding protein factor (termed NFEa) in K562 cells, which can bind specifically to the PCR of human β-globin gene. The sequence of the binding site is 5'ACTGATG3' (between -222 bp and -216 bp). The NFEa is erythroid-specific and perhaps specific for K562 cells. It seemed that this factor differed from the erythroid-specific tran-scriptional factor (NFE-1) using competition assay. The presence of the NFEa further supported that the function of the cis-acting element PCR was specific for K562 cells, and helps us to understand the mechanism of the regulation of the expression of human β-globin gene in the human K562 cells.

Sequence polymorphism of human mitochondrial DNA control region in Chinese Dongxiang unrelated individuals

Objective: To investigate the mitochondrial DNA sequence polymorphism in Chinese Dongxiang ethnic group and to provide basic data used in ethnic origin investigation and forensic purpose. Methods: Genomic DNA was extracted from the whole blood of 100 unrelated individuals of Chinese Dongxiang ethnic group by standard Chelex-100 method. The sequence polymorphism was determined by PCR amplification and direct sequencing. Results: Eighty-two polymorphic sites were identified in mtDNA D-loop region 16 091 - 16 418 np, and 88 haplotypes were found. The genetic diversity was calculated to he 0.9969, and the genetic identity was 0.013 2. Conclusion: There are some particular polymorphic sites in Chinese Dongxiang ethnic group, and these sites provide an important basis to investigate the origin of Dongxiang and the relationship between Dongxiang and other ethnic groups. The result also suggested that sequence polymorphism from 16 091 -16 418 np in human mitochondrial DNA control region can be an useful tool for forensic identity.

The Genetic Structure and Diversity of Repomucenus curvicornis Inhabiting Liaoning Coast Based on Mitochondrial COⅠ Gene and Control Region

[Object] This study was conducted to explore the genetic diversity and structure of the wild Repomucenus curvicornis inhabiting Liaoning Coast, China. [Method] The mitochondrial COⅠ gene and control region（CR） were PCR amplified from the wild R. curvicornis populations from the Liaodong Bay（n=22） and the northern Yellow Sea（n=18）, sequenced and analyzed for genetic diversity. [Result] The contents of A, T, C and G of 624 bp COⅠ gene were 24.09%, 31.04%, 25.28%, and 19.59%, and those of 460 bp CR fragment were 32.96%, 32.80%, 14.86% and 19.38%, respectively. The total number of variable sites, average number of nucleotide differences（ k）, haplotype diversity（H） and nucleotide diversity（π） based on COⅠ gene were 38, 4.67,（0.96±0.02） and（0.007 5±0.004 2）, and those based on CR fragment were 26, 3.35,（0.97 ±0.02） and（0.007 3±0.004 3）, respectively. Based on mitochondrial COⅠ gene and CR, the genetic diversity of Liaodong Bay population was lower than that of the northern Yellow Sea population. The AMOVA analysis based on CR fragments revealed almost significant genetic divergence between the Liaodong Bay and the northern Yellow Sea populations, while there was no significant genetic divergence based on COⅠ gene. The results showed that CR and COⅠ gene are effective molecular markers for detecting the genetic diversity of R. curvicornis population, while CR is more reliable than COⅠ gene in detecting the genetic structure. [Conclusion] CR is an appropriate marker for genetic analysis of marine fish population.

Shallow Genetic Structure of Pholis fangi in Bohai Sea and Yellow Sea Inferred from mt DNA Control Region

Pholis fangi is an ecologically important fish species inhabiting Chinese coastal waters of Yellow Sea and Bohai Sea. To investigate the genetic diversity and population genetic structure of P. fangi, a fragment of 487 bp in the first hypervariable region (HVR-1) of the mitochondrial DNA (mtDNA) control region was sequenced for 181 individuals collected from Bohai Sea and Yel- low Sea. A total of 18 polymorphic sites were detected, which defined 25 haplotypes. A moderate level of haplotype diversity (h = 0.7052) and a low level of nucleotide diversity (π= 0.0028) were detected. Both the phylogenetic tree and the haplotype network showed no significant genealogical structure difference among sampling locations. Pairwise FST comparison and hierarchical mo- lecular variance analysis (AMOVA) revealed that no significant genetic structure difference existed throughout the investigated re- gions, suggesting a high gene exchange among different populations. The results of neutrality test and mismatch distribution analysis indicated that a late Pleistocene population expansion (38000 127000 years ago) happened. Seasonal schooling migration may con- tribute to the genetically homogeneous population structure of the species.

Mitochondrial DNA Control Region Variation from Bangladesh: Sequence Analysis for the Establishment of a Forensic Database

Mitochondrial DNA sequences of the entire control region and three coding regions were analyzed in 108 unrelated individuals from three regions of Bangladesh. Sequence evaluation was performed with validated primers and combined sequence comparison led to the identification of 14 different haplotypes characterized by 37 variable polymorphic sites. The Bangladeshi sequences exhibited high variations and low random match probability, indicating for forensic application. The mean pairwise difference between individual was 9.698 ± 1.8658 nucleotides (95% CI 9.67 - 9.69), compared to a mean pairwise difference of 9.890 ± 4.189 nucleotides reported from Northeast Asia and suggested significant differences in the mtDNA composition of the various populations. The sequence diversity of 108 Bangladeshi Bengali samples (n = 216 chromosomes) was estimated to be 0.8475 ± 0.13406. This study first time reports that the comparison of closely related mtDNA sequences can be very useful for improving mtDNA database quality, as well as provide haplotype information for forensic study in mainstream population of Bangladesh.

LMI Approach to Robust H_∞/H_2 Controller Design with Regional Poles Constraint of a Pump-Motor System

The time domain guideposts requirements of a pump-motor system is transfered into a series of constraints which express the robust performance upper bound and regional poles limits of the closed loop system. Then the servo system control problem is transferred into the problem of robust performance optimizing under regional poles constrains described by linear matrix inequality （LMI）. These LMIs are easy to solve through the Matlab LMI-toolbox. Simulations indicate that the controller has excellent dynamic, static and disturbance rejection performance, and the control system is robust and has perfect H2 performance to the bounded external torque disturbance.

Pinning-controlled synchronization of complex networks with bounded or unbounded synchronized regions

This paper studies pinning-controlled synchronization of complex networks with bounded or unbounded synchronized regions. To study a state-feedback pinning-controlled network with N nodes, it first converts the controlled network to an extended network of N＋1 nodes without controls. It is shown that the controlled synchronizability of the given network is determined by the real part of the smallest nonzero eigenvalue of the coupling matrix of its extended network when the synchronized region is unbounded; but it is determined by the ratio of the real parts of the largest and the smallest nonzero eigenvalues of the coupling matrix when the synchronized region is bounded. Both theoretical analysis and numerical simulation show that the portion of controlled nodes has no critical values when the synchronized region is unbounded, but it has a critical value when the synchronized region is bounded. In the former case, therefore, it is possible to control the network to achieve synchronization by pinning only one node. In the latter case, the network can achieve controlled synchronization only when the portion of controlled nodes is larger than the critical value.

Role of 3'-untranslated region translational control in cancer development, diagnostics and treatment

The messenger RNA 3'-untranslated region(3'UTR)plays an important role in regulation of gene expres-sion on the posttranscriptional level. The 3'UTR con-trols gene expression via orchestrated interactionbetween the structural components of mRNAs(cis-ele-ment) and the specific trans-acting factors(RNA bind-ing proteins and non-coding RNAs). The crosstalk ofthese factors is based on the binding sequences and/or direct protein-protein interaction, or just functionalinteraction. Much new evidence that has accumulatedsupports the idea that several RNA binding factors canbind to common mRNA targets: to the non-overlappingbinding sites or to common sites in a competitive fash-ion. Various factors capable of binding to the sameRNA can cooperate or be antagonistic in their actions.The outcome of the collective function of all factorsbound to the same mRNA 3'UTR depends on manycircumstances, such as their expression levels, affinity to the binding sites, and localization in the cell, which can be controlled by various physiological conditions. Moreover, the functional and/or physical interactions of the factors binding to 3'UTR can change the character of their actions. These interactions vary during the cell cycle and in response to changing physiological condi-tions. Abnormal functioning of the factors can lead to disease. In this review we will discuss how alterations of these factors or their interaction can affect cancer development and promote or enhance the malignant phenotype of cancer cells. Understanding these altera-tions and their impact on 3'UTR-directed posttran-scriptional gene regulation will uncover promising new targets for therapeutic intervention and diagnostics. We will also discuss emerging new tools in cancer di-agnostics and therapy based on 3'UTR binding factors and approaches to improve them.

Estimation of Attractive Regions of Nonlinear MPC Controller-A Feasible Solution-based Method

A new model predictive control(MPC) algorithm for nonlinear systems is presented,its stabilizing property is proved,and its attractive regions are estimated.The presented method is based on the feasible solution,which makes the attractive regions much larger than those of the normal MPC controller that is based on the optimal solution.

Directional region control of the thermal fractal diffusion of a space body

We present a directional region control （DRC） model of thermal diffusion fractal growth with active heat diffusion in three-dimensional space. This model can be applied to predict the space body heat fractal growth and study its directional region control. When the nonlinear interference term and the inner heat source term are generalized functions, the relationship between the particle aggregation probability and the interference terms can be obtained using the norm theory. We can then predict the aggregation form of particles in different regions. When the nonlinear interference terms in the model are expressed as a trigonometric function and its composite function, our simulations show that the DRC method of thermal fractal diffusion is effective and has reference value for the directional control of actual fractal growth systems.

Sexual Risk Behaviours among People Living with HIV and Implications for Control in the North West Region of Cameroon

In Cameroon, despite extensive control efforts against HIV/AIDS, the number of new HIV infections is still on the rise. The factors contributing to this are not clearly understood. We hypothesized that it may lie on people living with HIV (PLHIV). In a case-control descriptive study, we studied the characteristics and sexual risky behaviour of PLHIV in the North West Region of Cameroon which has the highest HIV prevalence. Participants were screened for HIV and a structured questionnaire was used in data collection. An equivalent number (350) of PLHIV and controls who did not differ with respect to age and sex participated. Relative to the control, PLHIV were generally less educated (P < 0.001), poorer and less privileged (P < 0.001) with no stable source of income. Among participants that were once married, a greater proportion of PLHIV were divorced (OR = 5.23, P = 0.007), and widows (OR = 2.73, P = 0.001). Among participants that were single, a relatively greater proportion of PLHIV practiced multi-partner sex (OR = 4.55, P< 0.001). History of STDs was higher in PLHIV than the control (OR = 1.88, P = 0.001). Out of 350 PLHIV, 280 (80%) admitted to having had sexual intercourse after being diagnosed of which only 127 (41.78%) admitted to using condoms and 132 (47.14%) admitted to concealing their HIV status from their sexual partner(s). These findings have implications in HIV control programs which should target the poor and the less educated, as well as the sexual behaviour of PLHIV, so as to reverse the current rising trend of new infections in the country.

Model Predictive Control of Nonlinear Systems: Stability Region and Feasible Initial Control

This paper proposes a new method for model predictive control （MPC） of nonlinear systems to calculate stability region and feasible initial control profile/sequence, which are important to the implementations of MPC. Different from many existing methods, this paper distinguishes stability region from conservative terminal region. With global linearization, linear differential inclusion （LDI） and linear matrix inequality （LMI） techniques, a nonlinear system is transformed into a convex set of linear systems, and then the vertices of the set are used off-line to design the controller, to estimate stability region, and also to determine a feasible initial control profile/sequence. The advantages of the proposed method are demonstrated by simulation study.