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Sample records for control region sequence

  1. Mitochondrial control region sequences from an Egyptian population sample.

    PubMed

    Saunier, Jessica L; Irwin, Jodi A; Strouss, Katharine M; Ragab, Hisham; Sturk, Kimberly A; Parsons, Thomas J

    2009-06-01

    Entire mitochondrial control region data was generated for 277 unrelated Egyptian individuals. High-throughput robotics, a redundant sequencing approach, and several quality control checks were implemented to generate a high-quality database. The data presented here will augment the limited Egyptian mtDNA reference data currently available for forensic comparisons. PMID:19414160

  2. Repetitive sequences in the crocodilian mitochondrial control region: poly-A sequences and heteroplasmic tandem repeats.

    PubMed

    Ray, David A; Densmore, Llewellyn D

    2003-06-01

    Heteroplasmic tandem repeats in the mitochondrial control region have been documented in a wide variety of vertebrate species. We have examined the control region from 11 species in the family Crocodylidae and identified two different types of heteroplasmic repetitive sequences in the conserved sequence block (CSB) domain-an extensive poly-A tract that appears to be involved in the formation of secondary structure and a series of tandem repeats located downstream ranging from approximately 50 to approximately 80 bp in length. We describe this portion of the crocodylian control region in detail and focus on members of the family Crocodylidae. We then address the origins of the tandemly repeated sequences in this family and suggest hypotheses to explain possible mechanisms of expansion/contraction of the sequences. We have also examined control region sequences from Alligator and Caiman and offer hypotheses for the origin of tandem repeats found in those taxa. Finally, we present a brief analysis of intraindividual and interindividual haplotype variation by examining representatives of Morelet's crocodile (Crocodylus moreletii). PMID:12716979

  3. Mitochondrial control-region sequence variation in aboriginal Australians.

    PubMed

    van Holst Pellekaan, S; Frommer, M; Sved, J; Boettcher, B

    1998-02-01

    The mitochondrial D-loop hypervariable segment 1 (mt HVS1) between nucleotides 15997 and 16377 has been examined in aboriginal Australian people from the Darling River region of New South Wales (riverine) and from Yuendumu in central Australia (desert). Forty-seven unique HVS1 types were identified, varying at 49 nucleotide positions. Pairwise analysis by calculation of BEPPI (between population proportion index) reveals statistically significant structure in the populations, although some identical HVS1 types are seen in the two contrasting regions. mt HVS1 types may reflect more-ancient distributions than do linguistic diversity and other culturally distinguishing attributes. Comparison with sequences from five published global studies reveals that these Australians demonstrate greatest divergence from some Africans, least from Papua New Guinea highlanders, and only slightly more from some Pacific groups (Indonesian, Asian, Samoan, and coastal Papua New Guinea), although the HVS1 types vary at different nucleotide sites. Construction of a median network, displaying three main groups, suggests that several hypervariable nucleotide sites within the HVS1 are likely to have undergone mutation independently, making phylogenetic comparison with global samples by conventional methods difficult. Specific nucleotide-site variants are major separators in median networks constructed from Australian HVS1 types alone and for one global selection. The distribution of these, requiring extended study, suggests that they may be signatures of different groups of prehistoric colonizers into Australia, for which the time of colonization remains elusive. PMID:9463317

  4. Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes.

    PubMed Central

    Stoneking, M; Hedgecock, D; Higuchi, R G; Vigilant, L; Erlich, H A

    1991-01-01

    A method for detecting sequence variation of hypervariable segments of the mtDNA control region was developed. The technique uses hybridization of sequence-specific oligonucleotide (SSO) probes to DNA sequences that have been amplified by PCR. The nucleotide sequences of the two hypervariable segments of the mtDNA control region from 52 individuals were determined; these sequences were then used to define nine regions suitable for SSO typing. A total of 23 SSO probes were used to detect sequence variants at these nine regions in 525 individuals from five ethnic groups (African, Asian, Caucasian, Japanese, and Mexican). The SSO typing revealed an enormous amount of variability, with 274 mtDNA types observed among these 525 individuals and with diversity values, for each population, exceeding .95. For each of the nine mtDNA regions significant differences in the frequencies of sequence variants were observed between these five populations. The mtDNA SSO-typing system was successfully applied to a case involving individual identification of skeletal remains; the probability of a random match was approximately 0.7%. The potential useful applications of this mtDNA SSO-typing system thus include the analysis of individual identity as well as population genetic studies. Images Figure 3 PMID:1990843

  5. Solving a sequencing problem in the vertebrate mitochondrial control region using phylogenetic comparisons.

    PubMed

    Feinstein, Julie; Cracraft, Joel

    2004-01-01

    The mitochondrial control region (mtCR) of the bird-of-paradise, Phonygammus keraudrenii, the Trumpet Manucode, contains a unique arrangement of homopolymers and short tandem repeats. Homopolymers occur within a few hundred bases of each other, trapping sequence information between unsequenceable barriers. A comparative strategy, involving other manucode species, allowed the prediction of primer sites in the inaccessible region. The method is suggested for similar sequencing problems. PMID:15621664

  6. Investigation of mtDNA control region sequences in an Egyptian population sample.

    PubMed

    Elmadawy, Mostafa Ali; Nagai, Atsushi; Gomaa, Ghada M; Hegazy, Hanaa M R; Shaaban, Fawzy Eid; Bunai, Yasuo

    2013-11-01

    The sequences of mitochondrial DNA (mtDNA) control region were investigated in 101 unrelated individuals living in the northern region of Nile delta (Gharbia, N=55 and Kafrelsheikh, N=46). DNA was extracted from blood stained filter papers or buccal swabs. HV1, HV2 and HV3 were PCR amplified and sequenced; the resulted sequences were aligned and compared with revised Cambridge sequence (rCRS). The results revealed presence of total 93 different haplotypes, 86 of them are unique and 7 are shared haplotypes, the most common haplotype, was observed with a frequency, 2.97% of population sample. High mtDNA diversity was observed with genetic diversity and power of discrimination, 0.9982 and 0.9883, respectively. In this dataset the west Eurasian haplogroups predominated over the African haplogroups. The results would be useful for forensic examinations and human genetic studies. PMID:23910099

  7. Mitochondrial DNA control region sequences study in Saraiki population from Pakistan.

    PubMed

    Hayat, Sikandar; Akhtar, Tanveer; Siddiqi, Muhammad Hassan; Rakha, Allah; Haider, Naeem; Tayyab, Muhammad; Abbas, Ghazanfar; Ali, Azam; Bokhari, Syed Yassir Abbas; Tariq, Muhammad Akram; Khan, Fazle Majid

    2015-03-01

    The analysis of mitochondrial DNA (mtDNA) control region was carried in 85 unrelated Sariki individuals living in the different provinces of Pakistan. DNA was extracted from blood preserved in EDTA vacutainers. Hypervariable regions (HV1, HV2 & HV3) were PCR amplified and sequenced. Sequencing results were aligned and compared with revised Cambridge reference sequence (rCRS). The sequencing results showed presence of total 63 different haplotypes, 58 of them are unique and 05 are common haplotypes shared by more than one individual. The most common haplotype observed was (W6) with a frequency 12.9% of population sample. The Saraiki population was detected with genetic diversity (0.9570) and power of discrimination (0.9458). This study will be beneficial for forensic casework. PMID:25465675

  8. Multiple independent transpositions of mitochondrial DNA control region sequences to the nucleus.

    PubMed

    Sorenson, M D; Fleischer, R C

    1996-12-24

    Transpositions of mtDNA sequences to the nuclear genome have been documented in a wide variety of individual taxa, but little is known about their taxonomic frequency or patterns of variation. We provide evidence of nuclear sequences homologous to the mtDNA control region in seven species of diving ducks (tribe Aythyini). Phylogenetic analysis places each nuclear sequence as a close relative of the mtDNA haplotypes of the specie(s) in which it occurs, indicating that they derive from six independent transposition events, all occurring within the last approximately 1.5 million years. Relative-rate tests and comparison of intraspecific variation in nuclear and mtDNA sequences confirm the expectation of a greatly reduced rate of evolution in the nuclear copies. By representing mtDNA haplotypes from ancestral populations, nuclear insertions may be valuable in some phylogenetic analyses, but they also confound the accurate determination of mtDNA sequences. In particular, our data suggest that the presumably nonfunctional but more slowly evolving nuclear sequences often will not be identifiable by changes incompatible with function and may be preferentially amplified by PCR primers based on mtDNA sequences from related taxa. PMID:8986794

  9. Mitochondrial DNA control region sequence variation in migraine headache and cyclic vomiting syndrome.

    PubMed

    Wang, Qingxue; Ito, Masamichi; Adams, Kathleen; Li, B U K; Klopstock, Thomas; Maslim, Audrey; Higashimoto, Tomoyasu; Herzog, Juergen; Boles, Richard G

    2004-11-15

    Migraine headache is a very common condition affecting about 10% of the population that results in substantial morbidity and economic loss. The two most common variants are migraine with (MA) and without (MO) aura. Often considered to be a migraine-like variant, cyclic vomiting syndrome (CVS) is a predominately childhood condition characterized by severe, discrete episodes of nausea, vomiting, and lethargy. Disease-associated mitochondrial DNA (mtDNA) sequence variants are suggested in common migraine and CVS based upon a strong bias towards the maternal inheritance of disease, and several other factors. Temporal temperature gradient gel electrophoresis (TTGE) followed by cyclosequencing and RFLP was used to screen almost 90% of the mtDNA, including the control region (CR), for heteroplasmy in 62 children with CVS and neuromuscular disease (CVS+) and in 95 control subjects. One or two rare mtDNA-CR heteroplasmic sequence variants were found in six CVS+ and in zero control subjects (P = 0.003). These variants comprised 6 point and 2 length variants in hypervariable regions 1 and 2 (HV1 and HV2, both part of the mtDNA-CR), one half of which were clustered in the nt 16040-16188 segment of HV1 that includes the termination associated sequence (TAS), a functional location important in the regulation of mtDNA replication. Based upon our findings, sequencing and statistical analysis looking for homoplasmic nucleotide changes was performed in HV1 among 30 CVS+, 30 randomly-ascertained CVS (rCVS), 18 MA, 32 MO, and 35 control haplogroup H cases. Within the nt 16040-16188 segment, homoplasmic sequence variants were three-fold more common relative to control subjects in both CVS groups (P = 0.01 combined data) and in MO (P = 0.02), but not in MA (P = 0.5 vs. control subjects and 0.02 vs. MO). No group differences were noted in the remainder of HV1. We conclude that sequence variation in this small "peri-TAS" segment is associated with CVS and MO, but not MA. These variants

  10. Distribution of sequence variation in the mtDNA control region of Native North Americans.

    PubMed

    Lorenz, J G; Smith, D G

    1997-12-01

    The distributions of mtDNA diversity within and/or among North American haplogroups, language groups, and tribes were used to characterize the process of tribalization that followed the colonization of the New World. Approximately 400 bp from the mtDNA control region of 1 Na-Dene and 33 Amerind individuals representing a wide variety of languages and geographic origins were sequenced. With the inclusion of data from previous studies, 225 native North American (284 bp) sequences representing 85 distinct mtDNA lineages were analyzed. Mean pairwise sequence differences between (and within) tribes and language groups were primarily due to differences in the distribution of three of the four major haplogroups that evolved before settlement of the New World. Pairwise sequence differences within each of these three haplogroups were more similar than previous studies based on restriction enzyme analysis have indicated. The mean of pairwise sequence differences between Amerind members of haplogroup A, the most common of the four haplogroups in North America, was only slightly higher than that for the Eskimo, providing no evidence of separate ancestry, but was about two-thirds higher than that for the Na-Dene. However, analysis of pairwise sequence divergence between only tribal-specific lineages, unweighted for sample size, suggests that random evolutionary processes have reduced sequence diversity within the Na-Dene and that members of all three language groups possess approximately equally diverse mtDNA lineages. Comparisons of diversity within and between specific ethnic groups with the largest sample size were also consistent with this outcome. These data are not consistent with the hypothesis that the New World was settled by more than a single migration. Because lineages tended not to cluster by tribe and because lineage sharing among linguistically unrelated groups was restricted to geographically proximate groups, the tribalization process probably did not occur

  11. Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores.

    PubMed

    Hoelzel, A R; Lopez, J V; Dover, G A; O'Brien, S J

    1994-08-01

    We describe a repetitive DNA region at the 3' end of the mitochondrial DNA (mtDNA) control region and compare it in 21 carnivore species representing eight carnivore families. The sequence and organization of the repetitive motifs can differ extensively between arrays; however, all motifs appear to be derived from the core motif "ACGT." Sequence data and Southern blot analysis demonstrate extensive heteroplasmy. The general form of the array is similar between heteroplasmic variants within an individual and between individuals within a species (varying primarily in the length of the array, though two clones from the northern elephant seal are exceptional). Within certain families, notably ursids, the array structure is also similar between species. Similarity between species was not apparent in other carnivore families, such as the mustelids, suggesting rapid changes in the organization and sequence of some arrays. The pattern of change seen within and between species suggests that a dominant mechanism involved in the evolution of these arrays is DNA slippage. A comparative analysis shows that the motifs that are being reiterated or deleted vary within and between arrays, suggesting a varying rate of DNA turnover. We discuss the evolutionary implications of the observed patterns of variation and extreme levels of heteroplasmy. PMID:7932782

  12. Sequence polymorphism of the mitochondrial DNA control region in the population of Vojvodina Province, Serbia.

    PubMed

    Zgonjanin, Dragana; Veselinović, Igor; Kubat, Milovan; Furac, Ivana; Antov, Mirjana; Loncar, Eva; Tasić, Milos; Vuković, Radenko; Omorjan, Radovan

    2010-03-01

    In order to generate and establish the database for forensic identification purposes in Vojvodina Province (Serbia), the sequence of the hypervariable regions 1 (HV1) and 2 (HV2) of the mtDNA control region were determined in a population of 104 unrelated individuals from Vojvodina Province, using a fluorescent-based capillary electrophoresis sequencing method. A total of 93 different haplotypes were found, of these 83 mtDNA types were unique, nine haplotypes were shared by two individuals and one haplotype by three individuals. The variation of mtDNA HV1 and HV2 regions was confined to 116 nucleotide positions, of which 72 were observed in the HV1 and 44 in the HV2. A statistical estimate of the results for this population showed the genetic diversity of 0.9977 and the random match probability of 1.18%. Haplogroup H was the most common haplogroup (43.3%). Haplogroups observed at intermediate levels included clusters U (13.5%), T (10.6%), J (8.6%) and W (5.8%). PMID:19962932

  13. Genetic structure of Florida green turtle rookeries as indicated by mitochondrial DNA control region sequences

    USGS Publications Warehouse

    Shamblin, Brian M.; Bagley, Dean A.; Ehrhart, Llewellyn M.; Desjardin, Nicole A.; Martin, R. Erik; Hart, Kristen M.; Naro-Maciel, Eugenia; Rusenko, Kirt; Stiner, John C.; Sobel, Debra; Johnson, Chris; Wilmers, Thomas; Wright, Laura J.; Nairn, Campbell J.

    2014-01-01

    Green turtle (Chelonia mydas) nesting has increased dramatically in Florida over the past two decades, ranking the Florida nesting aggregation among the largest in the Greater Caribbean region. Individual beaches that comprise several hundred kilometers of Florida’s east coast and Keys support tens to thousands of nests annually. These beaches encompass natural to highly developed habitats, and the degree of demographic partitioning among rookeries was previously unresolved. We characterized the genetic structure of ten Florida rookeries from Cape Canaveral to the Dry Tortugas through analysis of 817 base pair mitochondrial DNA (mtDNA) control region sequences from 485 nesting turtles. Two common haplotypes, CM-A1.1 and CM-A3.1, accounted for 87 % of samples, and the haplotype frequencies were strongly partitioned by latitude along Florida’s Atlantic coast. Most genetic structure occurred between rookeries on either side of an apparent genetic break in the vicinity of the St. Lucie Inlet that separates Hutchinson Island and Jupiter Island, representing the finest scale at which mtDNA structure has been documented in marine turtle rookeries. Florida and Caribbean scale analyses of population structure support recognition of at least two management units: central eastern Florida and southern Florida. More thorough sampling and deeper sequencing are necessary to better characterize connectivity among Florida green turtle rookeries as well as between the Florida nesting aggregation and others in the Greater Caribbean region.

  14. Control region sequences indicate that multiple externae represent multiple infections by Sacculina carcini (Cirripedia: Rhizocephala).

    PubMed

    Rees, David; Glenner, Henrik

    2014-08-01

    The rhizocephalan barnacle, Sacculina carcini, is a common parasite of the European shore crab, Carcinus maenas, in which it causes significant detrimental physical and behavioral modifications. In the vast majority of cases, the external portion of the parasite is present in the form of a single sac-like externa; in rare cases, double or even triple externae may occur on the same individual host. Here, we use a highly variable DNA marker, the mitochondrial control region (CR), to investigate whether multiple externae in S. carcini represent infection by multiple parasites or asexual cloning developed by a single parasite individual. Sequences for multiple externae from C. maenas hosts from the Danish inlet, Limfjorden, and from the mud flates at Roscoff, France, were compared. In almost all cases, double or triple externae from an individual host yielded different haplotypes. In the few cases where identical haplotypes were identified from externae on a multiple-infected host, this always represented the most commonly found haplotype in the population. This indicates that in Sacculina carcini, the presence of multiple externae on a single host reflects infection by different individual parasites. A haplotype network of CR sequences also suggests a degree of geographical partitioning, with no shared haplotypes between the Limfjorden and Roscoff. Our data represent the first complete CR sequences for a rhizocephalan, and a unique gene order was also revealed. Although the utility of CR sequences for population-level work must be investigated further, the CR has proved a simple to use and highly variable marker for studies of S. carcini and can easily be applied to a variety of studies in this important parasite. PMID:25473481

  15. Haplogroup Classification of Korean Cattle Breeds Based on Sequence Variations of mtDNA Control Region

    PubMed Central

    Kim, Jae-Hwan; Lee, Seong-Su; Kim, Seung Chang; Choi, Seong-Bok; Kim, Su-Hyun; Lee, Chang Woo; Jung, Kyoung-Sub; Kim, Eun Sung; Choi, Young-Sun; Kim, Sung-Bok; Kim, Woo Hyun; Cho, Chang-Yeon

    2016-01-01

    Many studies have reported the frequency and distribution of haplogroups among various cattle breeds for verification of their origins and genetic diversity. In this study, 318 complete sequences of the mtDNA control region from four Korean cattle breeds were used for haplogroup classification. 71 polymorphic sites and 66 haplotypes were found in these sequences. Consistent with the genetic patterns in previous reports, four haplogroups (T1, T2, T3, and T4) were identified in Korean cattle breeds. In addition, T1a, T3a, and T3b sub-haplogroups were classified. In the phylogenetic tree, each haplogroup formed an independent cluster. The frequencies of T3, T4, T1 (containing T1a), and T2 were 66%, 16%, 10%, and 8%, respectively. Especially, the T1 haplogroup contained only one haplotype and a sample. All four haplogroups were found in Chikso, Jeju black and Hanwoo. However, only the T3 and T4 haplogroups appeared in Heugu, and most Chikso populations showed a partial of four haplogroups. These results will be useful for stable conservation and efficient management of Korean cattle breeds. PMID:26954229

  16. Variability of the human mitochondrial DNA control region sequences in the Lithuanian population.

    PubMed

    Kasperaviciūte, Dalia; Kucinskas, Vaidutis

    2002-01-01

    The Lithuanians and Latvians are the only two Baltic cultures that survived until today. Since the Neolithic period the native inhabitants of the present-day Lithuanian territory have not been replaced by any other ethnic group. Therefore the genetic characterization of the present-day Lithuanians may shed some light on the early history of the Balts. We have analysed 120 DNA samples from two Lithuanian ethnolinguistic groups (Aukstaiciai and Zemaiciai) by direct sequencing of the first hypervariable segment (HVI) of the control region of mitochondrial DNA (mtDNA) and restriction enzyme digestion for polymorphic site 00073. On the basis of specific nucleotide substitutions the obtained sequences were classified to mtDNA haplogroups. This revealed the presence of almost all European haplogroups (except X) in the Lithuanian sample, including those that expanded through Europe in the Palaeolithic and those whose expansion occurred during the Neolithic. Molecular diversity indices (gene diversity 0.97, nucleotide diversity 0.012 and mean number of pairwise differences 4.5) were within the range usually reported in European populations. No significant differences between Aukstaiciai and Zemaiciai subgroups were found, but some slight differences need further investigation. PMID:12080181

  17. Haplogroup Classification of Korean Cattle Breeds Based on Sequence Variations of mtDNA Control Region.

    PubMed

    Kim, Jae-Hwan; Lee, Seong-Su; Kim, Seung Chang; Choi, Seong-Bok; Kim, Su-Hyun; Lee, Chang Woo; Jung, Kyoung-Sub; Kim, Eun Sung; Choi, Young-Sun; Kim, Sung-Bok; Kim, Woo Hyun; Cho, Chang-Yeon

    2016-05-01

    Many studies have reported the frequency and distribution of haplogroups among various cattle breeds for verification of their origins and genetic diversity. In this study, 318 complete sequences of the mtDNA control region from four Korean cattle breeds were used for haplogroup classification. 71 polymorphic sites and 66 haplotypes were found in these sequences. Consistent with the genetic patterns in previous reports, four haplogroups (T1, T2, T3, and T4) were identified in Korean cattle breeds. In addition, T1a, T3a, and T3b sub-haplogroups were classified. In the phylogenetic tree, each haplogroup formed an independent cluster. The frequencies of T3, T4, T1 (containing T1a), and T2 were 66%, 16%, 10%, and 8%, respectively. Especially, the T1 haplogroup contained only one haplotype and a sample. All four haplogroups were found in Chikso, Jeju black and Hanwoo. However, only the T3 and T4 haplogroups appeared in Heugu, and most Chikso populations showed a partial of four haplogroups. These results will be useful for stable conservation and efficient management of Korean cattle breeds. PMID:26954229

  18. Complete mitochondrial control region sequences indicate a distinct variety of brown trout Salmo trutta in the Aral Sea.

    PubMed

    Griffiths, A M; Bright, D; Stevens, J R

    2009-04-01

    Complete sequencing of the mtDNA control region (CR) from five specimens of brown trout Salmo trutta from the Amu Darya River identified two novel haplotypes belonging to the Danubian lineage. This finding supports the long-standing hypothesis that brown trout in the Aral Sea represent a distinct genetic stock and also illustrates the benefits that complete sequencing of the CR can provide for elucidating phylogeographic relationships. PMID:20735624

  19. Investigation of mtDNA control region sequences in a Tibetan population sample from China.

    PubMed

    Wang, Yun-Ke; Yao, Jun; Han, Xuan; Ding, Mei; Pang, Hao; Wang, Bao-Jie; Zhang, Zhi-Qiang

    2016-05-01

    Mitochondrial hypervariable region sequences including HVI and HVII (15,751-520) were investigated from 174 unrelated Tibetan individuals living in Tibet Autonomous Region in People's Republic of China. The resulted sequences were aligned and compared with revised Cambridge sequence (rCRS). This sequence variability rendered a high gene diversity value (0.9940 ± 0.0021) and a high random match probability (0.0118) was determined with PIC of 0.9882. Among a total of 174 samples, 217 polymorphic sites were identified, which defined 135 haplotypes. A total of 135 different haplotypes were detected, 113 of them were unique and 22 were shared. The most common haplogroup was M9a1a1c1b1 (16.09%), followed by A11 (6.32%), A (5.17%), R (4.60%), A15 (4.60%), and G3a1 (3.45). The proportions of macro-haplogroups M, N, and L were 54.60%, 42.53%, and 2.87%, respectively. By principal component analysis (PCA), there was no special cluster between Tibetans and other populations except that the structure of Tibetans closely resembled that of Uygur in component 2. PMID:25423521

  20. Optimization of human mtDNA control region sequencing for forensic applications.

    PubMed

    Bourdon, Véronique; Ng, Carolyn; Harris, Jessica; Prinz, Mechthild; Shapiro, Eli

    2014-07-01

    Sequencing mitochondrial DNA hypervariable regions I and II (HVI and HVII) is useful in forensic missing person and unidentified remains cases. Improvements in ease and sensitivity of testing will yield results from more samples in a timely fashion. Routinely, amplification of HVI and HVII is followed by Sanger sequencing using the BigDye(®) Terminator v3.1 Cycle Sequencing kit (Applied Biosystems) using 4 μL of ready reaction mix (RRM). Each sequencing reaction is then purified through column filtration before capillary electrophoresis. Using lower amounts of RRM (2 μL or 1 μL) and purification using BigDye(®) XTerminator(™) (Applied Biosystems) instead of columns showed no loss of sequence length and increased the quality and the sensitivity of testing, allowing HVI and HVII typing from mitochondrial genome equivalent to 125 fg of nuclear DNA, or 100 pg of HVI/HVII amplicons. Using this methodology, testing can be completed in 1 day, and the cost of testing is reduced. PMID:24666098

  1. Controlled processing during sequencing

    PubMed Central

    Thothathiri, Malathi; Rattinger, Michelle

    2015-01-01

    Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6) in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region’s activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations. PMID:26578941

  2. Massively parallel sequencing of the entire control region and targeted coding region SNPs of degraded mtDNA using a simplified library preparation method.

    PubMed

    Lee, Eun Young; Lee, Hwan Young; Oh, Se Yoon; Jung, Sang-Eun; Yang, In Seok; Lee, Yang-Han; Yang, Woo Ick; Shin, Kyoung-Jin

    2016-05-01

    The application of next-generation sequencing (NGS) to forensic genetics is being explored by an increasing number of laboratories because of the potential of high-throughput sequencing for recovering genetic information from multiple markers and multiple individuals in a single run. A cumbersome and technically challenging library construction process is required for NGS. In this study, we propose a simplified library preparation method for mitochondrial DNA (mtDNA) analysis that involves two rounds of PCR amplification. In the first-round of multiplex PCR, six fragments covering the entire mtDNA control region and 22 fragments covering interspersed single nucleotide polymorphisms (SNPs) in the coding region that can be used to determine global haplogroups and East Asian haplogroups were amplified using template-specific primers with read sequences. In the following step, indices and platform-specific sequences for the MiSeq(®) system (Illumina) were added by PCR. The barcoded library produced using this simplified workflow was successfully sequenced on the MiSeq system using the MiSeq Reagent Nano Kit v2. A total of 0.4 GB of sequences, 80.6% with base quality of >Q30, were obtained from 12 degraded DNA samples and mapped to the revised Cambridge Reference Sequence (rCRS). A relatively even read count was obtained for all amplicons, with an average coverage of 5200 × and a less than three-fold read count difference between amplicons per sample. Control region sequences were successfully determined, and all samples were assigned to the relevant haplogroups. In addition, enhanced discrimination was observed by adding coding region SNPs to the control region in in silico analysis. Because the developed multiplex PCR system amplifies small-sized amplicons (<250 bp), NGS analysis using the library preparation method described here allows mtDNA analysis using highly degraded DNA samples. PMID:26844917

  3. The complete mitochondrial genome sequence of the tubeworm Lamellibrachia satsuma and structural conservation in the mitochondrial genome control regions of Order Sabellida.

    PubMed

    Patra, Ajit Kumar; Kwon, Yong Min; Kang, Sung Gyun; Fujiwara, Yoshihiro; Kim, Sang-Jin

    2016-04-01

    The control region of the mitochondrial genomes shows high variation in conserved sequence organizations, which follow distinct evolutionary patterns in different species or taxa. In this study, we sequenced the complete mitochondrial genome of Lamellibrachia satsuma from the cold-seep region of Kagoshima Bay, as a part of whole genome study and extensively studied the structural features and patterns of the control region sequences. We obtained 15,037 bp of mitochondrial genome using Illumina sequencing and identified the non-coding AT-rich region or control region (354 bp, AT=83.9%) located between trnH and trnR. We found 7 conserved sequence blocks (CSB), scattered throughout the control region of L. satsuma and other taxa of Annelida. The poly-TA stretches, which commonly form the stem of multiple stem-loop structures, are most conserved in the CSB-I and CSB-II regions. The mitochondrial genome of L. satsuma encodes a unique repetitive sequence in the control region, which forms a unique secondary structure in comparison to Lamellibrachia luymesi. Phylogenetic analyses of all protein-coding genes indicate that L. satsuma forms a monophyletic clade with L. luymesi along with other tubeworms found in cold-seep regions (genera: Lamellibrachia, Escarpia, and Seepiophila). In general, the control region sequences of Annelida could be aligned with certainty within each genus, and to some extent within the family, but with a higher rate of variation in conserved regions. PMID:26776396

  4. Sequencing Complex Genomic Regions

    SciTech Connect

    Eichler, Evan

    2009-05-28

    Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 1 of 2

  5. Sequencing Complex Genomic Regions

    SciTech Connect

    Eichler, Evan

    2009-05-28

    Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 2 of 2

  6. [Polymorphism and Genetic Structure of Microtus maximowiczii (Schrenck, 1858) (Rodentia, Cricetidae) from the Middle Amur River Region as Inferred from Sequencing of the mtDNA Control Region].

    PubMed

    Sheremetyeva, I N; Kartavtseva, I V; Frisman, L V; Vasil'eva, T V; Adnagulova, A V

    2015-10-01

    The genetic variability of the mitochondrial DNA control region sequences was estimated for the Maximowicz's vole Microtus maximowiczii from the Middle Amur River region located between the confluence of Amur River with Ussuri River and Zeya River. The species as a whole was characterized by a high level of genetic variability. For each individual sample, low nucleotide diversity was observed, except for two samples in which a more than twofold increase in this index was revealed. The presence of the contact zone of two genetically distinct populations in the area between Bira and Bidzhan rivers is suggested. PMID:27169230

  7. Sequence analysis of the mitochondrial DNA control region of ciscoes (genus Coregonus): Taxonomic implications for the Great Lakes species flock

    USGS Publications Warehouse

    Reed, Kent M.; Dorschner, Michael O.; Todd, Thomas N.; Phillips, Ruth B.

    1998-01-01

    Sequence variation in the control region (D-loop) of the mitochondrial DNA (mtDNA) was examined to assess the genetic distinctiveness of the shortjaw cisco (Coregonus zenithicus). Individuals from within the Great Lakes Basin as well as inland lakes outside the basin were sampled. DNA fragments containing the entire D-loop were amplified by PCR from specimens ofC. zenithicus and the related species C. artedi, C. hoyi, C. kiyi, and C. clupeaformis. DNA sequence analysis revealed high similarity within and among species and shared polymorphism for length variants. Based on this analysis, the shortjaw cisco is not genetically distinct from other cisco species.

  8. Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control.

    PubMed

    Lee, Hwan Young; Yoo, Ji-Eun; Park, Myung Jin; Chung, Ukhee; Shin, Kyoung-Jin

    2006-01-01

    We have established a high-quality mtDNA control region sequence database for Koreans. To identify polymorphic sites and to determine their frequencies and haplotype frequencies, the complete mtDNA control region was sequenced in 593 Koreans, and major length variants of poly-cytosine tracts in HV2 and HV3 were determined in length heteroplasmic individuals by PCR analysis using fluorescence-labeled primers. Sequence comparison showed that 494 haplotypes defined by 285 variable sites were found when the major poly-cytosine tract genotypes were considered in distinguishing haplotypes, whereas 441 haplotypes were found when the poly-cytosine tracts were ignored. Statistical parameters indicated that analysis of partial mtDNA control region which encompasses the extended regions of HV1 and HV2, CA dinucleotide repeats in HV3 and nucleotide position 16497, 16519, 456, 489 and 499 (HV1ex+HV2ex+HV3CA+5SNPs) and the analysis of another partial mtDNA control region including extended regions of HV1 and HV2, HV3 region and nucleotide position 16497 and 16519 (HV1ex+HV2ex+HV3+2SNPs) can be used as efficient alternatives for the analysis of the entire mtDNA control region in Koreans. Also, we collated the basic informative SNPs, suggested the important mutation motifs for the assignment of East Asian haplogroups, and classified 592 Korean mtDNAs (99.8%) into various East Asian haplogroups or sub-haplogroups. Haplogroup-directed database comparisons confirmed the absence of any major systematic errors in our data, e.g., a mix-up of site designations, base shifts or mistypings. PMID:16177905

  9. The H19 Imprinting Control Region Mediates Preimplantation Imprinted Methylation of Nearby Sequences in Yeast Artificial Chromosome Transgenic Mice

    PubMed Central

    Okamura, Eiichi; Matsuzaki, Hitomi; Sakaguchi, Ryuuta; Takahashi, Takuya; Fukamizu, Akiyoshi

    2013-01-01

    In the mouse Igf2/H19 imprinted locus, differential methylation of the imprinting control region (H19 ICR) is established during spermatogenesis and is maintained in offspring throughout development. Previously, however, we observed that the paternal H19 ICR, when analyzed in yeast artificial chromosome transgenic mice (YAC-TgM), was preferentially methylated only after fertilization. To identify the DNA sequences that confer methylation imprinting, we divided the H19 ICR into two fragments (1.7 and 1.2 kb), ligated them to both ends of a λ DNA fragment into which CTCF binding sites had been inserted, and analyzed this in YAC-TgM. The maternally inherited λ sequence, normally methylated after implantation in the absence of H19 ICR sequences, became hypomethylated, demonstrating protective activity against methylation within the ICR. Meanwhile, the paternally inherited λ sequence was hypermethylated before implantation only when a 1.7-kb fragment was ligated. Consistently, when two subfragments of the H19 ICR were individually investigated for their activities in YAC-TgM, only the 1.7-kb fragment was capable of introducing paternal allele-specific DNA methylation. These results show that postfertilization methylation imprinting is conferred by a paternal allele-specific methylation activity present in a 1.7-kb DNA fragment of the H19 ICR, while maternal allele-specific activities protect the allele from de novo DNA methylation. PMID:23230275

  10. Minding the gap: Frequency of indels in mtDNA control region sequence data and influence on population genetic analyses

    USGS Publications Warehouse

    Pearce, J.M.

    2006-01-01

    Insertions and deletions (indels) result in sequences of various lengths when homologous gene regions are compared among individuals or species. Although indels are typically phylogenetically informative, occurrence and incorporation of these characters as gaps in intraspecific population genetic data sets are rarely discussed. Moreover, the impact of gaps on estimates of fixation indices, such as FST, has not been reviewed. Here, I summarize the occurrence and population genetic signal of indels among 60 published studies that involved alignments of multiple sequences from the mitochondrial DNA (mtDNA) control region of vertebrate taxa. Among 30 studies observing indels, an average of 12% of both variable and parsimony-informative sites were composed of these sites. There was no consistent trend between levels of population differentiation and the number of gap characters in a data block. Across all studies, the average influence on estimates of ??ST was small, explaining only an additional 1.8% of among population variance (range 0.0-8.0%). Studies most likely to observe an increase in ??ST with the inclusion of gap characters were those with < 20 variable sites, but a near equal number of studies with few variable sites did not show an increase. In contrast to studies at interspecific levels, the influence of indels for intraspecific population genetic analyses of control region DNA appears small, dependent upon total number of variable sites in the data block, and related to species-specific characteristics and the spatial distribution of mtDNA lineages that contain indels. ?? 2006 Blackwell Publishing Ltd.

  11. Irritable Bowel Syndrome may be associated with maternal inheritance and mitochondrial DNA control region sequence variants

    PubMed Central

    van Tilburg, Miranda A.L.; Zaki, Essam A.; Venkatesan, Thangam; Boles, Richard G.

    2014-01-01

    Background & Aims Mitochondrial dysfunction has been implicated in various functional disorders that are co-morbid to Irritable Bowel Syndrome (IBS) such as migraine, depression and chronic fatigue syndrome. The aim of the current case-control pilot study was to determine if functional symptoms in IBS show a maternal inheritance bias, and if the degree of this maternal inheritance is related to mitochondrial DNA (mtDNA) polymorphisms. Methods Pedigrees were obtained from N=308 adult IBS patients, N=102 healthy controls, and N=36 controls with Inflammatory Bowel Disease (IBD), all from Caucasian heritage, to determine probable maternal inheritance. Two mtDNA polymorphisms (16519T and 3010A), which have previously been implicated in other functional disorders, were assayed in mtDNA haplogroup H IBS subjects and compared to genetic data from N=344 published haplogroup H controls. Results Probable Maternal Inheritance was found in 17.5% IBS, 2% healthy controls and 0% IBD controls (p < 0.0001). No difference was found between IBS and control for 3010A, and a trend was found for 16519T (p=.05). IBS with maternal inheritance were significantly more likely to have the 16519T than controls (OR=5.8; 95%CI=1.5–23.1) or IBS without maternal inheritance (OR=5.2; 95%CI=1.2–22.6). Conclusions This small pilot study shows that a significant minority (1/6) of IBS patients have pedigrees suggestive of maternal inheritance. The mtDNA polymorphism 16519T, which has been previously implicated in other functional disorders, is also associated with IBS patients who display maternal inheritance. These findings suggest that mtDNA-related mitochondrial dysfunction may constitute a sub-group within IBS. Future replication studies in larger samples are needed. PMID:24500451

  12. [Genetic variation of Manchurian pheasant (Phasianus colchicus pallasi Rotshild, 1903) inferred from mitochondrial DNA control region sequences].

    PubMed

    Kozyrenko, M M; Fisenko, P V; Zhuravlev, Iu N

    2009-04-01

    Sequence variation of the mitochondrial DNA control region was studied in Manchurian pheasants (Phasianus colchicus pallasi Rotshild, 1903) representing three geographic populations from the southern part of the Russian Far East. Extremely low population genetic differentiation (F(ST) = 0.0003) pointed to a very high gene exchange between the populations. Combination of such characters as high haplotype diversity (0.884 to 0.913), low nucleotide diversity (0.0016 to 0.0022), low R2 values (0.1235 to 0.1337), certain patterns of pairwise-difference distributions, and the absence of phylogenetic structure suggested that the phylogenetic history of Ph. C. pallasi included passing through a bottleneck with further expansion in the postglacial period. According to the data obtained, it was suggested that differentiation between the mitochondrial lineages started approximately 100 000 years ago. PMID:19507706

  13. Constraining controls on carbonate sequences with high-resolution chronostratigraphy: Upper Miocene, Cabo de Gata region, SE Spain

    USGS Publications Warehouse

    Montgomery, P.; Farr, M.R.; Franseen, E.K.; Goldstein, R.H.

    2001-01-01

    A high-resolution chronostratigraphy has been developed for Miocene shallow-water carbonate strata in the Cabo de Gata region of SE Spain for evaluation of local, regional and global factors that controlled platform architecture prior to and during the Messinian salinity crisis. Paleomagnetic data were collected from strata at three localities. Mean natural remanent magnetization (NRM) ranges between 1.53 ?? 10-8 and 5.2 ?? 10-3 Am2/kg. Incremental thermal and alternating field demagnetization isolated the characteristic remanent magnetization (ChRM). Rock magnetic studies show that the dominant magnetic mineral is magnetite, but mixtures of magnetite and hematite occur. A composite chronostratigraphy was derived from five stratigraphic sections. Regional stratigraphic data, biostratigraphic data, and an 40Ar/39Ar date of 8.5 ?? 0.1 Ma, for an interbedded volcanic flow, place the strata in geomagnetic polarity Chrons C4r to C3r. Sequence-stratigraphic and diagenetic evidence indicate a major unconformity at the base of depositional sequence (DS)3 that contains a prograding reef complex, suggesting that approximately 250 000 yr of record (Subchrons C3Br.2r to 3Br.1r) are missing near the Messinian-Tortonian boundary. Correlation to the GPTS shows that the studied strata represent five third- to fourth-order DSs. Basal units are temperate to subtropical ramps (DS1A, DS1B, DS2); these are overlain by subtropical to tropical reefal platforms (DS3), which are capped by subtropical to tropical cyclic carbonates (Terminal Carbonate Complex, TCC). Correlation of the Cabo de Gata record to the Melilla area of Morocco, and the Sorbas basin of Spain indicate that early - Late Tortonian ramp strata from these areas are partially time-equivalent. Similar strata are extensively developed in the Western Mediterranean and likely were influenced by a cool climate or influx of nutrients during an overall rise in global sea-level. After ramp deposition, a sequence boundary (SB3) in

  14. Analyses of nuclear ldhA gene and mtDNA control region sequences of Atlantic northern bluefin tuna populations.

    PubMed

    Ely, B; Stoner, D S; Bremer, Alvarado J R; Dean, J M; Addis, P; Cau, A; Thelen, E J; Jones, W J; Black, D E; Smith, L; Scott, K; Naseri, I; Quattro, J M

    2002-12-01

    There has been considerable debate about whether the Atlantic northern bluefin tuna exist as a single panmictic unit. We have addressed this issue by examining both mitochondrial DNA control region nucleotide sequences and nuclear gene ldhA allele frequencies in replicate size or year class samples of northern bluefin tuna from the Mediterranean Sea and the northwestern Atlantic Ocean. Pairwise comparisons of multiple year class samples from the 2 regions provided no evidence for population subdivision. Similarly, analyses of molecular variance of both mitochondrial and ldhA data revealed no significant differences among or between samples from the 2 regions. These results demonstrate the importance of analyzing multiple year classes and large sample sizes to obtain accurate estimates when using allele frequencies to characterize a population. It is important to note that the absence of genetic evidence for population substructure does not unilaterally constitute evidence of a single panmictic population, as genetic differentiation can be prevented by large population sizes and by migration. PMID:14961233

  15. The Phylogeographical Pattern and Conservation of the Chinese Cobra (Naja atra) across Its Range Based on Mitochondrial Control Region Sequences

    PubMed Central

    Lin, Long-Hui; Hua, Lei; Qu, Yan-Fu; Gao, Jian-Fang; Ji, Xiang

    2014-01-01

    The vulnerable Chinese cobra (Naja atra) ranges from southeastern China south of the Yangtze River to northern Vietnam and Laos. Large mountain ranges and water bodies may influence the pattern of genetic diversity of this species. We sequenced the mitochondrial DNA control region (1029 bp) using 285 individuals collected from 23 localities across the species' range and obtained 18 sequences unique to Taiwan from GenBank for phylogenetic and population analysis. Two distinct clades were identified, one including haplotypes from the two westernmost localities (Hekou and Miyi) and the other including haplotypes from all sampling sites except Miyi. A strong population structure was found (Φst = 0.76, P<0.0001) with high haplotype diversity (h = 1.00) and low nucleotide diversity (π = 0.0049). The Luoxiao and Nanling Mountains act as historical geographical barriers limiting gene exchange. In the haplotype network there were two “star” clusters. Haplotypes from populations east of the Luoxiao Mountains were represented within one cluster and haplotypes from populations west of the mountain range within the other, with haplotypes from populations south of the Nanling Mountains in between. Lineage sorting between mainland and island populations is incomplete. It remains unknown as to how much adaptive differentiation there is between population groups or within each group. We caution against long-distance transfers within any group, especially when environmental differences are apparent. PMID:25184236

  16. Population genetic diversity of the northern snakehead (Channa argus) in China based on the mitochondrial DNA control region and adjacent regions sequences.

    PubMed

    Zhou, Aiguo; Zhuo, Xiaolei; Zou, Qing; Chen, Jintao; Zou, Jixing

    2015-06-01

    Genetic variation and population structure of northern snakehead (Channa argus) from eight locations in China were investigated using mitochondrial DNA control region and adjacent regions sequences. Sequence analysis showed that there were 105 haplotypes in 260 individuals, 48 unique haplotypes and 57 shared haplotypes, but no common haplotype shared by all populations. As a whole, the haplotype diversity was high (h=0.989), while the nucleotide diversity was low (π=0.00482). AMOVA analysis detected significant genetic differentiation among all eight populations (FST=0.328, p<0.01) and 66.17% of the total variance was resulted from intra-population differentiation. UPGMA analysis indicated that the eight populations could be divided into four major clusters, which was consistent with that the eight sampled locations were belonged to four isolated river systems. The neutrality and mismatch distribution tests suggested that the eight populations of C. argus in the sampling locations underwent recent population expansion. Among the eight populations, the Erhai Lake population may represent a unique genetic resource and therefore needs to be conserved. PMID:24724976

  17. Genetic relationships among some subspecies of the Peregrine Falcon (Falco peregrinus L.), inferred from mitochondrial DNA control-region sequences

    USGS Publications Warehouse

    White, Clayton M.; Sonsthagen, Sarah A.; Sage, George K.; Anderson, Clifford; Talbot, Sandra L.

    2013-01-01

    The ability to successfully colonize and persist in diverse environments likely requires broad morphological and behavioral plasticity and adaptability, and this may partly explain why the Peregrine Falcon (Falco peregrinus) exhibits a large range of morphological characteristics across their global distribution. Regional and local differences within Peregrine Falcons were sufficiently variable that ∼75 subspecies have been described; many were subsumed, and currently 19 are generally recognized. We used sequence information from the control region of the mitochondrial genome to test for concordance between genetic structure and representatives of 12 current subspecies and from two areas where subspecies distributions overlap. Haplotypes were broadly shared among subspecies, and all geographic locales shared a widely distributed common haplotype (FalconCR2). Haplotypes were distributed in a star-like phylogeny, consistent with rapid expansion of a recently derived species, with observed genetic patterns congruent with incomplete lineage sorting and/or differential rates of evolution on morphology and neutral genetic characters. Hierarchical analyses of molecular variance did not uncover genetic partitioning at the continental level, despite strong population-level structure (FST = 0.228). Similar analyses found weak partitioning, albeit significant, among subspecies (FCT = 0.138). All reconstructions placed the hierofalcons' (Gyrfalcon [F. rusticolus] and Saker Falcon [F. cherrug]) haplotypes in a well-supported clade either basal or unresolved with respect to the Peregrine Falcon. In addition, haplotypes representing Taita Falcon (F. fasciinucha) were placed within the Peregrine Falcon clade.

  18. Inferring Invasion History of Red Swamp Crayfish (Procambarus clarkii) in China from Mitochondrial Control Region and Nuclear Intron Sequences

    PubMed Central

    Li, Yanhe; Guo, Xianwu; Chen, Liping; Bai, Xiaohui; Wei, Xinlan; Zhou, Xiaoyun; Huang, Songqian; Wang, Weimin

    2015-01-01

    Identifying the dispersal pathways of an invasive species is useful for adopting the appropriate strategies to prevent and control its spread. However, these processes are exceedingly complex. So, it is necessary to apply new technology and collect representative samples for analysis. This study used Approximate Bayesian Computation (ABC) in combination with traditional genetic tools to examine extensive sample data and historical records to infer the invasion history of the red swamp crayfish, Procambarus clarkii, in China. The sequences of the mitochondrial control region and the proPOx intron in the nuclear genome of samples from 37 sites (35 in China and one each in Japan and the USA) were analyzed. The results of combined scenarios testing and historical records revealed a much more complex invasion history in China than previously believed. P. clarkii was most likely originally introduced into China from Japan from an unsampled source, and the species then expanded its range primarily into the middle and lower reaches and, to a lesser extent, into the upper reaches of the Changjiang River in China. No transfer was observed from the upper reaches to the middle and lower reaches of the Changjiang River. Human-mediated jump dispersal was an important dispersal pathway for P. clarkii. The results provide a better understanding of the evolutionary scenarios involved in the rapid invasion of P. clarkii in China. PMID:26132567

  19. The emerging tree of West Eurasian mtDNAs: a synthesis of control-region sequences and RFLPs.

    PubMed Central

    Macaulay, V; Richards, M; Hickey, E; Vega, E; Cruciani, F; Guida, V; Scozzari, R; Bonné-Tamir, B; Sykes, B; Torroni, A

    1999-01-01

    Variation in the human mitochondrial genome (mtDNA) is now routinely described and used to infer the histories of peoples, by means of one of two procedures, namely, the assaying of RFLPs throughout the genome and the sequencing of parts of the control region (CR). Using 95 samples from the Near East and northwest Caucasus, we present an analysis based on both systems, demonstrate their concordance, and, using additional available information, present the most refined phylogeny to date of west Eurasian mtDNA. We describe and apply a nomenclature for mtDNA clusters. Hypervariable nucleotides are identified, and the relative mutation rates of the two systems are evaluated. We point out where ambiguities remain. The identification of signature mutations for each cluster leads us to apply a hierarchical scheme for determining the cluster composition of a sample of Berber speakers, previously analyzed only for CR variation. We show that the main indigenous North African cluster is a sister group to the most ancient cluster of European mtDNAs, from which it diverged approximately 50,000 years ago. PMID:9915963

  20. Inferring the phylogeny of disjunct populations of the azure-winged magpie Cyanopica cyanus from mitochondrial control region sequences.

    PubMed

    Fok, Koon Wah; Wade, Christopher M; Parkin, David T

    2002-08-22

    The azure-winged magpie (AWM), Cyanopica cyanus, is found in Asia and Iberia. This remarkable disjunct distribution has been variously explained by either the sixteenth-century introduction of birds into Iberia from the Far East, or by the loss of individuals from the central part of their range as a result of Pleistocene glaciations. We have used the mitochondrial control region to undertake a molecular phylogenetic analysis of the AWM, with sequences examined from individuals collected from across the current distribution range and incorporating representatives of all currently defined subspecies. The Western birds are genetically distinct from their Asian congeners and their divergence is basal in the phylogenetic tree. This indicates that the AWM is native to Iberia and not the result of a recent introduction from Asia. In Asia, two major mitochondrial DNA lineages were identified. These correspond to an Inland Asia group and a Pacific Seaboard group, and are separated topographically by the Da Hingan Ling mountains and the Yellow Sea. Molecular clock estimates suggest that these divergences are associated with Pleistocene glaciations. Furthermore, our data do not support the current classification of the AWM into 10 subspecies, as defined based on morphology and geographical distribution. PMID:12204127

  1. Control regions for chromosome replication are conserved with respect to sequence and location among Escherichia coli strains

    PubMed Central

    Frimodt-Møller, Jakob; Charbon, Godefroid; Krogfelt, Karen A.; Løbner-Olesen, Anders

    2015-01-01

    In Escherichia coli, chromosome replication is initiated from oriC by the DnaA initiator protein associated with ATP. Three non-coding regions contribute to the activity of DnaA. The datA locus is instrumental in conversion of DnaAATP to DnaAADP (datA dependent DnaAATP hydrolysis) whereas DnaA rejuvenation sequences 1 and 2 (DARS1 and DARS2) reactivate DnaAADP to DnaAATP. The structural organization of oriC, datA, DARS1, and DARS2 were found conserved among 59 fully sequenced E. coli genomes, with differences primarily in the non-functional spacer regions between key protein binding sites. The relative distances from oriC to datA, DARS1, and DARS2, respectively, was also conserved despite of large variations in genome size, suggesting that the gene dosage of either region is important for bacterial growth. Yet all three regions could be deleted alone or in combination without loss of viability. Competition experiments during balanced growth in rich medium and during mouse colonization indicated roles of datA, DARS1, and DARS2 for bacterial fitness although the relative contribution of each region differed between growth conditions. We suggest that this fitness advantage has contributed to conservation of both sequence and chromosomal location for datA, DARS1, and DARS2. PMID:26441936

  2. Sequence comparison in the crossover region of an oncogenic avian retrovirus recombinant and its nononcogenic parent: Genetic regions that control growth rate and oncogenic potential

    SciTech Connect

    Tsichlis, P.N.; Donehower, L.; Hager, G.; Zeller, N.; Malavarca, R.; Astrin, S.; Skalka, A.M.

    1982-11-01

    NTRE is an avian retrovirus recombinant of the endogeneous nononcogenic Rous-associated virus-0 (RAV-0) and the oncogenic, exogeneous, transformation-defective (td) Prague strain of Rous sarcoma virus B (td-PrRSV-B). Oligonucleotide mapping had shown that the recombinant virus is indistinguishable from its RAV-0 parent except for the 3'-end sequences, which were derived from td-PrRSV-B. However, the virus exhibits properties which are typical of an exogenous virus: it grows to high titers in tissue culture, and it is oncogenic in vivo. To accurately define the genetic region responsible for these properties, the authors determined the nucleotide sequences of the recombinant and its RAV-0 parent by using molecular clones of their DNA. These were compared with sequences already available for PrRSV-C, a virus closely related to the exogenous parent td-PrRSV-B. The results suggested that the crossover event which generated NTRE 7 took place in a region -501 to -401 nucleotides from the 3' end of the td-PrRSV parental genome and that sequences to the right of the recombination region were responsible for its growth properties and oncogenic potential. Since the exogenous-virus-specific sequences are expected to be missing from transformation-defective mutants of the Schmidt-Ruppin strain of RSV, which, like other exogeneous viruses, grow to high tiers in tissue culture and are oncogenic in vivo, the authors concluded that the growth properties and oncogenic potential of the exogeneous viruses are determined by sequences in the U3 region of the long terminal repeat. However, the authors propose that the exogeneous-virus-specific region may play a role in determining the oncogenic spectrum of a given oncogenic virus.

  3. Application of 16S rRNA, cytochrome b and control region sequences for understanding the phylogenetic relationships in Oryx species.

    PubMed

    Khan, H A; Arif, I A; Al Homaidan, A A; Al Farhan, A H

    2008-01-01

    The present study reports the application of mitochondrial markers for the molecular phylogeny of Oryx species, including the Arabian oryx (AO), scimitar-horned oryx (SHO) and plains oryx (PO), using the Addax as an outgroup. Sequences of three molecular markers, 16S rRNA, cytochrome b and a control region, for the above four taxa were aligned and the topologies of respective phylogenetic trees were compared. All these markers clearly differentiated the genus Addax from Oryx. However, for species-level grouping, while 16S rRNA and cytochrome b produced similar phylogeny (SHO grouped with PO), the control region grouped SHO with AO. Further studies are warranted to generate more sequencing data, apply multiple bioinformatics tools and to include relevant nuclear markers for phylogenetic analysis of Oryx species. PMID:19224456

  4. DNA sequence of the control region of phage D108: the N-terminal amino acid sequences of repressor and transposase are similar both in phage D108 and in its relative, phage Mu.

    PubMed Central

    Mizuuchi, M; Weisberg, R A; Mizuuchi, K

    1986-01-01

    We have determined the DNA sequence of the control region of phage D108 up to position 1419 at the left end of the phage genome. Open reading frames for the repressor gene, ner gene, and the 5' part of the A gene (which codes for transposase) are found in the sequence. The genetic organization of this region of phage D108 is quite similar to that of phage Mu in spite of considerable divergence, both in the nucleotide sequence and in the amino acid sequences of the regulatory proteins of the two phages. The N-terminal amino acid sequences of the transposases of the two phages also share only limited homology. On the other hand, a significant amino acid sequence homology was found within each phage between the N-terminal parts of the repressor and transposase. We propose that the N-terminal domains of the repressor and transposase of each phage interact functionally in the process of making the decision between the lytic and the lysogenic mode of growth. PMID:3012481

  5. Quantitative controls on location and architecture of carbonate depositional sequences: upper miocene, cabo de gata region, se Spain

    USGS Publications Warehouse

    Franseen, E.K.; Goldstein, R.H.; Farr, M.R.

    1998-01-01

    Sequence stratigraphy, pinning-point relative sea-level curves, and magnetostratigraphy provide the quantitative data necessary to understand how rates of sea-level change and different substrate paleoslopes are dominant controls on accumulation rate, carbonate depositional sequence location, and internal architecture. Five third-order (1-10 my) and fourth-order (0.1-1.0 my) upper Miocene carbonate depositional sequences (DS1A, DS1B, DS2, DS3, TCC) formed with superimposed higher-frequency sea-level cycles in an archipelago setting in SE Spain. Overall, our study indicates when areas of high substrate slope (> 15??) are in shallow water, independent of climate, the location and internal architecture of carbonate deposits are not directly linked to sea-level position but, instead, are controlled by location of gently sloping substrates and processes of bypass. In contrast, if carbonate sediments are generated where substrates of low slope ( 15.6 cm/ky to ??? 2 cm/ky and overall relative sea level rose at rates of 17-21.4 cm/ky. Higher frequency sea-level rates were about 111 to more than 260 cm/ky, producing onlapping, fining- (deepening-) upward cycles. Decreasing accumulation rates resulted from decreasing surface area for shallow-water sediment production, drowning of shallow-water substrates, and complex sediment dispersal related to the archipelago setting. Typical systems tract and parasequence development should not be expected in "bypass ramp" settings; facies of onlapping strata do not track base level and are likely to be significantly different compared to onlapping strata associated with coastal onlap. Basal and upper DS2 reef megabreccias (indicating the transition from cool to warmer climatic conditions) were eroded from steep upslope positions and redeposited downslope onto areas of gentle substrate during rapid sea-level falls (> 22.7 cm/ky) of short duration. Such rapid sea-level falls and presence of steep slopes are not conducive to formation of

  6. Quantitative controls on location and architecture of carbonate depositional sequences: Upper miocene, cabo de gata region, SE Spain

    USGS Publications Warehouse

    Franseen, E.K.; Goldstein, R.H.; Farr, M.R.

    1997-01-01

    Sequence stratigraphy, pinning-point relative sea-level curves, and magnetostratigraphy provide the quantitative data necessary to understand how rates of sea-level change and different substrate paleoslopes are dominant controls on accumulation rate, carbonate depositional sequence location, and internal architecture. Five third-order (1-10 my) and fourth-order (0.1-1.0 my) upper Miocene carbonate depositional sequences (DS1A, DS1B, DS2, DS3, TCC) formed with superimposed higher-frequency sea-level cycles in an archipelago setting in SE Spain. Overall, our study indicates when areas of high substrate slope (> 15??) are in shallow water, independent of climate, the location and internal architecture of carbonate deposits are not directly linked to sea-level position but, instead, are controlled by location of gently sloping substrates and processes of bypass. In contrast, if carbonate sediments are generated where substrates of low slope ( 15.6 cm/ky to ??? 2 cm/ky and overall relative sea level rose at rates of 17-21.4 cm/ky. Higher frequency sea-level rates were about 111 to more than 260 cm/ky, producing onlapping, fining- (deepening-) upward cycles. Decreasing accumulation rates resulted from decreasing surface area for shallow-water sediment production, drowning of shallow-water substrates, and complex sediment dispersal related to the archipelago setting. Typical systems tract and parasequence development should not be expected in "bypass ramp" settings; facies of onlapping strata do not track base level and are likely to be significantly different compared to onlapping strata associated with coastal onlap. Basal and upper DS2 reef megabreccias (indicating the transition from cool to warmer climatic conditions) were eroded from steep upslope positions and redeposited downslope onto areas of gentle substrate during rapid sea-level falls (> 22.7 cm/ky) of short duration. Such rapid sea-level falls and presence of steep slopes are not conducive to formation of

  7. Dpb11 Controls the Association between DNA Polymerases α and ɛ and the Autonomously Replicating Sequence Region of Budding Yeast

    PubMed Central

    Masumoto, Hiroshi; Sugino, Akio; Araki, Hiroyuki

    2000-01-01

    Dpb11 is required for chromosomal DNA replication and the S-phase checkpoint in Saccharomyces cerevisiae. Here, we report detection of a physical complex containing Dpb11 and DNA polymerase ɛ (Dpb11-Polɛ complex). During the S phase of the cell cycle, Dpb11 associated preferentially with DNA fragments containing autonomously replicating sequences (ARSs), at the same time as Polɛ associated with these fragments. Association of Dpb11 and Polɛ with these fragments was mutually dependent, suggesting that the Dpb11-Polɛ complex associates with the ARS. Moreover, Dpb11 was required for the association of Polα-primase with the fragments. Thus, it seems likely that association of the Dpb11-Polɛ complex with the ARS fragments is required for the association of the Polα-primase complex. Hydroxyurea inhibits late-origin firing in S. cerevisiae, and the checkpoint genes, RAD53 and MEC1, are involved in this inhibition. In the presence of hydroxyurea at temperatures permissive for cell growth, Polɛ in dpb11-1 cells associated with early- and late-origin fragments. In wild-type cells, however, it associated only with early-origin fragments. This indicates that Dpb11 may also be involved in the regulation of late-origin firing. Overall, these results suggest that Dpb11 controls the association between DNA polymerases α and ɛ and the ARS. PMID:10733584

  8. mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences

    PubMed Central

    Lee, Hwan Young; Song, Injee; Ha, Eunho; Cho, Sung-Bae; Yang, Woo Ick; Shin, Kyoung-Jin

    2008-01-01

    Background For the past few years, scientific controversy has surrounded the large number of errors in forensic and literature mitochondrial DNA (mtDNA) data. However, recent research has shown that using mtDNA phylogeny and referring to known mtDNA haplotypes can be useful for checking the quality of sequence data. Results We developed a Web-based bioinformatics resource "mtDNAmanager" that offers a convenient interface supporting the management and quality analysis of mtDNA sequence data. The mtDNAmanager performs computations on mtDNA control-region sequences to estimate the most-probable mtDNA haplogroups and retrieves similar sequences from a selected database. By the phased designation of the most-probable haplogroups (both expected and estimated haplogroups), mtDNAmanager enables users to systematically detect errors whilst allowing for confirmation of the presence of clear key diagnostic mutations and accompanying mutations. The query tools of mtDNAmanager also facilitate database screening with two options of "match" and "include the queried nucleotide polymorphism". In addition, mtDNAmanager provides Web interfaces for users to manage and analyse their own data in batch mode. Conclusion The mtDNAmanager will provide systematic routines for mtDNA sequence data management and analysis via easily accessible Web interfaces, and thus should be very useful for population, medical and forensic studies that employ mtDNA analysis. mtDNAmanager can be accessed at . PMID:19014619

  9. A Novel SRP Recognition Sequence in the Homeostatic Control Region of Heat Shock Transcription Factor σ32

    PubMed Central

    Miyazaki, Ryoji; Yura, Takashi; Suzuki, Takehiro; Dohmae, Naoshi; Mori, Hiroyuki; Akiyama, Yoshinori

    2016-01-01

    Heat shock response (HSR) generally plays a major role in sustaining protein homeostasis. In Escherichia coli, the activity and amount of the dedicated transcription factor σ32 transiently increase upon heat shock. The initial induction is followed by chaperone-mediated negative feedback to inactivate and degrade σ32. Previous work reported that signal recognition particle (SRP)-dependent targeting of σ32 to the membrane is essential for feedback control, though how SRP recognizes σ32 remained unknown. Extensive photo- and disulfide cross-linking studies in vivo now reveal that the highly conserved regulatory region of σ32 that lacks a consecutive hydrophobic stretch interacts with the signal peptide-binding site of Ffh (the protein subunit of SRP). Importantly, the σ32–Ffh interaction observed was significantly affected by mutations in this region that compromise the feedback regulation, but not by deleting the DnaK/DnaJ chaperones. Homeostatic regulation of HSR thus requires a novel type of SRP recognition mechanism. PMID:27052372

  10. A Novel SRP Recognition Sequence in the Homeostatic Control Region of Heat Shock Transcription Factor σ32.

    PubMed

    Miyazaki, Ryoji; Yura, Takashi; Suzuki, Takehiro; Dohmae, Naoshi; Mori, Hiroyuki; Akiyama, Yoshinori

    2016-01-01

    Heat shock response (HSR) generally plays a major role in sustaining protein homeostasis. In Escherichia coli, the activity and amount of the dedicated transcription factor σ(32) transiently increase upon heat shock. The initial induction is followed by chaperone-mediated negative feedback to inactivate and degrade σ(32). Previous work reported that signal recognition particle (SRP)-dependent targeting of σ(32) to the membrane is essential for feedback control, though how SRP recognizes σ(32) remained unknown. Extensive photo- and disulfide cross-linking studies in vivo now reveal that the highly conserved regulatory region of σ(32) that lacks a consecutive hydrophobic stretch interacts with the signal peptide-binding site of Ffh (the protein subunit of SRP). Importantly, the σ(32)-Ffh interaction observed was significantly affected by mutations in this region that compromise the feedback regulation, but not by deleting the DnaK/DnaJ chaperones. Homeostatic regulation of HSR thus requires a novel type of SRP recognition mechanism. PMID:27052372

  11. Helena, the hidden beauty: Resolving the most common West Eurasian mtDNA control region haplotype by massively parallel sequencing an Italian population sample.

    PubMed

    Bodner, Martin; Iuvaro, Alessandra; Strobl, Christina; Nagl, Simone; Huber, Gabriela; Pelotti, Susi; Pettener, Davide; Luiselli, Donata; Parson, Walther

    2015-03-01

    The analysis of mitochondrial (mt)DNA is a powerful tool in forensic genetics when nuclear markers fail to give results or maternal relatedness is investigated. The mtDNA control region (CR) contains highly condensed variation and is therefore routinely typed. Some samples exhibit an identical haplotype in this restricted range. Thus, they convey only weak evidence in forensic queries and limited phylogenetic information. However, a CR match does not imply that also the mtDNA coding regions are identical or samples belong to the same phylogenetic lineage. This is especially the case for the most frequent West Eurasian CR haplotype 263G 315.1C 16519C, which is observed in various clades within haplogroup H and occurs at a frequency of 3-4% in many European populations. In this study, we investigated the power of massively parallel complete mtGenome sequencing in 29 Italian samples displaying the most common West Eurasian CR haplotype - and found an unexpected high diversity. Twenty-eight different haplotypes falling into 19 described sub-clades of haplogroup H were revealed in the samples with identical CR sequences. This study demonstrates the benefit of complete mtGenome sequencing for forensic applications to enforce maximum discrimination, more comprehensive heteroplasmy detection, as well as highest phylogenetic resolution. PMID:25303789

  12. Involvement of long terminal repeat U3 sequences overlapping the transcription control region in human immunodeficiency virus type 1 mRNA 3' end formation.

    PubMed Central

    DeZazzo, J D; Kilpatrick, J E; Imperiale, M J

    1991-01-01

    In retroviral proviruses, the poly(A) site is present in both long terminal repeats (LTRs) but used only in the 3' position. One mechanism to account for this selective poly(A) site usage is that LTR U3 sequences, transcribed only from the 3' poly(A) site, are required in the RNA for efficient processing. To test this possibility, mutations were made in the human immunodeficiency virus type 1 (HIV-1) U3 region and the mutated LTRs were inserted into simple and complex transcription units. HIV-1 poly(A) site usage was then quantitated by S1 nuclease analysis following transfection of each construct into human 293 cells. The results showed that U3 sequences confined to the transcription control region were required for efficient usage of the HIV-1 poly(A) site, even when it was placed 1.5 kb from the promoter. Although the roles of U3 in processing and transcription activation were separable, optimal 3' end formation was partly dependent on HIV-1 enhancer and SP1 binding site sequences. Images PMID:1996111

  13. Heteroplasmy, length and sequence variation in the mtDNA control regions of three percid fish species (Perca fluviatilis, Acerina cernua, Stizostedion lucioperca).

    PubMed Central

    Nesbø, C L; Arab, M O; Jakobsen, K S

    1998-01-01

    The nucleotide sequence of the control region and flanking tRNA genes of perch (Perca fluviatilis) mtDNA was determined. The organization of this region is similar to that of other vertebrates. A tandem array of 10-bp repeats, associated with length variation and heteroplasmy was observed in the 5' end. While the location of the array corresponds to that reported in other species, the length of the repeated unit is shorter than previously observed for tandem repeats in this region. The repeated sequence was highly similar to the Mt5 element which has been shown to specifically bind a putative D-loop DNA termination protein. Of 149 perch analyzed, 74% showed length variation heteroplasmy. Single-cell PCR on oocytes suggested that the high level of heteroplasmy is passively maintained by maternal transmission. The array was also observed in the two other percid species, ruffe (Acerina cernua) and zander (Stizostedion lucioperca). The array and the associated length variation heteroplasmy are therefore likely to be general features of percid mtDNAs. Among the perch repeats, the mutation pattern is consistent with unidirectional slippage, and statistical analyses supported the notion that the various haplotypes are associated with different levels of heteroplasmy. The variation in array length among and within species is ascribed to differences in predicted stability of secondary structures made between repeat units. PMID:9560404

  14. Population structure and genetic variability of six bar wrasse (Thallasoma hardwicki) in northern South China Sea revealed by mitochondrial control region sequences.

    PubMed

    Chen, Chaolun Allen; Ablan, Maria Carmen Anonuevo; McManus, John Williams; Bell, Johann Diepernk; Tuan, Vo Si; Cabanban, Annadel Sarmiento; Shao, Kwang-Tsao

    2004-01-01

    The genetic relationships among northern South China Sea populations of the six bar wrasse (Thallasoma hardwicki) were investigated. Fish collected from the Solomon Islands were used for geographic comparison. In 1998 and 1999, a total of 100 fish were sampled from 6 localities of the northern South China Sea and 3 localities of the Solomon Islands. Genetic variations in DNA sequences were examined from the first hypervariable region (HVR-1) of the mitochondrial control region, as amplified by polymerase chain reaction. High levels of haplotypic diversity (h = 0.944 +/- 0.0016, pi = 0.0224 +/- 0.01171) in the HVR-1 region of the mitochondrial control region of T. hardwicki were detected. This yielded 94 haplotypes that exhibited a minimum spanning tree with a starburst structure, suggestive of a very recent origin for most haplotypes. Neutrality tests indicated that the pattern of genetic variability in T. hardwicki is consistent either with genetic hitchhiking by an advantageous mutation or with population expansion. Partitioning populations into coherent geographic groups divided the northern South China Sea samples (Phi(CT) = 0.0313, P < 0.001) into 3 major groups: a north-central group composed of northwestern Taiwan and northern Vietnam; a southwestern group containing southern Vietnam; and a southern group including the central Philippines. These results are in concordance with mesoscale boundaries proposed by allozyme markers, thus highlighting the importance of identifying transboundary units for the conservation and management of fisheries in the South China Sea. PMID:15129326

  15. Development of a control region-based mtDNA SNaPshot™ selection tool, integrated into a mini amplicon sequencing method.

    PubMed

    Weiler, Natalie E C; de Vries, Gerda; Sijen, Titia

    2016-03-01

    Mitochondrial DNA (mtDNA) analysis is regularly applied to forensic DNA samples with limited amounts of nuclear DNA (nDNA), such as hair shafts and bones. Generally, this mtDNA analysis involves examination of the hypervariable control region by Sanger sequencing of amplified products. When samples are severely degraded, small-sized amplicons can be applied and an earlier described mini-mtDNA method by Eichmann et al. [1] that accommodates ten mini amplicons in two multiplexes is found to be a very robust approach. However, in cases with large numbers of samples, like when searching for hairs with an mtDNA profile deviant from that of the victim, the method is time (and cost) consuming. Previously, Chemale et al. [2] described a SNaPshot™-based screening tool for a Brazilian population that uses standard-size amplicons for HVS-I and HVS-II. Here, we describe a similar tool adapted to the full control region and compatible with mini-mtDNA amplicons. Eighteen single nucleotide polymorphisms (SNPs) were selected based on their relative frequencies in a European population. They showed a high discriminatory power in a Dutch population (97.2%). The 18 SNPs are assessed in two SNaPshot™ multiplexes that pair to the two mini-mtDNA amplification multiplexes. Degenerate bases are included to limit allele dropout due to SNPs at primer binding site positions. Three SNPs provide haplogroup information. Reliability testing showed no differences with Sanger sequencing results. Since mini-mtSNaPshot screening uses only a small portion of the same PCR products used for Sanger sequencing, no additional DNA extract is consumed, which is forensically advantageous. PMID:26976467

  16. Low Genetic Diversity and Strong Geographical Structure of the Critically Endangered White-Headed Langur (Trachypithecus leucocephalus) Inferred from Mitochondrial DNA Control Region Sequences

    PubMed Central

    Wang, Weiran; Qiao, Yu; Pan, Wenshi; Yao, Meng

    2015-01-01

    Many Asian colobine monkey species are suffering from habitat destruction and population size decline. There is a great need to understand their genetic diversity, population structure and demographic history for effective species conservation. The white-headed langur (Trachypithecus leucocephalus) is a Critically Endangered colobine species endemic to the limestone karst forests in southwestern China. We analyzed the mitochondrial DNA (mtDNA) control region sequences of 390 fecal samples from 40 social groups across the main distribution areas, which represented one-third of the total extant population. Only nine haplotypes and 10 polymorphic sites were identified, indicating remarkably low genetic diversity in the species. Using a subset of 77 samples from different individuals, we evaluated genetic variation, population structure, and population demographic history. We found very low values of haplotype diversity (h = 0.570 ± 0.056) and nucleotide diversity (π = 0.00323 ± 0.00044) in the hypervariable region I (HVRI) of the mtDNA control region. Distribution of haplotypes displayed marked geographical pattern, with one population (Chongzuo, CZ) showing a complete lack of genetic diversity (having only one haplotype), whereas the other population (Fusui, FS) having all nine haplotypes. We detected strong population genetic structure among habit patches (ΦST = 0.375, P < 0.001). In addition, the Mantel test showed a significant correlation between the pairwise genetic distances and geographical distances among social groups in FS (correlation coefficient = 0.267, P = 0.003), indicting isolation-by-distance pattern of genetic divergence in the mtDNA sequences. Analyses of demographic history suggested an overall stable historical population size and modest population expansion in the last 2,000 years. Our results indicate different genetic diversity and possibly distinct population history for different local populations, and suggest that CZ and FS should be

  17. Atypical regions in large genomic DNA sequences

    SciTech Connect

    Scherer, S. |; McPeek, M.S.; Speed, T.P.

    1994-07-19

    Large genomic DNA sequences contain regions with distinctive patterns of sequence organization. The authors describe a method using logarithms of probabilities based on seventh-order Markov chains to rapidly identify genomic sequences that do not resemble models of genome organization built from compilations of octanucleotide usage. Data bases have been constructed from Escherichia coli and Saccharomyces cerevisiae DNA sequences of >1000 nt and human sequences of >10,000 nt. Atypical genes and clusters of genes have been located in bacteriophage, yeast, and primate DNA sequences. The authors consider criteria for statistical significance of the results, offer possible explanations for the observed variation in genome organization, and give additional applications of these methods in DNA sequence analysis.

  18. Classification and phylogeny of sika deer (Cervus nippon) subspecies based on the mitochondrial control region DNA sequence using an extended sample set.

    PubMed

    Ba, Hengxing; Yang, Fuhe; Xing, Xiumei; Li, Chunyi

    2015-06-01

    To further refine the classification and phylogeny of sika deer subspecies, the well-annotated sequences of the complete mitochondrial DNA (mtDNA) control region of 13 sika deer subspecies from GenBank were downloaded, aligned and analyzed in this study. By reconstructing the phylogenetic tree with an extended sample set, the results revealed a split between Northern and Southern Mainland Asia/Taiwan lineages, and moreover, two subspecies, C.n.mantchuricus and C.n.hortulorum, were existed in Northern Mainland Asia. Unexpectedly, Dybowskii's sika deer that was thought to originate from Northern Mainland Asia joins the Southern Mainland Asia/Taiwan lineage. The genetic divergences were ranged from 2.1% to 4.7% between Dybowskii's sika deer and all the other established subspecies at the mtDNA sequence level, which suggests that the maternal lineage of uncertain sika subspecies in Europe had been maintained until today. This study also provides a better understanding for the classification, phylogeny and phylogeographic history of sika deer subspecies. PMID:24063645

  19. mtDNA control-region sequence variation suggests multiple independent origins of an "Asian-specific" 9-bp deletion in sub-Saharan Africans.

    PubMed Central

    Soodyall, H.; Vigilant, L.; Hill, A. V.; Stoneking, M.; Jenkins, T.

    1996-01-01

    The intergenic COII/tRNA(Lys) 9-bp deletion in human mtDNA, which is found at varying frequencies in Asia, Southeast Asia, Polynesia, and the New World, was also found in 81 of 919 sub-Saharan Africans. Using mtDNA control-region sequence data from a subset of 41 individuals with the deletion, we identified 22 unique mtDNA types associated with the deletion in Africa. A comparison of the unique mtDNA types from sub-Saharan Africans and Asians with the 9-bp deletion revealed that sub-Saharan Africans and Asians have sequence profiles that differ in the locations and frequencies of variant sites. Both phylogenetic and mismatch-distribution analysis suggest that 9-bp deletion arose independently in sub-Saharan Africa and Asia and that the deletion has arisen more than once in Africa. Within Africa, the deletion was not found among Khoisan peoples and was rare to absent in western and southwestern African populations, but it did occur in Pygmy and Negroid populations from central Africa and in Malawi and southern African Bantu-speakers. The distribution of the 9-bp deletion in Africa suggests that the deletion could have arisen in central Africa and was then introduced to southern Africa via the recent "Bantu expansion." PMID:8644719

  20. Mitochondrial DNA control region sequence variation suggests an independent origin of an {open_quotes}Asian-specific{close_quotes} 9-bp deletion in Africans

    SciTech Connect

    Soodyall, H.; Redd, A.; Vigilant

    1994-09-01

    The intergenic noncoding region between the cytochrome oxidase II and lysyl tRNA genes of human mitochondrial DNA (mtDNA) is associated with two tandemly arranged copies of a 9-bp sequence. A deletion of one of these repeats has been found at varying frequencies in populations of Asian descent, and is commonly referred to as an {open_quotes}Asian-specific{close_quotes} marker. We report here that the 9-bp deletion is also found at a frequency of 10.2% (66/649) in some indigenous African populations, with frequencies of 28.6% (20/70) in Pygmies, 26.6% (12/45) in Malawians and 15.4% (31/199) in southeastern Bantu-speaking populations. The deletion was not found in 123 Khoisan individuals nor in 209 western Bantu-speaking individuals, with the exception of 3 individuals from one group that was admixed with Pygmies. Sequence analysis of the two hypervariable segments of the mtDNA control region reveals that the types associated with the African 9-bp deletion are different from those found in Asian-derived populations with the deletion. Phylogenetic analysis separates the {open_quotes}African{close_quotes} and {open_quotes}Asian{close_quotes} 9-bp deletion types into two different clusters which are statistically supported. Mismatch distributions based on the number of differences between pairs of mtDNA types are consistent with this separation. These findings strongly support the view that the 9-bp deletion originated independently in Africa and in Asia.

  1. Comparison of mitochondrial DNA control region sequence and microsatellite DNA analyses in estimating population structure and gene flow rates in Atlantic sturgeon Acipenser oxyrinchus

    USGS Publications Warehouse

    Wirgin, I.; Waldman, J.; Stabile, J.; Lubinski, B.; King, T.

    2002-01-01

    Atlantic sturgeon Acipenser oxyrinchus is large, long-lived, and anadromous with subspecies distributed along the Atlantic (A. oxyrinchus oxyrinchus) and Gulf of Mexico (A. o. desotoi) coasts of North America. Although it is not certain if extirpation of some population units has occurred, because of anthropogenic influences abundances of all populations are low compared with historical levels. Informed management of A. oxyrinchus demands a detailed knowledge of its population structure, levels of genetic diversity, and likelihood to home to natal rivers. We compared the use of mitochondrial DNA (mtDNA) control region sequence and microsatellite nuclear DNA (nDNA) analyses in identifying the stock structure and homing fidelity of Atlantic and Gulf coast populations of A. oxyrinchus. The approaches were concordant in that they revealed moderate to high levels of genetic diversity and suggested that populations of Atlantic sturgeon are highly structured. At least six genetically distinct management units were detected using the two approaches among the rivers surveyed. Mitochondrial DNA sequences revealed a significant cline in haplotype diversity along the Atlantic coast with monomorphism observed in Canadian populations. High levels of nDNA diversity were also observed among populations along the Atlantic coast, including the two Canadian populations, probably resulting from the more rapid rate of mutational and evolutionary change at microsatellite loci. Estimates of gene flow among populations were similar between both approaches with the exception that because of mtDNA monomorphism in Canadian populations, gene flow estimates between them were unobtainable. Analyses of both genomes provided high resolution and confidence in characterizing the population structure of Atlantic sturgeon. Microsatellite analysis was particularly informative in delineating population structure in rivers that were recently glaciated and may prove diagnostic in rivers that are

  2. Mitochondrial sequences of Seriatopora corals show little agreement with morphology and reveal the duplication of a tRNA gene near the control region

    NASA Astrophysics Data System (ADS)

    Flot, J.-F.; Licuanan, W. Y.; Nakano, Y.; Payri, C.; Cruaud, C.; Tillier, S.

    2008-12-01

    The taxonomy of corals of the genus Seriatopora has not previously been studied using molecular sequence markers. As a first step toward a re-evaluation of species boundaries in this genus, mitochondrial sequence variability was analyzed in 51 samples collected from Okinawa, New Caledonia, and the Philippines. Four clusters of sequences were detected that showed little concordance with species currently recognized on a morphological basis. The most likely explanation is that the skeletal characters used for species identification are highly variable (polymorphic or phenotypically plastic); alternative explanations include introgression/hybridization, or deep coalescence and the retention of ancestral mitochondrial polymorphisms. In all individuals sequenced, two copies of trnW were found on either side of the atp8 gene near the putative D-loop, a novel mitochondrial gene arrangement that may have arisen from a duplication of the trnW-atp8 region followed by a deletion of one atp8.

  3. Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae

    PubMed Central

    Zhou, Kai; Lokate, Mariette; Deurenberg, Ruud H.; Tepper, Marga; Arends, Jan P.; Raangs, Erwin G. C.; Lo-Ten-Foe, Jerome; Grundmann, Hajo; Rossen, John W. A.; Friedrich, Alexander W.

    2016-01-01

    The study describes the transmission of a CTX-M-15-producing ST15 Klebsiella pneumoniae between patients treated in a single center and the subsequent inter-institutional spread by patient referral occurring between May 2012 and September 2013. A suspected epidemiological link between clinical K. pneumoniae isolates was supported by patient contact tracing and genomic phylogenetic analysis from May to November 2012. By May 2013, a patient treated in three institutions in two cities was involved in an expanding cluster caused by this high-risk clone (HiRiC) (local expansion, CTX-M-15 producing, and containing hypervirulence factors). A clone-specific multiplex PCR was developed for patient screening by which another patient was identified in September 2013. Genomic phylogenetic analysis including published ST15 genomes revealed a close homology with isolates previously found in the USA. Environmental contamination and lack of consistent patient screening were identified as being responsible for the clone dissemination. The investigation addresses the advantages of whole-genome sequencing in the early detection of HiRiC with a high propensity of nosocomial transmission and prolonged circulation in the regional patient population. Our study suggests the necessity for inter-institutional/regional collaboration for infection/outbreak management of K. pneumoniae HiRiCs. PMID:26864946

  4. The complete mitochondrial genome sequence of Cynoglossus abbreviatus (Pleuronectiformes: Cynoglossidae) with control region translocation and tRNA-Gln gene inversion.

    PubMed

    Shi, Wei; Gong, Li; Kong, Xiao-Yu

    2016-05-01

    Cynoglossus abbreviatus (Cynoglossidae, Soleoidei) is characterized by a bilaterally asymmetrical with both eyes on the left side. In this study, the complete mitogenome of this tongue sole has been reported for the first time. The gene order in C. abbreviatus mitogenome possesses a novel rearrangement like other tonguefish. The tRNA-Gln gene moves from the light strand to the heavy strand, accompanied by tRNA-Ile gene shuffling, leaving a large non-coding region (88 bp) between these two tRNAs. Additionally, the control region translocates to the place between ND1 and tRNA-Gln genes. The total length is 16,417 bp, with 30.9%, 29.5%, 24.9% and 14.7% for A, T, C and G, respectively (60.4% for AT content). These molecular data will provide useful information about the mechanism of gene reorganization in Cynoglossidae mitogenome and further phylogenetic study on Pleuronectiformes. PMID:25427811

  5. Structure and evolution of the Phasianidae mitochondrial DNA control region.

    PubMed

    Huang, Zuhao; Ke, Dianhua

    2016-01-01

    The mitochondrial DNA control region is an area of the mitochondrial genome which is non-coding DNA. To infer the structural and evolutionary characteristics of Phasianidae mitochondrial DNA control region, the entire control region sequences of 34 species were analyzed. The length of the control region sequences ranged from 1144 bp (Phasianus colchicus) to 1555 bp (Coturnix japonica) and can be separated into three domains. The average genetic distances among the species within the genera varied from 1.96% (Chrysolophus) to 12.05% (Coturnix). The average genetic distances showed significantly negative correlation with ts/tv. In most genera (except Coturnix), domain I is the most variable among the three domains. However, the first 150 nucleotides apparently evolved at unusually low rates. Four conserved sequence boxes in the domain II of Phasianidae sequences were identified. The alignment of the Phasianidae four boxes and CSB-1 sequences showed considerable sequence variation. PMID:24617466

  6. Characterization of the red knot (Calidris canutus) mitochondrial control region.

    PubMed

    Buehler, Deborah M; Baker, Allan J

    2003-08-01

    We sequenced the complete mitochondrial control regions of 11 red knots (Calidris canutus). The control region is 1168 bp in length and is flanked by tRNA glutamate (glu) and the gene ND6 at its 5' end and tRNA phenylalanine (phe) and the gene 12S on its 3' end. The sequence possesses conserved sequence blocks F, E, D, C, CSB-1, and the bird similarity box (BSB), as expected for a mitochondrial copy. Flanking tRNA regions show correct secondary structure, and a relative rate test indicated no significant difference between substitution rates in the sequence we obtained versus the known mitochondrial sequence of turnstones (Charadriiformes: Scolopacidae). These characteristics indicate that the sequence is mitochondrial in origin. To confirm this, we sequenced the control region of a single individual using both purified mitochondrial DNA and genomic DNA. The sequences were identical using both methods. The sequence and methods presented in this paper may now serve as a reference for future studies using knot and other avian control regions. Furthermore, the discovery of five variable sites in 11 knots towards the 3' end of the control region, and the variability of this region in contrast to the more conserved central domain in the alignment between knots and other Charadriiformes, highlights the importance of this area as a source of variation for future studies in knots and other birds. PMID:12897864

  7. Two control regions for eukaryotic tRNA gene transcription.

    PubMed Central

    DeFranco, D; Schmidt, O; Söll, D

    1980-01-01

    Two Drosophila tRNALys genes with identical coding sequences were shown to transcribe with very different efficiences in nuclear extracts from Xenopus oocytes. The use of recombinant plasmids in which the 5'-flanking sequences of these genes were either "switched" or replaced by defined pBR322 sequences revealed two control regions for tRNA gene transcription. An internal control region comprising the mature tRNA coding sequence (and possibly its 3'-flanking sequences) is sufficient for transcription initiation, and an external control region comprising the 5'-flanking sequences represses this transcription. All transcripts have short leader sequences. Altered precursor tRNAs transcribed from truncated tRNALys genes (missing a single base pair in the acceptor stem) are not processed well in vitro. Images PMID:6774336

  8. Time Separation Between Events in a Sequence: a Regional Property?

    NASA Astrophysics Data System (ADS)

    Muirwood, R.; Fitzenz, D. D.

    2013-12-01

    understand the rate controlling processes that determine such sequences per tectonic region and fluid/heat flow provinces.

  9. TAG Sequence Identification of Genomic Regions Using TAGdb.

    PubMed

    Ruperao, Pradeep

    2016-01-01

    Second-generation sequencing (SGS) technology has enabled the sequencing of genomes and identification of genes. However, large complex plant genomes remain particularly difficult for de novo assembly. Access to the vast quantity of raw sequence data may facilitate discoveries; however the volume of this data makes access difficult. This chapter discusses the Web-based tool TAGdb that enables researchers to identify paired read second-generation DNA sequence data that share identity with a submitted query sequence. The identified reads can be used for PCR amplification of genomic regions to identify genes and promoters without the need for genome assembly. PMID:26519409

  10. Wiggle—Predicting Functionally Flexible Regions from Primary Sequence

    PubMed Central

    Gu, Jenny; Gribskov, Michael; Bourne, Philip E

    2006-01-01

    The Wiggle series are support vector machine–based predictors that identify regions of functional flexibility using only protein sequence information. Functionally flexible regions are defined as regions that can adopt different conformational states and are assumed to be necessary for bioactivity. Many advances have been made in understanding the relationship between protein sequence and structure. This work contributes to those efforts by making strides to understand the relationship between protein sequence and flexibility. A coarse-grained protein dynamic modeling approach was used to generate the dataset required for support vector machine training. We define our regions of interest based on the participation of residues in correlated large-scale fluctuations. Even with this structure-based approach to computationally define regions of functional flexibility, predictors successfully extract sequence-flexibility relationships that have been experimentally confirmed to be functionally important. Thus, a sequence-based tool to identify flexible regions important for protein function has been created. The ability to identify functional flexibility using a sequence based approach complements structure-based definitions and will be especially useful for the large majority of proteins with unknown structures. The methodology offers promise to identify structural genomics targets amenable to crystallization and the possibility to engineer more flexible or rigid regions within proteins to modify their bioactivity. PMID:16839194

  11. Dynamics and control of DNA sequence amplification

    SciTech Connect

    Marimuthu, Karthikeyan; Chakrabarti, Raj E-mail: rajc@andrew.cmu.edu

    2014-10-28

    DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.

  12. Dynamics and control of DNA sequence amplification

    NASA Astrophysics Data System (ADS)

    Marimuthu, Karthikeyan; Chakrabarti, Raj

    2014-10-01

    DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.

  13. [On the Population Genetic Portrait of Kaluga, Acipenser dauricus Georgi, 1775 Analysis of Sequence Variation in the Mitochondrial DNA Control Region].

    PubMed

    Shedko, S V; Miroshnichenko, I L; Nemkova, G A; Shedko, M B

    2015-09-01

    The variability of the mtDNA D-loop was examined in kaluga endemic to the Amur River, which is classified as critically endangered by the IUCN Red List of Threatened species. Sequencing of the D-loop fragment (819 bp) in 122 kaluga specimens collected in Lower Amur revealed 27 unique genotypes. The sample was characterized by a relatively low level of haplotypic (0.927) and nucleotide (0.0044) diversity. No considerable deviations from the neutral mutation model of DNA polymorphism were observed. Overall, the mismatch distribution patterns and the results of testing of simple demographic models (sudden demographic expansion and exponential population growth) pointed to a past increase in the number of kaluga sturgeons. According to the Bayesian skyline, the kaluga population doubled over the last two to three thousand years. The number of mature females in the modern kaluga population and the assessment of their long-term effective population size (Nef) are roughly at the same level (about three thousand individuals), which confirms the validity of assigning kaluga to the category of species on the brink of extinction. PMID:26606799

  14. Correlation approach to identify coding regions in DNA sequences

    NASA Technical Reports Server (NTRS)

    Ossadnik, S. M.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Peng, C. K.; Simons, M.; Stanley, H. E.

    1994-01-01

    Recently, it was observed that noncoding regions of DNA sequences possess long-range power-law correlations, whereas coding regions typically display only short-range correlations. We develop an algorithm based on this finding that enables investigators to perform a statistical analysis on long DNA sequences to locate possible coding regions. The algorithm is particularly successful in predicting the location of lengthy coding regions. For example, for the complete genome of yeast chromosome III (315,344 nucleotides), at least 82% of the predictions correspond to putative coding regions; the algorithm correctly identified all coding regions larger than 3000 nucleotides, 92% of coding regions between 2000 and 3000 nucleotides long, and 79% of coding regions between 1000 and 2000 nucleotides. The predictive ability of this new algorithm supports the claim that there is a fundamental difference in the correlation property between coding and noncoding sequences. This algorithm, which is not species-dependent, can be implemented with other techniques for rapidly and accurately locating relatively long coding regions in genomic sequences.

  15. Terminal region sequence variations in variola virus DNA.

    PubMed

    Massung, R F; Loparev, V N; Knight, J C; Totmenin, A V; Chizhikov, V E; Parsons, J M; Safronov, P F; Gutorov, V V; Shchelkunov, S N; Esposito, J J

    1996-07-15

    Genome DNA terminal region sequences were determined for a Brazilian alastrim variola minor virus strain Garcia-1966 that was associated with an 0.8% case-fatality rate and African smallpox strains Congo-1970 and Somalia-1977 associated with variola major (9.6%) and minor (0.4%) mortality rates, respectively. A base sequence identity of > or = 98.8% was determined after aligning 30 kb of the left- or right-end region sequences with cognate sequences previously determined for Asian variola major strains India-1967 (31% death rate) and Bangladesh-1975 (18.5% death rate). The deduced amino acid sequences of putative proteins of > or = 65 amino acids also showed relatively high identity, although the Asian and African viruses were clearly more related to each other than to alastrim virus. Alastrim virus contained only 10 of 70 proteins that were 100% identical to homologs in Asian strains, and 7 alastrim-specific proteins were noted. PMID:8661439

  16. The regions of sequence variation in caulimovirus gene VI.

    PubMed

    Sanger, M; Daubert, S; Goodman, R M

    1991-06-01

    The sequence of gene VI from figwort mosaic virus (FMV) clone x4 was determined and compared with that previously published for FMV clone DxS. Both clones originated from the same virus isolation, but the virus used to clone DxS was propagated extensively in a host of a different family prior to cloning whereas that used to clone x4 was not. Differences in the amino acid sequence inferred from the DNA sequences occurred in two clusters. An N-terminal conserved region preceded two regions of variation separated by a central conserved region. Variation in cauliflower mosaic virus (CaMV) gene VI sequences, all of which were derived from virus isolates from hosts from one host family, was similar to that seen in the FMV comparison, though the extent of variation was less. Alignment of gene VI domains from FMV and CaMV revealed regions of amino acid sequence identical in both viruses within the conserved regions. The similarity in the pattern of conserved and variable domains of these two viruses suggests common host-interactive functions in caulimovirus gene VI homologues, and possibly an analogy between caulimoviruses and certain animal viruses in the influence of the host on sequence variability of viral genes. PMID:2024500

  17. Kinetoplast DNA minicircles: regions of extensive sequence divergence.

    PubMed Central

    Rogers, W O; Wirth, D F

    1987-01-01

    Previous work has shown that the kinetoplast minicircle DNA of Leishmania species exhibits species-specific sequence divergence and this observation has led to the development of a DNA probe-based diagnostic test for leishmaniasis. In the work reported here, we demonstrate that the minicircle is composed of three types of DNA sequences with differing specificities reflecting different rates of DNA sequence change. A library of cloned fragments of kinetoplast DNA (kDNA) from Leishmania mexicana amazonensis was prepared and the cloned subfragments were found to contain DNA sequences with different taxonomic specificities based on hybridization analysis with various species of Leishmania. Four groups of subfragments were found, those that hybridized with a large number of Leishmania sp. as well as sequences unique to the species, subspecies, or isolate. Analysis of nested deletions of a single, full-length minicircle demonstrates that these different taxonomic specificities are contained within a single minicircle. This implies that different regions of a single minicircle have DNA sequences that diverge at different rates. These sequences represent potentially valuable tools in diagnostic, epidemiologic, and ecological studies of leishmaniasis and provide the basis for a model of kDNA sequence evolution. Images PMID:3025880

  18. Rapid Evolution of Virus Sequences in Intrinsically Disordered Protein Regions

    PubMed Central

    Gitlin, Leonid; Hagai, Tzachi; LaBarbera, Anthony; Solovey, Mark; Andino, Raul

    2014-01-01

    Nodamura Virus (NoV) is a nodavirus originally isolated from insects that can replicate in a wide variety of hosts, including mammals. Because of their simplicity and ability to replicate in many diverse hosts, NoV, and the Nodaviridae in general, provide a unique window into the evolution of viruses and host-virus interactions. Here we show that the C-terminus of the viral polymerase exhibits extreme structural and evolutionary flexibility. Indeed, fewer than 10 positively charged residues from the 110 amino acid-long C-terminal region of protein A are required to support RNA1 replication. Strikingly, this region can be replaced by completely unrelated protein sequences, yet still produce a functional replicase. Structure predictions, as well as evolutionary and mutational analyses, indicate that the C-terminal region is structurally disordered and evolves faster than the rest of the viral proteome. Thus, the function of an intrinsically unstructured protein region can be independent of most of its primary sequence, conferring both functional robustness and sequence plasticity on the protein. Our results provide an experimental explanation for rapid evolution of unstructured regions, which enables an effective exploration of the sequence space, and likely function space, available to the virus. PMID:25502394

  19. The Main Sequence of Explosive Solar Active Regions: Comparison of Emerging and Mature Active Regions

    NASA Technical Reports Server (NTRS)

    Falconer, David; Moore, Ron

    2011-01-01

    For mature active regions, an active region s magnetic flux content determines the maximum free energy the active region can have. Most Large flares and CMEs occur in active regions that are near their free-energy limit. Active-region flare power radiated in the GOES 1-8 band increases steeply as the free-energy limit is approached. We infer that the free-energy limit is set by the rate of release of an active region s free magnetic energy by flares, CMEs and coronal heating balancing the maximum rate the Sun can put free energy into the active region s magnetic field. This balance of maximum power results in explosive active regions residing in a "mainsequence" in active-region (flux content, free energy content) phase space, which sequence is analogous to the main sequence of hydrogen-burning stars in (mass, luminosity) phase space.

  20. A database of mitochondrial DNA hypervariable regions I and II sequences of individuals from Slovakia.

    PubMed

    Lehocký, Ivan; Baldovic, Marian; Kádasi, Ludevít; Metspalu, Ene

    2008-09-01

    In order to identify polymorphic positions and to determine their frequencies and the frequency of haplotypes in the human mitochondrial control region, two hypervariable regions (HV1 and HV2) of the mitochondrial DNA (mtDNA) of 374 unrelated individuals from Slovakia were amplified and sequenced. Sequence comparison led to the identification of 284 mitochondrial lineages as defined by 163 variable sites. Genetic diversity (GD) was estimated at 0.997 and the probability of two randomly selected individuals from population having identical mtDNA types (random match probability, RMP) for the both regions is 0.60%. PMID:19083829

  1. Climatic controls on Pennsylvanian sequences, United States

    SciTech Connect

    Cecil, C.B.; Dulong, F.T.; Edgar, N.T.

    1996-08-01

    Temporal and spatial paleoclimate changes were primary controls on changes in sediment supply, both siliciclastic and chemical, in Pennsylvanian deposystems of the United States. Tectonic and eustatic processes, as well as climatically induced changes in sediment supply, controlled accommodation space and sequence stratigraphy within these deposystems. Interbasinal correlations of lithologies sensitive to climate, such as coeval paleosols, provide continental-scale records of climatic and eustatic conditions. Pennsylvanian bio- and lithostratigraphy are indicative of climate change at time scales that range from long-term (tens of millions of years) as Pangea formed and North America moved northward through the paleoequator, to intermediate-term hundred thousand year cycles controlled by orbital forcing, to very short-term events perhaps analogous to El Nino. Because of proximity to the humid tropics, the long-term climate of eastern basins of the United States was generally wetter than western basins. In the east, pluvial parts of climate cycles occur during low-stand events and are recorded by intense chemical weathering, high terrestrial organic productivity, restricted erosion, and siliciclastic sediment starvation. These conditions resulted in highly leached mineral paleosols (Ultisols) and coal beds (Histosols) of interbasinal extent. Drier parts of climate cycles in the east occurred during highstands of sea level when erosion and siliciclastic transport were maximum. In the western basins pluvial periods are generally indicated by shifts from eolian to fluvial and lacustrine sedimentary regimes in continental environments and from evaporate and carbonate to siliciclastic deposition, including black shale petroleum source rocks, in marine environments. Tectonics controlled basin development and glacial eustasy controlled sea level cycles. Climate, however, was the primary control on sediment supply and lithostratigraphy.

  2. Non-standard D region usage by human TCRB sequences

    SciTech Connect

    Bowman, S.J.; Lanchbury, J.S.

    1996-06-01

    T-cell receptor P (TCRB) chain variability is primarily created by a specific process of rearrangement of three sets of gene segments, V D, and J regions, with deletion of the intervening DNA. This process utilizes one of at least 51 TCRBV gene segments, downstream of which are two clusters of D, J, and C region genes. The TCRBC1 cluster contains a TCRBD1 (DB1) gene, six TCRBJ1 genes and the TCRBC1 (CB1) gene. The TCRBC2 cluster is similar, with a TCRBD2 (DB2) gene, seven TCRBJ2 genes, and the TCRBC2 (CB2) gene. The TCRBD genes are unusual in that they can be translated in all three reading frames. The region between the V and J region segments (the junctional region) shows the greatest sequence variability and there is good evidence that this region contacts the major histocompatibility complex peptide complex. Complexity at the V-D and D-J junctions is enhanced by exonuclease activity, the addition of a variable number of template-independent N nucleotides by terminal deoxynucleotidyl transferase, and by P nucleotide addition by a DNA polymerase. As a result of these processes and the sequence similarity between the germline TCRBD1 and TCRBD2 segments, it is not always possible to clearly assign TCRBD gene segment usage to either TCRBD1 or TCRBD2. Where TCRBD1 is used, {open_quotes}standard{close_quotes} downstream rearrangement can occur either to the TCRBJ1-CB1 cluster or the TCRBJ2-CB2 cluster. Only the TCRBJ2-CB2 cluster is downstream of TCRBD2, and hence is generally utilized in sequences containing TCRBD2. In the TCRD locus, however, multiple TCRDD segment usage is not uncommon. Sequences have also been reported for the TCRB locus in which both TCRBD1 and TCRBD2 were used in a single sequence, and more recently, TCRBD2 - TCRBJ1, and occasional TCRBD2 - TCRBD1 - TCRBJ1 and TCRBD1 - TCRBD2 - TCRBJ1 {open_quotes}non-standard{close_quotes} rearrangements have been reported. 11 refs., 1 fig.

  3. Hierarchical Control of Cognitive Processes: Switching Tasks in Sequences

    ERIC Educational Resources Information Center

    Schneider, Darryl W.; Logan, Gordon D.

    2006-01-01

    Hierarchical control of cognitive processes was studied by examining the relationship between sequence- and task-level processing in the performance of explicit, memorized task sequences. In 4 experiments, switch costs in task-switching performance were perturbed by sequence initiation times that varied with sequence complexity, preparation time,…

  4. Regional correlation of deposition sequences in the southern Mesozoic marine province, northwestern Nevada

    SciTech Connect

    Satterfield, J.I.; Oldow, J.S. . Dept. of Geology and Geophysics)

    1993-04-01

    Strata of the Mesozoic marine province of a northwestern Nevada, deposited in subaerial to deep marine environment in a backarc basin, underwent severe deformation during the late Mesozoic. Restoration of stratigraphic relations among constituent volcanic, volcanogenic, carbonate, and continentally-derived siliciclastic rocks has been hampered by sparse biostratigraphic age control. Regional correlation of coeval facies is made possible by coupling depositional sequences with biostratigraphic control in the southwestern Gabbs Valley Range, the southern Shoshone Mountains, and the southern Clan Alpine Mountains, which serve as reference sections for Late Triassic and Early Jurassic ammonite zonation of western North America. Differentiation between regionally significant sequence boundaries and those of limited areal extent is possible only by linking the biostratigraphy and physical stratigraphic relations, such as abrupt vertical transitions in lithology corresponding to large facies changes. Physical stratigraphic relations alone are not adequate for correlation ad indicated by the diachronous initiation of Early to Middle( ) Jurassic deposition in half-graben basins (Dunlap Formation) which locally cloaks eustatically( ) controlled depositional sequences. Within these limitations, three regionally extensive sequences are recognized in the reference sections and have lower boundaries at the base of Upper Triassic shallow marine to deltaic carbonate-clastic rocks (Luning Formation) and at the base and within subtidal to offshore-marine carbonate and clastic rocks (Triassic and Jurassic Volcano Peak Group).

  5. Detecting pore-lining regions in transmembrane protein sequences

    PubMed Central

    2012-01-01

    Background Alpha-helical transmembrane channel and transporter proteins play vital roles in a diverse range of essential biological processes and are crucial in facilitating the passage of ions and molecules across the lipid bilayer. However, the experimental difficulties associated with obtaining high quality crystals has led to their significant under-representation in structural databases. Computational methods that can identify structural features from sequence alone are therefore of high importance. Results We present a method capable of automatically identifying pore-lining regions in transmembrane proteins from sequence information alone, which can then be used to determine the pore stoichiometry. By labelling pore-lining residues in crystal structures using geometric criteria, we have trained a support vector machine classifier to predict the likelihood of a transmembrane helix being involved in pore formation. Results from testing this approach under stringent cross-validation indicate that prediction accuracy of 72% is possible, while a support vector regression model is able to predict the number of subunits participating in the pore with 62% accuracy. Conclusion To our knowledge, this is the first tool capable of identifying pore-lining regions in proteins and we present the results of applying it to a data set of sequences with available crystal structures. Our method provides a way to characterise pores in transmembrane proteins and may even provide a starting point for discovering novel routes of therapeutic intervention in a number of important diseases. This software is freely available as source code from: http://bioinf.cs.ucl.ac.uk/downloads/memsat-svm/. PMID:22805427

  6. Comparison of Sequencing (Barcode Region) and Sequence-Tagged-Site PCR for Blastocystis Subtyping

    PubMed Central

    2013-01-01

    Blastocystis is the most common nonfungal microeukaryote of the human intestinal tract and comprises numerous subtypes (STs), nine of which have been found in humans (ST1 to ST9). While efforts continue to explore the relationship between human health status and subtypes, no consensus regarding subtyping methodology exists. It has been speculated that differences detected in subtype distribution in various cohorts may to some extent reflect different approaches. Blastocystis subtypes have been determined primarily in one of two ways: (i) sequencing of small subunit rRNA gene (SSU-rDNA) PCR products and (ii) PCR with subtype-specific sequence-tagged-site (STS) diagnostic primers. Here, STS primers were evaluated against a panel of samples (n = 58) already subtyped by SSU-rDNA sequencing (barcode region), including subtypes for which STS primers are not available, and a small panel of DNAs from four other eukaryotes often present in feces (n = 18). Although the STS primers appeared to be highly specific, their sensitivity was only moderate, and the results indicated that some infections may go undetected when this method is used. False-negative STS results were not linked exclusively to certain subtypes or alleles, and evidence of substantial genetic variation in STS loci was obtained. Since the majority of DNAs included here were extracted from feces, it is possible that STS primers may generally work better with DNAs extracted from Blastocystis cultures. In conclusion, due to its higher applicability and sensitivity, and since sequence information is useful for other forms of research, SSU-rDNA barcoding is recommended as the method of choice for Blastocystis subtyping. PMID:23115257

  7. Artificial Intelligence Controls Tape-Recording Sequence

    NASA Technical Reports Server (NTRS)

    Schwuttke, Ursula M.; Otamura, Roy M.; Zottarelli, Lawrence J.

    1989-01-01

    Developmental expert-system computer program intended to schedule recording of large amounts of data on limited amount of magnetic tape. Schedules recording using two sets of rules. First set incorporates knowledge of locations for recording of new data. Second set incorporates knowledge about issuing commands to recorder. Designed primarily for use on Voyager Spacecraft, also applicable to planning and sequencing in industry.

  8. Time Sequence of Jupiter's Equatorial Region (Time Sets 2 & 4)

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Time sequence of Jupiter's equatorial region at 756 nanometers (nm). The mosaics cover an area of 34,000 kilometers by 22,000 kilometers and were taken ten hours (approximately one Jovian rotation) apart. The dark region near the center of the mosaic is an equatorial 'hotspot' similar to the Galileo Probe entry site. The near-infrared continuum filter shows the features of Jupiter's main visible cloud deck.

    Jupiter's atmospheric circulation is dominated by alternating jets of east/west (zonal) winds. The bands have different widths and wind speeds but have remained constant as long as telescopes and spacecraft have measured them. The top half of these mosaics lies within Jupiter's North Equatorial Belt, a westward (left) current. The bottom half shows part of the Equatorial Zone, a fast moving eastward current. The clouds near the hotspot are the fastest moving features in these mosaics, moving at about 100 meters per second, or 224 miles per hour.

    North is at the top. The mosaics cover latitudes 1 to 19 degrees and are centered at longitude 336 degrees West. The grid lines, fixed in longitude, mark 350 degrees west (on the left edge) with decreasing longitude lines marking every 5 degrees moving east (to the right). The smallest resolved features are tens of kilometers in size. These images were taken on December 17, 1996, at a range of 1.5 million kilometers by the Solid State Imaging system aboard NASA's Galileo spacecraft.

    The Jet Propulsion Laboratory, Pasadena, CA manages the mission for NASA's Office of Space Science, Washington, DC.

    This image and other images and data received from Galileo are posted on the World Wide Web, on the Galileo mission home page at URL http://galileo.jpl.nasa.gov. Background information and educational context for the images can be found at URL http://www.jpl.nasa.gov/galileo/sepo

  9. PRE-MAIN-SEQUENCE STARS IN THE CEPHEUS FLARE REGION

    SciTech Connect

    Kun, Maria; Balog, Zoltan; Kenyon, Scott J.; Mamajek, Eric E.; Gutermuth, Robert A.

    2009-12-01

    We present results of optical spectroscopic and BVR {sub C} I {sub C} photometric observations of 77 pre-main-sequence (PMS) stars in the Cepheus flare region. A total of 64 of these are newly confirmed PMS stars, originally selected from various published candidate lists. We estimate effective temperatures and luminosities for the PMS stars, and comparing the results with PMS evolutionary models, we estimate stellar masses of 0.2-2.4 M {sub sun} and stellar ages of 0.1-15 Myr. Among the PMS stars, we identify 15 visual binaries with separations of 2-10 arcsec. From archival IRAS, Two Micron All Sky Survey, and Spitzer data, we construct their spectral energy distributions (SEDs) and classify 5% of the stars as Class I, 10% as Flat SED, 60% as Class II, and 3% as Class III young stellar objects. We identify 12 classical T Tauri stars and two weak-line T Tauri stars as members of NGC 7023, with a mean age of 1.6 Myr. The 13 PMS stars associated with L1228 belong to three small aggregates: RNO 129, L1228A, and L1228S. The age distribution of the 17 PMS stars associated with L1251 suggests that star formation has propagated with the expansion of the Cepheus flare shell. We detect sparse aggregates of {approx}6-7 Myr old PMS stars around the dark clouds L1177 and L1219, at a distance of {approx}400 pc. Three T Tauri stars appear to be associated with the Herbig Ae star SV Cep at a distance of 600 pc. Our results confirm that the molecular complex in the Cepheus flare region contains clouds of various distances and star-forming histories.

  10. Iterative exponential growth of stereo- and sequence-controlled polymers

    NASA Astrophysics Data System (ADS)

    Barnes, Jonathan C.; Ehrlich, Deborah J. C.; Gao, Angela X.; Leibfarth, Frank A.; Jiang, Yivan; Zhou, Erica; Jamison, Timothy F.; Johnson, Jeremiah A.

    2015-10-01

    Chemists have long sought sequence-controlled synthetic polymers that mimic nature's biopolymers, but a practical synthetic route that enables absolute control over polymer sequence and structure remains a key challenge. Here, we report an iterative exponential growth plus side-chain functionalization (IEG+) strategy that begins with enantiopure epoxides and facilitates the efficient synthesis of a family of uniform >3 kDa macromolecules of varying sequence and stereoconfiguration that are coupled to produce unimolecular polymers (>6 kDa) with sequences and structures that cannot be obtained using traditional polymerization techniques. Selective side-chain deprotection of three hexadecamers is also demonstrated, which imbues each compound with the ability to dissolve in water. We anticipate that these new macromolecules and the general IEG+ strategy will find broad application as a versatile platform for the scalable synthesis of sequence-controlled polymers.

  11. Intrusion Detection in Control Systems using Sequence Characteristics

    NASA Astrophysics Data System (ADS)

    Kiuchi, Mai; Onoda, Takashi

    Intrusion detection is considered effective in control systems. Sequences of the control application behavior observed in the communication, such as the order of the control device to be controlled, are important in control systems. However, most intrusion detection systems do not effectively reflect sequences in the application layer into the detection rules. In our previous work, we considered utilizing sequences for intrusion detection in control systems, and demonstrated the usefulness of sequences for intrusion detection. However, manually writing the detection rules for a large system can be difficult, so using machine learning methods becomes feasible. Also, in the case of control systems, there have been very few observed cyber attacks, so we have very little knowledge of the attack data that should be used to train the intrusion detection system. In this paper, we use an approach that combines CRF (Conditional Random Field) considering the sequence of the system, thus able to reflect the characteristics of control system sequences into the intrusion detection system, and also does not need the knowledge of attack data to construct the detection rules.

  12. Colorectal Cancer Genetic Heterogeneity Delineated by Multi-Region Sequencing

    PubMed Central

    Liang, Rui; Xie, Zhen-Rong; Luo, Hua-You; Zeng, Yu-Jian; Xu, Yu; Wang, La-Mei; Kong, Xiang-Yang; Wang, Kun-Hua

    2016-01-01

    Intratumor heterogeneity (ITH) leads to an underestimation of the mutational landscape portrayed by a single needle biopsy and consequently affects treatment precision. The extent of colorectal cancer (CRC) genetic ITH is not well understood in Chinese patients. Thus, we conducted deep sequencing by using the OncoGxOne™ Plus panel, targeting 333 cancer-specific genes in multi-region biopsies of primary and liver metastatic tumors from three Chinese CRC patients. We determined that the extent of ITH varied among the three cases. On average, 65% of all the mutations detected were common within individual tumors. KMT2C aberrations and the NCOR1 mutation were the only ubiquitous events. Subsequent phylogenetic analysis showed that the tumors evolved in a branched manner. Comparison of the primary and metastatic tumors revealed that PPP2R1A (E370X), SETD2 (I1608V), SMAD4 (G382T), and AR splicing site mutations may be specific to liver metastatic cancer. These mutations might contribute to the initiation and progression of distant metastasis. Collectively, our analysis identified a substantial level of genetic ITH in CRC, which should be considered for personalized therapeutic strategies. PMID:27023146

  13. Trypanosoma cruzi: sequence analysis of the variable region of kinetoplast minicircles.

    PubMed

    Telleria, Jenny; Lafay, Bénédicte; Virreira, Myrna; Barnabé, Christian; Tibayrenc, Michel; Svoboda, Michal

    2006-12-01

    The comparisons of 170 sequences of kinetoplast DNA minicircle hypervariable region obtained from 19 stocks of Trypanosoma cruzi and 2 stocks of Trypanosoma cruzi marenkellei showed that only 56% exhibited a significant homology one with other sequences. These sequences could be grouped into homology classes showing no significant sequence similarity with any other homology group. The 44% remaining sequences thus corresponded to unique sequences in our data set. In the DTU I ("Discrete Typing Units") 51% of the sequences were unique. In contrast, in the DTU IId, 87.5% of sequences were distributed into three classes. The results obtained for T. cruzi marinkellei, showed that all sequences were unique, without any similarity between them and T. cruzi sequences. Analysis of palindromes in all sequence sets show high frequency of the EcoRI site. Analysis of repetitive sequences suggested a common ancestral origin of the kDNA. The editing mechanism that occurs in kinetoplastidae is discussed. PMID:16730709

  14. Development of a species-specific sequence-characterized amplified region marker for roses.

    PubMed

    Riaz, S; Sadia, B; Awan, F S; Khan, I A; Sadaqat, H A; Khan, I A

    2012-01-01

    DNA fingerprints of four rose species, Rosa centifolia, R. Gruss-an-Teplitz, R. bourboniana, and R. damascena, were developed using RAPD-PCR. We identified a unique polymorphic band in R. centifolia. This 762-bp fragment was produced by the random primer GLI-2. The fragment was eluted and directly cloned in a TA cloning vector, pTZ57R/T. Digestion of the plasmid with EcoRI confirmed the cloning of GLI-2(762) in pTZ57R/T. A second enzyme, PstI, used in combination with EcoRI, gave complete digestion of the plasmid, and the 762-bp fragment was confirmed on the gel. Subsequently, the polymorphic amplicon was sequenced with an AB1 373 DNA sequencer system using the PRISM(TM) Ready Reaction DyeDeoxy(TM) Terminator Cycle Sequencing kit. After sequencing, specific primers (23 bp long) were designed based on the sequence of the flanking regions of the original RAPD fragment. These primers will effectively allow fingerprinting for the identification of R. centifolia species. In essence, we developed an SCAR marker to authenticate the identity of R. centifolia species and to distinguish it from its substitutes. Such techniques are required not only to complement conventional parameters in creating the passport data of commercial and medicinal products of rose, but also for routine quality control in commercial and government rosaries and rose nurseries. PMID:22427036

  15. Phaneorozoic sequence stratigraphy of Bolivia and adjacent regions

    SciTech Connect

    Sempere, T. )

    1993-02-01

    Phaneorozoic sequence stratigraphy of the Pacific margin of western South America, particularly the Bolivian section, has been completed and new interpretations and hypotheses have been proposed as a result of data analyses of this information. The Paleozoic margin was initially passive (late Cambrian-Llanvirn, [open quotes]Puna aulacogen[close quotes]), but became active during a middle Ordovician compressional episode. Most of late Cambrian to early Triassic Bolivian rocks are of marine origin, with dark shale units recording sea level rises, whereas middle Triassic to Recent rocks were mainly deposited in continental environments (except six restricted-marine ingressions in the late Cretaceous-Danian, and one in the late Miocene, all with hydrocarbon potential). A noteworthy similarity exists between the Devonian to Jurassic stratigraphies of Bolivia and the Parana basin, suggesting that Bolivia behaved as part of the Brazilian craton from late Cambrian to late Jurassic, when it was captured into the Pacific margin geotectonic system. Organic-rich units correlate with Paleozoic highstand deposits and younger ingressions. The Bolivian Phanerozoic strata is characterized by thick layers, partly due to middle Ordovician-Carboniferous and late Cretaceous-Cenozoic foreland basins. Paleozoic foreland geometries include northeastern onlaps and, potentially, stratigraphic traps. Hydrocarbon generation, migration and trapping mainly depended on Cenozoic structural loading and burial and on propagation of Andean deformation which are comprised of Paleozoic shale decollements. Precise knowledge of the evolution of the Phanerozoic geodynamic contexts and basin geometries through sedimentation and subsequent deformations is crucial for hydrocarbon exploration strategies in these regions.

  16. Visual attention control in image sequences using multiple knowledge sources

    NASA Astrophysics Data System (ADS)

    Bernasch, Jost

    1993-05-01

    Both biological visual systems and image understanding systems are forced by resource limitations to reduce input data to their essential part, to keep the amount of data manageable in succeeding processing levels and to maintain a realistic chance to achieve real-time performance even for complex tasks. We present a new design and implementation of a visual attention control system (GOAL) for a significant reduction of data while maintaining salient information. The visual attention system deals not with synthetic images or simple static images but is developed for complex dynamic real image sequences emphasizing arbitrary traffic scenes recorded from a car built-in camera. GOAL is part of the image understanding system MOVIE for real-time interpretation of traffic scenes and supports the model-based scene analysis (MOSAIC) by directing high-level vision processes to salient regions. Based on a model of human attention (the guided search model from Wolfe and Cave) requirements for the module `visual attention' of an image understanding system are derived. GOAL combines different knowledge sources (both motion and shape-oriented) to achieve a robust, spatially restricting, and expectation-driven attention control system. The knowledge sources consist of four very basic image operations, namely (1) enhanced difference image method, (2) direct depth method, (3) local symmetry detection, and (4) 2D - 3D line movement. Each knowledge source contributes to an accumulated evidence for the existence of attention fields. The knowledge sources are temporally stabilized by using a Kalman filter. The nonlinear combination of multiple knowledge sources makes the selection of attention fields much more robust even with merely increasing computational power. This is shown with results from various real image sequences.

  17. Sequence analysis of mitochondrial DNA hypervariable regions using infrared fluorescence detection.

    PubMed

    Steffens, D L; Roy, R

    1998-06-01

    The non-coding region of the mitochondrial genome provides an attractive target for human forensic identification studies. Two hypervariable (HV) regions, each approximately 250-350 bp in length, contain the majority of mitochondrial DNA (mtDNA) sequence variability among different individuals. Various approaches to determine mtDNA sequence were evaluated utilizing highly sensitive infrared (IR) fluorescence detection. HV regions were amplified either together or separately and cycle-sequenced using a Thermo Sequenase protocol. An M13 universal primer sequence tail covalently attached to the 5' terminus of an amplification primer facilitated electrophoretic analysis and direct sequencing of the amplification products using IR detection. PMID:9631201

  18. Automated manual transmission shift sequence controller

    DOEpatents

    Lawrie, Robert E.; Reed, Richard G.; Rausen, David J.

    2000-02-01

    A powertrain system for a hybrid vehicle. The hybrid vehicle includes a heat engine, such as a diesel engine, and an electric machine, which operates as both, an electric motor and an alternator, to power the vehicle. The hybrid vehicle also includes a manual-style transmission configured to operate as an automatic transmission from the perspective of the driver. The engine and the electric machine drive an input shaft which in turn drives an output shaft of the transmission. In addition to driving the transmission, the electric machine regulates the speed of the input shaft in order to synchronize the input shaft during either an upshift or downshift of the transmission by either decreasing or increasing the speed of the input shaft. When decreasing the speed of the input shaft, the electric motor functions as an alternator to produce electrical energy which may be stored by a storage device. Operation of the transmission is controlled by a transmission controller which receives input signals and generates output signals to control shift and clutch motors to effect smooth launch, upshift shifts, and downshifts of the transmission, so that the transmission functions substantially as an automatic transmission from the perspective of the driver, while internally substantially functioning as a manual transmission.

  19. Control for stochastic sampling variation and qualitative sequencing error in next generation sequencing

    PubMed Central

    Blomquist, Thomas; Crawford, Erin L.; Yeo, Jiyoun; Zhang, Xiaolu; Willey, James C.

    2015-01-01

    Background Clinical implementation of Next-Generation Sequencing (NGS) is challenged by poor control for stochastic sampling, library preparation biases and qualitative sequencing error. To address these challenges we developed and tested two hypotheses. Methods Hypothesis 1: Analytical variation in quantification is predicted by stochastic sampling effects at input of (a) amplifiable nucleic acid target molecules into the library preparation, (b) amplicons from library into sequencer, or (c) both. We derived equations using Monte Carlo simulation to predict assay coefficient of variation (CV) based on these three working models and tested them against NGS data from specimens with well characterized molecule inputs and sequence counts prepared using competitive multiplex-PCR amplicon-based NGS library preparation method comprising synthetic internal standards (IS). Hypothesis 2: Frequencies of technically-derived qualitative sequencing errors (i.e., base substitution, insertion and deletion) observed at each base position in each target native template (NT) are concordant with those observed in respective competitive synthetic IS present in the same reaction. We measured error frequencies at each base position within amplicons from each of 30 target NT, then tested whether they correspond to those within the 30 respective IS. Results For hypothesis 1, the Monte Carlo model derived from both sampling events best predicted CV and explained 74% of observed assay variance. For hypothesis 2, observed frequency and type of sequence variation at each base position within each IS was concordant with that observed in respective NTs (R2 = 0.93). Conclusion In targeted NGS, synthetic competitive IS control for stochastic sampling at input of both target into library preparation and of target library product into sequencer, and control for qualitative errors generated during library preparation and sequencing. These controls enable accurate clinical diagnostic reporting of

  20. Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease.

    PubMed

    Zhou, Fusheng; Cao, Hongzhi; Zuo, Xianbo; Zhang, Tao; Zhang, Xiaoguang; Liu, Xiaomin; Xu, Ricong; Chen, Gang; Zhang, Yuanwei; Zheng, Xiaodong; Jin, Xin; Gao, Jinping; Mei, Junpu; Sheng, Yujun; Li, Qibin; Liang, Bo; Shen, Juan; Shen, Changbing; Jiang, Hui; Zhu, Caihong; Fan, Xing; Xu, Fengping; Yue, Min; Yin, Xianyong; Ye, Chen; Zhang, Cuicui; Liu, Xiao; Yu, Liang; Wu, Jinghua; Chen, Mengyun; Zhuang, Xuehan; Tang, Lili; Shao, Haojing; Wu, Longmao; Li, Jian; Xu, Yu; Zhang, Yijie; Zhao, Suli; Wang, Yu; Li, Ge; Xu, Hanshi; Zeng, Lei; Wang, Jianan; Bai, Mingzhou; Chen, Yanling; Chen, Wei; Kang, Tian; Wu, Yanyan; Xu, Xun; Zhu, Zhengwei; Cui, Yong; Wang, Zaixing; Yang, Chunjun; Wang, Peiguang; Xiang, Leihong; Chen, Xiang; Zhang, Anping; Gao, Xinghua; Zhang, Furen; Xu, Jinhua; Zheng, Min; Zheng, Jie; Zhang, Jianzhong; Yu, Xueqing; Li, Yingrui; Yang, Sen; Yang, Huanming; Wang, Jian; Liu, Jianjun; Hammarström, Lennart; Sun, Liangdan; Wang, Jun; Zhang, Xuejun

    2016-07-01

    The human major histocompatibility complex (MHC) region has been shown to be associated with numerous diseases. However, it remains a challenge to pinpoint the causal variants for these associations because of the extreme complexity of the region. We thus sequenced the entire 5-Mb MHC region in 20,635 individuals of Han Chinese ancestry (10,689 controls and 9,946 patients with psoriasis) and constructed a Han-MHC database that includes both variants and HLA gene typing results of high accuracy. We further identified multiple independent new susceptibility loci in HLA-C, HLA-B, HLA-DPB1 and BTNL2 and an intergenic variant, rs118179173, associated with psoriasis and confirmed the well-established risk allele HLA-C*06:02. We anticipate that our Han-MHC reference panel built by deep sequencing of a large number of samples will serve as a useful tool for investigating the role of the MHC region in a variety of diseases and thus advance understanding of the pathogenesis of these disorders. PMID:27213287

  1. Mitochondrial DNA hypervariable region-1 sequence variation and phylogeny of the concolor gibbons, Nomascus.

    PubMed

    Monda, Keri; Simmons, Rachel E; Kressirer, Philipp; Su, Bing; Woodruff, David S

    2007-11-01

    The still little known concolor gibbons are represented by 14 taxa (five species, nine subspecies) distributed parapatrically in China, Myanmar, Vietnam, Laos and Cambodia. To set the stage for a phylogeographic study of the genus we examined DNA sequences from the highly variable mitochondrial hypervariable region-1 (HVR-1 or control region) in 51 animals, mostly of unknown geographic provenance. We developed gibbon-specific primers to amplify mtDNA noninvasively and obtained >477 bp sequences from 38 gibbons in North American and European zoos and >159 bp sequences from ten Chinese museum skins. In hindsight, we believe these animals represent eight of the nine nominal subspecies and four of the five nominal species. Bayesian, maximum likelihood and maximum parsimony haplotype network analyses gave concordant results and show Nomascus to be monophyletic. Significant intraspecific variation within N. leucogenys (17 haplotypes) is comparable with that reported earlier in Hylobates lar and less than half the known interspecific pairwise distances in gibbons. Sequence data support the recognition of five species (concolor, leucogenys, nasutus, gabriellae and probably hainanus) and suggest that nasutus is the oldest and leucogenys, the youngest taxon. In contrast, the subspecies N. c. furvogaster, N. c. jingdongensis, and N. leucogenys siki, are not recognizable at this otherwise informative genetic locus. These results show that HVR-1 sequence is variable enough to define evolutionarily significant units in Nomascus and, if coupled with multilocus microsatellite or SNP genotyping, more than adequate to characterize their phylogeographic history. There is an urgent need to obtain DNA from gibbons of known geographic provenance before they are extirpated to facilitate the conservation genetic management of the surviving animals. PMID:17455231

  2. Chronology of Eocene-Miocene sequences on the New Jersey shallow shelf: implications for regional, interregional, and global correlations

    USGS Publications Warehouse

    Browning, James V.; Miller, Kenneth G.; Sugarman, Peter J.; Barron, John; McCarthy, Francine M.G.; Kulhanek, Denise K.; Katz, Miriam E.; Feigenson, Mark D.

    2013-01-01

    Integrated Ocean Drilling Program Expedition 313 continuously cored and logged latest Eocene to early-middle Miocene sequences at three sites (M27, M28, and M29) on the inner-middle continental shelf offshore New Jersey, providing an opportunity to evaluate the ages, global correlations, and significance of sequence boundaries. We provide a chronology for these sequences using integrated strontium isotopic stratigraphy and biostratigraphy (primarily calcareous nannoplankton, diatoms, and dinocysts [dinoflagellate cysts]). Despite challenges posed by shallow-water sediments, age resolution is typically ±0.5 m.y. and in many sequences is as good as ±0.25 m.y. Three Oligocene sequences were sampled at Site M27 on sequence bottomsets. Fifteen early to early-middle Miocene sequences were dated at Sites M27, M28, and M29 across clinothems in topsets, foresets (where the sequences are thickest), and bottomsets. A few sequences have coarse (∼1 m.y.) or little age constraint due to barren zones; we constrain the age estimates of these less well dated sequences by applying the principle of superposition, i.e., sediments above sequence boundaries in any site are younger than the sediments below the sequence boundaries at other sites. Our age control provides constraints on the timing of deposition in the clinothem; sequences on the topsets are generally the youngest in the clinothem, whereas the bottomsets generally are the oldest. The greatest amount of time is represented on foresets, although we have no evidence for a correlative conformity. Our chronology provides a baseline for regional and interregional correlations and sea-level reconstructions: (1) we correlate a major increase in sedimentation rate precisely with the timing of the middle Miocene climate changes associated with the development of a permanent East Antarctic Ice Sheet; and (2) the timing of sequence boundaries matches the deep-sea oxygen isotopic record, implicating glacioeustasy as a major driver

  3. Sequence analysis of two genomic regions containing the KIT and the FMS receptor tyrosine kinase genes

    SciTech Connect

    Andre, C.; Hampe, A.; Lachaume, P.

    1997-01-15

    The KIT and FMS tyrosine kinase receptors, which are implicated in the control of cell growth and differentiation, stem through duplications from a common ancestor. We have conducted a detailed structural analysis of the two loci containing the KIT and FMS genes. The sequence of the {approximately}90-kb KIT locus reveals the position and size of the 21 introns and of the 5{prime} regulatory region of the KIT gene. The introns and the 3{prime}-untranslated parts of KIT and FMS have been analyzed in parallel. Comparison of the two sequences shows that, while introns of both genes have extensively diverged in size and sequence, this divergence is, at least in part, due to intron expansion through internal duplications, as suggested by the discrete extant analogies. Repetitive elements as well as exon predictions obtained using the GRAIL and GENEFINDER programs are described in detail. These programs led us to identify a novel gene, designated SMF, immediately downstream of FMS, in the opposite orientation. This finding emphasizes the gene-rich characteristic of this genomic region. 49 refs., 4 figs., 7 tabs.

  4. OrfPredictor: predicting protein-coding regions in EST-derived sequences.

    PubMed

    Min, Xiang Jia; Butler, Gregory; Storms, Reginald; Tsang, Adrian

    2005-07-01

    OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects. OrfPredictor is available at https://fungalgenome.concordia.ca/tools/OrfPredictor.html. PMID:15980561

  5. Sequence of the dog immunoglobulin alpha and epsilon constant region genes

    SciTech Connect

    Patel, M.; Selinger, D.; Mark, G.E.; Hollis, G.F.; Hickey, G.J.

    1995-03-01

    The immunoglobulin alpha (IGHAC) and epsilon (IGHEC) germline constant region genes were isolated from a dog liver genomic DNA library. Sequence analysis indicates that the dog IGHEC gene is encoded by four exons spread out over 1.7 kilobases (kb). The IGHAC sequence encompasses 1.5 kb and includes all three constant region coding exons. The complete exon/intron sequence of these genes is described. 28 refs., 2 figs., 2 tabs.

  6. Sequence analysis of the 3' non-coding region of mouse immunoglobulin light chain messenger RNA.

    PubMed Central

    Hamlyn, P H; Gillam, S; Smith, M; Milstein, C

    1977-01-01

    Using an oligonucleotide d(pT10-C-A) as primer, cDNA has been transcribed from the 3' non-coding region of mouse immunoglobulin light chain mRNA and sequenced by a modification1 of the 'plus-minus' gel method2. The sequence obtained has partially corrected and extended a previously obtained sequence3. The new data contains an unusual sequence in which a trinucleotide is repeated seven times. Images PMID:405661

  7. [Structure analysis of mtDNA control region of spotted halibut (Verasper variegatus) and its related species].

    PubMed

    He, Chong-Bo; Cao, Jie; Liu, Wei-Dong; Zhou, Zun-Chun; Ge, Long-Li; Gao, Xiang-Gang; Wang, Xiao-Min

    2007-07-01

    Spotted halibut (Verasper variegatus) is the only species of Genus Verasper in China. The fish was naturally distributed in Yellow Sea and Bohai Sea in northern China and Kyushu in Japan and in Korean sea area. Using PCR product direct sequencing, mitochondrial control region sequences of 24 individuals of spotted halibut was confirmed and analyzed. 4 control region haplotypes, resulting from length heteroplamy of the tandem repeat region, was obtained from these 24 fish. Sequence analysis demonstrated that there were four similar structures in the control region, i.e., extended terminal associated sequences (ETAS), central conserved sequence block (CSB), conserved sequence block (CSB), and repeat region, in V. moseri, Limanda ferruginea, Reinhardtius hippoglossoides, Heppoglossoides platessoides, Paralichthys olivaceous, Solea solea, S. senegalensis, and S. lascari. By comparing with other vertebrates, we found that there were similar repeated sequences immediately after the CSB-3 in all of the anuran species. PMID:17646149

  8. Modular sequence elements associated with origin regions in eukaryotic chromosomal DNA.

    PubMed Central

    Dobbs, D L; Shaiu, W L; Benbow, R M

    1994-01-01

    We have postulated that chromosomal replication origin regions in eukaryotes have in common clusters of certain modular sequence elements (Benbow, Zhao, and Larson, BioEssays 14, 661-670, 1992). In this study, computer analyses of DNA sequences from six origin regions showed that each contained one or more potential initiation regions consisting of a putative DUE (DNA unwinding element) aligned with clusters of SAR (scaffold associated region), and ARS (autonomously replicating sequence) consensus sequences, and pyrimidine tracts. The replication origins analyzed were from the following loci: Tetrahymena thermophila macronuclear rDNA gene, Chinese hamster ovary dihydrofolate reductase amplicon, human c-myc proto-oncogene, chicken histone H5 gene, Drosophila melanogaster chorion gene cluster on the third chromosome, and Chinese hamster ovary rhodopsin gene. The locations of putative initiation regions identified by the computer analyses were compared with published data obtained using diverse methods to map initiation sites. For at least four loci, the potential initiation regions identified by sequence analysis aligned with previously mapped initiation events. A consensus DNA sequence, WAWTTDDWWWDHWGWHMAWTT, was found within the potential initiation regions in every case. An additional 35 kb of combined flanking sequences from the six loci were also analyzed, but no additional copies of this consensus sequence were found. Images PMID:8041609

  9. Intra-Genomic Internal Transcribed Spacer Region Sequence Heterogeneity and Molecular Diagnosis in Clinical Microbiology

    PubMed Central

    Zhao, Ying; Tsang, Chi-Ching; Xiao, Meng; Cheng, Jingwei; Xu, Yingchun; Lau, Susanna K. P.; Woo, Patrick C. Y.

    2015-01-01

    Internal transcribed spacer region (ITS) sequencing is the most extensively used technology for accurate molecular identification of fungal pathogens in clinical microbiology laboratories. Intra-genomic ITS sequence heterogeneity, which makes fungal identification based on direct sequencing of PCR products difficult, has rarely been reported in pathogenic fungi. During the process of performing ITS sequencing on 71 yeast strains isolated from various clinical specimens, direct sequencing of the PCR products showed ambiguous sequences in six of them. After cloning the PCR products into plasmids for sequencing, interpretable sequencing electropherograms could be obtained. For each of the six isolates, 10–49 clones were selected for sequencing and two to seven intra-genomic ITS copies were detected. The identities of these six isolates were confirmed to be Candida glabrata (n = 2), Pichia (Candida) norvegensis (n = 2), Candida tropicalis (n = 1) and Saccharomyces cerevisiae (n = 1). Multiple sequence alignment revealed that one to four intra-genomic ITS polymorphic sites were present in the six isolates, and all these polymorphic sites were located in the ITS1 and/or ITS2 regions. We report and describe the first evidence of intra-genomic ITS sequence heterogeneity in four different pathogenic yeasts, which occurred exclusively in the ITS1 and ITS2 spacer regions for the six isolates in this study. PMID:26506340

  10. Timing, Sequencing, and Executive Control in Repetitive Movement Production.

    ERIC Educational Resources Information Center

    Krampe, Ralf Th.; Mayr, Ulrich; Kliegl, Reinhold

    2005-01-01

    The authors demonstrate that the timing and sequencing of target durations require low-level timing and executive control. Sixteen young (M-sub(age) = 19 years) and 16 older (M-sub(age) = 70 years) adults participated in 2 experiments. In Experiment 1, individual mean-variance functions for low-level timing (isochronous tapping) and the sequencing…

  11. Control of Task Sequences: What Is the Role of Language?

    ERIC Educational Resources Information Center

    Mayr, Ulrich; Kleffner-Canucci, Killian; Kikumoto, Atsushi; Redford, Melissa A.

    2014-01-01

    It is almost a truism that language aids serial-order control through self-cuing of upcoming sequential elements. We measured speech onset latencies as subjects performed hierarchically organized task sequences while "thinking aloud" each task label. Surprisingly, speech onset latencies and response times (RTs) were highly synchronized,…

  12. MAIN-SEQUENCE STAR POPULATIONS IN THE VIRGO OVERDENSITY REGION

    SciTech Connect

    Jerjen, H.; Da Costa, G. S.; Tisserand, P.; Willman, B.; Arimoto, N.; Okamoto, S.; Mateo, M.; Saviane, I.; Walsh, S.; Geha, M.; Jordan, A.; Zoccali, M.; Olszewski, E.; Walker, M.; Kroupa, P.

    2013-05-20

    We present deep color-magnitude diagrams (CMDs) for two Subaru Suprime-Cam fields in the Virgo Stellar Stream (VSS)/Virgo Overdensity (VOD) and compare them to a field centered on the highest concentration of Sagittarius (Sgr) Tidal Stream stars in the leading arm, Branch A of the bifurcation. A prominent population of main-sequence stars is detected in all three fields and can be traced as faint as g Almost-Equal-To 24 mag. Using theoretical isochrone fitting, we derive an age of 9.1{sup +1.0}{sub -1.1} Gyr, a median abundance of [Fe/H] = -0.70{sup +0.15}{sub -0.20} dex, and a heliocentric distance of 30.9 {+-} 3.0 kpc for the main sequence of the Sgr Stream Branch A. The dominant main-sequence populations in the two VSS/VOD fields ({Lambda}{sub Sun} Almost-Equal-To 265 Degree-Sign , B{sub Sun} Almost-Equal-To 13 Degree-Sign ) are located at a mean distance of 23.3 {+-} 1.6 kpc and have an age of {approx}8.2 Gyr, and an abundance of [Fe/H] = -0.67{sup +0.16}{sub -0.12} dex, similar to the Sgr Stream stars. These statistically robust parameters, derived from the photometry of 260 main-sequence stars, are also in good agreement with the age of the main population in the Sgr dwarf galaxy (8.0 {+-} 1.5 Gyr). They also agree with the peak in the metallicity distribution of 2-3 Gyr old M giants, [Fe/H] Almost-Equal-To -0.6 dex, in the Sgr north leading arm. We then compare the results from the VSS/VOD fields with the Sgr Tidal Stream model by Law and Majewski based on a triaxial Galactic halo shape that is empirically calibrated with Sloan Digital Sky Survey Sgr A-branch and Two Micron All Sky Survey M-giant stars. We find that the most prominent feature in the CMDs, the main-sequence population at 23 kpc, is not explained by the model. Instead the model predicts in these directions a low-density filamentary structure of Sgr debris stars at {approx}9 kpc and a slightly higher concentration of Sgr stars spread over a heliocentric distance range of 42-53 kpc. At best

  13. Pre-main-sequence population in NGC 1893 region

    NASA Astrophysics Data System (ADS)

    Pandey, A. K.; Samal, M. R.; Chauhan, N.; Eswaraiah, C.; Pandey, J. C.; Chen, W. P.; Ojha, D. K.

    2013-02-01

    In this paper we continued our efforts to understand the star formation scenario in and around the young cluster NGC 1893. We used a sample of the young stellar sources (YSOs) identified on the basis of multiwavelength data (optical, near-infrared (NIR), mid-infrared (MIR) and X-ray) to study the nature of YSOs associated with the region. The identified YSOs show an age spread of ~ 5 Myr. The YSOs located near the nebulae at the periphery of the cluster are relatively younger in comparison to those located within the cluster region. The present results are in accordance with those obtained by us in previous studies. Other main results from the present study are: 1) the fraction of disk bearing stars increases towards the periphery of the cluster; 2) there is an evidence supporting the notion that the mechanisms for disk dispersal operate less efficiently for low-mass stars; 3) the sample of Class II sources is found to be relatively older in comparison to that of Class III sources. A comparison of various properties of YSOs in the NGC 1893 region with those in the Tr 37/ IC 1396 region is also discussed.

  14. Sequence Controlled Self-Knotting Colloidal Patchy Polymers

    NASA Astrophysics Data System (ADS)

    Coluzza, Ivan; van Oostrum, Peter D. J.; Capone, Barbara; Reimhult, Erik; Dellago, Christoph

    2013-02-01

    Knotted chains are a promising class of polymers with many applications for materials science and drug delivery. Here we introduce an experimentally realizable model for the design of chains with controllable topological properties. Recently, we have developed a systematic methodology to construct self-assembling chains of simple particles, with final structures fully controlled by the sequence of particles along the chain. The individual particles forming the chain are colloids decorated with mutually interacting patches, which can be manufactured in the laboratory with current technology. Our methodology is applied to the design of sequences folding into self-knotting chains, in which the end monomers are by construction always close together in space. The knotted structure can then be externally locked simply by controlling the interaction between the end monomers, paving the way to applications in the design and synthesis of active materials and novel carriers for drugs delivery.

  15. Characterization and evolution of the mitochondrial DNA control region in hornbills (Bucerotiformes).

    PubMed

    Delport, Wayne; Ferguson, J Willem H; Bloomer, Paulette

    2002-06-01

    We determined the mitochondrial DNA control region sequences of six Bucerotiformes. Hornbills have the typical avian gene order and their control region is similar to other avian control regions in that it is partitioned into three domains: two variable domains that flank a central conserved domain. Two characteristics of the hornbill control region sequence differ from that of other birds. First, domain I is AT rich as opposed to AC rich, and second, the control region is approximately 500 bp longer than that of other birds. Both these deviations from typical avian control region sequence are explainable on the basis of repeat motifs in domain I of the hornbill control region. The repeat motifs probably originated from a duplication of CSB-1 as has been determined in chicken, quail, and snowgoose. Furthermore, the hornbill repeat motifs probably arose before the divergence of hornbills from each other but after the divergence of hornbills from other avian taxa. The mitochondrial control region of hornbills is suitable for both phylogenetic and population studies, with domains I and II probably more suited to population and phylogenetic analyses, respectively. PMID:12029361

  16. Sequence analysis and compositional properties of untranslated regions of human mRNAs.

    PubMed

    Pesole, G; Fiormarino, G; Saccone, C

    1994-03-25

    A detailed computer analysis of the untranslated regions, 5'-UTR and 3'-UTR, of human mRNA sequences is reported. The compositional properties of these regions, compared with those of the corresponding coding regions, indicate that 5'-UTR and 3'-UTR are less affected by the isochore compartmentalization than the corresponding third codon positions of mRNAs. The presence of higher functional constraints in 5'-UTR is also reported. Dinucleotide analysis shows a depletion of CpG and TpA in both sequences. A search for significant sequence motifs using the WORDUP algorithm reveals the patterns already known to have a functional role in the mRNA UTR, and several other motifs whose functional roles remain to be demonstrated. This type of analysis may be particularly useful for guiding site-directed mutagenesis experiments. In addition, it can be used for assessing the nature of anonymous sequences now produced in large amounts in megabase sequencing projects. PMID:8144029

  17. Multiple interdependent sequence elements control splicing of a fibroblast growth factor receptor 2 alternative exon.

    PubMed Central

    Del Gatto, F; Plet, A; Gesnel, M C; Fort, C; Breathnach, R

    1997-01-01

    The fibroblast growth factor receptor 2 gene contains a pair of mutually exclusive alternative exons, one of which (K-SAM) is spliced specifically in epithelial cells. We have described previously (F. Del Gatto and R. Breathnach, Mol. Cell. Biol. 15:4825-4834, 1995) some elements controlling K-SAM exon splicing, namely weak exon splice sites, an exon-repressing sequence, and an intron-activating sequence. We identify here two additional sequences in the intron downstream from the K-SAM exon which activate splicing of the exon. The first sequence (intron-activating sequence 2 [IAS2]) lies 168 to 186 nucleotides downstream from the exon's 5' splice site. The second sequence (intron-activating sequence 3 [IAS3]) lies 933 to 1,052 nucleotides downstream from the exon's 5' splice site. IAS3 is a complex region composed of several parts, one of which (nucleotides 963 to 983) can potentially form an RNA secondary structure with IAS2. This structure is composed of two stems separated by an asymmetric bulge. Mutations which disrupt either stem decrease activation, while compensatory mutations which reestablish the stem restore activation, either completely or partially, depending on the mutation. We present a model for K-SAM exon splicing involving the intervention of multiple, interdependent pre-mRNA sequence elements. PMID:9271388

  18. Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions.

    PubMed

    Maughan, Heather; Wang, Pauline W; Diaz Caballero, Julio; Fung, Pauline; Gong, Yunchen; Donaldson, Sylva L; Yuan, Lijie; Keshavjee, Shaf; Zhang, Yu; Yau, Yvonne C W; Waters, Valerie J; Tullis, D Elizabeth; Hwang, David M; Guttman, David S

    2012-01-01

    The characterization of bacterial communities using DNA sequencing has revolutionized our ability to study microbes in nature and discover the ways in which microbial communities affect ecosystem functioning and human health. Here we describe Serial Illumina Sequencing (SI-Seq): a method for deep sequencing of the bacterial 16S rRNA gene using next-generation sequencing technology. SI-Seq serially sequences portions of the V5, V6 and V7 hypervariable regions from barcoded 16S rRNA amplicons using an Illumina short-read genome analyzer. SI-Seq obtains taxonomic resolution similar to 454 pyrosequencing for a fraction of the cost, and can produce hundreds of thousands of reads per sample even with very high multiplexing. We validated SI-Seq using single species and mock community controls, and via a comparison to cystic fibrosis lung microbiota sequenced using 454 FLX Titanium. Our control runs show that SI-Seq has a dynamic range of at least five orders of magnitude, can classify >96% of sequences to the genus level, and performs just as well as 454 and paired-end Illumina methods in estimation of standard microbial ecology diversity measurements. We illustrate the utility of SI-Seq in a pilot sample of central airway secretion samples from cystic fibrosis patients. PMID:23056217

  19. Analysis of the regions flanking the human insulin gene and sequence of an Alu family member.

    PubMed Central

    Bell, G I; Pictet, R; Rutter, W J

    1980-01-01

    The regions around the human insulin gene have been studied by heteroduplex, hybridization and sequence analysis. These studies indicated that there is a region of heterogeneous length located approximately 700 bp before the 5' end of the gene; and that the 19 kb of cloned DNA which includes the 1430 bp insulin gene as well as 5650 bp before and 11,500 bp after the gene is single copy sequence except for 500 bp located 6000 bp from the 3' end of the gene. This 500 bp segment contains a member of the Alu family of dispersed middle repetitive sequences as well as another less highly repeated homopolymeric segment. The sequence of this region was determined. This Alu repeat is bordered by 19 bp direct repeats and also contains an 83 bp sequence which is present twice. The regions flanking the human and rat I insulin genes were compared by heteroduplex analysis to localize homologous sequences in the flanking regions which could be involved in the regulation of insulin biosynthesis. The homology between the two genes is restricted to the region encoding preproinsulin and a short region of approximately 60 bp flanking the 5' side of the genes. Images PMID:6253909

  20. Sequence of the Saccharomyces GAL region and its transcription in vivo.

    PubMed Central

    Citron, B A; Donelson, J E

    1984-01-01

    In Saccharomyces, the enzymes used to convert galactose to glucose are specified by three coordinately expressed, tightly linked genes, GAL7, GAL10, and GAL1. These genes are induced by galactose and are controlled by the positive regulator gene gal4 and the negative regulator gene gal80. GAL81 mutations, which are known to alter the gal4 protein, produce a constitutive phenotype. We have cloned fragments of Saccharomyces carlsbergensis DNA that span 26.3 kilobases surrounding the three clustered GAL genes. About 5 kilobases of the sequence was determined, which includes the entire GAL1 gene, the two intercistronic regions, and portions of the coding sequences of GAL10 and GAL7. Some amino acid homology between the GAL1 gene product, galactokinase, and the Escherichia coli galactokinase was detected. By using various Saccharomyces DNA fragments, the accumulation of GAL1 and GAL10 RNA in yeast cells after induction with galactose was studied. Our results, using wild-type, gal4-, gal80-, and GAL81-1- yeast cells, support the hypothesis that control is exerted at the transcriptional level. Images PMID:6715281

  1. Biothems: Sequence stratigraphic units and their implications for regional tectono-stratigraphic interpretations

    SciTech Connect

    Lane, H.R. ); Frye, M.W. ); Couples, G.D. )

    1992-01-01

    Biothems are regional wedge- or lens-shaped bodies of strata that are bounded shelfward or cratonward by paleontologically recognizable unconformities; generally thicken on marine shelves, where they are typically conformable with underlying and overlying biothems; are commonly thinner or represent starved sequences further basinward; and in their most basinward extent, are either bounded by biostratigraphically recognizable unconformities or are conformable with underlying and overlying biothems. As recognized to date, biothems have a logical distribution of faunal and floral components, as well as facies groupings that represent internally consistent and logical sequences of depositional environments. A west-to-east transect within the North American Mississippian System which extends from the Basin and Range Province, across the Transcontinental Arch (TA), into the Anadarko Basin, was constructed to demonstrate the regional distribution and tectono-stratigraphic significance of biothems relative to the axis of the TA. The relationships portrayed on the transect, tied to an understanding of North American Mississippian paleogeography, imply that biothems deposited during relative highstand events on one flank of the TA are time-equivalent to biothems deposited during relative lowstand events on the opposite flank of the TA. This distribution is interpreted to have been controlled by intraplate tectonic events that formed piano key basins along the flanks of the TA. The spatial patterns of these basins are not consistent with published models of basin evolution. A further conclusion is that the lack of coincident, transgressive or regressive Mississippian biothems on either flank of the TA suggests that it is inadvisable to impose the Mississippi Valley-derived eustasy curve on western flank depositional sequences.

  2. Proximal and distal sequences control UV cone pigment gene expression in transgenic zebrafish.

    PubMed

    Luo, Wenqin; Williams, John; Smallwood, Philip M; Touchman, Jeffrey W; Roman, Laura M; Nathans, Jeremy

    2004-04-30

    The molecular basis of cone photoreceptor-specific gene expression is largely unknown. In this study, we define cis-acting DNA sequences that control the cell type-specific expression of the zebrafish UV cone pigment gene by transient expression of green fluorescent protein transgenes following their injection into zebrafish embryos. These experiments show that 4.8 kb of 5'-flanking sequences from the zebrafish UV pigment gene direct expression specifically to UV cones and that this activity requires both distal and proximal sequences. In addition, we demonstrate that a proximal region located between -215 and -110 bp (with respect to the initiator methionine codon) can function in the context of a zebrafish rhodopsin promotor to convert its specificity from rod-only expression to rod and UV cone expression. These experiments demonstrate the power of transient transgenesis in zebrafish to efficiently define cis-acting regulatory sequences in an intact vertebrate. PMID:14966125

  3. Isolation and sequencing of a putative promoter region of the murine G protein beta 1 subunit (GNB1) gene.

    PubMed

    Kitanaka, Junichi; Kitanaka, Nobue; Takemura, Motohiko; Wang, Xiao-Bing; Hembree, Cambria M; Goodman, Nancy L; Uhl, George R

    2002-02-01

    The expression of the heterotrimeric GTP-binding protein beta 1 subunit gene (GNB1) is regulated by psychostimulants such as cocaine and amphetamines. Since the up-regulation appears to be one of the candidate processes of sensitization, it is necessary to elucidate the cellular and molecular mechanism of the GNB1 gene regulation for a better understanding the establishment of sensitization. In the present study, we describe the isolation and nucleotide sequence analysis of the GNB1 gene promoter region. We have isolated approximately 10 kb of the 5'-flanking region of the mouse of GNB1 gene and found potential elements involved in putative transcriptional control of the GNB1, such as AP1, AP2, Sp1, cyclic AMP response element, and nuclear factor kappa B recognition sites, within the sequences 0.3 kb upstream from the putative transcription start site. This region was highly rich in G + C content, but lacked TATA or CATT boxes. Comparing the nucleotide sequence of the cDNA clone with the human genome databases using the BLAST program a region containing putative exon 1 and promoter of the human GNB1 gene in chromosome 1 was found. The cloning and sequence analysis of an extensive portion of the 5'-flanking regulatory region of the GNB1 gene provides new insights into the factors involved in the regulation by psychostimulants of GNB1 expression. PMID:12180136

  4. Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein‐Coding Regions

    PubMed Central

    Lelieveld, Stefan H.; Spielmann, Malte; Mundlos, Stefan; Veltman, Joris A.

    2015-01-01

    ABSTRACT For next‐generation sequencing technologies, sufficient base‐pair coverage is the foremost requirement for the reliable detection of genomic variants. We investigated whether whole‐genome sequencing (WGS) platforms offer improved coverage of coding regions compared with whole‐exome sequencing (WES) platforms, and compared single‐base coverage for a large set of exome and genome samples. We find that WES platforms have improved considerably in the last years, but at comparable sequencing depth, WGS outperforms WES in terms of covered coding regions. At higher sequencing depth (95x–160x), WES successfully captures 95% of the coding regions with a minimal coverage of 20x, compared with 98% for WGS at 87‐fold coverage. Three different assessments of sequence coverage bias showed consistent biases for WES but not for WGS. We found no clear differences for the technologies concerning their ability to achieve complete coverage of 2,759 clinically relevant genes. We show that WES performs comparable to WGS in terms of covered bases if sequenced at two to three times higher coverage. This does, however, go at the cost of substantially more sequencing biases in WES approaches. Our findings will guide laboratories to make an informed decision on which sequencing platform and coverage to choose. PMID:25973577

  5. Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA

    PubMed Central

    2015-01-01

    With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization. PMID:26401685

  6. Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA.

    PubMed

    Belkin, Maxim; Chao, Shu-Han; Jonsson, Magnus P; Dekker, Cees; Aksimentiev, Aleksei

    2015-11-24

    With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization. PMID:26401685

  7. Whole-genome sequencing to control antimicrobial resistance

    PubMed Central

    Köser, Claudio U.; Ellington, Matthew J.; Peacock, Sharon J.

    2014-01-01

    Following recent improvements in sequencing technologies, whole-genome sequencing (WGS) is positioned to become an essential tool in the control of antibiotic resistance, a major threat in modern healthcare. WGS has already found numerous applications in this area, ranging from the development of novel antibiotics and diagnostic tests through to antibiotic stewardship of currently available drugs via surveillance and the elucidation of the factors that allow the emergence and persistence of resistance. Numerous proof-of-principle studies have also highlighted the value of WGS as a tool for day-to-day infection control and, for some pathogens, as a primary diagnostic tool to detect antibiotic resistance. However, appropriate data analysis platforms will need to be developed before routine WGS can be introduced on a large scale. PMID:25096945

  8. Research on the timing sequence control in large laser facility

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaolu; Wang, Lingfang; Wang, Chao; Tang, Ling; Chen, Ji; Zhang, Xin

    2015-11-01

    The timing sequence, between different pulses in SG-III laser facility, is controlled with three arbitrary waveform generators. The external clock and trigger are used to inhibit the timing jitter, which is provided by the synchronization system. Close-loop monitoring is used to make sure that the temporal phase can be recovered after reboot of the arbitrary waveform generator. The verification experiment shows that the three arbitrary waveform generators can work synchronously , which ensures the synchronization error control of the SG-III laser facility.

  9. Flagellar transcriptional activators FlbB and FlaI: gene sequences and 5' consensus sequences of operons under FlbB and FlaI control.

    PubMed Central

    Bartlett, D H; Frantz, B B; Matsumura, P

    1988-01-01

    The regulation of the expression of the operons in the flagella-chemotaxis regulon in Escherichia coli has been shown to be a highly ordered cascade which closely parallels the assembly of the flagellar structure and the chemotaxis machinery (T. Iino, Annu. Rev. Genet. 11:161-182, 1977; Y. Komeda, J. Bacteriol. 168: 1315-1318). The master operon, flbB, has been sequenced, and one of its gene products (FlaI) has been identified. On the basis of the deduced amino acid sequence, the FlbB protein has similarity to an alternate sigma factor which is responsible for expression of flagella in Bacillus subtilis. In addition, we have sequenced the 5' regions of a number of flagellar operons and compared these sequences with the 5' region of flagellar operons directly and indirectly under FlbB and FlaI control. We found both a consensus sequence which has been shown to be in all other flagellar operons (J. D. Helmann and M. J. Chamberlin, Proc. Natl. Acad. Sci. USA 84:6422-6424) and a derivative consensus sequence, which is found only in the 5' region of operons directly under FlbB and FlaI control. Images PMID:2832369

  10. Mapping of retrotransposon sequences in the unstable region surrounding the spinal muscular atrophy locus in 5q13

    SciTech Connect

    Francis, M.J.; Nesbit, M.A.; Theodosiou, A.M.

    1995-05-20

    The mutation that underlies the autosomal recessive disorder spinal muscular atrophy (SMA) is located on chromosome 5q13. Recent studies show that SMA patients frequently have deletions and rearrangements in this region compared to normal controls. During the isolation of candidate cDNAs for the disease, the authors identified a sequence that shows high homology to the THE-1 retrotransposon gene family. Using YAC fragmentation techniques, they have refined the localization of this sequence to the domain known to show instability in SMA patients. The implication of these results for the mechanism of the mutation in SMA is discussed. 20 refs., 1 fig.

  11. Automatic detection of regions of interest in complex video sequences

    NASA Astrophysics Data System (ADS)

    Osberger, Wilfried M.; Rohaly, Ann M.

    2001-06-01

    Studies of visual attention and eye movements have shown that people generally attend to only a few areas in typical scenes. These areas are commonly referred to as regions of interest (ROIs). When scenes are viewed with the same context and motivation, these ROIs are often highly correlated amongst different people, motivating the development of computational models of visual attention. This paper describes a novel model of visual attention designed to provide an accurate and robust prediction of a viewer's locus of attention across a wide range of typical video content. The model has been calibrated and verified using data gathered in an experiment in which the eye movements of 24 viewers were recorded while viewing material form a large database of still and video scenes. Certain characteristics of the scene content, such as moving objects, people, foreground and centrally-located objects, were found to exert a strong influence on viewers' attention. The results of comparing model predictions to experimental data demonstrate a strong correlation between the predicted ROIs and viewers' fixations.

  12. Hemispheric asymmetries and the control of motor sequences.

    PubMed

    Serrien, Deborah J; Sovijärvi-Spapé, Michiel M

    2015-04-15

    Sequencing of finger positions reflects a prototype of skilled behaviour. In order to perform sequencing, cognitive control supports the requirements and postural transitions. In this electroencephalography (EEG) study, we evaluate the effects of hand dominance and assess the neural correlates of unimanual and bimanual sequencing in left- and right-handers. The behavioural measurements provided an index of response planning (response time to first key press) and response execution (time between successive key presses, taps/s and percentage of correct responses), whereas the neural dynamics was determined by means of EEG coherence, expressing the functional connectivity between brain areas. Correlations between brain activity and behaviour were calculated for exploring the neural correlates that are functionally relevant for sequencing. Brain-behavioural correlations during response planning and execution revealed the significance of circuitry in the left hemisphere, underlining its significant role in the organisation of goal-directed behaviour. This lateralisation profile was independent of intrinsic constraints (hand dominance) and extrinsic demands (task requirements), suggesting essential higher-order computations in the left hemisphere. Overall, the observations highlight that the left hemisphere is specialised for sequential motor organisation in left- and right-handers, suggesting an endogenous hemispheric asymmetry for compound actions and the representation of skill; processes that can be separated from those that are involved in hand dominance. PMID:25617529

  13. Tracking TCRβ Sequence Clonotype Expansions during Antiviral Therapy Using High-Throughput Sequencing of the Hypervariable Region

    PubMed Central

    Robinson, Mark W.; Hughes, Joseph; Wilkie, Gavin S.; Swann, Rachael; Barclay, Stephen T.; Mills, Peter R.; Patel, Arvind H.; Thomson, Emma C.; McLauchlan, John

    2016-01-01

    To maintain a persistent infection viruses such as hepatitis C virus (HCV) employ a range of mechanisms that subvert protective T cell responses. The suppression of antigen-specific T cell responses by HCV hinders efforts to profile T cell responses during chronic infection and antiviral therapy. Conventional methods of detecting antigen-specific T cells utilize either antigen stimulation (e.g., ELISpot, proliferation assays, cytokine production) or antigen-loaded tetramer staining. This limits the ability to profile T cell responses during chronic infection due to suppressed effector function and the requirement for prior knowledge of antigenic viral peptide sequences. Recently, high-throughput sequencing (HTS) technologies have been developed for the analysis of T cell repertoires. In the present study, we have assessed the feasibility of HTS of the TCRβ complementarity determining region (CDR)3 to track T cell expansions in an antigen-independent manner. Using sequential blood samples from HCV-infected individuals undergoing antiviral therapy, we were able to measure the population frequencies of >35,000 TCRβ sequence clonotypes in each individual over the course of 12 weeks. TRBV/TRBJ gene segment usage varied markedly between individuals but remained relatively constant within individuals across the course of therapy. Despite this stable TRBV/TRBJ gene segment usage, a number of TCRβ sequence clonotypes showed dramatic changes in read frequency. These changes could not be linked to therapy outcomes in the present study; however, the TCRβ CDR3 sequences with the largest fold changes did include sequences with identical TRBV/TRBJ gene segment usage and high junction region homology to previously published CDR3 sequences from HCV-specific T cells targeting the HLA-B*0801-restricted 1395HSKKKCDEL1403 and HLA-A*0101-restricted 1435ATDALMTGY1443 epitopes. The pipeline developed in this proof of concept study provides a platform for the design of future

  14. Identification of Medically Important Yeast Species by Sequence Analysis of the Internal Transcribed Spacer Regions

    PubMed Central

    Leaw, Shiang Ning; Chang, Hsien Chang; Sun, Hsiao Fang; Barton, Richard; Bouchara, Jean-Philippe; Chang, Tsung Chain

    2006-01-01

    Infections caused by yeasts have increased in previous decades due primarily to the increasing population of immunocompromised patients. In addition, infections caused by less common species such as Pichia, Rhodotorula, Trichosporon, and Saccharomyces spp. have been widely reported. This study extensively evaluated the feasibility of sequence analysis of the rRNA gene internal transcribed spacer (ITS) regions for the identification of yeasts of clinical relevance. Both the ITS1 and ITS2 regions of 373 strains (86 species), including 299 reference strains and 74 clinical isolates, were amplified by PCR and sequenced. The sequences were compared to reference data available at the GenBank database by using BLAST (basic local alignment search tool) to determine if species identification was possible by ITS sequencing. Since the GenBank database currently lacks ITS sequence entries for some yeasts, the ITS sequences of type (or reference) strains of 15 species were submitted to GenBank to facilitate identification of these species. Strains producing discrepant identifications between the conventional methods and ITS sequence analysis were further analyzed by sequencing of the D1-D2 domain of the large-subunit rRNA gene for species clarification. The rates of correct identification by ITS1 and ITS2 sequence analysis were 96.8% (361/373) and 99.7% (372/373), respectively. Of the 373 strains tested, only 1 strain (Rhodotorula glutinis BCRC 20576) could not be identified by ITS2 sequence analysis. In conclusion, identification of medically important yeasts by ITS sequencing, especially using the ITS2 region, is reliable and can be used as an accurate alternative to conventional identification methods. PMID:16517841

  15. PROTEINS FROM EIGHT EUKARYOTIC CYTOCHROME P-450 FAMILIES SHARE A SEGMENTED REGION OF SEQUENCE SIMILARITY

    EPA Science Inventory

    Proteins from eight eukaryotic families in the cytochrome P-450 superfamily share one region of sequence similarity. his region begins 275-310 amino acids from the amino terminus of each P-450, continues for 170 residues, and ends 35-50 amino acids before the carboxyl terminus. h...

  16. DNA Replication Control Is Linked to Genomic Positioning of Control Regions in Escherichia coli.

    PubMed

    Frimodt-Møller, Jakob; Charbon, Godefroid; Krogfelt, Karen A; Løbner-Olesen, Anders

    2016-09-01

    Chromosome replication in Escherichia coli is in part controlled by three non-coding genomic sequences, DARS1, DARS2, and datA that modulate the activity of the initiator protein DnaA. The relative distance from oriC to the non-coding regions are conserved among E. coli species, despite large variations in genome size. Here we use a combination of i) site directed translocation of each region to new positions on the bacterial chromosome and ii) random transposon mediated translocation followed by culture evolution, to show genetic evidence for the importance of position. Here we provide evidence that the genomic locations of these regulatory sequences are important for cell cycle control and bacterial fitness. In addition, our work shows that the functionally redundant DARS1 and DARS2 regions play different roles in replication control. DARS1 is mainly involved in maintaining the origin concentration, whether DARS2 is also involved in maintaining single cell synchrony. PMID:27589233

  17. A strategy for sequence control in vinyl polymers via iterative controlled radical cyclization.

    PubMed

    Hibi, Yusuke; Ouchi, Makoto; Sawamoto, Mitsuo

    2016-01-01

    There is a growing interest in sequence-controlled polymers toward advanced functional materials. However, control of side-chain order for vinyl polymers has been lacking feasibility in the field of polymer synthesis because of the inherent feature of chain-growth propagation. Here we show a general and versatile strategy to control sequence in vinyl polymers through iterative radical cyclization with orthogonally cleavable and renewable bonds. The proposed methodology employs a repetitive and iterative intramolecular cyclization via a radical intermediate in a one-time template with a radical-generating site at one end and an alkene end at the other, each of which is connected to a linker via independently cleavable and renewable bonds. The unique design specifically allowed control of radical addition reaction although inherent chain-growth intermediate (radical species) was used, as well as the iterative cycle and functionalization for resultant side chains, to lead to sequence-controlled vinyl polymers (or oligomers). PMID:26996881

  18. A strategy for sequence control in vinyl polymers via iterative controlled radical cyclization

    PubMed Central

    Hibi, Yusuke; Ouchi, Makoto; Sawamoto, Mitsuo

    2016-01-01

    There is a growing interest in sequence-controlled polymers toward advanced functional materials. However, control of side-chain order for vinyl polymers has been lacking feasibility in the field of polymer synthesis because of the inherent feature of chain-growth propagation. Here we show a general and versatile strategy to control sequence in vinyl polymers through iterative radical cyclization with orthogonally cleavable and renewable bonds. The proposed methodology employs a repetitive and iterative intramolecular cyclization via a radical intermediate in a one-time template with a radical-generating site at one end and an alkene end at the other, each of which is connected to a linker via independently cleavable and renewable bonds. The unique design specifically allowed control of radical addition reaction although inherent chain-growth intermediate (radical species) was used, as well as the iterative cycle and functionalization for resultant side chains, to lead to sequence-controlled vinyl polymers (or oligomers). PMID:26996881

  19. A strategy for sequence control in vinyl polymers via iterative controlled radical cyclization

    NASA Astrophysics Data System (ADS)

    Hibi, Yusuke; Ouchi, Makoto; Sawamoto, Mitsuo

    2016-03-01

    There is a growing interest in sequence-controlled polymers toward advanced functional materials. However, control of side-chain order for vinyl polymers has been lacking feasibility in the field of polymer synthesis because of the inherent feature of chain-growth propagation. Here we show a general and versatile strategy to control sequence in vinyl polymers through iterative radical cyclization with orthogonally cleavable and renewable bonds. The proposed methodology employs a repetitive and iterative intramolecular cyclization via a radical intermediate in a one-time template with a radical-generating site at one end and an alkene end at the other, each of which is connected to a linker via independently cleavable and renewable bonds. The unique design specifically allowed control of radical addition reaction although inherent chain-growth intermediate (radical species) was used, as well as the iterative cycle and functionalization for resultant side chains, to lead to sequence-controlled vinyl polymers (or oligomers).

  20. Relative rates of evolution in the coding and control regions of African mtDNAs.

    PubMed

    Howell, Neil; Elson, Joanna L; Howell, Corinna; Turnbull, Douglass M

    2007-10-01

    Reduced median networks of African haplogroup L mitochondrial DNA (mtDNA) sequences were analyzed to determine the pattern of substitutions in both the noncoding control and coding regions. In particular, we attempted to determine the causes of the previously reported (Howell et al. 2004) violation of the molecular clock during the evolution of these sequences. In the coding region, there was a significantly higher rate of substitution at synonymous sites than at nonsynonymous sites as well as in the tRNA and rRNA genes. This is further evidence for the operation of purifying selection during human mtDNA evolution. For most sites in the control region, the relative rate of substitution was similar to the rate of neutral evolution (assumed to be most closely approximated by the substitution rate at 4-fold degenerate sites). However, there are a number of mutational hot spots in the control region, approximately 3% of the total sites, that have a rate of substitution greater than the neutral rate, at some sites by more than an order of magnitude. It is possible either that these sites are evolving under conditions of positive selection or that the substitution rate at some sites in the control region is strongly dependent upon sequence context. Finally, we obtained preliminary evidence for "nonideal" evolution in the control region, including haplogroup-specific substitution patterns and a decoupling between relative rates of substitution in the control and coding regions. PMID:17642471

  1. Proteome-Wide Discovery of Evolutionary Conserved Sequences in Disordered Regions

    PubMed Central

    Nguyen Ba, Alex N.; Yeh, Brian J.; van Dyk, Dewald; Davidson, Alan R.; Andrews, Brenda J.; Weiss, Eric L.; Moses, Alan M.

    2016-01-01

    At least 30% of human proteins are thought to contain intrinsically disordered regions, which lack stable structural conformation. Despite lacking enzymatic functions and having few protein domains, disordered regions are functionally important for protein regulation and contain short linear motifs (short peptide sequences involved in protein-protein interactions), but in most disordered regions, the functional amino acid residues remain unknown. We searched for evolutionarily conserved sequences within disordered regions according to the hypothesis that conservation would indicate functional residues. Using a phylogenetic hidden Markov model (phylo-HMM), we made accurate, specific predictions of functional elements in disordered regions even when these elements are only two or three amino acids long. Among the conserved sequences that we identified were previously known and newly identified short linear motifs, and we experimentally verified key examples, including a motif that may mediate interaction between protein kinase Cbk1 and its substrates. We also observed that hub proteins, which interact with many partners in a protein interaction network, are highly enriched in these conserved sequences. Our analysis enabled the systematic identification of the functional residues in disordered regions and suggested that at least 5% of amino acids in disordered regions are important for function. PMID:22416277

  2. Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences.

    PubMed

    Pang, Erli; Wu, Xiaomei; Lin, Kui

    2016-06-01

    Protein evolution plays an important role in the evolution of each genome. Because of their functional nature, in general, most of their parts or sites are differently constrained selectively, particularly by purifying selection. Most previous studies on protein evolution considered individual proteins in their entirety or compared protein-coding sequences with non-coding sequences. Less attention has been paid to the evolution of different parts within each protein of a given genome. To this end, based on PfamA annotation of all human proteins, each protein sequence can be split into two parts: domains or unassigned regions. Using this rationale, single nucleotide polymorphisms (SNPs) in protein-coding sequences from the 1000 Genomes Project were mapped according to two classifications: SNPs occurring within protein domains and those within unassigned regions. With these classifications, we found: the density of synonymous SNPs within domains is significantly greater than that of synonymous SNPs within unassigned regions; however, the density of non-synonymous SNPs shows the opposite pattern. We also found there are signatures of purifying selection on both the domain and unassigned regions. Furthermore, the selective strength on domains is significantly greater than that on unassigned regions. In addition, among all of the human protein sequences, there are 117 PfamA domains in which no SNPs are found. Our results highlight an important aspect of protein domains and may contribute to our understanding of protein evolution. PMID:26833483

  3. THE 'MAIN SEQUENCE' OF EXPLOSIVE SOLAR ACTIVE REGIONS: DISCOVERY AND INTERPRETATION

    SciTech Connect

    Falconer, David A.; Moore, Ronald L.; Adams, Mitzi; Gary, G. Allen

    2009-08-01

    We examine the location and distribution of the production of coronal mass ejections (CMEs) and major flares by sunspot active regions in the phase space of two whole-active-region magnetic quantities measured from 1897 SOHO/MDI magnetograms. These magnetograms track the evolution of 44 active regions across the central disk of radius 0.5 R {sub Sun}. The two quantities are {sup L}WL{sub SG}, a gauge of the total free energy in an active region's magnetic field, and {sup L}{phi}, a measure of the active region's total magnetic flux. From these data and each active region's history of production of CMEs, X flares, and M flares, we find (1) that CME/flare-productive active regions are concentrated in a straight-line 'main sequence' in (log {sup L}WL{sub SG}, log {sup L}{phi}) space, (2) that main-sequence active regions have nearly their maximum attainable free magnetic energy, and (3) evidence that this arrangement plausibly results from equilibrium between input of free energy to an explosive active region's magnetic field in the chromosphere and corona by contortion of the field via convection in and below the photosphere and loss of free energy via CMEs, flares, and coronal heating, an equilibrium between energy gain and loss that is analogous to that of the main sequence of hydrogen-burning stars in (mass, luminosity) space.

  4. Sequence Ready Characterization of the Pericentromeric Region of 19p12

    SciTech Connect

    Evan E. Eichler

    2006-08-31

    Current mapping and sequencing strategies have been inadequate within the proximal portion of 19p12 due, in part, to the presence of a recently expanded ZNF (zinc-finger) gene family and the presence of large (25-50 kb) inverted beta-satellite repeat structures which bracket this tandemly duplicated gene family. The virtual of absence of classically defined “unique” sequence within the region has hampered efforts to identify and characterize a suitable minimal tiling path of clones which can be used as templates required for finished sequencing of the region. The goal of this proposal is to develop and implement a novel sequence-anchor strategy to generate a contiguous BAC map of the most proximal portion of chromosome 19p12 for the purpose of complete sequence characterization. The target region will be an estimated 4.5 Mb of DNA extending from STS marker D19S450 (the beginning of the ZNF gene cluster) to the centromeric (alpha-satellite) junction of 19p11. The approach will entail 1) pre-selection of 19p12 BAC and cosmid clones (NIH approved library) utilizing both 19p12 -unique and 19p12-SPECIFIC repeat probes (Eichler et al., 1998); 2) the generation of a BAC/cosmid end-sequence map across the region with a density of one marker every 8kb; 3) the development of a second-generation of STS (sequence tagged sites) which will be used to identify and verify clonal overlap at the level of the sequence; 4) incorporation of these sequence-anchored overlapping clones into existing cosmid/BAC restriction maps developed at Livermore National Laboratory; and 5) validation of the organization of this region utilizing high-resolution FISH techniques (extended chromatin analysis) on monochromosomal 19 somatic cell hybrids and parental cell lines of source material. The data generated will be used in the selection of the most parsimonious tiling path of BAC clones to be sequenced as part of the JGI effort on chromosome 19 and should serve as a model for the sequence

  5. Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads

    PubMed Central

    Dong, Jiaqiang; Feng, Yaping; Kumar, Dibyendu; Zhang, Wei; Zhu, Tingting; Luo, Ming-Cheng; Messing, Joachim

    2016-01-01

    Haplotype variation not only involves SNPs but also insertions and deletions, in particular gene copy number variations. However, comparisons of individual genomes have been difficult because traditional sequencing methods give too short reads to unambiguously reconstruct chromosomal regions containing repetitive DNA sequences. An example of such a case is the protein gene family in maize that acts as a sink for reduced nitrogen in the seed. Previously, 41–48 gene copies of the alpha zein gene family that spread over six loci spanning between 30- and 500-kb chromosomal regions have been described in two Iowa Stiff Stalk (SS) inbreds. Analyses of those regions were possible because of overlapping BAC clones, generated by an expensive and labor-intensive approach. Here we used single-molecule real-time (Pacific Biosciences) shotgun sequencing to assemble the six chromosomal regions from the Non-Stiff Stalk maize inbred W22 from a single DNA sequence dataset. To validate the reconstructed regions, we developed an optical map (BioNano genome map; BioNano Genomics) of W22 and found agreement between the two datasets. Using the sequences of full-length cDNAs from W22, we found that the error rate of PacBio sequencing seemed to be less than 0.1% after autocorrection and assembly. Expressed genes, some with premature stop codons, are interspersed with nonexpressed genes, giving rise to genotype-specific expression differences. Alignment of these regions with those from the previous analyzed regions of SS lines exhibits in part dramatic differences between these two heterotic groups. PMID:27354512

  6. Sequencing of the Ribosomal Intergenic Spacer Region for Strain Identification of Porphyromonas gingivalis

    PubMed Central

    Rumpf, Robert W.; Griffen, Ann L.; Wen, Bo-Gui; Leys, Eugene J.

    1999-01-01

    The ribosomal intergenic spacer regions (ISRs) of 19 laboratory strains and 30 clinical samples of Porphyromonas gingivalis were amplified by PCR and sequenced to provide a strain identifier. The ISR is a variable region of DNA located between the conserved 16S and 23S rRNA genes. This makes it an ideal locus for differentiation of strains within a species: primers specific for the conserved flanking genes were used to amplify the ISR, which was then sequenced to identify the strain. We have constructed a P. gingivalis ISR sequence database to facilitate strain identification. ISR sequence analysis provides a strain identifier that can be easily reproduced among laboratories and catalogued for unambiguous comparison. PMID:10405432

  7. Structure-function studies of HIV-1: influence of long terminal repeat U3 region sequences on virus production.

    PubMed

    Velpandi, A; Nagashunmugam, T; Otsuka, T; Cartas, M; Srinivasan, A

    1992-06-01

    DNA sequence analyses of several human immunodeficiency virus (HIV) isolates revealed extensive genetic diversity in the env gene and, to a lesser extent, in other regions of the viral genome, including the long terminal repeat (LTR) sequences. Since the LTRs contain elements responsible for the control of transcription, the difference in the LTR region may play a crucial role in the overall replication rate of HIV. To evaluate the role of the LTR, we have constructed a number of infectious hybrid HIV molecular clones containing LTRs from different proviral DNAs linked to the body of the viral genome, and analyzed them in a transient expression system. Both parental and hybrid proviral DNAs were transfected into human rhabdomyosarcoma cells for monitoring virus production. Proviral DNA designate pZ6 (HIVZr6) showed a high level of virus in the medium of the transfected culture in comparison to the pHXB2 (HIVHTLV-III) and pARV (HIVSF-2) DNAs. Hybrid proviral DNAs containing viral genes from pZ6, linked to LTR U3 sequences of pHXB2 and pARV at the 5' end, showed virus production similar to the levels observed with pZ6. These results indicate that the extent of virus production does not correlate with the LTR U3 sequences, and may involve other regions of the viral genome. PMID:1351391

  8. Comparative Genomic Sequence Analysis of the Human Chromosome 21 Down Syndrome Critical Region

    PubMed Central

    Toyoda, Atsushi; Noguchi, Hideki; Taylor, Todd D.; Ito, Takehiko; Pletcher, Mathew T.; Sakaki, Yoshiyuki; Reeves, Roger H.; Hattori, Masahira

    2002-01-01

    Comprehensive knowledge of the gene content of human chromosome 21 (HSA21) is essential for understanding the etiology of Down syndrome (DS). Here we report the largest comparison of finished mouse and human sequence to date for a 1.35-Mb region of mouse chromosome 16 (MMU16) that corresponds to human chromosome 21q22.2. This includes a portion of the commonly described “DS critical region,” thought to contain a gene or genes whose dosage imbalance contributes to a number of phenotypes associated with DS. We used comparative sequence analysis to construct a DNA feature map of this region that includes all known genes, plus 144 conserved sequences ≥100 bp long that show ≥80% identity between mouse and human but do not match known exons. Twenty of these have matches to expressed sequence tag and cDNA databases, indicating that they may be transcribed sequences from chromosome 21. Eight putative CpG islands are found at conserved positions. Models for two human genes, DSCR4 and DSCR8, are not supported by conserved sequence, and close examination indicates that low-level transcripts from these loci are unlikely to encode proteins. Gene prediction programs give different results when used to analyze the well-conserved regions between mouse and human sequences. Our findings have implications for evolution and for modeling the genetic basis of DS in mice. [Sequence data described in this paper have been submitted to the DDBJ/GenBank under accession nos. AP003148 through AP003158, and AB066227. Supplemental material is available at http://www.genome.org.] PMID:12213769

  9. Delineation of the regulatory region sequences of Agrobacterium tumefaciens virB operon.

    PubMed Central

    Das, A; Pazour, G J

    1989-01-01

    A virB-lacZ translational fusion was constructed to monitor expression of the Agrobacterium tumefaciens virB operon. Expression of the fusion gene was dependent on the presence of pTiA6 virA, virG, and a plant factor acetosyringone. Analysis of deletion mutants, constructed by exonuclease Bal31 digestion, showed that 68 residues upstream of the virB transcription initiation site was necessary for its expression. A TT----CC substitution at positions -62 and -61 led to a 7 fold reduction in virB expression. The virB upstream region contains a tetradecameric sequence, dPuT/ATDCAATGHAAPy (D = A, G or T; H = A, C or T), that is conserved in the non-transcribed regions of all vir genes. Alteration of the position of this sequence relative to the promoter region sequences had a drastic negative effect on virB expression. PMID:2748333

  10. Structure of mitochondrial DNA control region of Pholis fangi and its phylogenetic implication

    NASA Astrophysics Data System (ADS)

    Li, Lin; Zhang, Hui; Sun, Dianrong; Gao, Tianxiang

    2014-06-01

    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.

  11. Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes

    PubMed Central

    Schirtzinger, Erin E.; Tavares, Erika S.; Gonzales, Lauren A.; Eberhard, Jessica R.; Miyaki, Cristina Y.; Sanchez, Juan J.; Hernandez, Alexis; Müeller, Heinrich; Graves, Gary R.; Fleischer, Robert C.; Wright, Timothy F.

    2012-01-01

    Mitochondrial genomes are generally thought to be under selection for compactness, due to their small size, consistent gene content, and a lack of introns or intergenic spacers. As more animal mitochondrial genomes are fully sequenced, rearrangements and partial duplications are being identified with increasing frequency, particularly in birds (Class Aves). In this study, we investigate the evolutionary history of mitochondrial control region states within the avian order Psittaciformes (parrots and cockatoos). To this aim, we reconstructed a comprehensive multi-locus phylogeny of parrots, used PCR of three diagnostic fragments to classify the mitochondrial control region state as single or duplicated, and mapped these states onto the phylogeny. We further sequenced 44 selected species to validate these inferences of control region state. Ancestral state reconstruction using a range of weighting schemes identified six independent origins of mitochondrial control region duplications within Psittaciformes. Analysis of sequence data showed that varying levels of mitochondrial gene and tRNA homology and degradation were present within a given clade exhibiting duplications. Levels of divergence between control regions within an individual varied from 0–10.9% with the differences occurring mainly between 51 and 225 nucleotides 3′ of the goose hairpin in domain I. Further investigations into the fates of duplicated mitochondrial genes, the potential costs and benefits of having a second control region, and the complex relationship between evolutionary rates, selection, and time since duplication are needed to fully explain these patterns in the mitochondrial genome. PMID:22543055

  12. Mitochondrial DNA control region of three mackerels, genus Rastrelliger: structure, molecular diversity and phylogenetic relationship.

    PubMed

    Jondeung, Amnuay; Karinthanyakit, Wirangrong

    2016-07-01

    The complete mitochondrial control regions (CR) of three mackerels (Rastrelliger spp.) were examined and analyzed. The CR contained three domains, in which three termination-associated sequences (TAS-I, TAS-II and TAS-III), two central conserved sequence blocks (CSB-E, CSB-D), three conserved sequence blocks (CSB-I, CSB-II, and CSB-III) and a putative promoter were detected. Molecular indices analyses of the aligned complete CR sequences showed high level of haplotype diversities and genetic divergences among the three species. The intraspecific divergence among species of this genus ranked from 0.25% to 1.62% and interspecific divergence from 1.90% to 4.30%. The phylogenetic tree shows monophyly with R. brachysoma as a basal species of Rastrelliger. Applying the average divergence rate for fish control regions, the results suggest that the time of separation among Rastrelligers could have occurred in the middle Pleistocene era. PMID:26119119

  13. Programmed factor binding to simian virus 40 GC-box replication and transcription control sequences.

    PubMed Central

    Buchanan, R L; Gralla, J D

    1990-01-01

    Nuclear footprinting revealed a temporal program involving factor binding to the repetitive GC-box DNA elements present in the simian virus 40 regulatory region. This program specified ordered and directional binding to these tandem regulatory sequences in vivo during the late phase of infection. The program was interrupted by the DNA replication inhibitor aphidicolin or by inactivation of the viral replication factor simian virus 40 T antigen, suggesting a link between viral DNA replication and new factor binding. Measurements of DNA accumulation in viruses lacking either the distal or proximal halves of the GC-box region suggested that the region has a dual role in replication control. Overall, the data point to important relationships between DNA replication and factor binding to the GC-box DNA, a multifunctional regulatory region. Images PMID:2152821

  14. Regional Changes in the Sequence of Cotton Leaf Curl Multan Betasatellite

    PubMed Central

    Akhtar, Sohail; Tahir, Muhammad Nouman; Baloch, Ghulam Rasool; Javaid, Shaista; Khan, Ali Qaiser; Amin, Imran; Briddon, Rob W.; Mansoor, Shahid

    2014-01-01

    Cotton leaf curl disease (CLCuD) in Pakistan and northwestern India is caused by monopartite begomoviruses in association with an essential, disease-specific satellite, Cotton leaf curl Multan betasatellite (CLCuMB). Following a recent upsurge in CLCuD problems in Sindh province (southern Pakistan), sequences of clones of CLCuMB were obtained from Sindh and Punjab province (central Pakistan), where CLCuD has been a problem since the mid-1980s. The sequences were compared to all sequences of CLCuMB available in the databases. Analysis of the sequences shows extensive sequence variation in CLCuMB, most likely resulting from recombination. The range of sequence variants differ between Sindh, the Punjab and northwestern India. The possible significance of the findings with respect to movement of the CLCuD between the three regions is discussed. Additionally, the lack of sequence variation within the only coding sequence of CLCuMB suggests that the betasatellite is not involved in resistance breaking which became a problem after 2001 in the Punjab and subsequently also in northwestern India. PMID:24859342

  15. Nucleotide sequence of the regulatory locus controlling expression of bacterial genes for bioluminescence.

    PubMed Central

    Engebrecht, J; Silverman, M

    1987-01-01

    Production of light by the marine bacterium Vibrio fischeri and by recombinant hosts containing cloned lux genes is controlled by the density of the culture. Density-dependent regulation of lux gene expression has been shown to require a locus consisting of the luxR and luxI genes and two closely linked divergent promoters. As part of a genetic analysis to understand the regulation of bioluminescence, we have sequenced the region of DNA containing this control circuit. Open reading frames corresponding to luxR and luxI were identified; transcription start sites were defined by S1 nuclease mapping and sequences resembling promoter elements were located. Images PMID:3697093

  16. Natural and artificial RNAs occupy the same restricted region of sequence space

    PubMed Central

    Kennedy, Ryan; Lladser, Manuel E.; Wu, Zhiyuan; Zhang, Chen; Yarus, Michael; De Sterck, Hans; Knight, Rob

    2010-01-01

    Different chemical and mutational processes within genomes give rise to sequences with different compositions and perhaps different capacities for evolution. The evolution of functional RNAs may occur on a “neutral network” in which sequences with any given function can easily mutate to sequences with any other. This neutral network hypothesis is more likely if there is a particular region of composition that contains sequences that are functional in general, and if many different functions are possible within this preferred region of composition. We show that sequence preferences in active sites recovered by in vitro selection combine with biophysical folding rules to support the neutral network hypothesis. These simple active-site specifications and folding preferences obtained by artificial selection experiments recapture the previously observed purine bias and specific spread along the GC axis of naturally occurring aptamers and ribozymes isolated from organisms, although other types of RNAs, such as miRNA precursors and spliceosomal RNAs, that act primarily through complementarity to other amino acids do not share these preferences. These universal evolved sequence features are therefore intrinsic in RNA molecules that bind small-molecule targets or catalyze reactions. PMID:20032164

  17. Functional analysis and nucleotide sequence of the promoter region of the murine hck gene.

    PubMed Central

    Lock, P; Stanley, E; Holtzman, D A; Dunn, A R

    1990-01-01

    The structure and function of the promoter region and exon 1 of the murine hck gene have been characterized in detail. RNase protection analysis has established that hck transcripts initiate from heterogeneous start sites located within the hck gene. Fusion gene constructs containing hck 5'-flanking sequences and the bacterial Neor gene have been introduced into the hematopoietic cell lines FDC-P1 and WEHI-265 by using a self-inactivating retroviral vector. The transcriptional start sites of the fusion gene are essentially identical to those of the endogenous hck gene. Analysis of infected WEHI-265 cell lines treated with bacterial lipopolysaccharide (LPS) reveals a 3- to 5-fold elevation in the levels of endogenous hck mRNA and a 1.4- to 2.6-fold increase in the level of Neor fusion gene transcripts, indicating that hck 5'-flanking sequences are capable of conferring LPS responsiveness on the Neor gene. The 5'-flanking region of the hck gene contains sequences similar to an element which is thought to be involved in the LPS responsiveness of the class II major histocompatibility gene A alpha k. A subset of these sequences are also found in the 5'-flanking regions of other LPS-responsive genes. Moreover, this motif is related to the consensus binding sequence of NF-kappa B, a transcription factor which is known to be regulated by LPS. Images PMID:2388619

  18. Translational control by lysine-encoding A-rich sequences

    PubMed Central

    Arthur, Laura L.; Pavlovic-Djuranovic, Slavica; Koutmou, Kristin S.; Green, Rachel; Szczesny, Pawel; Djuranovic, Sergej

    2015-01-01

    Regulation of gene expression involves a wide array of cellular mechanisms that control the abundance of the RNA or protein products of that gene. We describe a gene regulatory mechanism that is based on polyadenylate [poly(A)] tracks that stall the translation apparatus. We show that creating longer or shorter runs of adenosine nucleotides, without changes in the amino acid sequence, alters the protein output and the stability of mRNA. Sometimes, these changes result in the production of an alternative “frameshifted” protein product. These observations are corroborated using reporter constructs and in the context of recombinant gene sequences. About 2% of genes in the human genome may be subject to this uncharacterized yet fundamental form of gene regulation. The potential pool of regulated genes encodes many proteins involved in nucleic acid binding. We hypothesize that the genes we identify are part of a large network whose expression is fine-tuned by poly(A) tracks, and we provide a mechanism through which synonymous mutations may influence gene expression in pathological states. PMID:26322332

  19. Human phosphoribosylformylglycineamide amidotransferase (FGARAT): regional mapping, complete coding sequence, isolation of a functional genomic clone, and DNA sequence analysis.

    PubMed

    Patterson, D; Bleskan, J; Gardiner, K; Bowersox, J

    1999-11-01

    Purines play essential roles in many cellular functions, including DNA replication, transcription, intra- and extra-cellular signaling, energy metabolism, and as coenzymes for many biochemical reactions. The de-novo synthesis of purines requires 10 enzymatic steps for the production of inosine monophosphate (IMP). Defects in purine metabolism are associated with human diseases. Further, many anticancer agents function as inhibitors of the de-novo biosynthetic pathway. Genes or cDNAs for most of the enzymes comprising this pathway have been isolated from humans or other mammals. One notable exception is the phosphoribosylformylglycineamide amidotransferase (FGARAT) gene, which encodes the fourth step of this pathway. This gene has been cloned from numerous microorganisms and from Drosophila melanogaster and C. elegans. We report here the identification of a human cDNA containing the coding region of the FGARAT mRNA and the isolation of a P1 clone that contains an intact human FGARAT gene. The P1 clone corrects the purine auxotrophy and protein deficiency of Chinese hamster ovary (CHO) cell mutants (AdeB) deficient in both the activity and the protein for FGARAT. The P1 clone was used to regionally map the FGARAT gene to chromosome region 17p13, a location consistent with our prior assignment of this gene to chromosome 17. A comparison of the DNA sequence of the human FGARAT and FGARAT DNA sequence from 17 other organisms is reported. The isolation of this gene means that DNA clones for all the 10 steps of IMP synthesis have been isolated from humans or other mammals. PMID:10548741

  20. Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions

    PubMed Central

    Lorch, Yahli; Maier-Davis, Barbara; Kornberg, Roger D.

    2014-01-01

    AT-rich DNA is concentrated in the nucleosome-free regions (NFRs) associated with transcription start sites of most genes. We tested the hypothesis that AT-rich DNA engenders NFR formation by virtue of its rigidity and consequent exclusion of nucleosomes. We found that the AT-rich sequences present in many NFRs have little effect on the stability of nucleosomes. Rather, these sequences facilitate the removal of nucleosomes by the RSC chromatin remodeling complex. RSC activity is stimulated by AT-rich sequences in nucleosomes and inhibited by competition with AT-rich DNA. RSC may remove NFR nucleosomes without effect on adjacent ORF nucleosomes. Our findings suggest that many NFRs are formed and maintained by an active mechanism involving the ATP-dependent removal of nucleosomes rather than a passive mechanism due to the intrinsic instability of nucleosomes on AT-rich DNA sequences. PMID:25403179

  1. Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions.

    PubMed

    Lorch, Yahli; Maier-Davis, Barbara; Kornberg, Roger D

    2014-11-15

    AT-rich DNA is concentrated in the nucleosome-free regions (NFRs) associated with transcription start sites of most genes. We tested the hypothesis that AT-rich DNA engenders NFR formation by virtue of its rigidity and consequent exclusion of nucleosomes. We found that the AT-rich sequences present in many NFRs have little effect on the stability of nucleosomes. Rather, these sequences facilitate the removal of nucleosomes by the RSC chromatin remodeling complex. RSC activity is stimulated by AT-rich sequences in nucleosomes and inhibited by competition with AT-rich DNA. RSC may remove NFR nucleosomes without effect on adjacent ORF nucleosomes. Our findings suggest that many NFRs are formed and maintained by an active mechanism involving the ATP-dependent removal of nucleosomes rather than a passive mechanism due to the intrinsic instability of nucleosomes on AT-rich DNA sequences. PMID:25403179

  2. Human immunodeficiency virus type 1 LTR TATA and TAR region sequences required for transcriptional regulation.

    PubMed Central

    Garcia, J A; Harrich, D; Soultanakis, E; Wu, F; Mitsuyasu, R; Gaynor, R B

    1989-01-01

    The human immunodeficiency virus (HIV) type 1 LTR is regulated at the transcriptional level by both cellular and viral proteins. Using HeLa cell extracts, multiple regions of the HIV LTR were found to serve as binding sites for cellular proteins. An untranslated region binding protein UBP-1 has been purified and fractions containing this protein bind to both the TAR and TATA regions. To investigate the role of cellular proteins binding to both the TATA and TAR regions and their potential interaction with other HIV DNA binding proteins, oligonucleotide-directed mutagenesis of both these regions was performed followed by DNase I footprinting and transient expression assays. In the TATA region, two direct repeats TC/AAGC/AT/AGCTGC surround the TATA sequence. Mutagenesis of both of these direct repeats or of the TATA sequence interrupted binding over the TATA region on the coding strand, but only a mutation of the TATA sequence affected in vivo assays for tat-activation. In addition to TAR serving as the site of binding of cellular proteins, RNA transcribed from TAR is capable of forming a stable stem-loop structure. To determine the relative importance of DNA binding proteins as compared to secondary structure, oligonucleotide-directed mutations in the TAR region were studied. Local mutations that disrupted either the stem or loop structure were defective in gene expression. However, compensatory mutations which restored base pairing in the stem resulted in complete tat-activation. This indicated a significant role for the stem-loop structure in HIV gene expression. To determine the role of TAR binding proteins, mutations were constructed which extensively changed the primary structure of the TAR region, yet left stem base pairing, stem energy and the loop sequence intact. These mutations resulted in decreased protein binding to TAR DNA and defects in tat-activation, and revealed factor binding specifically to the loop DNA sequence. Further mutagenesis which inverted

  3. Rapid detection and sequencing of alleles in the 3' flanking region of the interleukin-6 gene.

    PubMed Central

    Bowcock, A M; Ray, A; Erlich, H; Sehgal, P B

    1989-01-01

    The 3' flanking region of the interleukin 6 gene is polymorphic due to insertions of different size. Within this region lies a sequence of approximately 500 base pairs that is AT rich. Based on flanking sequence information we have constructed oligonucleotides which prime the polymerase chain reaction (PCR) and amplify this AT rich region. The amplification products visualized by agarose gel electrophoresis gave fragment sizes for both homozygous and heterozygous individuals that were concordant with those observed by conventional genomic blotting techniques. Alleles that could not be typed by Southern analysis were resolved with this approach. These results illustrate the value of PCR for the rapid detection of length polymorphisms such as those due to variable numbers of tandem repeats. In contrast to RFLP analysis this procedure takes less than a day to perform, is cheaper, avoids the use of radioactivity and requires far less substrate DNA. Three different human alleles were sequenced, and differences were detected that were due to both large duplications and loss of one or two bases, suggesting that AT rich regions identify highly polymorphic loci. The same primers also amplified non-human primate DNA, allowing a comparison of the human sequence with that of the common chimpanzee and baboon. Images PMID:2789373

  4. POLYMORPHISM IN THE CODING REGION SEQUENCE OF GDF8 GENE IN INDIAN SHEEP.

    PubMed

    Pothuraju, M; Mishra, S K; Kumar, S N; Mohamed, N F; Kataria, R S; Yadav, D K; Arora, R

    2015-11-01

    The present study was undertaken to identify polymorphism in the coding sequence of GDF8gene across indigenous meat type sheep breeds. A 1647 bp sequence was generated, encompassing 208 bp of the 5'UTR, 1128 bp of coding region (exon1, 2 and 3) as well as 311 bp of 3'UTR. The sheep and goat GDF8 gene sequences were observed to be highly conserved as compared to cattle, buffalo, horse and pig. Several nucleotide variations were observed across coding sequence of GDF8 gene in Indian sheep. Three polymorphic sites were identified in the 5'UTR, one in exon 1 and one in the exon 2 regions. Both SNPs in the exonic region were found to be non-synonymous. The mutations c.539T > G and c.821T > A discovered in this study in the exon 1 and exon 2, respectively, have not been previously reported. The information generated provides preliminary indication of the functional diversity present in Indian sheep at the coding region of GDF8gene. The novel as well as the previously reported SNPs discovered in the Indian sheep warrant further analysis to see whether they affect the phenotype. Future studies will need to establish the affect of reported SNPs in the expression of the GDF8 gene in Indian sheep population. PMID:26845859

  5. Auditory sequence processing reveals evolutionarily conserved regions of frontal cortex in macaques and humans.

    PubMed

    Wilson, Benjamin; Kikuchi, Yukiko; Sun, Li; Hunter, David; Dick, Frederic; Smith, Kenny; Thiele, Alexander; Griffiths, Timothy D; Marslen-Wilson, William D; Petkov, Christopher I

    2015-01-01

    An evolutionary account of human language as a neurobiological system must distinguish between human-unique neurocognitive processes supporting language and evolutionarily conserved, domain-general processes that can be traced back to our primate ancestors. Neuroimaging studies across species may determine whether candidate neural processes are supported by homologous, functionally conserved brain areas or by different neurobiological substrates. Here we use functional magnetic resonance imaging in Rhesus macaques and humans to examine the brain regions involved in processing the ordering relationships between auditory nonsense words in rule-based sequences. We find that key regions in the human ventral frontal and opercular cortex have functional counterparts in the monkey brain. These regions are also known to be associated with initial stages of human syntactic processing. This study raises the possibility that certain ventral frontal neural systems, which play a significant role in language function in modern humans, originally evolved to support domain-general abilities involved in sequence processing. PMID:26573340

  6. Intra-tumor Heterogeneity in Localized Lung Adenocarcinomas Delineated by Multi-region Sequencing

    PubMed Central

    Zhang, Jianjun; Fujimoto, Junya; Zhang, Jianhua; Wedge, David C.; Song, Xingzhi; Zhang, Jiexin; Seth, Sahil; Chow, Chi-Wan; Cao, Yu; Gumbs, Curtis; Gold, Kathryn A.; Kalhor, Neda; Little, Latasha; Mahadeshwar, Harshad; Moran, Cesar; Protopopov, Alexei; Sun, Huandong; Tang, Jiabin; Wu, Xifeng; Ye, Yuanqing; William, William N.; Lee, Jack J.; Heymach, John V.; Hong, Waun Ki; Swisher, Stephen; Wistuba, Ignacio I.; Futreal, P. Andrew

    2015-01-01

    Cancers are composed of populations of cells with distinct molecular and phenotypic features, a phenomenon termed intra-tumor heterogeneity (ITH). ITH in lung cancers has not been well studied. We applied multi-region whole exome sequencing (WES) on 11 localized lung adenocarcinomas. All tumors showed clear evidence of ITH. On average, 76% of all mutations and 20/21 known cancer gene mutations were identified in all regions of individual tumors suggesting single-region sequencing may be adequate to identify the majority of known cancer gene mutations in localized lung adenocarcinomas. With a median follow-up of 21 months post-surgery, 3 patients have relapsed and all 3 patients had significantly larger fractions of subclonal mutations in their primary tumors than patients without relapse. These data indicate larger subclonal mutation fraction may be associated with increased likelihood of postsurgical relapse in patients with localized lung adenocarcinomas. PMID:25301631

  7. Auditory sequence processing reveals evolutionarily conserved regions of frontal cortex in macaques and humans

    PubMed Central

    Wilson, Benjamin; Kikuchi, Yukiko; Sun, Li; Hunter, David; Dick, Frederic; Smith, Kenny; Thiele, Alexander; Griffiths, Timothy D.; Marslen-Wilson, William D.; Petkov, Christopher I.

    2015-01-01

    An evolutionary account of human language as a neurobiological system must distinguish between human-unique neurocognitive processes supporting language and evolutionarily conserved, domain-general processes that can be traced back to our primate ancestors. Neuroimaging studies across species may determine whether candidate neural processes are supported by homologous, functionally conserved brain areas or by different neurobiological substrates. Here we use functional magnetic resonance imaging in Rhesus macaques and humans to examine the brain regions involved in processing the ordering relationships between auditory nonsense words in rule-based sequences. We find that key regions in the human ventral frontal and opercular cortex have functional counterparts in the monkey brain. These regions are also known to be associated with initial stages of human syntactic processing. This study raises the possibility that certain ventral frontal neural systems, which play a significant role in language function in modern humans, originally evolved to support domain-general abilities involved in sequence processing. PMID:26573340

  8. The Monitoring and Control of Task Sequences in Human and Non-Human Primates

    PubMed Central

    Desrochers, Theresa M.; Burk, Diana C.; Badre, David; Sheinberg, David L.

    2016-01-01

    Our ability to plan and execute a series of tasks leading to a desired goal requires remarkable coordination between sensory, motor, and decision-related systems. Prefrontal cortex (PFC) is thought to play a central role in this coordination, especially when actions must be assembled extemporaneously and cannot be programmed as a rote series of movements. A central component of this flexible behavior is the moment-by-moment allocation of working memory and attention. The ubiquity of sequence planning in our everyday lives belies the neural complexity that supports this capacity, and little is known about how frontal cortical regions orchestrate the monitoring and control of sequential behaviors. For example, it remains unclear if and how sensory cortical areas, which provide essential driving inputs for behavior, are modulated by the frontal cortex during these tasks. Here, we review what is known about moment-to-moment monitoring as it relates to visually guided, rule-driven behaviors that change over time. We highlight recent human work that shows how the rostrolateral prefrontal cortex (RLPFC) participates in monitoring during task sequences. Neurophysiological data from monkeys suggests that monitoring may be accomplished by neurons that respond to items within the sequence and may in turn influence the tuning properties of neurons in posterior sensory areas. Understanding the interplay between proceduralized or habitual acts and supervised control of sequences is key to our understanding of sequential task execution. A crucial bridge will be the use of experimental protocols that allow for the examination of the functional homology between monkeys and humans. We illustrate how task sequences may be parceled into components and examined experimentally, thereby opening future avenues of investigation into the neural basis of sequential monitoring and control. PMID:26834581

  9. Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region.

    PubMed Central

    Yura, T; Mori, H; Nagai, H; Nagata, T; Ishihama, A; Fujita, N; Isono, K; Mizobuchi, K; Nakata, A

    1992-01-01

    A contiguous 111,402-nucleotide sequence corresponding to the 0 to 2.4 min region of the E. coli chromosome was determined as a first step to complete structural analysis of the genome. The resulting sequence was used to predict open reading frames and to search for sequence similarity against the PIR protein database. A number of novel genes were found whose predicted protein sequences showed significant homology with known proteins from various organisms, including several clusters of genes similar to those involved in fatty acid metabolism in bacteria (e.g., betT, baiF) and higher organisms, iron transport (sfuA, B, C) in Serratia marcescens, and symbiotic nitrogen fixation or electron transport (fixA, B, C, X) in Azorhizobium caulinodans. In addition, several genes and IS elements that had been mapped but not sequenced (e.g., leuA, B, C, D) were identified. We estimate that about 90 genes are represented in this region of the chromosome with little spacer. Images PMID:1630901

  10. Analysis of mixtures using next generation sequencing of mitochondrial DNA hypervariable regions

    PubMed Central

    Kim, Hanna; Erlich, Henry A.; Calloway, Cassandra D.

    2015-01-01

    Aim To apply massively parallel and clonal sequencing (next generation sequencing or NGS) to the analysis of forensic mixed samples. Methods A duplex polymerase chain reaction (PCR) assay targeting the mitochondrial DNA (mtDNA) hypervariable regions I/II (HVI/HVII) was developed for NGS analysis on the Roche 454 GS Junior instrument. Eight sets of multiplex identifier-tagged 454 fusion primers were used in a combinatorial approach for amplification and deep sequencing of up to 64 samples in parallel. Results This assay was shown to be highly sensitive for sequencing limited DNA amounts ( ~ 100 mtDNA copies) and analyzing contrived and biological mixtures with low level variants ( ~ 1%) as well as “complex” mixtures (≥3 contributors). PCR artifact “hybrid” sequences generated by jumping PCR or template switching were observed at a low level (<2%) in the analysis of mixed samples but could be eliminated by reducing the PCR cycle number. Conclusion This study demonstrates the power of NGS technologies targeting the mtDNA HVI/HVII regions for analysis of challenging forensic samples, such as mixtures and specimens with limited DNA. PMID:26088845

  11. Spouse-to-Spouse Transmission and Evolution of Hypervariable Region 1 and 5’ Untranslated Region of Hepatitis C Virus Analyzed by Next-Generation Sequencing

    PubMed Central

    Caraballo Cortes, Kamila; Zagordi, Osvaldo; Jabłońska, Joanna; Pawełczyk, Agnieszka; Kubisa, Natalia; Perlejewski, Karol; Bukowska-Ośko, Iwona; Płoski, Rafał; Radkowski, Marek; Laskus, Tomasz

    2016-01-01

    Hepatitis C virus (HCV) transmission between spouses remains poorly characterized, largely due to the limited availability of samples from the early stage of infection, as well as methodological constraints. A fifty-eight year-old male developed acute hepatitis C infection and his 53-year old spouse has been HCV-positive for over 10 years. Serum samples were collected from both at the time of acute hepatitis C diagnosis in male (baseline) and then at 9 and 13 months. Hypervariable region 1 (HVR1) and 5’ untranslated region (5’UTR) sequences were amplified and subjected to next generation sequencing (NGS) using a pyrosequencing platform. Genetic variants were inferred by Shorah reconstruction method and compared by phylogenetic and sequence diversity analysis. As the sequencing error of the procedure was previously determined to be ≤ 1.5%, the analysis was conducted with and without the 1.5% cut-off with regard to the frequency of variants. No identical HVR1 variants were identified in spouses at baseline and follow-up samples regardless whether the cut-off was applied or not. However, there was high similarity (98.3%) between a minor baseline donor variant (1.7% frequency) and the most abundant baseline recipient variant (62.5% frequency). Furthermore, donor and recipient strains clustered together when compared to 10 control subjects from the same area and infected with the same HCV subtype. There was an increase in HVR1 complexity (number of genetic variants) over time in both spouses. In contrast, the 5'UTR region was stable and of low complexity throughout the study. In conclusion, intrafamilial HCV transmission may be established by a very minor variant and investigation of this phenomenon requires high-sensitivity assays, such as NGS. PMID:26918636

  12. Regions of the polytene chromosomes of Drosophila virilis carrying multiple dispersed p Dv 111 DNA sequences

    SciTech Connect

    Gubenko, I.S.; Evgen'ev, M.B.

    1986-09-01

    The cloned sequences of p Dv 111 DNA hybridized in situ with more than 170 regions of Drosophila virilis salivary gland chromosomes. Comparative autoradiography of in situ hybridization and the nature of pulse /sup 3/H-thymidine and /sup 3/H-deoxycytidine incorporation into the polytene chromosomes of D. virilis at the puparium formation stage showed that the hybridization sites of p Dv 111 are distributed not only in the heterochromatic regions but also in the euchromatic regions of the chromosomes that are not late replicating. Two distinct bands of hybridization of p Dv 111 /sup 3/H-DNA were observed in the region of the heat shock puff 20CD. The regions of the distal end of chromosome 2, in which breaks appeared during radiation-induced chromosomal rearrangements, hybridized with the p Dv 111 DNA.

  13. Digital Sequences and a Time Reversal-Based Impact Region Imaging and Localization Method

    PubMed Central

    Qiu, Lei; Yuan, Shenfang; Mei, Hanfei; Qian, Weifeng

    2013-01-01

    To reduce time and cost of damage inspection, on-line impact monitoring of aircraft composite structures is needed. A digital monitor based on an array of piezoelectric transducers (PZTs) is developed to record the impact region of impacts on-line. It is small in size, lightweight and has low power consumption, but there are two problems with the impact alarm region localization method of the digital monitor at the current stage. The first one is that the accuracy rate of the impact alarm region localization is low, especially on complex composite structures. The second problem is that the area of impact alarm region is large when a large scale structure is monitored and the number of PZTs is limited which increases the time and cost of damage inspections. To solve the two problems, an impact alarm region imaging and localization method based on digital sequences and time reversal is proposed. In this method, the frequency band of impact response signals is estimated based on the digital sequences first. Then, characteristic signals of impact response signals are constructed by sinusoidal modulation signals. Finally, the phase synthesis time reversal impact imaging method is adopted to obtain the impact region image. Depending on the image, an error ellipse is generated to give out the final impact alarm region. A validation experiment is implemented on a complex composite wing box of a real aircraft. The validation results show that the accuracy rate of impact alarm region localization is approximately 100%. The area of impact alarm region can be reduced and the number of PZTs needed to cover the same impact monitoring region is reduced by more than a half. PMID:24084123

  14. Digital sequences and a time reversal-based impact region imaging and localization method.

    PubMed

    Qiu, Lei; Yuan, Shenfang; Mei, Hanfei; Qian, Weifeng

    2013-01-01

    To reduce time and cost of damage inspection, on-line impact monitoring of aircraft composite structures is needed. A digital monitor based on an array of piezoelectric transducers (PZTs) is developed to record the impact region of impacts on-line. It is small in size, lightweight and has low power consumption, but there are two problems with the impact alarm region localization method of the digital monitor at the current stage. The first one is that the accuracy rate of the impact alarm region localization is low, especially on complex composite structures. The second problem is that the area of impact alarm region is large when a large scale structure is monitored and the number of PZTs is limited which increases the time and cost of damage inspections. To solve the two problems, an impact alarm region imaging and localization method based on digital sequences and time reversal is proposed. In this method, the frequency band of impact response signals is estimated based on the digital sequences first. Then, characteristic signals of impact response signals are constructed by sinusoidal modulation signals. Finally, the phase synthesis time reversal impact imaging method is adopted to obtain the impact region image. Depending on the image, an error ellipse is generated to give out the final impact alarm region. A validation experiment is implemented on a complex composite wing box of a real aircraft. The validation results show that the accuracy rate of impact alarm region localization is approximately 100%. The area of impact alarm region can be reduced and the number of PZTs needed to cover the same impact monitoring region is reduced by more than a half. PMID:24084123

  15. Controlling the bond scission sequence of oxygenates for energy applications

    NASA Astrophysics Data System (ADS)

    Stottlemyer, Alan L.

    intermediates was observed on the Pt and Pt/WC surfaces. For CH3OH decomposition, DFT calculations suggested that the bond scission sequence could be controlled using monolayer coverage of Pt on WC. The Ni/Pt bimetallic system was studied as an example for using oxygenates as a hydrogen source. There are two well characterized surface structures for the Ni/Pt system: the surface configuration, in which the Ni atoms reside primarily on the surface of the Pt bulk, and the subsurface configuration, in which the second atomic layer is enriched in Ni atoms and the surface is enriched in Pt atoms. These configurations are denoted NiPtPt and PtNiPt, respectively. DFT results revealed that trends established for the Ni/Pt(111) system extend to the Ni/Pt(100) analogue. TPD studies revealed that the NiPtPt surface was more active for oxygenate reforming than the Pt or PtNiPt surfaces. HREELS confirmed the presence of strongly bound reaction intermediates, including aldehyde-like species, and suggested that the first decomposition step was likely O-H bond scission. Thus, the binding energies of the deprotonated reaction intermediates are important parameters in controlling the decomposition pathways of oxygenates. These studies have demonstrated that the bond scission sequence of oxygenate decomposition can be controlled using bimetallic and transition metal carbide catalysts. While this study has focused on oxygenate decomposition for energy applications, the principles and methodology applied herein are universally applicable to the development of novel and marketable value-added products. The value in such a methodology is in the combination of both calculations to predict catalytic and chemical properties, and experiments to fine-tune theoretical predictions.

  16. A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence

    PubMed Central

    Forman, Joshua J.; Legesse-Miller, Aster; Coller, Hilary A.

    2008-01-01

    Recognition sites for microRNAs (miRNAs) have been reported to be located in the 3′ untranslated regions of transcripts. In a computational screen for highly conserved motifs within coding regions, we found an excess of sequences conserved at the nucleotide level within coding regions in the human genome, the highest scoring of which are enriched for miRNA target sequences. To validate our results, we experimentally demonstrated that the let-7 miRNA directly targets the miRNA-processing enzyme Dicer within its coding sequence, thus establishing a mechanism for a miRNA/Dicer autoregulatory negative feedback loop. We also found computational evidence to suggest that miRNA target sites in coding regions and 3′ UTRs may differ in mechanism. This work demonstrates that miRNAs can directly target transcripts within their coding region in animals, and it suggests that a complete search for the regulatory targets of miRNAs should be expanded to include genes with recognition sites within their coding regions. As more genomes are sequenced, the methodological approach that we used for identifying motifs with high sequence conservation will be increasingly valuable for detecting functional sequence motifs within coding regions. PMID:18812516

  17. Upstream regulatory regions required to stabilize binding to the TATA sequence in an adenovirus early promoter.

    PubMed

    Garcia, J; Wu, F; Gaynor, R

    1987-10-26

    Of the five early adenovirus promoters, the early region 3 (E3) promoter is one of the most strongly induced by the E1A protein. To identify cellular proteins involved in both the basal and E1A-induced transcriptional regulation of the E3 promoter, DNase I footprinting using partially purified Hela cell extracts was performed. Four regions of the E3 promoter serve as binding domains for cellular proteins. These regions are found between -156 to -179 (site IV), -83 to -103 (site III), -47 to -67 (site II), and -16 to -37 (site I), relative to the start of transcription. Examination of the DNA sequences in each binding domain suggests that site III likely serves as a binding site for activator protein 1 (AP-1), site II for the cyclic AMP regulatory element binding protein (CREB), and site I for a TATA binding factor. The factors binding to either site II or III were sufficient to stabilize binding to the TATA sequence (site I). Mutagenesis studies indicated that both sites II and III, in addition to site I, are needed for complete basal and E1A-induced transcription. These results suggest that multiple cellular factors are involved in both the basal and E1A-induced transcriptional regulation of the E3 promoter, and that either of two upstream regions are capable of stabilizing factor binding to the TATA sequence. PMID:2959908

  18. Nucleotide sequence of the hypervariable region of the human C2 gene

    SciTech Connect

    Zhu, Z.B.; Volanakis, J.V. )

    1991-03-15

    It has been previously suggested that the multiallelic Bam H1/Sst I RFLPs of the human C2 gene arose through deletion/insertion of a tandemly-repeated minisatellite region. In this study the authors subcloned and sequenced the Sst I polymorphic fragment of the b haplotype of the C2 gene. This restriction fragment is 2,450 bp long and maps 1,550 bp 3{prime} of exon 3. Its nucleotide sequence is characterized by the presence of at least 4 different repeated regions varying in size from 18 to 58 bp. One of these regions starting at position 1,413 is 48 bp long and is repeated five times. The first 3 repeats are in tandem and are separated by 72 bp from two additional tandem repeats. Sequence homology among the 5 repeats ranges between 93 and 98%. Eighty three percent of the nucleotides of the repeated-region are G or C. It seems likely that this nucleotide repeat resulted in the multiallelic RFLPs through a mechanism of unequal recombination or replication slippage.

  19. Upstream regulatory regions required to stabilize binding to the TATA sequence in an adenovirus early promoter.

    PubMed Central

    Garcia, J; Wu, F; Gaynor, R

    1987-01-01

    Of the five early adenovirus promoters, the early region 3 (E3) promoter is one of the most strongly induced by the E1A protein. To identify cellular proteins involved in both the basal and E1A-induced transcriptional regulation of the E3 promoter, DNase I footprinting using partially purified Hela cell extracts was performed. Four regions of the E3 promoter serve as binding domains for cellular proteins. These regions are found between -156 to -179 (site IV), -83 to -103 (site III), -47 to -67 (site II), and -16 to -37 (site I), relative to the start of transcription. Examination of the DNA sequences in each binding domain suggests that site III likely serves as a binding site for activator protein 1 (AP-1), site II for the cyclic AMP regulatory element binding protein (CREB), and site I for a TATA binding factor. The factors binding to either site II or III were sufficient to stabilize binding to the TATA sequence (site I). Mutagenesis studies indicated that both sites II and III, in addition to site I, are needed for complete basal and E1A-induced transcription. These results suggest that multiple cellular factors are involved in both the basal and E1A-induced transcriptional regulation of the E3 promoter, and that either of two upstream regions are capable of stabilizing factor binding to the TATA sequence. Images PMID:2959908

  20. DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences

    PubMed Central

    Meng, Fanchi; Kurgan, Lukasz

    2016-01-01

    Motivation: Disordered flexible linkers (DFLs) are disordered regions that serve as flexible linkers/spacers in multi-domain proteins or between structured constituents in domains. They are different from flexible linkers/residues because they are disordered and longer. Availability of experimentally annotated DFLs provides an opportunity to build high-throughput computational predictors of these regions from protein sequences. To date, there are no computational methods that directly predict DFLs and they can be found only indirectly by filtering predicted flexible residues with predictions of disorder. Results: We conceptualized, developed and empirically assessed a first-of-its-kind sequence-based predictor of DFLs, DFLpred. This method outputs propensity to form DFLs for each residue in the input sequence. DFLpred uses a small set of empirically selected features that quantify propensities to form certain secondary structures, disordered regions and structured regions, which are processed by a fast linear model. Our high-throughput predictor can be used on the whole-proteome scale; it needs <1 h to predict entire proteome on a single CPU. When assessed on an independent test dataset with low sequence-identity proteins, it secures area under the receiver operating characteristic curve equal 0.715 and outperforms existing alternatives that include methods for the prediction of flexible linkers, flexible residues, intrinsically disordered residues and various combinations of these methods. Prediction on the complete human proteome reveals that about 10% of proteins have a large content of over 30% DFL residues. We also estimate that about 6000 DFL regions are long with ≥30 consecutive residues. Availability and implementation: http://biomine.ece.ualberta.ca/DFLpred/. Contact: lkurgan@vcu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307636

  1. Sequence polymorphism of the mitochondrial DNA hypervariable regions I and II in 205 Singapore Malays.

    PubMed

    Wong, Hang Yee; Tang, June S W; Budowle, Bruce; Allard, Marc W; Syn, Christopher K C; Tan-Siew, Wai Fun; Chow, Shui Tse

    2007-01-01

    Mitochondrial DNA sequences of the hypervariable regions HV1 and HV2 were analyzed in 205 unrelated ethnic Malays residing in Singapore as an initial effort to generate a database for forensic identification purposes. Sequence polymorphism was detected using PCR and direct sequencing analysis. A total of 152 haplotypes was found containing 152 polymorphisms. Out of the 152 haplotypes, 115 were observed only once and 37 types were seen in multiple individuals. The most common haplotype (16223T, 16295T, 16362C, 73G, 146C, 199C, 263G, and 315.1C) was shared by 7 (3.41%) individuals, two haplotypes were shared by 4 individuals, seven haplotypes were shared by 3 individuals, and 27 haplotypes by 2 individuals. Haplotype diversity and random match probability were estimated to be 0.9961% and 0.87%, respectively. PMID:17150401

  2. Nonessential region of bacteriophage P4: DNA sequence, transcription, gene products, and functions.

    PubMed Central

    Ghisotti, D; Finkel, S; Halling, C; Dehò, G; Sironi, G; Calendar, R

    1990-01-01

    We sequenced the leftmost 2,640 base pairs of bacteriophage P4 DNA, thus completing the sequence of the 11,627-base-pair P4 genome. The newly sequenced region encodes three nonessential genes, which are called gop, beta, and cII (in order, from left to right). The gop gene product kills Escherichia coli when the beta protein is absent; the gop and beta genes are transcribed rightward from the same promoter. The cII gene is transcribed leftward to a rho-independent terminator. Mutation of this terminator creates a temperature-sensitive phenotype, presumably owing to a defect in expression of the beta gene. Images PMID:2403440

  3. Targeted enrichment of genomic DNA regions for next-generation sequencing

    PubMed Central

    ElSharawy, Abdou; Sauer, Sascha; van Helvoort, Joop M.L.M.; van der Zaag, P.J.; Franke, Andre; Nilsson, Mats; Lehrach, Hans; Brookes, Anthony J.

    2011-01-01

    In this review, we discuss the latest targeted enrichment methods and aspects of their utilization along with second-generation sequencing for complex genome analysis. In doing so, we provide an overview of issues involved in detecting genetic variation, for which targeted enrichment has become a powerful tool. We explain how targeted enrichment for next-generation sequencing has made great progress in terms of methodology, ease of use and applicability, but emphasize the remaining challenges such as the lack of even coverage across targeted regions. Costs are also considered versus the alternative of whole-genome sequencing which is becoming ever more affordable. We conclude that targeted enrichment is likely to be the most economical option for many years to come in a range of settings. PMID:22121152

  4. Local generation of multineuronal spike sequences in the hippocampal CA1 region

    PubMed Central

    Stark, Eran; Roux, Lisa; Eichler, Ronny; Buzsáki, György

    2015-01-01

    Sequential activity of multineuronal spiking can be observed during theta and high-frequency ripple oscillations in the hippocampal CA1 region and is linked to experience, but the mechanisms underlying such sequences are unknown. We compared multineuronal spiking during theta oscillations, spontaneous ripples, and focal optically induced high-frequency oscillations (“synthetic” ripples) in freely moving mice. Firing rates and rate modulations of individual neurons, and multineuronal sequences of pyramidal cell and interneuron spiking, were correlated during theta oscillations, spontaneous ripples, and synthetic ripples. Interneuron spiking was crucial for sequence consistency. These results suggest that participation of single neurons and their sequential order in population events are not strictly determined by extrinsic inputs but also influenced by local-circuit properties, including synapses between local neurons and single-neuron biophysics. PMID:26240336

  5. Hydraulic fracturing and the Crooked Lake Sequences: Insights gleaned from regional seismic networks

    NASA Astrophysics Data System (ADS)

    Schultz, Ryan; Stern, Virginia; Novakovic, Mark; Atkinson, Gail; Gu, Yu Jeffrey

    2015-04-01

    Within central Alberta, Canada, a new sequence of earthquakes has been recognized as of 1 December 2013 in a region of previous seismic quiescence near Crooked Lake, ~30 km west of the town of Fox Creek. We utilize a cross-correlation detection algorithm to detect more than 160 events to the end of 2014, which is temporally distinguished into five subsequences. This observation is corroborated by the uniqueness of waveforms clustered by subsequence. The Crooked Lake Sequences have come under scrutiny due to its strong temporal correlation (>99.99%) to the timing of hydraulic fracturing operations in the Duvernay Formation. We assert that individual subsequences are related to fracturing stimulation and, despite adverse initial station geometry, double-difference techniques allow us to spatially relate each cluster back to a unique horizontal well. Overall, we find that seismicity in the Crooked Lake Sequences is consistent with first-order observations of hydraulic fracturing induced seismicity.

  6. Sequence stratigraphic and tectonic controls on Shannon incised-valley distribution, Hartzog Draw, Wyoming

    SciTech Connect

    Sullivan, M.D.; Van Wagoner, J.C.; Jennette, D.C.

    1996-12-31

    The Upper Cretaceous Shannon Sandstone in the Powder River Basin, Wyoming is interpreted as stacked tidal bars infilling northwest-southeast trending incised valleys. The Shannon Sandstone can be subdivided into 3 sequences: Copenhagen Blue, Crimson Red, and Canary Yellow. The Copenhagen Blue sequence boundary is a regional unconformity at the base of the Shannon Sandstone marked by distal tidal-bar deposits resting on offshore mudstones of the Cody. The overlying Crimson Red sequence is the main reservoir interval at Hartzog Draw and is composed of proximal tidal-bar deposits. The highly erosional Canary Yellow sequence boundary forms the trap at Hartzog Draw by juxtaposing the reservoir sandstones of the Crimson Red sequence with the overlying offshore mudstones of the Canary Yellow sequence. The Shannon Sandstone is therefore an erosional remnant of originally more extensive tide-dominated deltas deposited within northwest-southeast trending incised valleys. The orientation and distribution of the Shannon incised valleys is the result of the interplay between tectonics and eustacy. During lowstand incised valley development the orientation of fluvial systems incising the shelf was strongly controlled by pre-existing northwest-southeast trending structural elements in the basin. During the subsequent sea-level rise the shoreline backstepped in a landward direction. The shoreline also gradually rotated from an east-west orientation during the lowstand to a north-south orientation during the highstand systems tract. Ultimately the highstand shorelines were located over 160 kms landward of the lowstand shorelines and oriented subparallel to the lowstand incised valleys.

  7. Sequence stratigraphic and tectonic controls on Shannon incised-valley distribution, Hartzog Draw, Wyoming

    SciTech Connect

    Sullivan, M.D.; Van Wagoner, J.C.; Jennette, D.C. )

    1996-01-01

    The Upper Cretaceous Shannon Sandstone in the Powder River Basin, Wyoming is interpreted as stacked tidal bars infilling northwest-southeast trending incised valleys. The Shannon Sandstone can be subdivided into 3 sequences: Copenhagen Blue, Crimson Red, and Canary Yellow. The Copenhagen Blue sequence boundary is a regional unconformity at the base of the Shannon Sandstone marked by distal tidal-bar deposits resting on offshore mudstones of the Cody. The overlying Crimson Red sequence is the main reservoir interval at Hartzog Draw and is composed of proximal tidal-bar deposits. The highly erosional Canary Yellow sequence boundary forms the trap at Hartzog Draw by juxtaposing the reservoir sandstones of the Crimson Red sequence with the overlying offshore mudstones of the Canary Yellow sequence. The Shannon Sandstone is therefore an erosional remnant of originally more extensive tide-dominated deltas deposited within northwest-southeast trending incised valleys. The orientation and distribution of the Shannon incised valleys is the result of the interplay between tectonics and eustacy. During lowstand incised valley development the orientation of fluvial systems incising the shelf was strongly controlled by pre-existing northwest-southeast trending structural elements in the basin. During the subsequent sea-level rise the shoreline backstepped in a landward direction. The shoreline also gradually rotated from an east-west orientation during the lowstand to a north-south orientation during the highstand systems tract. Ultimately the highstand shorelines were located over 160 kms landward of the lowstand shorelines and oriented subparallel to the lowstand incised valleys.

  8. Cell mutants defective in synthesizing a heparan sulfate proteoglycan with regions of defined monosaccharide sequence

    SciTech Connect

    De Agostini, A.L.; Lau, H.K.; Leone, C.; Youssoufian, H. ); Rosenberg, R.D. Beth Israel Hospital, Boston, MA Harvard Medical School, Boston, MA )

    1990-12-01

    The authors have demonstrated that mouse LTA cells synthesize cell-surface heparan sulfate proteoglycans (HSPGs) with regions of defined monosaccharide sequence that specifically interact with antithrombin (HSPG{sup act}). It remains unclear how HSPG{sup act} can be generated by a biosynthetic pathway with no simple template for directing the ordered assembly of monosaccharide units. To examine this issue, they treated LTA cells with ethyl methanesulfonate and then isolated seven stable mutants that synthesize only 8 - 27% of the wild-type HSPG{sup act} but produce normal amounts of other HSPGs. These mutants are recessive in nature and fall into at least two different complementation groups. The delineation of the molecular basis of these defects should help to elucidate the manner by which cells synthesize HSPGs with regions of defined monosaccharide sequence.

  9. Regulation and targeting of recombination in extrachromosomal substrates carrying immunoglobulin switch region sequences.

    PubMed Central

    Leung, H; Maizels, N

    1994-01-01

    We have used extrachromosomal substrates carrying immunoglobulin heavy-chain S mu and S gamma 3 switch region sequences to study activation and targeting of recombination by a transcriptional enhancer element. Substrates are transiently introduced into activated primary murine B cells, in which recombination involving S-region sequences deletes a conditionally lethal marker, and recombination is measured by transformation of Escherichia coli in the second step of the assay. Previously we found that as many as 25% of replicated substrates recombined during 40-h transfection of lipopolysaccharide (LPS)-stimulated primary cells and that efficient recombination was dependent on the presence of S-region sequences as well as a transcriptional activator region in the constructs (H. Leung and N. Maizels, Proc. Natl. Acad. Sci. USA 89:4154-4158, 1992). Here we show that recombination of the switch substrates is threefold more efficient in LPS-cultured primary B cells than in the T-cell line EL4; the activities responsible for switch substrate recombination thus appear to be more abundant or more active in cells which can carry out chromosomal switch recombination. We test the role of the transcriptional activator region and show that the immunoglobulin heavy-chain intron enhancer (E mu) alone stimulates recombination as well as E mu combined with a heavy-chain promoter and that mutations that diminish enhancer-dependent transcription 500-fold diminish recombinational activation less than 2-fold. These observations suggest that the enhancer stimulates recombination by a mechanism that does not depend on transcript production or that is insensitive to the level of transcript production over a very broad range. Furthermore, we find that E mu stimulates recombination when located either upstream or downstream of S mu but that the position of the recombinational activator does affect the targeting of recombination junctions, suggesting that the relatively imprecise targeting of

  10. A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

    PubMed Central

    Nilsson, R. Henrik; Tedersoo, Leho; Ryberg, Martin; Kristiansson, Erik; Hartmann, Martin; Unterseher, Martin; Porter, Teresita M.; Bengtsson-Palme, Johan; Walker, Donald M.; de Sousa, Filipe; Gamper, Hannes Andres; Larsson, Ellen; Larsson, Karl-Henrik; Kõljalg, Urmas; Edgar, Robert C.; Abarenkov, Kessy

    2015-01-01

    The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation. PMID:25786896

  11. Designing a Bioengine for Detection and Analysis of Base String on an Affected Sequence in High-Concentration Regions

    PubMed Central

    Mandal, Bijoy Kumar; Kim, Tai-hoon

    2013-01-01

    We design an Algorithm for bioengine. As a program are enable optimal alignments searching between two sequences, the host sequence (normal plant) as well as query sequence (virus). Searching for homologues has become a routine operation of biological sequences in 4 × 4 combination with different subsequence (word size). This program takes the advantage of the high degree of homology between such sequences to construct an alignment of the matching regions. There is a main aim which is to detect the overlapping reading frames. This program also enables to find out the highly infected colones selection highest matching region with minimum gap or mismatch zones and unique virus colones matches. This is a small, portable, interactive, front-end program intended to be used to find out the regions of matching between host sequence and query subsequences. All the operations are carried out in fraction of seconds, depending on the required task and on the sequence length. PMID:24000321

  12. Identifying Human Genome-Wide CNV, LOH and UPD by Targeted Sequencing of Selected Regions.

    PubMed

    Wang, Yu; Li, Wei; Xia, Yingying; Wang, Chongzhi; Tang, Y Tom; Guo, Wenying; Li, Jinliang; Zhao, Xia; Sun, Yepeng; Hu, Juan; Zhen, Hefu; Zhang, Xiandong; Chen, Chao; Shi, Yujian; Li, Lin; Cao, Hongzhi; Du, Hongli; Li, Jian

    2014-01-01

    Copy-number variations (CNV), loss of heterozygosity (LOH), and uniparental disomy (UPD) are large genomic aberrations leading to many common inherited diseases, cancers, and other complex diseases. An integrated tool to identify these aberrations is essential in understanding diseases and in designing clinical interventions. Previous discovery methods based on whole-genome sequencing (WGS) require very high depth of coverage on the whole genome scale, and are cost-wise inefficient. Another approach, whole exome genome sequencing (WEGS), is limited to discovering variations within exons. Thus, we are lacking efficient methods to detect genomic aberrations on the whole genome scale using next-generation sequencing technology. Here we present a method to identify genome-wide CNV, LOH and UPD for the human genome via selectively sequencing a small portion of genome termed Selected Target Regions (SeTRs). In our experiments, the SeTRs are covered by 99.73%~99.95% with sufficient depth. Our developed bioinformatics pipeline calls genome-wide CNVs with high confidence, revealing 8 credible events of LOH and 3 UPD events larger than 5M from 15 individual samples. We demonstrate that genome-wide CNV, LOH and UPD can be detected using a cost-effective SeTRs sequencing approach, and that LOH and UPD can be identified using just a sample grouping technique, without using a matched sample or familial information. PMID:25919136

  13. Identifying Human Genome-Wide CNV, LOH and UPD by Targeted Sequencing of Selected Regions

    PubMed Central

    Guo, Wenying; Li, Jinliang; Zhao, Xia; Sun, Yepeng; Hu, Juan; Zhen, Hefu; Zhang, Xiandong; Chen, Chao; Shi, Yujian; Li, Lin; Cao, Hongzhi; Du, Hongli; Li, Jian

    2015-01-01

    Copy-number variations (CNV), loss of heterozygosity (LOH), and uniparental disomy (UPD) are large genomic aberrations leading to many common inherited diseases, cancers, and other complex diseases. An integrated tool to identify these aberrations is essential in understanding diseases and in designing clinical interventions. Previous discovery methods based on whole-genome sequencing (WGS) require very high depth of coverage on the whole genome scale, and are cost-wise inefficient. Another approach, whole exome genome sequencing (WEGS), is limited to discovering variations within exons. Thus, we are lacking efficient methods to detect genomic aberrations on the whole genome scale using next-generation sequencing technology. Here we present a method to identify genome-wide CNV, LOH and UPD for the human genome via selectively sequencing a small portion of genome termed Selected Target Regions (SeTRs). In our experiments, the SeTRs are covered by 99.73%~99.95% with sufficient depth. Our developed bioinformatics pipeline calls genome-wide CNVs with high confidence, revealing 8 credible events of LOH and 3 UPD events larger than 5M from 15 individual samples. We demonstrate that genome-wide CNV, LOH and UPD can be detected using a cost-effective SeTRs sequencing approach, and that LOH and UPD can be identified using just a sample grouping technique, without using a matched sample or familial information. PMID:25919136

  14. Sequence determination of a new parrot bornavirus-5 strain in Japan: implications of clade-specific sequence diversity in the regions interacting with host factors.

    PubMed

    Komorizono, Ryo; Makino, Akiko; Horie, Masayuki; Honda, Tomoyuki; Tomonaga, Keizo

    2016-06-01

    In this study, the genome sequence of a new parrot bornavirus-5 (PaBV-5) detected in Eclectus roratus was determined. Phylogenetic analysis showed that the genus Bornavirus is divided into three major clades and that PaBV-5 belongs to clade 2, which contains avian viruses that exhibit infectivity to mammalian cells. Sequence comparisons of the regions known to interact with host factors indicated that the clade 2 avian viruses possess sequences intermediate between the clade 1 mammalian viruses and the clade 3 avian viruses, suggesting that the identified regions might contribute to the differences in virological properties between the three clades. PMID:27166599

  15. Phylogeographic patterns and evolution of the mitochondrial DNA control region in two neotropical cats (Mammalia, felidae).

    PubMed

    Eizirik, E; Bonatto, S L; Johnson, W E; Crawshaw, P G; Vié, J C; Brousset, D M; O'Brien, S J; Salzano, F M

    1998-11-01

    The ocelot (Leopardus pardalis) and margay (L. wiedii) are sister-species of Neotropical cats which evolved from a lineage that migrated into South America during the formation of the Panamanian land bridge 3-5 million years ago. Patterns of population genetic divergence of each species were studied by phylogenetic analyses of mitochondrial DNA (mtDNA) control region sequences in individuals sampled across the distribution of these taxa. Abundant genetic diversity and remarkably concordant phylogeographic partitions for both species were observed, identifying parallel geographic regions which likely reflect historical faunal barriers. Inferred aspects of phylogeography, population genetic structure, and demographic history were used to formulate conservation recommendations for these species. In addition, observed patterns of sequence variation provided insight into the molecular evolution of the mtDNA control region in closely related felids. PMID:9797412

  16. Genetic variability among Schistosoma japonicum isolates from different endemic regions in China revealed by sequences of three mitochondrial DNA genes.

    PubMed

    Zhao, G H; Mo, X H; Zou, F C; Li, J; Weng, Y B; Lin, R Q; Xia, C M; Zhu, X Q

    2009-05-26

    The present study examined sequence variation in three mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 3 (cox3), NADH dehydrogenase subunits 4 and 5 (nad4 and nad5), among Schistosoma japonicum isolates from different endemic regions in China, and their phylogenetic relationships were re-constructed. A portion of the cox3 gene (pcox3), a portion of the nad4 and nad5 genes (pnad4 and pnad5) were amplified separately from individual trematodes by polymerase chain reaction (PCR) and the amplicons were subjected to direct sequencing. In the mountainous areas, sequence variations between parasites from Yunnan and those from Sichuan were 0.3% for pcox3, 0.0-0.1% for pnad4, and 0.0-0.2% for pnad5. In the lake/marshland areas, sequence variations between male and female parasites among different geographical locations were 0.0-0.3% for pcox3, 0.0-0.7% for pnad4, and 0.0-1.6% for pnad5. Sequence variations between S. japonicum from mountainous areas and those from lake/marshland areas were 0.0-0.5% for pcox3, 0.0-0.7% for pnad4, and 0.0-1.6% for pnad5. Phylogenetic analyses based on the combined sequences of pcox3, pnad4 and pnad5 revealed that S. japonicum isolates from mountainous areas (Yunnan and Sichuan provinces) clustered together. For isolates from the lake/marshland areas, isolates from Anhui and Jiangsu provinces clustered together and was sister to samples from Jiangxi province, while isolates from Hubei and Zhejiang province clustered together. However, isolates from different geographical locations in Hunan province were in different clades. These findings demonstrated the usefulness and attributes of the three mtDNA sequences for population genetic studies of S. japonicum, and have implications for studying population biology, molecular epidemiology, and genetic structure of S. japonicum, as well as for the effective control of schistosomiasis. PMID:19303214

  17. Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources

    PubMed Central

    Mizianty, Marcin J.; Stach, Wojciech; Chen, Ke; Kedarisetti, Kanaka Durga; Disfani, Fatemeh Miri; Kurgan, Lukasz

    2010-01-01

    Motivation: Intrinsically disordered proteins play a crucial role in numerous regulatory processes. Their abundance and ubiquity combined with a relatively low quantity of their annotations motivate research toward the development of computational models that predict disordered regions from protein sequences. Although the prediction quality of these methods continues to rise, novel and improved predictors are urgently needed. Results: We propose a novel method, named MFDp (Multilayered Fusion-based Disorder predictor), that aims to improve over the current disorder predictors. MFDp is as an ensemble of 3 Support Vector Machines specialized for the prediction of short, long and generic disordered regions. It combines three complementary disorder predictors, sequence, sequence profiles, predicted secondary structure, solvent accessibility, backbone dihedral torsion angles, residue flexibility and B-factors. Our method utilizes a custom-designed set of features that are based on raw predictions and aggregated raw values and recognizes various types of disorder. The MFDp is compared at the residue level on two datasets against eight recent disorder predictors and top-performing methods from the most recent CASP8 experiment. In spite of using training chains with ≤25% similarity to the test sequences, our method consistently and significantly outperforms the other methods based on the MCC index. The MFDp outperforms modern disorder predictors for the binary disorder assignment and provides competitive real-valued predictions. The MFDp's outputs are also shown to outperform the other methods in the identification of proteins with long disordered regions. Availability: http://biomine.ece.ualberta.ca/MFDp.html Supplementary information: Supplementary data are available at Bioinformatics online. Contact: lkurgan@ece.ualberta.ca PMID:20823312

  18. Discrimination of two natural biocontrol agents in the Mediterranean region based on mitochondrial DNA sequencing data.

    PubMed

    Evangelou, V I; Bouga, M; Emmanouel, N G; Perdikis, D Ch; Papadoulis, G Th

    2013-12-01

    Macrolophus pygmaeus and M. melanotoma (Hemiptera: Miridae) are biological control agents used in greenhouse crops, the former preferring plants of the Solanaceae family and the latter the aster Dittrichia viscosa. The discrimination of these species is of high significance for effective biological pest control, but identification based on morphological characters of the host plant is not always reliable. In this study, sequencing analysis of mitochondrial gene segments 12S rDNA and COI has been combined with crossing experiments and morphological observations to develop new markers for Macrolophus spp. discrimination and to provide new data on their genetic variability. This is the first comprehensive research in Greece on M. pygmaeus and M. melanotoma genetic variability based on sequencing data from 12S rDNA and COI gene segments. The relationship of this variability to host plant preference must be investigated in an agricultural ecosystem. PMID:23839086

  19. Divergence of human [alpha]-chain constant region gene sequences: A novel recombinant [alpha]2 gene

    SciTech Connect

    Chintalacharuvu, K. R.; Morrison, S.L. ); Raines, M. )

    1994-06-01

    IgA is the major Ig synthesized in humans and provides the first line of defense at the mucosal surfaces. The constant region of IgA heavy chain is encoded by the [alpha] gene on chromosome 14. Previous studies have indicated the presence of two [alpha] genes, [alpha]1 and [alpha]2 existing in two allotypic forms, [alpha]2 m(1) and [alpha]2 m(2). Here the authors report the cloning and complete nucleotide sequence determination of a novel human [alpha] gene. Nucleotide sequence comparison with the published [alpha] sequences suggests that the gene arose as a consequence of recombination or gene conversion between the two [alpha]2 alleles. The authors have expressed the gene as a chimeric protein in myeloma cells indicating that it encodes a functional protein. The novel IgA resembles IgA2 m(2) in that disulfide bonds link H and L chains. This novel recombinant gene provides insights into the mechanisms of generation of different constant regions and suggests that within human populations, multiple alleles of [alpha] may be present providing IgAs of different structures.

  20. Partial sequence of Mongolian gerbil (Meriones unguiculatus) immunoglobulin gamma heavy chain constant region.

    PubMed

    Ukaji, Takao; Sumiyama, Daisuke; Kai, Osamu

    2011-10-01

    We determined the sequence of the immunoglobulin gamma heavy-chain constant (IGHC) region of the Mongolian gerbil (Meriones unguiculatus). To isolate a part of the IGHC complementary DNA, we designed primers on the basis of highly conserved sequences in mouse, rat and hamster. The deduced IGHC is structurally similar to counterparts in other mammalian species and shows 84.6% identity to the IGHC of hamster IgG, 76.6% to rat IgG1, 83.3% to rat IgG2a, 78.1% to mouse IgG1, 81.8% to mouse IgG2a, 79.1% to mouse IgG2b and 79.2% to mouse IgG3 at the nucleotide level. The results suggest that gerbil IgG is closely related to hamster IgG and rat IgG2a. PMID:21951909

  1. Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing

    PubMed Central

    Wang, Jingwen; Vesterlund, Liselotte; Kere, Juha; Jiao, Hong

    2016-01-01

    Zebrafish (Danio rerio) has emerged as a model organism to investigate vertebrate development and human genetic diseases. However, the zebrafish genome annotation is still ongoing and incomplete, and there are still new gene transcripts to be found. With the introduction of massive parallel sequencing, whole transcriptome studies became possible. In the present study, we aimed to discover novel transcribed regions (NTRs) using developmental transcriptome data from RNA sequencing. In order to achieve this, we developed an in-house bioinformatics pipeline for NTR discovery. Using the pipeline, we detected 152 putative NTRs that at the time of discovery were not annotated in Ensembl and NCBI gene database. Four randomly selected NTRs were successfully validated using RT-PCR, and expression profiles of 10 randomly selected NTRs were evaluated using qRT-PCR. The identification of these 152 NTRs provide new information for zebrafish genome annotation as well as new candidates for studies of zebrafish gene function. PMID:27462902

  2. Transcribed sequences of the Escherichia coli btuB gene control its expression and regulation by vitamin B12.

    PubMed Central

    Lundrigan, M D; Köster, W; Kadner, R J

    1991-01-01

    The Escherichia coli btuB gene product is an outer membrane protein required for the active transport of vitamin B12 and other cobalamins. Synthesis of BtuB is repressed when cells are grown in the presence of cobalamins. Mapping of the 5' end of the btuB transcript revealed that a 240-nucleotide transcribed leader precedes the coding sequence. Point mutations causing increased expression under repressing conditions were isolated by use of a btuB-lacZ gene fusion. Mutations at many sites within the leader region affected btuB-lacZ regulation, whereas some base changes upstream of the start of transcription affected the absolute level of expression but not its repressibility. Analysis of btuB-phoA gene fusions and btuB-lacZ operon and gene fusions of various lengths showed that sequences within the btuB coding region (between nucleotides +250 and +350) had to be present for proper expression and transcriptional regulation. Sequences within the leader region (up to +250) conferred regulation of translational fusions. These results indicate that btuB expression is controlled at both the transcriptional and translational levels and that different but possibly overlapping sequences in the transcribed region, including the coding region for the transport protein itself, mediate these two modes of regulation. Images PMID:1847525

  3. Similarity graphing and enzyme-reaction database: methods to detect sequence regions of importance for recognition of chemical structures.

    PubMed

    Sumi, K; Nishioka, T; Oda, J

    1991-04-01

    We developed a new method which searches sequence segments responsible for the recognition of a given chemical structure. These segments are detected as those locally conserved among a sequence to be analyzed (target sequence) and a set of sequences (reference sequences). Reference sequences are the sequences of functionally related proteins, ligands of which contain a common chemical substructure in their molecular structures. 'Similarity graphing' cuts target sequences into segments, aligns them with reference sequence pairwise, calculates the degree of similarity for each alignment, and shows graphically cumulative similarity values on target sequence. Any locally conserved regions, short or long in length and weak or strong in similarity, are detected at their optimal conditions by adjusting three parameters. The 'enzyme-reaction database' contains chemical structures and their related enzymes. When a chemical substructure is input into the database, sequences of the enzymes related to the input substructure are systematically searched from the NBRF sequence database and output as reference sequences. Examples of analysis using similarity graphing in combination with the enzyme-reaction database showed a great potentiality in the systematic analysis of the relationships between sequences and molecular recognitions for protein engineering. PMID:1881867

  4. lac repressor blocks in vivo transcription of lac control region DNA.

    PubMed Central

    Sellitti, M A; Pavco, P A; Steege, D A

    1987-01-01

    Transcription of the Escherichia coli lac repressor gene (lacI) in vivo produces monocistronic mRNAs with discrete 3' ends in the lac control region, although the DNA sequence of this region does not specify a strong termination signal of the traditional form. Direct analysis of lac transcripts was used to show that the DNA sequence alone does not provide the signal to end the repressor mRNA and to establish that of the proteins with specific binding sites on control region DNA only the lac repressor has a striking effect on the continuity of lacI gene transcription. RNAs with 3' ends in the control region sequence are major mRNA species produced from a repressor-bound template, reflecting as much as a 50-fold increase over their levels in the repressor's absence. Repressor binding to the operator thus has a dual function. In addition to blocking initiation of transcription from the lacZ promoter, repressor serves as a termination factor by setting the length of its own transcript and separating lacI and lacZYA into two distinct transcription units. Images PMID:3554233

  5. Comparative Sequence Analysis of the Sorghum Rph Region and the Maize Rp1 Resistance Gene Complex

    PubMed Central

    Ramakrishna, Wusirika; Emberton, John; SanMiguel, Phillip; Ogden, Matthew; Llaca, Victor; Messing, Joachim; Bennetzen, Jeffrey L.

    2002-01-01

    A 268-kb chromosomal segment containing sorghum (Sorghum bicolor) genes that are orthologous to the maize (Zea mays) Rp1 disease resistance (R) gene complex was sequenced. A region of approximately 27 kb in sorghum was found to contain five Rp1 homologs, but most have structures indicating that they are not functional. In contrast, maize inbred B73 has 15 Rp1 homologs in two nearby clusters of 250 and 300 kb. As at maize Rp1, the cluster of R gene homologs is interrupted by the presence of several genes that appear to have no resistance role, but these genes were different from the ones found within the maize Rp1 complex. More than 200 kb of DNA downstream from the sorghum Rp1-orthologous R gene cluster was sequenced and found to contain many duplicated and/or truncated genes. None of the duplications currently exist as simple tandem events, suggesting that numerous rearrangements were required to generate the current genomic structure. Four truncated genes were observed, including one gene that appears to have both 5′ and 3′ deletions. The maize Rp1 region is also unusually enriched in truncated genes. Hence, the orthologous maize and sorghum regions share numerous structural features, but all involve events that occurred independently in each species. The data suggest that complex R gene clusters are unusually prone to frequent internal and adjacent chromosomal rearrangements of several types. PMID:12481055

  6. The Complete Chloroplast Genome Sequences of Three Veroniceae Species (Plantaginaceae): Comparative Analysis and Highly Divergent Regions

    PubMed Central

    Choi, Kyoung Su; Chung, Myong Gi; Park, SeonJoo

    2016-01-01

    Previous studies of Veronica and related genera were weakly supported by molecular and paraphyletic taxa. Here, we report the complete chloroplast genome sequence of Veronica nakaiana and the related species Veronica persica and Veronicastrum sibiricum. The chloroplast genome length of V. nakaiana, V. persica, and V. sibiricum ranged from 150,198 bp to 152,930 bp. A total of 112 genes comprising 79 protein coding genes, 29 tRNA genes, and 4 rRNA genes were observed in three chloroplast genomes. The total number of SSRs was 48, 51, and 53 in V. nakaiana, V. persica, and V. sibiricum, respectively. Two SSRs (10 bp of AT and 12 bp of AATA) were observed in the same regions (rpoC2 and ndhD) in three chloroplast genomes. A comparison of coding genes and non-coding regions between V. nakaiana and V. persica revealed divergent sites, with the greatest variation occurring petD-rpoA region. The complete chloroplast genome sequence information regarding the three Veroniceae will be helpful for elucidating Veroniceae phylogenetic relationships. PMID:27047524

  7. The organisation of repetitive sequences in the pericentromeric region of human chromosome 10.

    PubMed Central

    Jackson, M S; Slijepcevic, P; Ponder, B A

    1993-01-01

    Three satellite DNA families are present in the pericentromeric region of chromosome 10; the alpha satellite and two 5 bp satellite families defined here as satellites 2 and 3. Pulsed field gel electrophoresis (PFGE) demonstrates that these sequences are organised into five discrete arrays which are linked within a region of approximately 5.3 Megabases (Mb) of DNA. The alpha satellite is largely confined to a 2.2 Mb array which is flanked on its p arm side by two 100-150 kb satellite 3 arrays and on its q arm side by a 900 kb satellite 2 array and a further 320 kb satellite 3 array. This linear order is corroborated by fluorescent in situ hybridisation analyses. In total, these arrays account for 3.6 Mb of DNA in the pericentromeric region of chromosome 10. These data provide both physical information on sequences which may be involved in centromere function and a map across the centromere which has the potential to link yeast artificial chromosome (YAC) contigs currently being developed on both arms of this chromosome. Images PMID:8290346

  8. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: The Adh region

    SciTech Connect

    Ashburner, M.; Misra, S.; Roote, J.; Lewis, S.E.; Blazej, R.; Davis, T.; Doyle, C.; Galle, R.; George, R.; Harris, N.; Hartzell, G.; Harvey, D.; Hong, L.; Houston, K.; Hoskins, R.; Johnson, G.; Martin, C.; Moshrefi, A.; Palazzolo, M.; Reese, M.G.; Spradling, A.; Tsang, G.; Wan, K.; Whitelaw, K.; Kimmel, B.; Celniker, S.; Rubin, G.M.

    1999-03-24

    A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized

  9. A General Approach to Sequence-Controlled Polymers Using Macrocyclic Ring Opening Metathesis Polymerization

    PubMed Central

    2015-01-01

    A new and general strategy for the synthesis of sequence-defined polymers is described that employs relay metathesis to promote the ring opening polymerization of unstrained macrocyclic structures. Central to this approach is the development of a small molecule “polymerization trigger” which when coupled with a diverse range of sequence-defined units allows for the controlled, directional synthesis of sequence controlled polymers. PMID:26053158

  10. Quality Control Test for Sequence-Phenotype Assignments

    PubMed Central

    Ortiz, Maria Teresa Lara; Rosario, Pablo Benjamín Leon; Luna-Nevarez, Pablo; Gamez, Alba Savin; Martínez-del Campo, Ana; Del Rio, Gabriel

    2015-01-01

    Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10–20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas. PMID:25700273

  11. Control of Integrated Task Sequences Shapes Components of Reaching.

    PubMed

    Viswanathan, Priya; Whitall, Jill; Kagerer, Florian A

    2016-01-01

    Reaching toward an object usually consists of a sequence of elemental actions. Using a reaching task sequence, the authors investigated how task elements of that sequence affected feedforward and feedback components of the reaching phase of the movement. Nine right-handed adults performed, with their dominant and nondominant hands, 4 tasks of different complexities: a simple reaching task; a reach-to-grasp task; a reach-to-grasp and lift object task; and a reach-to-grasp, lift, and place object task. Results showed that in the reach-to-grasp and lift object task more time was allocated to the feedforward component of the reach phase, while latency between the task elements decreased. We also found between-hand differences, supporting previous findings of increased efficiency of processing planning-related information in the preferred hand. The presence of task-related modifications supports the concept of contextual effects when planning a movement. PMID:27254601

  12. Quality control test for sequence-phenotype assignments.

    PubMed

    Ortiz, Maria Teresa Lara; Rosario, Pablo Benjamín Leon; Luna-Nevarez, Pablo; Gamez, Alba Savin; Martínez-del Campo, Ana; Del Rio, Gabriel

    2015-01-01

    Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10-20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas. PMID:25700273

  13. Contamination-controlled high-throughput whole genome sequencing for influenza A viruses using the MiSeq sequencer.

    PubMed

    Lee, Hong Kai; Lee, Chun Kiat; Tang, Julian Wei-Tze; Loh, Tze Ping; Koay, Evelyn Siew-Chuan

    2016-01-01

    Accurate full-length genomic sequences are important for viral phylogenetic studies. We developed a targeted high-throughput whole genome sequencing (HT-WGS) method for influenza A viruses, which utilized an enzymatic cleavage-based approach, the Nextera XT DNA library preparation kit, for library preparation. The entire library preparation workflow was adapted for the Sentosa SX101, a liquid handling platform, to automate this labor-intensive step. As the enzymatic cleavage-based approach generates low coverage reads at both ends of the cleaved products, we corrected this loss of sequencing coverage at the termini by introducing modified primers during the targeted amplification step to generate full-length influenza A sequences with even coverage across the whole genome. Another challenge of targeted HTS is the risk of specimen-to-specimen cross-contamination during the library preparation step that results in the calling of false-positive minority variants. We included an in-run, negative system control to capture contamination reads that may be generated during the liquid handling procedures. The upper limits of 99.99% prediction intervals of the contamination rate were adopted as cut-off values of contamination reads. Here, 148 influenza A/H3N2 samples were sequenced using the HTS protocol and were compared against a Sanger-based sequencing method. Our data showed that the rate of specimen-to-specimen cross-contamination was highly significant in HTS. PMID:27624998

  14. A compendium of human mitochondrial DNA control region: development of an international standard forensic database.

    PubMed

    Miller, K W; Budowle, B

    2001-06-01

    A compendium of human mitochondrial DNA (mtDNA) control region types has been constructed. This updated compilation indexes over 10,000 population-specific mtDNA nucleotide sequences in a standardized format. The sequences represent mtDNA types from the Scientific Working Group on DNA Analysis Methods (SWGDAM) mtDNA database and from the public literature. The SWGDAM data are considered to be of higher quality than the public data, particularly for counting the number of times a particular haplotype has been observed. PMID:11387646

  15. [Variability of the mtDNA Control Region in Goose Anser albifrons Scopoli, 1769].

    PubMed

    Volkovsky, D V; Fisenko, P V; Gerasimov, Yu N; Zhuravlev, Yu N

    2016-03-01

    Sequence variation of the mtDNA (D loop) control region was examined in greater white-fronted goose Anser albifrons Scopoli, 1769 individuals (n = 71). The obtained sequences were compared with those from the NCBI GenBank database. The high level of similarity of the sample from Primorye (A. albifrons) with the sample from Japan (A. a. frontalis) at the level of molecular variation, genetic distance, phylogenetic reconstruction, and haplotype network was demonstrated. A hypothesis on the ways of spring goose migration in the Far East was made. It was confirmed that white-fronted geese wintering in Japan fly to their breeding grounds through Kamchatka. PMID:27281856

  16. Kinematic Distances of Pre-main Sequence Stars in the Lupus Star-Forming Region

    NASA Astrophysics Data System (ADS)

    Galli, P. A. B.; Teixeira, R.; Ducourant, C.; Bertout, C.

    2014-06-01

    The problem of the determination of distances has always played a central role in astronomy. However, little recent progress has been made in the distance determination of faint young stellar objects such as pre-main sequence (PMS) stars. Many of the PMS stars were neither observed by the Hipparcos satellite due to their magnitude nor have any trigonometric parallax measured from the ground due to their distance. Here we investigate the kinematic properties of the Lupus moving group with the primary objective of deriving individual parallaxes for each group member of this star-forming region.

  17. A genome walking strategy for the identification of nucleotide sequences adjacent to known regions.

    PubMed

    Wang, Hailong; Yao, Ting; Cai, Mei; Xiao, Xiuqing; Ding, Xuezhi; Xia, Liqiu

    2013-02-01

    To identify the transposon insertion sites in a soil actinomycete, Saccharopolyspora spinosa, a genome walking approach, termed SPTA-PCR, was developed. In SPTA-PCR, a simple procedure consisting of TA cloning and a high stringency PCR, following the single primer-mediated, randomly-primed PCR, can eliminate non-target DNA fragments and obtain target fragments specifically. Using SPTA-PCR, the DNA sequence adjacent to the highly conserved region of lectin coding gene in onion plant, Allium chinense, was also cloned. PMID:23108875

  18. Defining the functional domains in the control region of the adenovirus type 2 specific VARNA1 gene.

    PubMed

    Wu, G J; Railey, J F; Cannon, R E

    1987-04-01

    The outer boundaries of the internal transcriptional control region in the VARNA1 gene have been located from positions +10 to +69. To further define the detailed organization of the functional domains in this region and the function(s) of the 5' flanking sequence, and to obtain a more detailed insight into other transcriptionally important sequences, we have constructed 77 mutants with deletion endpoints at almost every one to five base-pairs in the entire region from -30 to +160 for transcriptional studies. Using our highly active crude extract under our assay conditions, and quantitatively measuring the transcriptional efficiency and competing strength of each mutant, we have revealed new features of important transcriptional control sequences and defined the transcriptional functions of several functional domains in this gene. The essential domain is from +59/+63 to +66/+68, which corresponds to the B block sequence. This is smaller than that defined previously. The second most important domain is the region from +12/14 to +40, which includes the A block sequence that dictates the wild-type major start site and amplifies the events started by the B block region, mediated through factors and RNA polymerase III. Furthermore, the domain from -5 to +11 affects the use of certain start site(s). Moreover, the 5' flanking region from -30 to +1 contributes 80 to 90% of the overall transcriptional efficiency of the gene. Finally, our transcriptional studies of mutants deleted of the A block sequence and all of the upstream sequence indicated that an intimate interaction between the two blocks is essential for initiation of transcription. Furthermore, the B block sequence is more important than the A block sequence in the transcription reaction. The mechanism and control of transcriptional initiation in the VARNA1 gene is similar to that in some tRNA genes, but differs from that in others. PMID:3625769

  19. 40 CFR 81.112 - Charleston Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Regions § 81.112 Charleston Intrastate Air Quality Control Region. The Charleston Intrastate Air Quality Control Region (South Carolina) consists of the territorial area encompassed by the... Quality Control Region: Region 1. 81.107Greenwood Intrastate Air Quality Control Region: Region 2....

  20. 40 CFR 81.112 - Charleston Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Regions § 81.112 Charleston Intrastate Air Quality Control Region. The Charleston Intrastate Air Quality Control Region (South Carolina) consists of the territorial area encompassed by the... Quality Control Region: Region 1. 81.107Greenwood Intrastate Air Quality Control Region: Region 2....

  1. Sequence stratigraphic control on prolific HC reservoir development, Southwest Iran

    USGS Publications Warehouse

    Lasemi, Y.; Kondroud, K.N.

    2008-01-01

    An important carbonate formation in the Persian Gulf and the onshore oil fields of Southwest Iran is the Lowermost Cretaceous Fahliyan formation. The formation in Darkhowain field consists of unconformity-bounded depositional sequences containing prolific hydrocarbon reservoirs of contrasting origin. Located in the high stand systems tract (HST) of the lower sequence encompassing over 200m of oil column are the most prolific reservoir. Another reservoir is over 80m thick consisting of shallowing-upward cycles that are best developed within the transgressive systems tract of the upper sequence. Vertical facies distribution and their paleobathymetry and geophysical log signatures of the Fahliyan formation in the Darkhowain platform reveal the presence of two unconformity-bounded depositional sequences in Vail et al., Van Wagoner et al., and Sarg. The Fahliyan formation mainly consists of platform carbonates composed of restricted bioclastic lime mudstone to packstone of the platform interior, Lithocodium boundstone or ooid-intraclast-bioclast grainstone of the high energy platform margin and the bioclast packstone to lime mudstone related to the off-platform setting.

  2. HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data.

    PubMed

    Ward, Ben J; van Oosterhout, Cock

    2016-03-01

    HYBRIDCHECK is a software package to visualize the recombination signal in large DNA sequence data set, and it can be used to analyse recombination, genetic introgression, hybridization and horizontal gene transfer. It can scan large (multiple kb) contigs and whole-genome sequences of three or more individuals. HYBRIDCHECK is written in the r software for OS X, Linux and Windows operating systems, and it has a simple graphical user interface. In addition, the r code can be readily incorporated in scripts and analysis pipelines. HYBRIDCHECK implements several ABBA-BABA tests and visualizes the effects of hybridization and the resulting mosaic-like genome structure in high-density graphics. The package also reports the following: (i) the breakpoint positions, (ii) the number of mutations in each introgressed block, (iii) the probability that the identified region is not caused by recombination and (iv) the estimated age of each recombination event. The divergence times between the donor and recombinant sequence are calculated using a JC, K80, F81, HKY or GTR correction, and the dating algorithm is exceedingly fast. By estimating the coalescence time of introgressed blocks, it is possible to distinguish between hybridization and incomplete lineage sorting. HYBRIDCHECK is libré software and it and its manual are free to download from http://ward9250.github.io/HybridCheck/. PMID:26394708

  3. Earthquake sequence in East Vrancea crustal region (Romania): source characteristics and seismotectonics

    NASA Astrophysics Data System (ADS)

    Popescu, Emilia; Borleanu, Felix; Otilia Placinta, Anica; Popa, Mihaela; Radulian, Mircea; Moldovan, Iren Adelina

    2016-04-01

    The goal of the paper is to investigate the crustal earthquake sequence generated in the East Vrancea crustal zone at the end of 2014 (22 November 2014). The main shock, occurred on 22 November 2014, 19:14 (45.860N, 27.160E, h = 39 km, ML = 5.7), is the greatest instrumentally recorded earthquake produced in this region. The aftershocks are unusually small for the sequences characterizing the Vrancea foredeep area (around 200 events with magnitude below 2). The largest aftershocks were recorded on 7 December 2015 (ML = 4.4) and 19 January 2015 (ML = 3.8). We apply cross-correlation analysis together with empirical Green's function (EGF) deconvolution and spectral ratios techniques to optimise the source parameters determination. At the same time we applied inversion techniques to retrieve the moment tensor solution for the largest shocks. For EGF and spectral ratios applications, we associated to the main event many co-located aftershocks (2.0 ≤ ML ≤ 4.4), selected according to the requirements for empirical Green's functions. The source parameters are estimated as mean values for all the available earthquake pairs. Source scaling properties and focal mechanism are investigated and discussed in terms of the regional seismotectonics and comparatively with the source scaling relationships for the Vrancea intermediate-depth earthquakes.

  4. The 2012 Ferrara seismic sequence: Regional crustal structure, earthquake sources, and seismic hazard

    NASA Astrophysics Data System (ADS)

    Malagnini, Luca; Herrmann, Robert B.; Munafò, Irene; Buttinelli, Mauro; Anselmi, Mario; Akinci, Aybige; Boschi, E.

    2012-10-01

    Inadequate seismic design codes can be dangerous, particularly when they underestimate the true hazard. In this study we use data from a sequence of moderate-sized earthquakes in northeast Italy to validate and test a regional wave propagation model which, in turn, is used to understand some weaknesses of the current design spectra. Our velocity model, while regionalized and somewhat ad hoc, is consistent with geophysical observations and the local geology. In the 0.02-0.1 Hz band, this model is validated by using it to calculate moment tensor solutions of 20 earthquakes (5.6 ≥ MW ≥ 3.2) in the 2012 Ferrara, Italy, seismic sequence. The seismic spectra observed for the relatively small main shock significantly exceeded the design spectra to be used in the area for critical structures. Observations and synthetics reveal that the ground motions are dominated by long-duration surface waves, which, apparently, the design codes do not adequately anticipate. In light of our results, the present seismic hazard assessment in the entire Pianura Padana, including the city of Milan, needs to be re-evaluated.

  5. Molecular phylogenetic analysis of Indonesia Solanaceae based on DNA sequences of internal transcribed spacer region

    NASA Astrophysics Data System (ADS)

    Hidayat, Topik; Priyandoko, Didik; Islami, Dina Karina; Wardiny, Putri Yunitha

    2016-02-01

    Solanaceae is one of largest family in Angiosperm group with highly diverse in morphological character. In Indonesia, this group of plant is very popular due to its usefulness as food, ornamental and medicinal plants. However, investigation on phylogenetic relationship among the member of this family in Indonesia remains less attention. The purpose of this study was to evaluate the phylogenetics relationship of the family especially distributed in Indonesia. DNA sequences of Internal Transcribed Spacer (ITS) region of 19 species of Solanaceae and three species of outgroup, which belongs to family Convolvulaceae, Apocynaceae, and Plantaginaceae, were isolated, amplified, and sequenced. Phylogenetic tree analysis based on parsimony method was conducted with using data derived from the ITS-1, 5.8S, and ITS-2, separately, and the combination of all. Results indicated that the phylogenetic tree derived from the combined data established better pattern of relationship than separate data. Thus, three major groups were revealed. Group 1 consists of tribe Datureae, Cestreae, and Petunieae, whereas group 2 is member of tribe Physaleae. Group 3 belongs to tribe Solaneae. The use of the ITS region as a molecular markers, in general, support the global Solanaceae relationship that has been previously reported.

  6. Genetic organization, size, and complete sequence of early region 3 genes of human adenovirus type 41.

    PubMed Central

    Yeh, H Y; Pieniazek, N; Pieniazek, D; Luftig, R B

    1996-01-01

    The complete nucleotide and predicted amino acid sequences for open reading frames (ORFs) of the human adenovirus type 41 (Ad41) early region 3 (E3) gene have been determined. The sequence of the Ad41 E3 gene (map units 74 to 83.9) consists of 3,373 nucleotides and has one TATA box and two polyadenylation signals (AATAAA). Analysis of the nucleotide sequence reveals that the E3 gene can encode six ORFs, designated RL1 to RL6. These are all expressed at the mRNA level, as determined by reverse transcription-PCR analysis of AD41-infected cell RNA. When compared with known E3 sequences of most other human adenoviruses deposited in GenBank, the sequences of RL1 to RL3 were found to be unique to subgroup F adenoviruses (Ad40 and Ad41). They encode putative proteins of 173 amino acids (19.4 kDa) and 276 amino acids (31.6 kDa) in one reading frame as well as a 59- amino-acid (6.7 kDa) protein in an overlapping reading frame. RL4 encodes a 90-amino-acid protein (10.1 kDa) with 40% homology to the Ad2 E3 10.4-kDa protein, which induces degradation of the epidermal growth factor receptor and functions together with the Ad2 E3 14.5-kDa protein to protect mouse cell lines against lysis. RL5 encodes a protein of 107 amino acid residues (12.3 kDa) and is analogous to the Ad E3 14.5-kDa protein. RL6 codes for a protein of 122 amino acids (14.7 kDa) that is analogous to the Ad2 14.7-kDa protein, which functions to protect Ad-infected cells from tumor necrosis factor-induced cytolysis. This finding of three unique (RL1 to RL3) E3 gene ORFs may explain why subgroup F adenoviruses differ substantially from other human adenoviruses in their host range; i.e., they replicate predominantly in the host's gastrointestinal rather than respiratory tract. A recent phylogenetic study that compared subgroup F Ad40 DNA sequences with representatives of subgroups B (Ad3), C (Ad2), and E (Ad4) reached a similar conclusion about the uniqueness of RL1 and RL2. PMID:8642703

  7. Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines.

    PubMed Central

    Powell, W; Morgante, M; McDevitt, R; Vendramin, G G; Rafalski, J A

    1995-01-01

    Simple sequence repeats (SSRs), consisting of tandemly repeated multiple copies of mono-, di-, tri-, or tetranucleotide motifs, are ubiquitous in eukaryotic genomes and are frequently used as genetic markers, taking advantage of their length polymorphism. We have examined the polymorphism of such sequences in the chloroplast genomes of plants, by using a PCR-based assay. GenBank searches identified the presence of several (dA)n.(dT)n mononucleotide stretches in chloroplast genomes. A chloroplast (cp) SSR was identified in three pine species (Pinus contorta, Pinus sylvestris, and Pinus thunbergii) 312 bp upstream of the psbA gene. DNA amplification of this repeated region from 11 pine species identified nine length variants. The polymorphic amplified fragments were isolated and the DNA sequence was determined, confirming that the length polymorphism was caused by variation in the length of the repeated region. In the pines, the chloroplast genome is transmitted through pollen and this PCR assay may be used to monitor gene flow in this genus. Analysis of 305 individuals from seven populations of Pinus leucodermis Ant. revealed the presence of four variants with intrapopulational diversities ranging from 0.000 to 0.629 and an average of 0.320. Restriction fragment length polymorphism analysis of cpDNA on the same populations previously failed to detect any variation. Population subdivision based on cpSSR was higher (Gst = 0.22, where Gst is coefficient of gene differentiation) than that revealed in a previous isozyme study (Gst = 0.05). We anticipate that SSR loci within the chloroplast genome should provide a highly informative assay for the analysis of the genetic structure of plant populations. Images Fig. 2 PMID:7644491

  8. Sequence comparisons of the variable VP2 region of eight infectious bursal disease virus isolates.

    PubMed

    Dormitorio, T V; Giambrone, J J; Duck, L W

    1997-01-01

    The VP2 gene is part of the genomic segment A of infectious bursal disease virus (IBDV). It has been identified as the major host-protective antigen of IBDV and is known to contain conformationally dependent protective epitopes. A 643-base pair segment covering the hypervariable region of this gene from three recent serologic variant IBDV isolates from the southeastern United States, two variants from the Delmarva Peninsula, and three serologic standard viruses were amplified and sequenced using the reverse transcription polymerase chain reaction and cycle sequencing techniques. This was done to determine the molecular similarity among isolates that differ antigenically and pathologically. Sequence analysis suggested that the Arkansas (Ark) and Mississippi (Miss) isolates evolved closely and separately from the Delmarva variants (GLS and DELE), in contrast to the other southeastern variant Georgia (Ga), which is more closely related (98.32%) to Delaware E (DELE). All variants, except for Miss, underwent a shift in amino acid number 222 from proline to threonine. The sequence of Univax BD virus, a commercially available intermediate vaccine, was markedly different, evolving from a separate lineage than the others. Restriction enzyme sites could differentiate most isolates. Except for Miss, variants do not have EcoRII site at the larger hydrophilic domain. All variants lost their HaeIII, StuI, and StyI cutting sites with a change in base number 856. The TaqI site is in DELE, whereas the SpeI site is absent in the standard vaccine viruses. The SWASASGS heptapeptide is conserved in all virulent viruses, including APHIS, but not in the attenuated (Univax BD and Bursa Vac 3) and published (D78 and PBG98) vaccines. PMID:9087318

  9. MiRNA Expression Profile for the Human Gastric Antrum Region Using Ultra-Deep Sequencing

    PubMed Central

    Hamoy, Igor G.; Darnet, Sylvain; Burbano, Rommel; Khayat, André; Gonçalves, André Nicolau; Alencar, Dayse O.; Cruz, Aline; Magalhães, Leandro; Araújo Jr., Wilson; Silva, Artur; Santos, Sidney; Demachki, Samia; Assumpção, Paulo; Ribeiro-dos-Santos, Ândrea

    2014-01-01

    Background MicroRNAs are small non-coding nucleotide sequences that regulate gene expression. These structures are fundamental to several biological processes, including cell proliferation, development, differentiation and apoptosis. Identifying the expression profile of microRNAs in healthy human gastric antrum mucosa may help elucidate the miRNA regulatory mechanisms of the human stomach. Methodology/Principal Findings A small RNA library of stomach antrum tissue was sequenced using high-throughput SOLiD sequencing technology. The total read count for the gastric mucosa antrum region was greater than 618,000. After filtering and aligning using with MirBase, 148 mature miRNAs were identified in the gastric antrum tissue, totaling 3,181 quality reads; 63.5% (2,021) of the reads were concentrated in the eight most highly expressed miRNAs (hsa-mir-145, hsa-mir-29a, hsa-mir-29c, hsa-mir-21, hsa-mir-451a, hsa-mir-192, hsa-mir-191 and hsa-mir-148a). RT-PCR validated the expression profiles of seven of these highly expressed miRNAs and confirmed the sequencing results obtained using the SOLiD platform. Conclusions/Significance In comparison with other tissues, the antrum’s expression profile was unique with respect to the most highly expressed miRNAs, suggesting that this expression profile is specific to stomach antrum tissue. The current study provides a starting point for a more comprehensive understanding of the role of miRNAs in the regulation of the molecular processes of the human stomach. PMID:24647245

  10. Sequence Level Analysis of Recently Duplicated Regions in the Soybean [Glycine max (L.) Merr.] Genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A single recessive gene, rxp, on linkage group (LG) D2 controls bacterial leaf pustule resistance in soybean. Markers linked to rxp were used to develop BAC contigs spanning the Rxp region. We identified two homoeologous contigs (GmA and GmA’) composed of five bacterial artificial chromosomes (BAC...

  11. Variable Genome Sequences of the Murine Pneumotropic Virus (Polyomaviridae) Regulatory Region Isolated from an Infected Mouse Tissue Viral Suspension

    PubMed Central

    Libbey, Jane E.

    2016-01-01

    The murine pneumotropic virus genome, isolated from an infected murine tissue homogenate, was sequenced to completion. The lungs, liver, spleen, and kidneys were the source of the tissue homogenate in order to mirror the heterogeneity of the virus population in vivo. The regulatory region sequence was found to be highly variable. PMID:27231357

  12. Intergenic Sequence Ribotyping using a region neighboring dkgB links genovar to Kauffman-White serotype of Salmonella enterica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Intergenic Sequence Ribotyping using a region neighboring dkgB links genovar to Kauffman-White serotype of Salmonella enterica Previous research identified that the 5S ribosomal (rrn) gene and associated flanking sequences that are closely linked to the dkgB gene of Salmonella enterica were highly ...

  13. Variable Genome Sequences of the Murine Pneumotropic Virus (Polyomaviridae) Regulatory Region Isolated from an Infected Mouse Tissue Viral Suspension.

    PubMed

    Libbey, Jane E; Fujinami, Robert S

    2016-01-01

    The murine pneumotropic virus genome, isolated from an infected murine tissue homogenate, was sequenced to completion. The lungs, liver, spleen, and kidneys were the source of the tissue homogenate in order to mirror the heterogeneity of the virus population in vivo The regulatory region sequence was found to be highly variable. PMID:27231357

  14. Spliced synthetic genes as internal controls in RNA sequencing experiments.

    PubMed

    Hardwick, Simon A; Chen, Wendy Y; Wong, Ted; Deveson, Ira W; Blackburn, James; Andersen, Stacey B; Nielsen, Lars K; Mattick, John S; Mercer, Tim R

    2016-09-01

    RNA sequencing (RNA-seq) can be used to assemble spliced isoforms, quantify expressed genes and provide a global profile of the transcriptome. However, the size and diversity of the transcriptome, the wide dynamic range in gene expression and inherent technical biases confound RNA-seq analysis. We have developed a set of spike-in RNA standards, termed 'sequins' (sequencing spike-ins), that represent full-length spliced mRNA isoforms. Sequins have an entirely artificial sequence with no homology to natural reference genomes, but they align to gene loci encoded on an artificial in silico chromosome. The combination of multiple sequins across a range of concentrations emulates alternative splicing and differential gene expression, and it provides scaling factors for normalization between samples. We demonstrate the use of sequins in RNA-seq experiments to measure sample-specific biases and determine the limits of reliable transcript assembly and quantification in accompanying human RNA samples. In addition, we have designed a complementary set of sequins that represent fusion genes arising from rearrangements of the in silico chromosome to aid in cancer diagnosis. RNA sequins provide a qualitative and quantitative reference with which to navigate the complexity of the human transcriptome. PMID:27502218

  15. Sequence comparisons in the aminoacyl-tRNA synthetases with emphasis on regions of likely homology with sequences in the Rossmann fold in the methionyl and tyrosyl enzymes.

    PubMed

    Walker, E J; Jeffrey, P D

    1988-02-01

    Amino acid sequences of aminoacyl-tRNA synthetases specific for 12 different amino acids have now been published. Differences in origin at the species and organelle level result in 20 distinct sequences being available for comparison. Some of these were compared in small groups as they were determined and, although some homologies were detected, it was generally concluded that there was surprisingly little sequence homology in this functionally related group of enzymes. We have made comparisons of all of the available sequences by using a combination of computer and manual alignment methods and knowledge of the sequences in the Rossmann fold region of methionyl-tRNA synthetase from E. coli and tyrosyl-tRNA synthetase from B. stearothermophilus, enzymes whose three-dimensional structures have been described. It emerges that all of the aminoacyl-tRNA synthetase sequences thus examined show considerable homology with each other over at least parts of this region, some over virtually all of it. We conclude that a great deal more similarity than had previously been suspected exists in these proteins. In particular, the alignments we have made strongly imply the existence of a mononucleotide binding site of the Rossmann fold configuration in all of the synthetases compared. PMID:3283733

  16. NO and temperature control of the D region

    NASA Astrophysics Data System (ADS)

    Danilov, A. D.; Taubenheim, J.

    1983-04-01

    It is postulated that the behavior of the D region parameters, first and foremost the electron concentration, is controlled not only (and probably not primarily) by the variations in solar and geophysical parameters but also by the changes in the characteristics of the strato-mesosphere, its thermal and dynamical regime. This is seen as the essence of the meteorological control of the D region. The way that this meteorological control is exercised, that is, the influence of the meteorological parameter on the D region characteristics, is investigated. The goal is to determine the indices which, together with the well known solar and geophysical indices, could be used to adequately describe the behavior of the D region. Calculations are performed showing that the experimentally observed seasonal variations in the ion composition, which lead to the systematic summer-to-winter difference in the electron concentration, can be accounted for by the seasonal changes in the mesospheric temperature.

  17. Bacterial interspersed mosaic elements (BIMEs) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence.

    PubMed

    Bachellier, S; Clément, J M; Hofnung, M; Gilson, E

    1997-03-01

    A significant fraction of Escherichia coli intergenic DNA sequences is composed of two families of repeated bacterial interspersed mosaic elements (BIME-1 and BIME-2). In this study, we determined the sequence organization of six intergenic regions in 51 E. coli and Shigella natural isolates. Each region contains a BIME in E. coli K-12. We found that multiple sequence variations are located within or near these BIMEs in the different bacteria. Events included excisions of a whole BIME-1, expansion/deletion within a BIME-2 and insertions of non-BIME sequences like the boxC repeat or a new IS element, named IS 1397. Remarkably, 14 out of IS 1397 integration sites correspond to a BIME sequence, strongly suggesting that this IS element is specifically associated with BIMEs, and thus inserts only in extragenic regions. Unlike BIMEs, IS 1397 is not detected in all E. coli isolates. Possible relationships between the presence of this IS element and the evolution of BIMEs are discussed. PMID:9055066

  18. Holocene fire activity in the Carpathian region: regional climate vs. local controls

    NASA Astrophysics Data System (ADS)

    Florescu, Gabriela; Feurdean, Angelica

    2015-04-01

    Introduction. Fire drives significant changes in ecosystem structure and function, diversity, species evolution, biomass dynamics and atmospheric composition. Palaeodata and model-based studies have pointed towards a strong connection between fire activity, climate, vegetation and people. Nevertheless, the relative importance of these factors appears to be strongly variable and a better understanding of these factors and their interaction needs a thorough investigation over multiple spatial (local to global) and temporal (years to millennia) scales. In this respect, sedimentary charcoal, associated with other proxies of climate, vegetation and human impact, represents a powerful tool of investigating changes in past fire activity, especially in regions with scarce fire dataset such as the CE Europe. Aim. To increase the spatial and temporal coverage of charcoal records and facilitate a more critical examination of the patterns, drivers and consequences of biomass burning over multiple spatial and temporal scales in CE Europe, we have investigated 6 fossil sequences in the Carpathian region (northern Romania). These are located in different geographical settings, in terms of elevation, vegetation composition, topography and land-use. Specific questions are: i) determine trends in timing and magnitude of fire activity, as well as similarities and differences between elevations; ii) disentangle the importance of regional from local controls in fire activity; iii) evaluate ecological consequences of fire on landscape composition, structure and diversity. Methods. We first determine the recent trends in fire activity (the last 150 years) from charcoal data and compare them with instrumental records of temperature, precipitation, site history and topography for a better understanding of the relationship between sedimentary charcoal and historical fire activity. We then statistically quantify centennial to millennial trends in fire activity (frequency, magnitude) based on

  19. Characterization of the mouse beta maj globin transcription termination region: a spacing sequence is required between the poly(A) signal sequence and multiple downstream termination elements.

    PubMed Central

    Tantravahi, J; Alvira, M; Falck-Pedersen, E

    1993-01-01

    For the majority of mRNA encoding eukaryotic transcription units, there is little or no knowledge of the elements responsible for transcription termination or how they may interact with RNA polymerase. In this report, we have used recombinant adenovirus reporter vectors to characterize the mouse beta maj globin sequence elements that cause transcription termination. Within the globin 3' termination region, we have identified at least three sequence elements which induce significant levels of transcription termination (> 50%). The smallest functionally active element (64% termination) is 69 bp in length. The natural arrangement of these elements results in a cumulative termination which is greater than 90%. Recognition of the termination elements by RNA polymerase II depends on the presence of a functional poly(A) signal sequence. We demonstrate that efficient transcription termination depends on appropriate spacing between the poly(A) signal sequence and the termination element. Images PMID:8417354

  20. Automatic sequencing and control of Space Station airlock operations

    NASA Technical Reports Server (NTRS)

    Himel, Victor; Abeles, Fred J.; Auman, James; Tqi, Terry O.

    1989-01-01

    Procedures that have been developed as part of the NASA JSC-sponsored pre-prototype Checkout, Servicing and Maintenance (COSM) program for pre- and post-EVA airlock operations are described. This paper addresses the accompanying pressure changes in the airlock and in the Advanced Extravehicular Mobility Unit (EMU). Additionally, the paper focuses on the components that are checked out, and includes the step-by-step sequences to be followed by the crew, the required screen displays and prompts that accompany each step, and a description of the automated processes that occur.

  1. Pre-main-sequence population in NGC 1893 region: X-ray properties

    NASA Astrophysics Data System (ADS)

    Pandey, A. K.; Samal, M. R.; Yadav, Ram Kesh; Richichi, Andrea; Lata, Sneh; Pandey, J. C.; Ojha, D. K.; Chen, W. P.

    2014-05-01

    Continuing the attempt to understand the properties of the stellar content in the young cluster NGC 1893 we have carried out a comprehensive multi-wavelength study of the region. The present study focuses on the X-ray properties of T-Tauri Stars (TTSs) in the NGC 1893 region. We found a correlation between the X-ray luminosity, LX, and the stellar mass (in the range 0.2-2.0 M) of TTSs in the NGC 1893 region, similar to those reported in some other young clusters, however the value of the power-law slope obtained in the present study (∼0.9) for NGC 1893 is smaller than those (∼1.4-3.6) reported in the case of TMC, ONC, IC 348 and Chameleon star forming regions. However, the slope in the case of Class III sources (Weak line TTSs) is found to be comparable to that reported in the case of NGC 6611 (∼1.1). It is found that the presence of circumstellar disks has no influence on the X-ray emission. The X-ray luminosity for both CTTSs and WTTSs is found to decrease systematically with age (in the range ∼0.4-5 Myr). The decrease of the X-ray luminosity of TTSs (slope ∼-0.6) in the case of NGC 1893 seems to be faster than observed in the case of other star-forming regions (slope -0.2 to -0.5). There is indication that the sources having relatively large NIR excess have relatively lower LX values. TTSs in NGC 1893 do not follow the well established X-ray activity - rotation relation as in the case of main-sequence stars.

  2. swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing

    PubMed Central

    Shao, Qianzhi; Liu, Qi; Chen, BingYu; Huang, Dongsheng

    2015-01-01

    DNA methylation is a widespread epigenetic modification that plays an essential role in gene expression through transcriptional regulation and chromatin remodeling. The emergence of whole genome bisulfite sequencing (WGBS) represents an important milestone in the detection of DNA methylation. Characterization of differential methylated regions (DMRs) is fundamental as well for further functional analysis. In this study, we present swDMR (http://sourceforge.net/projects/swdmr/) for the comprehensive analysis of DMRs from whole genome methylation profiles by a sliding window approach. It is an integrated tool designed for WGBS data, which not only implements accessible statistical methods to perform hypothesis test adapted to two or more samples without replicates, but false discovery rate was also controlled by multiple test correction. Downstream analysis tools were also provided, including cluster, annotation and visualization modules. In summary, based on WGBS data, swDMR can produce abundant information of differential methylated regions. As a convenient and flexible tool, we believe swDMR will bring us closer to unveil the potential functional regions involved in epigenetic regulation. PMID:26176536

  3. Computational and biological analysis of 680 kb of DNA sequence from the human 5q31 cytokine gene cluster region.

    PubMed

    Frazer, K A; Ueda, Y; Zhu, Y; Gifford, V R; Garofalo, M R; Mohandas, N; Martin, C H; Palazzolo, M J; Cheng, J F; Rubin, E M

    1997-05-01

    With the human genome project advancing into what will be a 7- to 10-year DNA sequencing phase, we are presented with the challenge of developing strategies to convert genomic sequence data, as they become available, into biologically meaningful information. We have analyzed 680 kb of noncontiguous DNA sequence from a 1-Mb region of human chromosome 5q31, coupling computational analysis with gene expression studies of tissues isolated from humans as well as from mice containing human YAC transgenes. This genomic interval has been noted previously for containing the cytokine gene cluster and a quantitative trait locus associated with inflammatory diseases. Our analysis identified and verified expression of 16 new genes, as well as 7 previously known genes. Of the total of 23 genes in this region, 78% had similarity matches to sequences in protein databases and 83% had exact expressed sequence tag (EST) database matches. Comparative mapping studies of eight of the new human genes discovered in the 5q31 region revealed that all are located in the syntenic region of mouse chromosome 11q. Our analysis demonstrates an approach for examining human sequence as it is made available from large sequencing programs and has resulted in the discovery of several biomedically important genes, including a cyclin, a transcription factor that is homologous to an oncogene, a protein involved in DNA repair, and several new members of a family of transporter proteins. PMID:9149945

  4. The regional costs and benefits of acid rain control

    SciTech Connect

    Berkman, M.P.

    1991-01-01

    Congress recently enacted acid rain control legislation as part of the 1990 Clean Air Act Amendments following a decade-long debate among disparate regional interests. Although Congress succeeded in drafting a law acceptable to all regions, the regional costs and benefits of the legislation remain uncertain. The research presented here attempts to estimate the regional costs and benefits and the economic impacts of acid rain controls. These estimates are made using a modeling system composed of econometric, linear programming and input-output models. The econometric and linear programming components describe markets for electricity and coal. The outputs of these components including capital investment, electricity demand, and coal production are taken as exogenous inputs by a multiregional input-output model. The input-output model produces estimates of changes in final demand, gross output, and employment. The utility linear programming model also predicts sulfur dioxide emissions (an acid-rain precursor). According to model simulations, the costs of acid rain control exceed the benefits for many regions including several regions customarily thought to be the major beneficiaries of acid rain control such as New England.

  5. Opportunistic DNA Recombination With Epstein-Barr Virus at Sites of Control Region Rearrangements Mediating JC Virus Neurovirulence.

    PubMed

    Wortman, Margaret J; Lundberg, Patric S; Dagdanova, Ayuna V; Venkataraman, Pranav; Daniel, Dianne C; Johnson, Edward M

    2016-05-01

    We document a unique DNA recombination between polyomavirus JC (JC virus [JCV]) and Epstein-Barr virus (EBV) at sequences of JCV found infecting the brain. Archetype JCV is present in bone marrow and uroepithelial cells of most adults. During immunosuppression, JCV can infect the brain, causing a demyelinating disease, progressive multifocal leukoencephalopathy. Rearrangements in the archetype noncoding control region are necessary for neurovirulence. Two NCCR deletions and a duplication occur at sequences of homology with EBV, present latently in B cells, which may be coinfected with both viruses. Recombination between JCV and EBV occurs in B lymphoblasts at a sequence essential for JCV neurovirulence and in cerebrospinal fluid of immunosuppressed patients with multiple sclerosis, those susceptible to progressive multifocal leukoencephalopathy. Interviral recombination is a model for conferring advantages on JCV in the brain. It can alter a critical noncoding control region sequence and potentially facilitate use of EBV DNA abilities to transfer among different cell types. PMID:26690342

  6. Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1.

    PubMed Central

    Simmonds, P; Balfe, P; Ludlam, C A; Bishop, J O; Brown, A J

    1990-01-01

    Nucleotide sequences in three hypervariable regions of the human immunodeficiency virus type 1 (HIV-1) env gene were obtained by sequencing provirus present in peripheral blood mononuclear cells of HIV-infected individuals. Single molecules of target sequences were isolated by limiting dilution and amplified in two stages by the polymerase chain reaction, using nested primers. The product was directly sequenced to avoid errors introduced by Taq polymerase during the amplification process. There was extensive variation between sequences from the same individual as well as between sequences from different individuals. Interpatient variability was markedly less in individuals infected from a common source. A high proportion of amino acid substitutions in the hypervariable regions altered the number and positions of potential N-linked glycosylation sites. Sequences in two hypervariable regions frequently contained short (3- to 15-bp) duplications or deletions, and by amplifying peripheral blood mononuclear cell DNA containing 10(2) or 10(3) proviral molecules and analyzing the product by high-resolution electrophoresis, the total number and abundance of distinct length variants within an individual could be estimated, providing a more comprehensive analysis of the variants present than would be obtained by sequencing alone. Sequences from many individuals showed frequent amino acid substitutions at certain key positions for neutralizing-antibody and cytotoxic T-cell recognition in the immunodominant loop. The rates of synonymous and nonsynonymous nucleotide substitution in the region of this and flanking regions indicate that strong positive selection for amino acid change is operating in the generation of antigenic diversity. Images PMID:2243378

  7. Identification of six Trypanosoma cruzi lineages by sequence-characterised amplified region markers.

    PubMed

    Brisse, S; Dujardin, J C; Tibayrenc, M

    2000-11-01

    Six discrete phylogenetic lineages were recently identified in Trypanosoma cruzi, on the basis of multilocus enzyme electrophoresis and random amplified polymorphic DNA (RAPD) characterisation. The objective of the present study was to develop specific PCR-based markers for the identification of each of the six lineages. Eighty-seven T. cruzi stocks representative of all the lineages were characterised by RAPD with three primers, resulting in the identification of three fragments that were specifically amplified in the given sets of lineages. After cloning and sequencing these fragments, three pairs of sequence-characterised amplified region (SCAR) primers were designed. After PCR amplification using the SCAR primers, the initial polymorphism was retained either as the presence or absence of amplification, or as size variation between the PCR products. Although most PCR products, taken individually, were distributed across several lineages, the combination of the three SCAR markers resulted in characteristic patterns that were distinct in the six lineages. Furthermore, T. cruzi lineages were distinguished from Trypanosoma rangeli, T. cruzi marinkellei and T. cruzi-like organisms. The excellent correspondence of these new PCR markers with the phylogenetic lineages, allied with their sensitivity, makes them reliable tools for lineage identification and strain characterisation in T. cruzi. The approach described here could be generalised to any species of microorganism harbouring clear-cut phylogenetic subdivisions. PMID:11087920

  8. Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons

    PubMed Central

    Lexa, Matej; Kejnovský, Eduard; Šteflová, Pavlína; Konvalinová, Helena; Vorlíčková, Michaela; Vyskot, Boris

    2014-01-01

    Retrotransposons with long terminal repeats (LTR) form a significant proportion of eukaryotic genomes, especially in plants. They have gag and pol genes and several regulatory regions necessary for transcription and reverse transcription. We searched for potential quadruplex-forming sequences (PQSs) and potential triplex-forming sequences (PTSs) in 18 377 full-length LTR retrotransposons collected from 21 plant species. We found that PQSs were often located in LTRs, both upstream and downstream of promoters from which the whole retrotransposon is transcribed. Upstream-located guanine PQSs were dominant in the minus DNA strand, whereas downstream-located guanine PQSs prevailed in the plus strand, indicating their role both at transcriptional and post-transcriptional levels. Our circular dichroism spectroscopy measurements confirmed that these PQSs readily adopted guanine quadruplex structures—some of them were paralell-stranded, while others were anti-parallel-stranded. The PQS often formed doublets at a mutual distance of up to 400 bp. PTSs were most abundant in 3′UTR (but were also present in 5′UTR). We discuss the potential role of quadruplexes and triplexes as the regulators of various processes participating in LTR retrotransposon life cycle and as potential recombination sites during post-insertional retrotransposon-based genome rearrangements. PMID:24106085

  9. Isolation of expressed sequences from the region commonly deleted in Velo-cardio-facial syndrome

    SciTech Connect

    Sirotkin, H.; Morrow, B.; DasGupta, R.

    1994-09-01

    Velo-cardio-facial syndrome (VCFS) is a relatively common autosomal dominant genetic disorder characterized by cleft palate, cardiac abnormalities, learning disabilities and a characteristic facial dysmorphology. Most VCFS patients have interstitial deletions of 22q11 of 1-2 mb. In an effort to isolate the gene(s) responsible for VCFS we have utilized a hybrid selection protocol to recover expressed sequences from three non-overlapping YACs comprising almost 1 mb of the commonly deleted region. Total yeast genomic DNA or isolated YAC DNA was immobilized on Hybond-N filters, blocked with yeast and human ribosomal and human repetitive sequences and hybridized with a mixture of random primed short fragment cDNA libraries. Six human short fragment libraries derived from total fetus, fetal brain, adult brain, testes, thymus and spleen have been used for the selections. Short fragment cDNAs retained on the filter were passed through a second round of selection and cloned into lambda gt10. cDNAs shown to originate from the YACs and from chromosome 22 are being used to isolate full length cDNAs. Three genes known to be present on these YACs, catechol-O-methyltransferase, tuple 1 and clathrin heavy chain have been recovered. Additionally, a gene related to the murine p120 gene and a number of novel short cDNAs have been isolated. The role of these genes in VCFS is being investigated.

  10. Complete sequence and gene organization of the Nosema heliothidis ribosomal RNA gene region.

    PubMed

    Dong, Shinan; Shen, Zhongyuan; Zhu, Feng; Tang, Xudong; Xu, Li

    2011-01-01

    By sequencing the entire ribosomal RNA (rRNA) gene region of Nosema heliothidis isolated from cotton bollworm (Helicoverpa armigera), we showed that its gene organization is similar to the type species, Nosema bombycis: the 5'-large subunit rRNA (2,490 bp)-internal transcribed spacer (192 bp)-small subunit rRNA (1,232 bp)-intergenic spacer (274 bp)-5S rRNA (115 bp)-3'. We constructed two phylogenetic trees, analyzed phylogenetic relationships, examined rRNA organization of microsporidia, and compared the secondary structure of small subunit rRNA with closely related microsporidia. The latter two features may provide important information for the classification and phylogenetic analysis of microsporidia. PMID:21895841

  11. Nucleotide sequence analysis of the DNA binding region of the chicken fibronectin gene.

    PubMed

    Karasaki, Y; Gotoh, S; Kubomura, S; Higashi, K; Hirano, H

    1988-12-01

    We have determined the nucleotide sequence of 2.0 kb EcoRI segment from the clone lambda FC32 of the genomic chicken fibronectin gene, which is called DNA binding domain. This segment overlapped another clone lambda FC36 and contained three exons which were 16, 17 and 18. They were classified as Type III repeat as originally shown in bovine plasma fibronectin. The average homologies of these three exons among the chicken, rat and human fibronectins in amino acid level are very high (87-98%) compared with that (79-88%) of the exons in the cell binding domain, indicating that this region is highly conservative during the evolution. PMID:3212295

  12. Size Sequencing as a Window on Executive Control in Children with Autism and Asperger's Syndrome

    ERIC Educational Resources Information Center

    McGonigle-Chalmers, Margaret; Bodner, Kimberly; Fox-Pitt, Alicia; Nicholson, Laura

    2008-01-01

    A study is reported in which size sequencing on a touch screen is used as a measure of executive control in 20 high-functioning children with Autistic Spectrum Disorders (ASD). The data show a significant and age-independent effect of the length of sequence that can be executed without errors by these children, in comparison with a chronologically…

  13. Mitochondrial DNA control region polymorphism in the population of Alagoas state, north-eastern Brazil.

    PubMed

    Barbosa, Adriana B G; da Silva, Luiz Antonio F; Azevedo, Dalmo A; Balbino, Valdir Q; Mauricio-da-Silva, Luiz

    2008-01-01

    The sequences of the two hypervariable (HV) segments of the mitochondrial DNA (mtDNA) control region were determined in 167 randomly selected, unrelated individuals living in the state of Alagoas, north-eastern Brazil. One hundred and forty-five different haplotypes, associated with 139 variable positions, were determined. More than 95% of the mtDNA sequences could be allocated to specific mtDNA haplogroups according to the mutational motifs. Length heteroplasmy in the C-stretch HV1 and HV2 regions was observed in 22 and 11%, respectively, of the population sample. The genetic diversity was estimated to be 0.9975 and the probability of two random individuals presenting identical mtDNA haplotypes was 0.0084. The most frequent haplotype was shared by six individuals. All sequences showed high-quality values and phantom mutations were not detected. The diversity revealed in the mitochondrial control region indicates the importance of this locus for forensic casework and population studies within Alagoas, Brazil. PMID:18279250

  14. Regional Implications of Ypresian Flysch Sequence From South of Marmara Sea: Structural, Stratigraphic and Paleontological Data

    NASA Astrophysics Data System (ADS)

    Ülgen, S. C.; Okay, A. I.; Özcan, E.; Şengör, A. M. C.; Akbayram, K.

    2012-04-01

    The study of a Ypresian flysch sequence, immediately southern of the Intra-Pontid suture zone and overlying the Upper Cretaceous basement rocks, permit us to comment on the late Cretaceous-early Tertiary tectonic history of the region This flysch sequence with a thickness 1500-2000 m consisting of sandstones, shales and conglomerates derived from the Upper-Cretaceous basement rocks. These clastics are intercalated with andesitic tuffs, pyroclasts, agglomerates and lenticular limestones. The flysch contains some larger foraminifera levels including Orbitoclypeus douvillei douvillei, O. douvillei yesilyurtensis, O. schopeni ex. interc. suvlukayensis-crimensis, O. schopeni crimensis, O.munieri munieri, Asterocyclina alticostata cf. gallica, , Discocyclina fortisi simferopolensis. The Ypresian flysch overlies a unit which consists of quartz conglomerate and boulders, chert, serpentinite , metamorphic rock blocks and conglomerates. Some think this unit to be a debris flow, but the range of rock types, the style of deformation and the its areal extent clearly shows it could be a mélange. Gravity flows like mudflows, slump folds and NW-SE trending anticline and synclines are observed and mapped in Ypresian flysch which suggest that it was tectonized during or soon after deposition. Anticlines, synclines and north-nortwest dipping thrust faults point SE vergance in the region. Also earlier published apatite fission track data from metamorphic rocks cropping out at south of Marmara Sea shows that nearby areas uplifted during Early Eocene (~ 52 Ma). We suggest that there are two probable sources for this tectonism in northwest Turkey; the compression related to the consumption of the Intra-Pontide Ocean in the north or the Late Cretaceous-Paleocene collision of Pontides and Taurides in the south.

  15. Rapid profiling of the antigen regions recognized by serum antibodies using massively parallel sequencing of antigen-specific libraries.

    PubMed

    Domina, Maria; Lanza Cariccio, Veronica; Benfatto, Salvatore; D'Aliberti, Deborah; Venza, Mario; Borgogni, Erica; Castellino, Flora; Biondo, Carmelo; D'Andrea, Daniel; Grassi, Luigi; Tramontano, Anna; Teti, Giuseppe; Felici, Franco; Beninati, Concetta

    2014-01-01

    There is a need for techniques capable of identifying the antigenic epitopes targeted by polyclonal antibody responses during deliberate or natural immunization. Although successful, traditional phage library screening is laborious and can map only some of the epitopes. To accelerate and improve epitope identification, we have employed massive sequencing of phage-displayed antigen-specific libraries using the Illumina MiSeq platform. This enabled us to precisely identify the regions of a model antigen, the meningococcal NadA virulence factor, targeted by serum antibodies in vaccinated individuals and to rank hundreds of antigenic fragments according to their immunoreactivity. We found that next generation sequencing can significantly empower the analysis of antigen-specific libraries by allowing simultaneous processing of dozens of library/serum combinations in less than two days, including the time required for antibody-mediated library selection. Moreover, compared with traditional plaque picking, the new technology (named Phage-based Representation OF Immuno-Ligand Epitope Repertoire or PROFILER) provides superior resolution in epitope identification. PROFILER seems ideally suited to streamline and guide rational antigen design, adjuvant selection, and quality control of newly produced vaccines. Furthermore, this method is also susceptible to find important applications in other fields covered by traditional quantitative serology. PMID:25473968

  16. Dopamine neurons control striatal cholinergic neurons via regionally heterogeneous dopamine and glutamate signaling

    PubMed Central

    Chuhma, Nao; Mingote, Susana; Moore, Holly; Rayport, Stephen

    2014-01-01

    Summary Midbrain dopamine neurons fire in bursts conveying salient information. Bursts are associated with pauses in tonic firing of striatal cholinergic interneurons. While the reciprocal balance of dopamine and acetylcholine in the striatum is well known, how dopamine neurons control cholinergic neurons has not been elucidated. Here we show that dopamine neurons make direct fast dopaminergic and glutamatergic connections with cholinergic interneurons, with regional heterogeneity. Dopamine neurons drive a burst-pause firing sequence in cholinergic interneurons in the medial shell of the nucleus accumbens, mixed actions in the accumbens core, and a pause in the dorsal striatum. This heterogeneity is due mainly to regional variation in dopamine-neuron glutamate cotransmission. A single dose of amphetamine attenuates dopamine neuron connections to cholinergic interneurons with dose-dependent regional specificity. Overall, the present data indicate that dopamine neurons control striatal circuit function via discrete, plastic connections with cholinergic interneurons. PMID:24559678

  17. The 2007 Sumatra seismic sequence revealed by a regional seismic network in Indonesia

    NASA Astrophysics Data System (ADS)

    Nakano, M.; Inoue, H.; Kumagai, H.; Yamashina, T.; Sunarjo; Fauzi; Suhardjono

    2007-12-01

    distributed in a region extending about 300 km along the subduction zone of the Indo-Australian Plate. The depths of aftershocks range from 15 to 60 km. In the off-Bengkulu region, the earthquakes with M8 or above occurred in 1381, 1608 and 1833, approximately every 230 years. Now 174 years have been passed since the last event in 1833. We did not experience M8 class earthquakes during the last 210 years in the off-Padang region, which is to the north of off-Bengkulu. The off-Padang region corresponds to a seismic gap between the source regions of the 2007 Sumatra seismic sequence and M8.7 Nias earthquake on March 2005. The sequence of the M8.4, M8.0, and M6.8 earthquakes moving towards the northwest from off-Bengkulu in the 2007 seismic activity suggests the imminency of a large earthquake off Padang. We have been deploying broadband seismograph networks in Indonesia, including JISNET, by an international cooperation among Indonesia, Germany, China, and Japan, aiming at improving the capabilities to monitor seismic activity and tsunami generation in Indonesia. The seismic networks are now in operation, and totally 150 seismic stations will be installed by the end of 2008. Seismic monitoring based on these regional networks would contribute to early notification of a large earthquake anticipated to occur in the off-Padang region.

  18. An analytic study of near terminal area optimal sequencing and flow control techniques

    NASA Technical Reports Server (NTRS)

    Park, S. K.; Straeter, T. A.; Hogge, J. E.

    1973-01-01

    Optimal flow control and sequencing of air traffic operations in the near terminal area are discussed. The near terminal area model is based on the assumptions that the aircraft enter the terminal area along precisely controlled approach paths and that the aircraft are segregated according to their near terminal area performance. Mathematical models are developed to support the optimal path generation, sequencing, and conflict resolution problems.

  19. Gene identification and DNA sequence analysis in the GC-poor 20 megabase region of human chromosome 21.

    PubMed

    Yu, J; Tong, S; Shen, Y; Kao, F T

    1997-06-24

    In contrast to the distal half of the long arm of chromosome 21, the proximal half of approximately 20 megabases of DNA, including 21q11-21 bands, is low in GC content, CpG islands, and identified genes. Despite intensive searches, very few genes and cDNAs have been found in this region. Since the 21q11-21 region is associated with certain Down syndrome pathologies like mental retardation, the identification of relevant genes in this region is important. We used a different approach by constructing microdissection libraries specifically for this region and isolating unique sequence microclones for detailed molecular analysis. We found that this region is enriched with middle and low-copy repetitive sequences, and is also heavily methylated. By sequencing and homology analysis, we identified a significant number of genes/cDNAs, most of which appear to belong to gene families. In addition, we used unique sequence microclones in direct screening of cDNA libraries and isolated 12 cDNAs for this region. Thus, although the 21q11-21 region is gene poor, it is not completely devoid of genes/cDNAs. The presence of high proportions of middle and low-copy repetitive sequences in this region may have evolutionary significance in the genome organization and function of this region. Since 21q11-21 is heavily methylated, the expression of genes in this region may be regulated by a delicate balance of methylation and demethylation, and the presence of an additional copy of chromosome 21 may seriously disturb this balance and cause specific Down syndrome anomalies including mental retardation. PMID:9192657

  20. Region based Brain Computer Interface for a home control application.

    PubMed

    Akman Aydin, Eda; Bay, Omer Faruk; Guler, Inan

    2015-08-01

    Environment control is one of the important challenges for disabled people who suffer from neuromuscular diseases. Brain Computer Interface (BCI) provides a communication channel between the human brain and the environment without requiring any muscular activation. The most important expectation for a home control application is high accuracy and reliable control. Region-based paradigm is a stimulus paradigm based on oddball principle and requires selection of a target at two levels. This paper presents an application of region based paradigm for a smart home control application for people with neuromuscular diseases. In this study, a region based stimulus interface containing 49 commands was designed. Five non-disabled subjects were attended to the experiments. Offline analysis results of the experiments yielded 95% accuracy for five flashes. This result showed that region based paradigm can be used to select commands of a smart home control application with high accuracy in the low number of repetitions successfully. Furthermore, a statistically significant difference was not observed between the level accuracies. PMID:26736451

  1. D0 Silicon Strip Detector Upgrade Project SVX Sequencer Controller Board

    SciTech Connect

    Utes, M.; /Fermilab

    2001-05-29

    The Sequencer Controller boards are 9U by 340mm circuit boards that will reside in slot 1 of each of eight Sequencer crates in the D0 detector platform. The primary purpose is to control the Sequencers during data acquisition based on trigger information from the D0 Trigger Framework. Functions and features are as follows: (1) Receives the Serial Command Link (SCL) from the D0 Trigger System and controls the operation of the Sequencers by forming a custom serial control link (NRZ/Clock) which is distributed individually to each Sequencer via the 11 Backplane; (2) Controllable delays adjust NRZ control link phasing to compensate for the various cable-length delays between the Sequencers and SVX chips, delay control is common for slots 2-11, and for slots 12-21 of the crate; (3) Each NRZ control link is phase controlled so that commands reach each Sequencer in a given half-crate simultaneously, i.e., the link is compensated for backplane propagation delays; (4) External communication via MIL-STD-1553; (5) Stand-alone operation via 1553 trigger commands in absence of an SCL link; (6) 1553-writeable register for triggering a laser, etc. followed by an acquisition cycle; (7) TTL front panel input to trigger an acquisition cycle, e.g. from a scintillator; (8) Synch Trig, Veto, Busy and Preamp Reset TTL outputs on front panel LEMOs; (9) On-board 53.104 MHz oscillator for stand-alone operation; (10) 1553 or SCL-triggerable Cal-inject cycle; (11) Front-panel inputs to accept NRZ/Clock link from the VRB Controller; (12) Front panel displays and LEDs show the board status at a glance; and (13) In-system programmable EPLDs are programmed via Altera's 'Byteblaster'.

  2. Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications.

    PubMed

    Sbisà, E; Tanzariello, F; Reyes, A; Pesole, G; Saccone, C

    1997-12-31

    This paper reports the first comprehensive analysis of Displacement loop (D-loop) region sequences from ten different mammalian orders. It represents a systematic evolutionary study at the molecular level on regulatory homologous regions in organisms belonging to a well defined class, mammalia, which radiated about 150 million years ago (Mya). We have aligned and analyzed 26 complete D-loop region sequences available in the literature and the fat dormouse sequence, recently determined in our laboratory. The novelty of our alignment consists of the extensive manual revision of the preliminary output obtained by computer program to optimize sequence similarity, particularly for the two peripheral domains displaying heterogeneity in length and the presence of repeated sequences. The multialignment is available at the WWW site: http://www.ba.cnr.it/dloop.html. Our comparative study has allowed us to identify new conserved sequence blocks present in all the species under consideration and events of insertion/deletion which have important implications in both functional and evolutionary aspects. In particular we have detected two blocks, about 60 bp long, extended termination associated sequences (ETAS1 and ETAS2) conserved in all the organisms considered. Evaluation against experimental work suggests a possible functional role of ETAS1 and ETAS2 in the regulation of replication and transcription and targeted experimental approaches. The analyses on conserved sequence blocks (CSBs) clearly indicate that CSB1 is the only very essential element, common to all mammalian mt genomes, while CSB2 and CSB3 could be involved in different though related functions, probably species specific, and thus more linked to nuclear mitochondrial coevolutionary processes. Our hypothesis on the different functional implications of the conserved elements, CSBs and TASs, reported so far as main regulatory signals, would explain the different conservation of these elements in evolution. Moreover

  3. Early regional LGM (MIS 3) reflected in Central European Loess-Paleosol Sequences?

    NASA Astrophysics Data System (ADS)

    Zoeller, Ludwig; Fuchs, Markus

    2014-05-01

    The age of the "Brandenburg Phase", representing the regional LGM in Northern Germany and Poland, has been under debate. Evidence was found recently by OSL dating that it occurred during late MIS 3. In a new loess profile in the famous quarry of Nußloch south of Heidelberg (Germany) an exceptionally thick (6 m) loess-paleosol sequence (LPS) starts with a boreal brown soil regionally known as "Lohne soil", which terminates the Middle Pleniglacial LPS, according to classical stratigraphies. This paleosol is overlain by loess beds interbedding with weakly developed tundra-gley soils of typically Upper Pleniglacial habitus. Mean OSL ages from quartz fine and middle grains range between ca. 29 ka and ca. 35 ka in this part of the section which is much thicker than in previously studied corresponding parts of the loess stratigraphy at the Nußloch site. Our surprising dating results are, however, supported by recently dated loess beds in the Central European corridor between the ice margin of the Brandenburg Phase and the Northern Alpine LGM terminal moraines. Paleoenvironmental reconstructions point to cold but rather humid climatic conditions favouring rapid ice advance. We, thus, hypothesize that the rapid advance of Scandinavian ice into northern Central Europe which may have occurred ca. 10 ka prior to the global LGM, is reflected in some well-preserved Central European loess sections covering the last glacial cycle.

  4. Genomic region operation kit for flexible processing of deep sequencing data.

    PubMed

    Ovaska, Kristian; Lyly, Lauri; Sahu, Biswajyoti; Jänne, Olli A; Hautaniemi, Sampsa

    2013-01-01

    Computational analysis of data produced in deep sequencing (DS) experiments is challenging due to large data volumes and requirements for flexible analysis approaches. Here, we present a mathematical formalism based on set algebra for frequently performed operations in DS data analysis to facilitate translation of biomedical research questions to language amenable for computational analysis. With the help of this formalism, we implemented the Genomic Region Operation Kit (GROK), which supports various DS-related operations such as preprocessing, filtering, file conversion, and sample comparison. GROK provides high-level interfaces for R, Python, Lua, and command line, as well as an extension C++ API. It supports major genomic file formats and allows storing custom genomic regions in efficient data structures such as red-black trees and SQL databases. To demonstrate the utility of GROK, we have characterized the roles of two major transcription factors (TFs) in prostate cancer using data from 10 DS experiments. GROK is freely available with a user guide from >http://csbi.ltdk.helsinki.fi/grok/. PMID:23702556

  5. Nucleotide sequence of the 3' region of an infectious human T-cell leukemia virus type II genome.

    PubMed Central

    Shimotohno, K; Wachsman, W; Takahashi, Y; Golde, D W; Miwa, M; Sugimura, T; Chen, I S

    1984-01-01

    The nucleic acid sequence of the 3' region of human T-cell leukemia virus type II (HTLV-II) proviral DNA was determined using a HTLV-II proviral clone that could be recovered as infectious, transforming virus. The sequence data indicate a region of unknown function of approximately equal to 1.6 kilobase pairs in the 3' region, analogous to the X region previously identified in human T-cell leukemia virus type I (HTLV-I). Three overlapping open reading frames are present in the X region of HTLV-II. One of these open reading frames, Xc, is most likely to encode a protein product, because it has greater predicted amino acid sequence homology (78%) with the X-IV region of HTLV-I and a greater percentage of its base differences with X-IV at the third nucleotide position of codons than do the other open reading frames. Sequences of the X-region that include the open reading frames are conserved in two deletion mutants of HTLV-II, which are associated with a subline of Mo cells with a decreased dependence on fetal bovine serum. Images PMID:6093110

  6. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region.

    PubMed Central

    Ashburner, M; Misra, S; Roote, J; Lewis, S E; Blazej, R; Davis, T; Doyle, C; Galle, R; George, R; Harris, N; Hartzell, G; Harvey, D; Hong, L; Houston, K; Hoskins, R; Johnson, G; Martin, C; Moshrefi, A; Palazzolo, M; Reese, M G; Spradling, A; Tsang, G; Wan, K; Whitelaw, K; Celniker, S

    1999-01-01

    A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized "Adh region." A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species.Before beginning a Hunt, it is wise to ask someone what you are looking for before you begin looking for it. Milne 1926 PMID:10471707

  7. Inhibition of pepsin by analogues of pepsinogen-(1-12)-peptide with substitutions in the 4-7 sequence region.

    PubMed Central

    Dunn, B M; Lewitt, M; Pham, C

    1983-01-01

    Derivatives of the 1-12 sequence of pig pepsinogen were prepared by solid-phase peptide synthesis. The three derivatives contain substitutions in the 4-7 region of the 1-12 sequence. Glycine was used to replace the hydrophobic residues -Val-Pro-Leu-Val- in pairs. After cleavage and purification, the synthetic peptides were compared with a synthetic peptide of the native sequence, prepared at the same time, with respect to their ability to inhibit the pepsin-catalysed clotting of milk. Inhibitory potency, determined from plots of percentage inhibition versus concentration of synthetic peptide, is inversely correlated with the substitution of glycine residues for the hydrophobic residues. Therefore the equilibrium inhibition of pepsin by these peptides is dominated by the hydrophobic nature of the 4-7 sequence region. PMID:6405735

  8. A micronucleus-specific sequence exists in the 5'-upstream region of calmodulin gene in Tetrahymena thermophila.

    PubMed Central

    Katoh, M; Hirono, M; Takemasa, T; Kimura, M; Watanabe, Y

    1993-01-01

    Tetrahymena thermophila possesses a transcriptionally inactive micronucleus and an active macronucleus. Both nuclei are developed from micronucleus-derived germ nuclei during conjugation. Extensive DNA rearrangement and transcriptional activation are known to be involved in macronuclear development, but little has been known about these processes in a particular functional gene. Therefore the micro- and macronuclear genomic DNAs for calmodulin gene were analyzed. A 1,384 bp micronucleus-specific sequence located about 3.5 kb upstream of calmodulin gene has been found, suggesting DNA rearrangement during macronuclear development. The micronucleus-specific sequence had 85% A + T, no extensive ORF, ATTAs at both ends, and two palindromic structures just outside of both ends. Interestingly, the micronucleus-specific sequence included a T-rich tract, T16CT5, in the middle, and a nearly complementary A-rich tract, A5TA10GA5, existed 7 bp upstream from the initiation codon. In addition, there was a 20 bp repetitive sequence TAAT(TAAC)4 about 100 bp upstream of the micronucleus-specific sequence and also in the promoter region of calmodulin gene. Although the functional significance of the micronucleus-specific sequence remains unclear, T16CT5 and TAAT(TAAC)4 elements might exert an influence on transcription of the calmodulin gene. Stringent Southern hybridization revealed that this micronucleus-specific sequence or very similar sequence(s) were abundant in the Tetrahymena micronuclear genome. Images PMID:8506136

  9. Cloning and sequencing of the blood meal-induced late trypsin gene from the mosquito Aedes aegypti and characterization of the upstream regulatory region.

    PubMed

    Barillas-Mury, C; Wells, M A

    1993-01-01

    A 4.1 kb genomic clone of the late trypsin gene from the mosquito Aedes aegypti was isolated, mapped and subcloned. A 1.6 kb subclone, corresponding to 1.1 kb of upstream regulatory region and 0.5 kb of coding region, was sequenced. The gene has no introns within the coding region. The 5' end of the mature mRNA was mapped using primer extension analysis. A TATA box consensus sequence (TATAAA) was found at position -31 from the 5' end of the mature mRNA. A cluster of five repeat sequences homologous to the yeast GCN4 DNA binding site was found within 200 nucleotides upstream of the cap site. GCN4 is required for derepression mediated control of general amino acid biosynthesis in response to amino acid starvation in yeast. It activates the transcription of at least twenty different genes coding for enzymes involved in amino acid biosynthesis. The presence of this cluster of consensus sequences suggests that a protein similar to GCN4 might regulate expression of the late trypsin gene in the mosquito. Southern blot analysis of genomic DNA indicates that late trypsin is a single copy gene. PMID:9087537

  10. Cenozoic prograding sequences of the Antarctic continental margin - What balance between structural and eustatic control

    SciTech Connect

    Cooper, A.K. ); Barrett, P. ); Hinz, K. ); Stagg, H. ); Traube, V. )

    1990-05-01

    Multichannel seismic reflection profiles across the Antarctic continental margin commonly reveal prograding sedimentary sequences that are bounded by unconformities. These sequences are as much as 5 km thick and, where sampled, are composed entirely of late Eocene( )-early Oligocene and younger glacial rocks. On nonpolar margins, prograding sequences generally are attributed to relative changes in sea level, sediment supply, and tectonism. Around Antarctica, ice sheets have also been important in controlling the geometry and location of prograding sequences. The Antarctic sequences may provide a proximal record of major Cenozoic ice volume changes and related sea level changes not obtainable from low-latitude continental shelves. Presently, the Antarctic record is poorly known because of limited core data. Two categories of prograding (P) and aggrading (A) sigmoidal sequences are observed around Antarctica: (1) P sequences that build principally outward (common) and (2) AP sequences that build largely upward and outward (less common). P sequences may result principally from grounded ice sheets, and AP sequences from open-marine basinal processes. Major rift embayments of Antarctica (e.g., eastern Ross Sea eastern Weddell Sea Lambert graben Wilkes basin) are also pathways for major ice movement. In general, most areas with P sequences lie within or adjacent to Mesozoic or older rift embayment, whereas the primary area with AP sequences (eastern Ross Sea) lies within a likely Cenozoic rift embayment. The Pacific side of the Antarctic Peninsula where Cenozoic ice sheets and Cenozoic tectonism have been active, is also marked by a P sequence. Scientific drilling on the Antarctic continental shelf has recovered openwater glacial deposits (Ross Sea) as well as glacial diamicts that were deposited beneath and in front of grounded glacier ice (Ross Sea and Prydz Bay).

  11. Going, going, gone? Proactive control prevents the congruency sequence effect from rapid decay.

    PubMed

    Duthoo, W; Abrahamse, E L; Braem, S; Notebaert, W

    2014-07-01

    The congruency sequence effect, the finding of a reduced congruency effect following incongruent trials in conflict tasks, has received considerable attention in the research on cognitive control over the last two decades. This effect can reflect either the expectancy-guided, preparatory biasing of attention in anticipation of the upcoming stimulus (i.e. proactive control), or the phasic enhancement of the attentional set in response to conflict on the previous trial (i.e. reactive control). A recent study by Egner et al. in Front Psychol 1 (2010) set out to contrast these two alternatives, by exploring the congruency sequence effect across a wide range of inter-trial intervals. It was found that congruency sequence effects were subject to rapid decay over time. This decay fits well with the notion of reactive control, while at the same time speaking against the involvement of proactive regulation—which should also (and even mainly) be evident at longer intervals. In the present study, we first replicate the reduction of the congruency sequence effect with increasing inter-trial interval in a face-word Stroop task. In a second experiment, we show that congruency sequence effects are observed at longer intervals, too, when the proportion of trials with the longest inter-trial interval is increased. Our findings indicate that proactive control can prevent the congruency sequence effect from decaying rapidly. PMID:24077774

  12. Sequence determination of the heavy-chain constant region in four immunoglobulin classes of Mongolian gerbils (Meriones unguiculatus).

    PubMed

    Ukaji, Takao; Sumiyama, Daisuke; Kai, Osamu

    2012-01-01

    We determined partial cDNA sequences of four immunoglobulin (Ig) classes-IgM, IgG1, IgE, and IgA-of Mongolian gerbil (Meriones unguiculatus). Each deduced Ig heavy-chain constant (IGHC) region-Cµ, Cγ1, Cε, and Cα-is structurally similar to its counterparts in the mouse and rat, and phylogenetic analysis suggests that the gerbil Igs are evolutionarily close to their counterparts. In spite of the high sequence homology to the other rodent Cγ sequences, the gerbil Cγ1 sequence differs from our previously reported Cγ2. This result indicates that the gerbil has at least two IgG subclasses. These four gerbil IGHC cDNA sequences will be useful for determining gerbil Ig isotypes and examining the expression of gerbil Ig mRNAs in response to parasitic and bacterial infections. PMID:22531724

  13. Identification of conserved genomic regions and variation therein amongst Cetartiodactyla species using next generation sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background Next Generation Sequencing has created an opportunity to genetically characterize an individual both inexpensively and comprehensively. In earlier work produced in our collaboration [1], it was demonstrated that, for animals without a reference genome, their Next Generation Sequence data ...

  14. Rationally Designing Aptamer Sequences with Reduced Affinity for Controlled Sensor Performance

    PubMed Central

    Schoukroun-Barnes, Lauren R.; White, Ryan J.

    2015-01-01

    The relative ease of predicting the secondary structure of nucleic acid sequences lends itself to the design of sequences to perform desired functions. Here, we combine the utility of nucleic acid aptamers with predictable control over the secondary structure to rationally design sequences with controlled affinity towards a target analyte when employed as the recognition element in an electrochemical sensor. Specifically, we present a method to modify an existing high-gain aptamer sequence to create sequences that, when employed in an electrochemical, aptamer-based sensor, exhibit reduced affinity towards a small molecule analyte tobramycin. Sensors fabricated with the high-gain parent sequence saturate at concentrations much below the therapeutic window for tobramycin (7–18 µM). Accordingly, the rationale behind modifying this high-gain sequence to reduce binding affinity was to tune sensor performance for optimal sensitivity in the therapeutic window. Using secondary structure predictions and analysis of the NMR structure of an aminoglycoside RNA aptamer bound to tobramycin, we are able to successfully modify the aptamer sequence to tune the dissociation constants of electrochemical aptamer-based sensors between 0.17 and 3 µM. The guidelines we present represent a general strategy to lessening binding affinity of sensors employing aptamer-modified electrodes. PMID:25835184

  15. Structural characteristics of the Relict Gull (Larus relictus) mitochondrial DNA control region and its comparison to other Laridae.

    PubMed

    Yang, Chao; Lian, Ting; Wang, Qing-Xiong; Huang, Yuan; Xiao, Hong

    2016-07-01

    The structure of the mitochondrial DNA control region in the Relict Gull (Larus relictus) was predicted and compared with data from the National Center for Biotechnology Information (NCBI) on five other gulls. The results showed that the control regions of the six gulls comprise three domains. Sequences of CSB-1-like (domain I) and CSB-1 (domain III) in L. relictus have the highest similarity with those in the other five gulls. The insertion fragments are located in downstream domain I of L. ridibundus, L. brunnicephalus, and L. saundersi. Seven conserved sequence boxes (additional box, F-box, E-box, D-box, C-box, bird-similarity-box, and B-box) are located in domain II in all six gulls. It is suggested that the CSB-2/3 sequence, the origin of H-strand replication, and bidirectional light- and heavy-strand transcription promoters in domain III of L. relictus have some distinguishing features to those of other gulls. Some repeat units are contained in the 3' end of the control region in the five gulls; however, no repeat units are found in the sequence CAAACAACAAA in L. relictus. The distribution of nucleotide diversity analysis will provide the useful information on the selected DNA fragment within the control region for genetic analyses among gulls. PMID:26016878

  16. Complete genome sequence of Deltapapillomavirus 4 (bovine papillomavirus 2) from a bovine papillomavirus lesion in Amazon Region, Brazil

    PubMed Central

    Daudt, Cíntia; da Silva, Flavio RC; Cibulski, Samuel P; Weber, Matheus N; Mayer, Fabiana Q; Varela, Ana Paula M; Roehe, Paulo M; Canal, Cláudio W

    2016-01-01

    The complete genome sequence of bovine papillomavirus 2 (BPV2) from Brazilian Amazon Region was determined using multiple-primed rolling circle amplification followed by Illumina sequencing. The genome is 7,947 bp long, with 45.9% GC content. It encodes seven early (E1, E2,E4, E5, E6,E7, and E8) and two late (L1 and L2) genes. The complete genome of a BPV2 can help in future studies since this BPV type is highly reported worldwide although the lack of complete genome sequences available. PMID:27074259

  17. Complete genome sequence of Deltapapillomavirus 4 (bovine papillomavirus 2) from a bovine papillomavirus lesion in Amazon Region, Brazil.

    PubMed

    Daudt, Cíntia; Silva, Flavio Rc da; Cibulski, Samuel P; Weber, Matheus N; Mayer, Fabiana Q; Varela, Ana Paula M; Roehe, Paulo M; Canal, Cláudio W

    2016-04-01

    The complete genome sequence of bovine papillomavirus 2 (BPV2) from Brazilian Amazon Region was determined using multiple-primed rolling circle amplification followed by Illumina sequencing. The genome is 7,947 bp long, with 45.9% GC content. It encodes seven early (E1, E2,E4, E5, E6,E7, and E8) and two late (L1 and L2) genes. The complete genome of a BPV2 can help in future studies since this BPV type is highly reported worldwide although the lack of complete genome sequences available. PMID:27074259

  18. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome.

    PubMed

    Muñoz-Amatriaín, María; Lonardi, Stefano; Luo, MingCheng; Madishetty, Kavitha; Svensson, Jan T; Moscou, Matthew J; Wanamaker, Steve; Jiang, Tao; Kleinhofs, Andris; Muehlbauer, Gary J; Wise, Roger P; Stein, Nils; Ma, Yaqin; Rodriguez, Edmundo; Kudrna, Dave; Bhat, Prasanna R; Chao, Shiaoman; Condamine, Pascal; Heinen, Shane; Resnik, Josh; Wing, Rod; Witt, Heather N; Alpert, Matthew; Beccuti, Marco; Bozdag, Serdar; Cordero, Francesca; Mirebrahim, Hamid; Ounit, Rachid; Wu, Yonghui; You, Frank; Zheng, Jie; Simková, Hana; Dolezel, Jaroslav; Grimwood, Jane; Schmutz, Jeremy; Duma, Denisa; Altschmied, Lothar; Blake, Tom; Bregitzer, Phil; Cooper, Laurel; Dilbirligi, Muharrem; Falk, Anders; Feiz, Leila; Graner, Andreas; Gustafson, Perry; Hayes, Patrick M; Lemaux, Peggy; Mammadov, Jafar; Close, Timothy J

    2015-10-01

    Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant. PMID:26252423

  19. Multiple Comparison Analysis of Two New Genomic Sequences of ILTV Strains from China with Other Strains from Different Geographic Regions

    PubMed Central

    Zhao, Yan; Kong, Congcong; Wang, Yunfeng

    2015-01-01

    To date, twenty complete genome sequences of ILTV strains have been published in GenBank, including one strain from China, and nineteen strains from Australian and the United States. To investigate the genomic information on ILTVs from different geographic regions, two additional individual complete genome sequences of WG and K317 strains from China were determined. The genomes of WG and K317 strains were 153,505 and 153,639 bp in length, respectively. Alignments performed on the amino acid sequences of the twelve glycoproteins showed that 13 out of 116 mutational sites were present only among the Chinese strain WG and the Australian strains SA2 and A20. The phylogenetic tree analysis suggested that the WG strain established close relationships with the Australian strain SA2. The recombination events were detected and confirmed in different subregions of the WG strain with the sequences of SA2 and K317 strains as parental. In this study, two new complete genome sequences of Chinese ILTV strains were used in comparative analysis with other complete genome sequences of ILTV strains from China, the United States, and Australia. The analysis of genome comparison, phylogenetic trees, and recombination events showed close relationships among the Chinese strain WG and the Australian strains SA2. The information of the two new complete genome sequences from China will help to facilitate the analysis of phylogenetic relationships and the molecular differences among ILTV strains from different geographic regions. PMID:26186451

  20. Multiple Comparison Analysis of Two New Genomic Sequences of ILTV Strains from China with Other Strains from Different Geographic Regions.

    PubMed

    Zhao, Yan; Kong, Congcong; Wang, Yunfeng

    2015-01-01

    To date, twenty complete genome sequences of ILTV strains have been published in GenBank, including one strain from China, and nineteen strains from Australian and the United States. To investigate the genomic information on ILTVs from different geographic regions, two additional individual complete genome sequences of WG and K317 strains from China were determined. The genomes of WG and K317 strains were 153,505 and 153,639 bp in length, respectively. Alignments performed on the amino acid sequences of the twelve glycoproteins showed that 13 out of 116 mutational sites were present only among the Chinese strain WG and the Australian strains SA2 and A20. The phylogenetic tree analysis suggested that the WG strain established close relationships with the Australian strain SA2. The recombination events were detected and confirmed in different subregions of the WG strain with the sequences of SA2 and K317 strains as parental. In this study, two new complete genome sequences of Chinese ILTV strains were used in comparative analysis with other complete genome sequences of ILTV strains from China, the United States, and Australia. The analysis of genome comparison, phylogenetic trees, and recombination events showed close relationships among the Chinese strain WG and the Australian strains SA2. The information of the two new complete genome sequences from China will help to facilitate the analysis of phylogenetic relationships and the molecular differences among ILTV strains from different geographic regions. PMID:26186451

  1. Regional Control of Nondisjunction of the B Chromosome in Maize

    PubMed Central

    Lin, Bor-Yaw

    1978-01-01

    Control of nondisjunction in the maize B chromosome was studied using a set of B-10 translocations. The study focused on the possible effect of the proximal region of the B long arm. The experimental procedure utilized a combination of a 10B chromosome from one translocation with a B10 from another translocation. The breakpoints of the two translocations were so located that combination of the two elements created a deletion in the proximal region of the B chromosome, but no deletion in chromosome 10. Two different types of deletions were established; one involved a portion of the euchromatic region and the other the entire heterochromatic portion comprising the distal half of the B long arm, except for the small euchromatic tip. Deletion of the heterochromatic portion did not exert any effect on nondisjunction. Deletions of different portions of the euchromatic region produce different responses. Some deletions resulted in typical B nondisjunctional activity; others resulted in the disappearance of this activity. It is concluded that a region within the euchromatic portion of the chromosome is critical for the nondisjunction of B chromosomes. Among 22 translocations with breakpoints in the euchromatic regions, three were proximal to the critical region, 16 were distal and the position of three others was not determined. PMID:17248872

  2. Evolution and strengthening of the Calabrian Regional Seismic Network during the Pollino sequence

    NASA Astrophysics Data System (ADS)

    D'Alessandro, Antonino; Gervasi, Anna; Guerra, Ignazio

    2013-04-01

    In the last three years the Calabria-Lucania border area is affected by an intense seismic activity generated by the activation of geological structures which be seat of clusters of microearthquakes, with energy release sufficient to be felt and to generate alarm and bother. Besides to the historical memory of the inhabitants of Mormanno (the town most affected of macroseismic effects) there are some historical documents that indicate the occurrence of a similar seismic crisis in 1888. A more recent seismic sequence, the first monitored by seismic instruments, occurred in 1973-1974. In the last case, the activity started in early 2010 and is still ongoing. The two shocks of ML = 4.3 and 5.0 and the the very long time duration differs this crisis from the previous ones. Given this background, in 1981 was installed at Mormanno a seismic station (MMN) belonging to Regional Seismic Network of the University of Calabria (RSRC), now also a station of the Italian National Seismic Network of the Istituto Nazionale di Geofisica Vulcanolgia (INSN-INGV). This seismic station made it possible to follow the evolution of seismicity in this area and in particular the progressive increase in seismic activity started in 2010. Since 2010, some 3D stand-alone, was installed by the University of Calabria. Further stations of INGV were installed in November 2011 after a sharp increase of the energy release and subsequently by the INGV and the GeoForschungsZentrum (Potsdam) after the main shock of the whole sequence. Seismic networks are powerful tools for understanding active tectonic processes in a monitored seismically active region. However, the optimal monitoring of a seismic region requires the assessment of the seismic network capabilities to identify seismogenic areas that are not adequately covered and to quantify measures that will allow the network improvement. In this paper we examine in detail the evolution and the strengthening of the RSRC in the last years analyzing the

  3. Assessment of potential jaw-tracking advantage using control point sequences of VMAT planning.

    PubMed

    Kim, Jung-in; Park, Jong Min; Park, So-Yeon; Choi, Chang Heon; Wu, Hong-Gyun; Ye, Sung-Joon

    2014-01-01

    This study aims to evaluate the potential jaw-tracking advantage using control point sequences of volume volumetric modulated arc therapy (VMAT) planning. VMAT plans for patients with prostate and head and neck (H&N) cancers were converted into new static arc (SA) plans. The SA plan consisted of a series of static fields at each control point of the VMAT plan. All other machine parameters of the SA plan were perfectly identical to those of the original VMAT plan. The jaw-tracking static arc (JTSA) plans were generated with fields that closed the jaws of each SA field into the multileaf collimators (MLCs) aperture. The dosimetric advantages of JTSA over SA were evaluated in terms of a dose-volume histogram (DVH) of organ at risk (OAR) after renormalizing both plans to make the same target coverage. Both plans were delivered to the MatriXX-based COMPASS system for 3D volume dose verification. The average jaw size reduction of the JTSA along the X direction was 3.1 ± 0.9 cm for prostate patients and 6.9 ± 1.9 cm for H&N patients. For prostate patients, the organs far from the target showed larger sparing (3.7%-8.1% on average) in JTSA than the organs adjacent to the target (1.1%-1.5%). For the H&N plans, the mean dose reductions for all organs ranged from 4.3% to 11.9%. The dose reductions were more significant in the dose regions of D80, D90, and D95 than the dose regions of D5, D10, and D20 for all patients. Likewise, the deliverability and reproducibility of jaw-tracking plan were validated. The measured dosimetric advantage of JTSA over SA coincided with the calculated one above. PMID:24710450

  4. The nucleotide sequence of the promoter region of hisS, the structural gene for histidyl-tRNA synthetase.

    PubMed

    Eisenbeis, S J; Parker, J

    1982-05-01

    A plasmid has been constructed which carries hisS, the structural gene for histidyl-RNA synthetase of E. coli, on a 1.6-kb fragment bounded by PvuII and BstEII sites. The DNA sequence of both ends of this fragment was determined. The amino-terminal sequence of histidyl-tRNA synthetase was also determined to locate the promoter proximal coding region and the frame in which it is read. Three promoters were identified by consensus criteria. The region surrounding these promoters contains extensive twofold symmetry. PMID:6290315

  5. Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers

    DOE PAGESBeta

    Wang, Jun; Bonnesen, Peter V; Rangel, E.; Vallejo, E.; Sanchez-Castillo, Ariadna; Cleaves, II, H. James; Baddorf, Arthur P; Sumpter, Bobby G; Pan, Minghu; Maksymovych, Petro; et al

    2016-01-04

    The self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N9-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two ormore » more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. The resulting characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Moreover, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.« less

  6. Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Bonnesen, Peter V.; Rangel, E.; Vallejo, E.; Sanchez-Castillo, Ariadna; James Cleaves, H., II; Baddorf, Arthur P.; Sumpter, Bobby G.; Pan, Minghu; Maksymovych, Petro; Fuentes-Cabrera, Miguel

    2016-01-01

    Self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N9-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two or more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. These characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Further, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.

  7. Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers

    PubMed Central

    Wang, Jun; Bonnesen, Peter V.; Rangel, E.; Vallejo, E.; Sanchez-Castillo, Ariadna; James Cleaves II, H.; Baddorf, Arthur P.; Sumpter, Bobby G.; Pan, Minghu; Maksymovych, Petro; Fuentes-Cabrera, Miguel

    2016-01-01

    Self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N9-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two or more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. These characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Further, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers. PMID:26725380

  8. Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers.

    PubMed

    Wang, Jun; Bonnesen, Peter V; Rangel, E; Vallejo, E; Sanchez-Castillo, Ariadna; James Cleaves Ii, H; Baddorf, Arthur P; Sumpter, Bobby G; Pan, Minghu; Maksymovych, Petro; Fuentes-Cabrera, Miguel

    2016-01-01

    Self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N(9)-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two or more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. These characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Further, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers. PMID:26725380

  9. Two structurally distinct {kappa}B sequence motifs cooperatively control LPS-induced KC gene transcription in mouse macrophages

    SciTech Connect

    Ohmori, Y.; Fukumoto, S.; Hamilton, T.A.

    1995-10-01

    The mouse KC gene is an {alpha}-chemokine gene whose transcription is induced in mononuclear phagocytes by LPS. DNA sequences necessary for transcriptional control of KC by LPS were identified in the region flanking the transcription start site. Transient transfection analysis in macrophages using deletion mutants of a 1.5-kb sequence placed in front of the chloramphenicol acetyl transferase (CAT) gene identified an LPS-responsive region between residues -104 and +30. This region contained two {kappa}B sequence motifs. The first motif (position -70 to -59, {kappa}B1) is highly conserved in all three human GRO genes and in the mouse macrophage inflammatory protein-2 (MIP-2) gene. The second {kappa}B motif (position -89 to -78, {kappa}B2) was conserved only between the mouse and the rat KC genes. Consistent with previous reports, the highly conserved {kappa}B site ({kappa}B1) was essential for LPS inducibility. Surprisingly, the distal {kappa}B site ({kappa}B2) was also necessary for optimal response; mutation of either {kappa}B site markedly reduced sensitivity to LPS in RAW264.7 cells and to TNF-{alpha} in NIH 3T3 fibroblasts. Although both {kappa}B1 and {kappa}B2 sequences were able to bind members of the Rel homology family, including NF{kappa}B1 (P50), RelA (65), and c-Rel, the {kappa}B1 site bound these factors with higher affinity and functioned more effectively than the {kappa}B2 site in a heterologous promoter. These findings demonstrate that transcriptional control of the KC gene requires cooperation between two {kappa}B sites and is thus distinct from that of the three human GRO genes and the mouse MIP-2 gene. 71 refs., 8 figs.

  10. Structural Control on South Napa Earthquake Sequence and Its Effects

    NASA Astrophysics Data System (ADS)

    Langenheim, V. E.; Graymer, R. W.; Jachens, R. C.

    2014-12-01

    Potential-field data indicate that the M6.0 South Napa earthquake and its aftershocks were influenced by complex structure among the West Napa-Carneros-Pinole-Franklin faults system. The West Napa and Carneros faults, although considered to be minor Quaternary players within the San Andreas fault system, are major faults that in part bound the Mayacamas Mountains, an uplifted block of Mesozoic basement between Sonoma and Napa Valleys, and that produce prominent potential-field gradients. These two faults may account for as much as 30-50 km of right-lateral offset since ~6 Ma based on offset magnetic anomalies, length of pull-apart basins, and correlation of Neogene units. Uplift of the block may be Quaternary in age because gravels found to the west of the range contain clasts of 2.8 Ma obsidian derived from the east of the range. The southern extent of the South Napa earthquake rupture and seismicity is bounded on the west by the north end of a pull-apart basin between the Carneros and Pinole faults reflected in gravity data. The prominent gravity and magnetic gradients associated with the West Napa fault weaken where mapped traces of the fault begin to splay at the southern extent of Mesozoic and Paleogene outcrops. This region also encompasses multiple linear north-northwest-trending features identified in UAVSAR and is where the Carneros and West Napa faults are closest at the surface. We suggest that the interaction of these two faults not only affects the South Napa earthquake, but also influenced the extent of seismicity following the 2000 Yountville earthquake as well as the diffuse zone of seismicity generally confined between these two faults as they curve northwestward towards the southern end of the Maacama fault. Damage produced by the South Napa and Yountville earthquakes may have been focused by the 2-3 km-deep basin beneath the city of Napa, concentrated not over the deepest parts of the basin, but rather along the periphery or over an intra

  11. Phase control of a two-photon transition with shaped femtosecond laser-pulse sequences

    SciTech Connect

    Praekelt, A.; Wollenhaupt, M.; Sarpe-Tudoran, C.; Baumert, T.

    2004-12-01

    Phase effects in a quantum control experiment on the two-photon transition 4s <-<- 3s of atomic sodium are studied. In our experiment, we combine the generation of phase-locked interferometrically generated pulses with pulse-shaping techniques to study in detail the interplay of optical and quantum-mechanical phases. Subtle differences in the physical realization of the pulse sequences produce large difference in the control objective--the 4s population. The control mechanisms of more complex pulse sequences generated by periodic and discontinuous phase-modulation functions are investigated systematically and analyzed on the basis of quantum-mechanical interference.

  12. Nucleotide sequence analysis of the hypervariable region III of mitochondrial DNA in Thais.

    PubMed

    Thongngam, Punlop; Leewattanapasuk, Worraanong; Bhoopat, Tanin; Sangthong, Padchanee

    2016-07-01

    This study analyzed the nucleotide sequences of the hypervariable region III (HVRIII) of mitochondrial DNA in Thai individuals. Buccal swab samples were randomly obtained from 100 healthy, unrelated, adult (18-60 years old), volunteer donors living in Thailand. Eighteen different haplotypes were found, of which 11 haplotypes were unique. The most frequent haplotypes observed were 522D-523D. Nucleotide transition from Thymine (T) to Cytosine (C) at position 489 (43%) was the most frequent substitution. Nucleotide transversions were also observed at position 433 (Adenine (A) to C, 1%) and position 499 (Guanine (G) to C, 1%). Fifty-three samples presented nucleotide insertion and deletion of C and A (CA) at position 514-523. Insertion of 1AC (3%) and 2AC (2%) were observed. Deletion of 1CA (53%) and 2CA (2%) at position 514-523 were revealed. The deletion of T at position 459 was observed. The haplotype diversity, random match probability, and discrimination power were calculated to be 0.7770, 0.2308, and 0.7692, respectively. PMID:27107562

  13. Transcriptome sequencing of purple petal spot region in tree peony reveals differentially expressed anthocyanin structural genes

    PubMed Central

    Zhang, Yanzhao; Cheng, Yanwei; Ya, Huiyuan; Xu, Shuzhen; Han, Jianming

    2015-01-01

    The pigmented cells in defined region of a petal constitute the petal spots. Petal spots attract pollinators and are found in many angiosperm families. Several cultivars of tree peony contain a single red or purple spot at the base of petal that makes the flower more attractive for the ornamental market. So far, the understanding of the molecular mechanism of spot formation is inadequate. In this study, we sequenced the transcriptome of the purple spot and the white non-spot of tree peony flower. We assembled and annotated 67,892 unigenes. Comparative analyses of the two transcriptomes showed 1,573 differentially expressed genes, among which 933 were up-regulated, and 640 were down-regulated in the purple spot. Subsequently, we examined four anthocyanin structural genes, including PsCHS, PsF3′H, PsDFR, and PsANS, which expressed at a significantly higher level in the purple spot than in the white non-spot. We further validated the digital expression data using quantitative real-time PCR. Our result uncovered transcriptome variance between the spot and non-spot of tree peony flower, and revealed that the co-expression of four anthocyanin structural genes was responsible for spot pigment in tree peony. The data will further help to unravel the genetic mechanism of peony flower spot formation. PMID:26583029

  14. Learner Control of Instructional Sequencing within an Adaptive Tutorial CAI Environment. Technical Report 75-7.

    ERIC Educational Resources Information Center

    Seidel, Robert J.; And Others

    A study to test the effects of learner control of the sequencing of instructional tasks when using computer-assisted instruction (CAI) systems is described. Using a series of CAI modules to teach the COBOL programing language to military personnel, students were able to control various aspects of their learning environment. Among the research…

  15. Learner Control of Instructional Sequencing Within an Adaptive Tutorial CAI Environment

    ERIC Educational Resources Information Center

    Seidel, Robert J.; And Others

    1978-01-01

    This study was designed to test effects of a specified degree of learner control over the sequencing of instructional materials in a self contained tutorial CAI course in COBOL programming. Findings describe contributions and interactions of learner controlled variables with respect to instructional effectiveness and efficiency. (RAO)

  16. The Effect of Joint Control Training on the Acquisition and Durability of a Sequencing Task

    ERIC Educational Resources Information Center

    DeGraaf, Allison; Schlinger, Henry D., Jr.

    2012-01-01

    Gutierrez (2006) experimentally demonstrated the effects of joint control and particularly the role of response mediation in the sequencing behavior of adults using an unfamiliar language. The purpose of the current study was to replicate and extend the procedures used by Gutierrez by comparing the effects of joint control training with the…

  17. Sequencing the GRHL3 Coding Region Reveals Rare Truncating Mutations and a Common Susceptibility Variant for Nonsyndromic Cleft Palate.

    PubMed

    Mangold, Elisabeth; Böhmer, Anne C; Ishorst, Nina; Hoebel, Ann-Kathrin; Gültepe, Pinar; Schuenke, Hannah; Klamt, Johanna; Hofmann, Andrea; Gölz, Lina; Raff, Ruth; Tessmann, Peter; Nowak, Stefanie; Reutter, Heiko; Hemprich, Alexander; Kreusch, Thomas; Kramer, Franz-Josef; Braumann, Bert; Reich, Rudolf; Schmidt, Gül; Jäger, Andreas; Reiter, Rudolf; Brosch, Sibylle; Stavusis, Janis; Ishida, Miho; Seselgyte, Rimante; Moore, Gudrun E; Nöthen, Markus M; Borck, Guntram; Aldhorae, Khalid A; Lace, Baiba; Stanier, Philip; Knapp, Michael; Ludwig, Kerstin U

    2016-04-01

    Nonsyndromic cleft lip with/without cleft palate (nsCL/P) and nonsyndromic cleft palate only (nsCPO) are the most frequent subphenotypes of orofacial clefts. A common syndromic form of orofacial clefting is Van der Woude syndrome (VWS) where individuals have CL/P or CPO, often but not always associated with lower lip pits. Recently, ∼5% of VWS-affected individuals were identified with mutations in the grainy head-like 3 gene (GRHL3). To investigate GRHL3 in nonsyndromic clefting, we sequenced its coding region in 576 Europeans with nsCL/P and 96 with nsCPO. Most strikingly, nsCPO-affected individuals had a higher minor allele frequency for rs41268753 (0.099) than control subjects (0.049; p = 1.24 × 10(-2)). This association was replicated in nsCPO/control cohorts from Latvia, Yemen, and the UK (pcombined = 2.63 × 10(-5); ORallelic = 2.46 [95% CI 1.6-3.7]) and reached genome-wide significance in combination with imputed data from a GWAS in nsCPO triads (p = 2.73 × 10(-9)). Notably, rs41268753 is not associated with nsCL/P (p = 0.45). rs41268753 encodes the highly conserved p.Thr454Met (c.1361C>T) (GERP = 5.3), which prediction programs denote as deleterious, has a CADD score of 29.6, and increases protein binding capacity in silico. Sequencing also revealed four novel truncating GRHL3 mutations including two that were de novo in four families, where all nine individuals harboring mutations had nsCPO. This is important for genetic counseling: given that VWS is rare compared to nsCPO, our data suggest that dominant GRHL3 mutations are more likely to cause nonsyndromic than syndromic CPO. Thus, with rare dominant mutations and a common risk variant in the coding region, we have identified an important contribution for GRHL3 in nsCPO. PMID:27018475

  18. Rapid evaluation and quality control of next generation sequencing data with FaQCs

    DOE PAGESBeta

    Lo, Chien -Chi; Chain, Patrick S. G.

    2014-12-01

    Background: Next generation sequencing (NGS) technologies that parallelize the sequencing process and produce thousands to millions, or even hundreds of millions of sequences in a single sequencing run, have revolutionized genomic and genetic research. Because of the vagaries of any platform's sequencing chemistry, the experimental processing, machine failure, and so on, the quality of sequencing reads is never perfect, and often declines as the read is extended. These errors invariably affect downstream analysis/application and should therefore be identified early on to mitigate any unforeseen effects. Results: Here we present a novel FastQ Quality Control Software (FaQCs) that can rapidly processmore » large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. Both the speed of processing and the memory footprint of storing all required information have been optimized via algorithmic and parallel processing solutions. The trimmed output compared side-by-side with the original data is part of the automated PDF output. We show how this tool can help data analysis by providing a few examples, including an increased percentage of reads recruited to references, improved single nucleotide polymorphism identification as well as de novo sequence assembly metrics. Conclusion: FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.« less

  19. Rapid evaluation and quality control of next generation sequencing data with FaQCs

    SciTech Connect

    Lo, Chien -Chi; Chain, Patrick S. G.

    2014-12-01

    Background: Next generation sequencing (NGS) technologies that parallelize the sequencing process and produce thousands to millions, or even hundreds of millions of sequences in a single sequencing run, have revolutionized genomic and genetic research. Because of the vagaries of any platform's sequencing chemistry, the experimental processing, machine failure, and so on, the quality of sequencing reads is never perfect, and often declines as the read is extended. These errors invariably affect downstream analysis/application and should therefore be identified early on to mitigate any unforeseen effects. Results: Here we present a novel FastQ Quality Control Software (FaQCs) that can rapidly process large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. Both the speed of processing and the memory footprint of storing all required information have been optimized via algorithmic and parallel processing solutions. The trimmed output compared side-by-side with the original data is part of the automated PDF output. We show how this tool can help data analysis by providing a few examples, including an increased percentage of reads recruited to references, improved single nucleotide polymorphism identification as well as de novo sequence assembly metrics. Conclusion: FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.

  20. Anabolic ornithine carbamoyltransferase of Pseudomonas aeruginosa: nucleotide sequence and transcriptional control of the argF structural gene.

    PubMed Central

    Itoh, Y; Soldati, L; Stalon, V; Falmagne, P; Terawaki, Y; Leisinger, T; Haas, D

    1988-01-01

    In Pseudomonas aeruginosa PAO the anabolic ornithine carbamoyltransferase (OTCase, EC 2.1.3.3) is the product of the argF gene and the only arginine biosynthetic enzyme whose synthesis is repressible by arginine. We have determined the complete nucleotide sequence of the argF gene including its promoter-control region. The deduced amino acid sequence of the anabolic OTCase consists of 305 residues (Mr 33,924), and this was confirmed by the N-terminal amino acid sequence, the total amino acid composition, and the subunit Mr of the purified enzyme. The native anabolic OTCase (Mr 110,000 to 125,000) was found to be a trimer by cross-linking experiments. P. aeruginosa also has a catabolic OTCase (the arcB gene product), which catalyzes the reverse reaction of the anabolic conversion. At the nucleotide sequence level, the P. aeruginosa argF gene had 52.4% identity with the arcB gene. The Escherichia coli argF and argI genes, which code for anabolic OTCase isoenzymes, had 47.3 and 44.9% identity, respectively, with the P. aeruginosa argF sequence. This suggests that these four genes have evolved from a common ancestral gene. The arcB gene appears to be more closely related to the E. coli argF gene than to the P. aeruginosa argF gene. Two transcripts (mRNA-1, mRNA-2) of the P. aeruginosa argF gene were identified by S1 mapping. The transcription initiation site for mRNA-1 was preceded by sequences having partial homology with the E. coli -35 and -10 consensus promoter sequences. No sequence similar to consensus promoters of enteric bacteria was found upstream of the 5' end of mRNA-2. E. coli carrying a P. aeruginosa argF+ recombinant plasmid produced mRNA-1 with low efficiency but no (or very little) mRNA-2. Arginine repressed argF transcription in P. aeruginosa. In the argF promoter region no sequence homologous to the "arg box" (arginine operator module) of E. coli was found. The mechanism of arginine repression in P. aeruginosa thus appears to be different from that in

  1. Complete mitochondrial genome of the frillneck lizard (Chlamydosaurus kingii, Reptilia; Agamidae), another squamate with two control regions.

    PubMed

    Ujvari, Beata; Madsen, Thomas

    2008-10-01

    Using PCR, the complete mitochondrial genome was sequenced in three frillneck lizards (Chlamydosaurus kingii). The mitochondria spanned over 16,761bp. As in other vertebrates, two rRNA genes, 22 tRNA genes and 13 protein coding genes were identified. However, similar to some other squamate reptiles, two control regions (CRI and CRII) were identified, spanning 801 and 812 bp, respectively. Our results were compared with another Australian member of the family Agamidae, the bearded dragon (Pogana vitticeps). The overall base composition of the light-strand sequence largely mirrored that observed in P vitticeps. Furthermore, similar to P. vitticeps, we observed an insertion 801 bp long between the ND5 and ND6 genes. However, in contrast to P vitticeps we did not observe a conserved sequence block III region. Based on a comparison among the three frillneck lizards, we also present data on the proportion of variable sites within the major mitochondrial regions. PMID:19489141

  2. Capture and identification of proteins that bind to a GGA-rich sequence from the ERBB2 gene promoter region.

    PubMed

    Zhang, Tian; Zhang, Huiping; Wang, Yuexi; McGown, Linda B

    2012-10-01

    The ERBB2 gene (HER2/neu) is overexpressed in many human breast cancers. It is an important therapeutic target and its product protein is a key biomarker for breast cancer. A 28-bp GGA repeat sequence (Pu28-mer) in the nuclease hypersensitive site of the ERBB2 promoter region may play an important role in the regulation of ERBB2 transcription, possibly involving the formation of a G-quadruplex. In order to investigate this possibility, an affinity MALDI-MS approach was used for in vitro protein capture from nuclear extracts from cultured MCF-7 and BT-474 cancer cells at Pu28-mer and control oligonucleotide-modified surfaces. Captured proteins from MCF-7 cells were analyzed by LC-MS/MS. Based on these results, Western blot was then used to interrogate captured proteins from both MCF-7 and the Her-2/neu-positive BT-474 cells. Results support the formation of a G-quadruplex by Pu28-mer, indicated by circular dichroism spectroscopy, that selectively captures transcription factors including Ku70, Ku80, PURA, nucleolin, and hnRNP K. Chromatin immunoprecipitation confirmed binding of Ku70, Ku80, PURA, and nucleolin to ERBB2 promoter in the live BT-474 cells. These findings may lead to a better understanding of the role of non-duplex DNA structures in gene regulation and provide a more complete picture of the regulation of ErbB2 expression in breast cancer. The results also provide a blueprint for development of "genome-inspired" aptamers based on the Pu28-mer sequence for in vitro and in vivo detection of proteins related to regulation of ERBB2 gene expression and breast cancer. PMID:22899247

  3. The human growth hormone gene is regulated by a multicomponent locus control region

    SciTech Connect

    Jones, B.; Cooke, N.E.; Liebhaber, S.A.; Monks, B.R.

    1995-12-01

    This article describes research involving the five-member human growth hormone (hGH)/chorionic somatomammotropin (hCS) gene cluster and its expression in the placenta. The results indicate that interactions among multiple elements are required to restrict hGH transcription to the pituitary and generate appropriate levels of expression in the mouse genome. In addition, the results suggest a role for shared and unique regulatory sequences in locus control region-mediated expression of the hGH/hCS gene cluster in the pituitary and possibly the placenta. 67 refs., 9 figs.

  4. Sequence-based definition of eight short tandem repeat loci located within the HLA-region in an Austrian population.

    PubMed

    Dauber, Eva-Maria; Wenda, Sabine; Schwartz-Jungl, Elisabeth Maria; Glock, Barbara; Mayr, Wolfgang R

    2015-01-01

    Sequenced allelic ladders are a prerequisite for reliable genotyping of short tandem repeat (STR) polymorphisms and consistent results across instrument platforms. For eight STR-loci located on the short arm of chromosome 6 (6p21.3), a sequenced based nomenclature was established according to international recommendations. Publicly available reference DNA samples were sequenced enabling interested laboratories to construct their own allelic ladders. Three tetrameric (D6S2691, D6S2678, DQIV), one trimeric (D6S2906) and four dimeric repeat loci (D6S2972, D6S2792, D6S2789, D6S273) were investigated. Apart from the very complex sequence structure at the DQIV locus, three loci showed a compound and four loci a simple repeat pattern. In the flanking regions of some loci additional single nucleotide and insertion/deletion polymorphisms occurred as well as sequence polymorphisms within the repeat region of alleles with the same length. In an Austrian Caucasoid population sample (n=293) between eight and 22 alleles were found. No significant deviation from Hardy-Weinberg expectations was observed, the power of discrimination ranged from 0.826 to 0.978. The loci cover the HLA-coding region from HLA-A to HLA-DQB1 and can be used for a better definition of HLA haplotypes for population and disease association studies, recombination point mapping, haematopoietic stem cell transplantation as well as for identity and relationship testing. PMID:25450788

  5. An approach to delineate primers for a group of poorly conserved sequences incorporating the common motif region.

    PubMed

    Sahu, Mousumi; Sahu, Jagajjit; Sahoo, Smita; Dehury, Budheswar; Sarma, Kishore; Sarmah, Ranjan; Sen, Priyabrata; Modi, Mahendra Kumar; Barooah, Madhumita

    2012-01-01

    Glutathione synthetase (gshB) has previously been reported to confer tolerance to acidic soil condition in Rhizobium species. Cloning the gene coding for this enzyme necessitates the designing of proper primer sets which in turn depends on the identification of high quality sequence similarity in multiple global alignments. In this experiment, a group of homologous gene sequences related to gshB gene (accession no: gi-86355669:327589-328536) of Rhizobium etli CFN 42, were extracted from NCBI nucleotide sequence databases using BLASTN and were analyzed for designing degenerate primers. However, the T-coffee multiple global alignment results did not show any block of conserved region for the above sequence set to design the primers. Therefore, we attempted to identify the location of common motif region based on multiple local alignments employing the MEME algorithm supported with MAST and Primer3. The results revealed some common motif regions that enabled us to design the primer sets for related gshB gene sequences. The result will be validated in wet lab. PMID:22419837

  6. Emerging infectious diseases in southeast Asia: regional challenges to control.

    PubMed

    Coker, Richard J; Hunter, Benjamin M; Rudge, James W; Liverani, Marco; Hanvoravongchai, Piya

    2011-02-12

    Southeast Asia is a hotspot for emerging infectious diseases, including those with pandemic potential. Emerging infectious diseases have exacted heavy public health and economic tolls. Severe acute respiratory syndrome rapidly decimated the region's tourist industry. Influenza A H5N1 has had a profound effect on the poultry industry. The reasons why southeast Asia is at risk from emerging infectious diseases are complex. The region is home to dynamic systems in which biological, social, ecological, and technological processes interconnect in ways that enable microbes to exploit new ecological niches. These processes include population growth and movement, urbanisation, changes in food production, agriculture and land use, water and sanitation, and the effect of health systems through generation of drug resistance. Southeast Asia is home to about 600 million people residing in countries as diverse as Singapore, a city state with a gross domestic product (GDP) of US$37,500 per head, and Laos, until recently an overwhelmingly rural economy, with a GDP of US$890 per head. The regional challenges in control of emerging infectious diseases are formidable and range from influencing the factors that drive disease emergence, to making surveillance systems fit for purpose, and ensuring that regional governance mechanisms work effectively to improve control interventions. PMID:21269678

  7. Control of bootstrap current in the pedestal region of tokamaks

    SciTech Connect

    Shaing, K. C.; Lai, A. L.

    2013-12-15

    The high confinement mode (H-mode) plasmas in the pedestal region of tokamaks are characterized by steep gradient of the radial electric field, and sonic poloidal U{sub p,m} flow that consists of poloidal components of the E×B flow and the plasma flow velocity that is parallel to the magnetic field B. Here, E is the electric field. The bootstrap current that is important for the equilibrium, and stability of the pedestal of H-mode plasmas is shown to have an expression different from that in the conventional theory. In the limit where ‖U{sub p,m}‖≫ 1, the bootstrap current is driven by the electron temperature gradient and inductive electric field fundamentally different from that in the conventional theory. The bootstrap current in the pedestal region can be controlled through manipulating U{sub p,m} and the gradient of the radial electric. This, in turn, can control plasma stability such as edge-localized modes. Quantitative evaluations of various coefficients are shown to illustrate that the bootstrap current remains finite when ‖U{sub p,m}‖ approaches infinite and to provide indications how to control the bootstrap current. Approximate analytic expressions for viscous coefficients that join results in the banana and plateau-Pfirsch-Schluter regimes are presented to facilitate bootstrap and neoclassical transport simulations in the pedestal region.

  8. Control of bootstrap current in the pedestal region of tokamaks

    NASA Astrophysics Data System (ADS)

    Shaing, K. C.; Lai, A. L.

    2013-12-01

    The high confinement mode (H-mode) plasmas in the pedestal region of tokamaks are characterized by steep gradient of the radial electric field, and sonic poloidal Up ,m flow that consists of poloidal components of the E ×B flow and the plasma flow velocity that is parallel to the magnetic field B. Here, E is the electric field. The bootstrap current that is important for the equilibrium, and stability of the pedestal of H-mode plasmas is shown to have an expression different from that in the conventional theory. In the limit where |Up ,m| ≫ 1, the bootstrap current is driven by the electron temperature gradient and inductive electric field fundamentally different from that in the conventional theory. The bootstrap current in the pedestal region can be controlled through manipulating Up ,m and the gradient of the radial electric. This, in turn, can control plasma stability such as edge-localized modes. Quantitative evaluations of various coefficients are shown to illustrate that the bootstrap current remains finite when |Up ,m| approaches infinite and to provide indications how to control the bootstrap current. Approximate analytic expressions for viscous coefficients that join results in the banana and plateau-Pfirsch-Schluter regimes are presented to facilitate bootstrap and neoclassical transport simulations in the pedestal region.

  9. Complex repetitive arrangements of gene sequence in the candidate region of the spinal muscular atrophy gene in 5q13

    SciTech Connect

    Theodosiou, A.M.; Nesbit, A.M.; Daniels, R.J.; Campbell, L.; Francis, M.J.; Christodoulou, Z.; Morrison, K.E.; Davies, K.E. |

    1994-12-01

    Childhood-onset proximal spinal muscular atrophy (SMA) is a heritable neurological disorder, which has been mapped by genetic linkage analysis to chromosome 5q13, in the interval between markers D5S435 and D5S557. Here, we present gene sequences that have been isolated from this interval, several of which show sequence homologies to exons of {beta}-glucuronidase. These gene sequences are repeated several times across the candidate region and are also present on chromosome 5p. The arrangement of these repetitive gene motifs is polymorphic between individuals. The high degree of variability observed may have some influence on the expression of the genes in the region. Since SMA is not inherited as a classical autosomal recessive disease, novel genomic rearrangements arising from aberrant recombination events between the complex repeats may be associated with the phenotype observed.

  10. Three Ingredients for Improved Global Aftershock Forecasts: Tectonic Region, Time-Dependent Catalog Incompleteness, and Inter-Sequence Variability

    NASA Astrophysics Data System (ADS)

    Page, M. T.; Hardebeck, J.; Felzer, K. R.; Michael, A. J.; van der Elst, N.

    2015-12-01

    Following a large earthquake, seismic hazard can be orders of magnitude higher than the long-term average as a result of aftershock triggering. Due to this heightened hazard, there is a demand from emergency managers and the public for rapid, authoritative, and reliable aftershock forecasts. In the past, USGS aftershock forecasts following large, global earthquakes have been released on an ad-hoc basis with inconsistent methods, and in some cases, aftershock parameters adapted from California. To remedy this, we are currently developing an automated aftershock product that will generate more accurate forecasts based on the Reasenberg and Jones (Science, 1989) method. To better capture spatial variations in aftershock productivity and decay, we estimate regional aftershock parameters for sequences within the Garcia et al. (BSSA, 2012) tectonic regions. We find that regional variations for mean aftershock productivity exceed a factor of 10. The Reasenberg and Jones method combines modified-Omori aftershock decay, Utsu productivity scaling, and the Gutenberg-Richter magnitude distribution. We additionally account for a time-dependent magnitude of completeness following large events in the catalog. We generalize the Helmstetter et al. (2005) equation for short-term aftershock incompleteness and solve for incompleteness levels in the global NEIC catalog following large mainshocks. In addition to estimating average sequence parameters within regions, we quantify the inter-sequence parameter variability. This allows for a more complete quantification of the forecast uncertainties and Bayesian updating of the forecast as sequence-specific information becomes available.

  11. Comparison of Sequences from the Ribosomal DNA Intergenic Region of Meloidogyne mayaguensis and Other Major Tropical Root-Knot Nematodes

    PubMed Central

    Blok, V. C.; Phillips, M. S.; Fargette, M.

    1997-01-01

    The unusual arrangement of the 5S ribosomal gene within the intergenic sequence (IGS) of the ribosomal cistron, previously reported for Meloidogyne arenaria, was also found in the ribosomal DNA of two other economically important species of tropical root-knot nematodes, M, incognita and M. javanica. This arrangement also was found in M. hapla, which is important in temperate regions, and M. mayaguensis, a virulent species of concern in West Africa. Amplification of the region between the 5S and 18S genes by PCR yielded products of three different sizes such that M. mayaguensis could be readily differentiated from the other species in this study. This product can be amplified from single juveniles, females, or egg masses. The sequences obtained in this region for one line of each of M. incognita, M. arenaria, and M. javanica were very similar, reflecting the close relationships of these lineages. The M. mayaguensis sequence for this region had a number of small deletions and insertions of various sizes, including possible sequence duplications. PMID:19274129

  12. Genetic Diversity of Toxoplasma gondii Strains from Different Hosts and Geographical Regions by Sequence Analysis of GRA20 Gene.

    PubMed

    Ning, Hong-Rui; Huang, Si-Yang; Wang, Jin-Lei; Xu, Qian-Ming; Zhu, Xing-Quan

    2015-06-01

    Toxoplasma gondii is a eukaryotic parasite of the phylum Apicomplexa, which infects all warm-blood animals, including humans. In the present study, we examined sequence variation in dense granule 20 (GRA20) genes among T. gondii isolates collected from different hosts and geographical regions worldwide. The complete GRA20 genes were amplified from 16 T. gondii isolates using PCR, sequence were analyzed, and phylogenetic reconstruction was analyzed by maximum parsimony (MP) and maximum likelihood (ML) methods. The results showed that the complete GRA20 gene sequence was 1,586 bp in length among all the isolates used in this study, and the sequence variations in nucleotides were 0-7.9% among all strains. However, removing the type III strains (CTG, VEG), the sequence variations became very low, only 0-0.7%. These results indicated that the GRA20 sequence in type III was more divergence. Phylogenetic analysis of GRA20 sequences using MP and ML methods can differentiate 2 major clonal lineage types (type I and type III) into their respective clusters, indicating the GRA20 gene may represent a novel genetic marker for intraspecific phylogenetic analyses of T. gondii. PMID:26174830

  13. Genetic Diversity of Toxoplasma gondii Strains from Different Hosts and Geographical Regions by Sequence Analysis of GRA20 Gene

    PubMed Central

    Ning, Hong-Rui; Huang, Si-Yang; Wang, Jin-Lei; Xu, Qian-Ming; Zhu, Xing-Quan

    2015-01-01

    Toxoplasma gondii is a eukaryotic parasite of the phylum Apicomplexa, which infects all warm-blood animals, including humans. In the present study, we examined sequence variation in dense granule 20 (GRA20) genes among T. gondii isolates collected from different hosts and geographical regions worldwide. The complete GRA20 genes were amplified from 16 T. gondii isolates using PCR, sequence were analyzed, and phylogenetic reconstruction was analyzed by maximum parsimony (MP) and maximum likelihood (ML) methods. The results showed that the complete GRA20 gene sequence was 1,586 bp in length among all the isolates used in this study, and the sequence variations in nucleotides were 0-7.9% among all strains. However, removing the type III strains (CTG, VEG), the sequence variations became very low, only 0-0.7%. These results indicated that the GRA20 sequence in type III was more divergence. Phylogenetic analysis of GRA20 sequences using MP and ML methods can differentiate 2 major clonal lineage types (type I and type III) into their respective clusters, indicating the GRA20 gene may represent a novel genetic marker for intraspecific phylogenetic analyses of T. gondii. PMID:26174830

  14. Sequence and analysis of the human ABL gene, the BCR gene, and regions involved in the Philadelphia chromosomal translocation

    SciTech Connect

    Burian, D.; Clifton, S.W.; Crabtree, J.

    1995-05-01

    The complete human BCR gene (152j-141 nt) on chromosome 22 and greater than 80% of the human ABL gene (179-512 nt) on chromosome 9 have been sequenced from mapped cosmid and plasmid clones via a shotgun strategy. Because these two chromosomes are translocated with breakpoints within the BCR and ABL genes in Philadelphia chromosome-positive leukemias, knowledge of these sequences also might provide insight into the validity of various theories of chromosomal rearrangements. Comparison of these genes with their cDNA sequences reveal the positions of 23 BCR exons and putative alternative BCR first and second exons, as well as the common ABL exons 2-11, respectively. Additionally, these regions include the alternative ABL first exons 1b and 1a, a new gene 5` to the first ABL exon, and an open reading frame with homology to an EST within the BCR fourth intron. Further analysis reveals an Alu homology of 38.83 and 39.35% for the BCR and ABL genes, respectively, with other repeat elements present to a lesser extent. Four new Philadelphia chromosome translocation breakpoints from chronic myelogenous leukemia patients also were sequenced, and the positions of these and several other previously sequenced breakpoints now have been mapped precisely, although no consistent breakpoint features immediately were apparent. Comparative analysis of genomic sequences encompassing the murine homologues to the human ABL exons 1b and 1a, as well as regions encompassing the ABL exons 2 and 3, reveals that although there is a high degree of homology in their corresponding exons and promoter regions, these two vertebrate species show a striking lack of homology outside these regions. 122 refs., 5 figs., 4 tabs.

  15. Overlapping signal sequences control nuclear localization and endoplasmic reticulum retention of GRP58

    SciTech Connect

    Adikesavan, Anbu Karani; Unni, Emmanual; Jaiswal, Anil K.

    2008-12-12

    Glucose-regulated GRP58 has shown clinical applications to endoplasmic reticulum (ER) stress and cancer. GRP58 is localized in the cytosol, endoplasmic reticulum (ER) and nucleus. Twenty-four amino acids at the N-terminal hydrophobic region are known to target GRP58 to ER for synthesis at the ER membrane and translocation into the ER lumen. In addition, GRP58 contains putative nuclear localization (494KPKKKKK500) and ER retention (502QEDL505) signals. However, the role of these signals in nuclear import and ER retention of GRP58 remains unknown. Present studies investigated the signals that control nuclear localization and ER retention of GRP58. Deletion/mutation of nuclear localization signal (NLS) abrogated nuclear import of GRP58. NLS attached to EGFP localized EGFP in the nucleus. However, deletion/mutation of putative ER retention signal alone did not alter ER retention of GRP58. Interestingly, a combined deletion/mutation of NLS and ER retention signals blocked the GRP58 retention in the ER. These results concluded that overlapping NLS and ER retention signal sequences regulate nuclear localization and ER retention of GRP58.

  16. Protein engineering of selected residues from conserved sequence regions of a novel Anoxybacillus α-amylase.

    PubMed

    Ranjani, Velayudhan; Janeček, Stefan; Chai, Kian Piaw; Shahir, Shafinaz; Abdul Rahman, Raja Noor Zaliha Raja; Chan, Kok-Gan; Goh, Kian Mau

    2014-01-01

    The α-amylases from Anoxybacillus species (ASKA and ADTA), Bacillus aquimaris (BaqA) and Geobacillus thermoleovorans (GTA, Pizzo and GtamyII) were proposed as a novel group of the α-amylase family GH13. An ASKA yielding a high percentage of maltose upon its reaction on starch was chosen as a model to study the residues responsible for the biochemical properties. Four residues from conserved sequence regions (CSRs) were thus selected, and the mutants F113V (CSR-I), Y187F and L189I (CSR-II) and A161D (CSR-V) were characterised. Few changes in the optimum reaction temperature and pH were observed for all mutants. Whereas the Y187F (t1/2 43 h) and L189I (t1/2 36 h) mutants had a lower thermostability at 65°C than the native ASKA (t1/2 48 h), the mutants F113V and A161D exhibited an improved t1/2 of 51 h and 53 h, respectively. Among the mutants, only the A161D had a specific activity, k(cat) and k(cat)/K(m) higher (1.23-, 1.17- and 2.88-times, respectively) than the values determined for the ASKA. The replacement of the Ala-161 in the CSR-V with an aspartic acid also caused a significant reduction in the ratio of maltose formed. This finding suggests the Ala-161 may contribute to the high maltose production of the ASKA. PMID:25069018

  17. Translational control by 5'-untranslated regions of eukaryotic mRNAs.

    PubMed

    Hinnebusch, Alan G; Ivanov, Ivaylo P; Sonenberg, Nahum

    2016-06-17

    The eukaryotic 5' untranslated region (UTR) is critical for ribosome recruitment to the messenger RNA (mRNA) and start codon choice and plays a major role in the control of translation efficiency and shaping the cellular proteome. The ribosomal initiation complex is assembled on the mRNA via a cap-dependent or cap-independent mechanism. We describe various mechanisms controlling ribosome scanning and initiation codon selection by 5' upstream open reading frames, translation initiation factors, and primary and secondary structures of the 5'UTR, including particular sequence motifs. We also discuss translational control via phosphorylation of eukaryotic initiation factor 2, which is implicated in learning and memory, neurodegenerative diseases, and cancer. PMID:27313038

  18. On Sequence Learning Models: Open-loop Control Not Strictly Guided by Hick's Law.

    PubMed

    Pavão, Rodrigo; Savietto, Joice P; Sato, João R; Xavier, Gilberto F; Helene, André F

    2016-01-01

    According to the Hick's law, reaction times increase linearly with the uncertainty of target stimuli. We tested the generality of this law by measuring reaction times in a human sequence learning protocol involving serial target locations which differed in transition probability and global entropy. Our results showed that sigmoid functions better describe the relationship between reaction times and uncertainty when compared to linear functions. Sequence predictability was estimated by distinct statistical predictors: conditional probability, conditional entropy, joint probability and joint entropy measures. Conditional predictors relate to closed-loop control models describing that performance is guided by on-line access to past sequence structure to predict next location. Differently, joint predictors relate to open-loop control models assuming global access of sequence structure, requiring no constant monitoring. We tested which of these predictors better describe performance on the sequence learning protocol. Results suggest that joint predictors are more accurate than conditional predictors to track performance. In conclusion, sequence learning is better described as an open-loop process which is not precisely predicted by Hick's law. PMID:26975409

  19. On Sequence Learning Models: Open-loop Control Not Strictly Guided by Hick’s Law

    PubMed Central

    Pavão, Rodrigo; Savietto, Joice P.; Sato, João R.; Xavier, Gilberto F.; Helene, André F.

    2016-01-01

    According to the Hick’s law, reaction times increase linearly with the uncertainty of target stimuli. We tested the generality of this law by measuring reaction times in a human sequence learning protocol involving serial target locations which differed in transition probability and global entropy. Our results showed that sigmoid functions better describe the relationship between reaction times and uncertainty when compared to linear functions. Sequence predictability was estimated by distinct statistical predictors: conditional probability, conditional entropy, joint probability and joint entropy measures. Conditional predictors relate to closed-loop control models describing that performance is guided by on-line access to past sequence structure to predict next location. Differently, joint predictors relate to open-loop control models assuming global access of sequence structure, requiring no constant monitoring. We tested which of these predictors better describe performance on the sequence learning protocol. Results suggest that joint predictors are more accurate than conditional predictors to track performance. In conclusion, sequence learning is better described as an open-loop process which is not precisely predicted by Hick’s law. PMID:26975409

  20. Regional seismic stratigraphy and controls on the Quaternary evolution of the Cape Hatteras region of the Atlantic passive margin, USA

    USGS Publications Warehouse

    Mallinson, D.J.; Culver, S.J.; Riggs, S.R.; Thieler, E.R.; Foster, D.; Wehmiller, J.; Farrell, K.M.; Pierson, J.

    2010-01-01

    Seismic and core data, combined with amino acid racemization and strontium-isotope age data, enable the definition of the Quaternary stratigraphic framework and recognition of geologic controls on the development of the modern coastal system of North Carolina, U.S.A. Seven regionally continuous high amplitude reflections are defined which bound six seismic stratigraphic units consisting of multiple regionally discontinuous depositional sequences and parasequence sets, and enable an understanding of the evolution of this margin. Data reveal the progressive eastward progradation and aggradation of the Quaternary shelf. The early Pleistocene inner shelf occurs at a depth of ca. 20-40 m beneath the western part of the modern estuarine system (Pamlico Sound). A mid- to outer shelf lowstand terrace (also early Pleistocene) with shelf sand ridge deposits comprising parasequence sets within a transgressive systems tract, occurs at a deeper level (ca. 45-70 m) beneath the modern barrier island system (the Outer Banks) and northern Pamlico Sound. Seismic and foraminiferal paleoenvironmental data from cores indicate the occurrence of lowstand strandplain shoreline deposits on the early to middle Pleistocene shelf. Middle to late Pleistocene deposits occur above a prominent unconformity and marine flooding surface that truncates underlying units, and contain numerous filled fluvial valleys that are incised into the early and middle Pleistocene deposits. The stratigraphic framework suggests margin progradation and aggradation modified by an increase in the magnitude of sea-level fluctuations during the middle to late Pleistocene, expressed as falling stage, lowstand, transgressive and highstand systems tracts. Thick stratigraphic sequences occur within the middle Pleistocene section, suggesting the occurrence of high capacity fluvial point sources debouching into the area from the west and north. Furthermore, the antecedent topography plays a significant role in the evolution

  1. Single nucleotide polymorphism mining and nucleotide sequence analysis of Mx1 gene in exonic regions of Japanese quail

    PubMed Central

    Niraj, Diwesh Kumar; Kumar, Pushpendra; Mishra, Chinmoy; Narayan, Raj; Bhattacharya, Tarun Kumar; Shrivastava, Kush; Bhushan, Bharat; Tiwari, Ashok Kumar; Saxena, Vishesh; Sahoo, Nihar Ranjan; Sharma, Deepak

    2015-01-01

    Aim: An attempt has been made to study the Myxovirus resistant (Mx1) gene polymorphism in Japanese quail. Materials and Methods: In the present, investigation four fragments viz. Fragment I of 185 bp (Exon 3 region), Fragment II of 148 bp (Exon 5 region), Fragment III of 161 bp (Exon 7 region), and Fragment IV of 176 bp (Exon 13 region) of Mx1 gene were amplified and screened for polymorphism by polymerase chain reaction-single-strand conformation polymorphism technique in 170 Japanese quail birds. Results: Out of the four fragments, one fragment (Fragment II) was found to be polymorphic. Remaining three fragments (Fragment I, III, and IV) were found to be monomorphic which was confirmed by custom sequencing. Overall nucleotide sequence analysis of Mx1 gene of Japanese quail showed 100% homology with common quail and more than 80% homology with reported sequence of chicken breeds. Conclusion: The Mx1 gene is mostly conserved in Japanese quail. There is an urgent need of comprehensive analysis of other regions of Mx1 gene along with its possible association with the traits of economic importance in Japanese quail. PMID:27047057

  2. Evolution of vertebrate IgM: complete amino acid sequence of the constant region of Ambystoma mexicanum mu chain deduced from cDNA sequence.

    PubMed

    Fellah, J S; Wiles, M V; Charlemagne, J; Schwager, J

    1992-10-01

    cDNA clones coding for the constant region of the Mexican axolotl (Ambystoma mexicanum) mu heavy immunoglobulin chain were selected from total spleen RNA, using a cDNA polymerase chain reaction technique. The specific 5'-end primer was an oligonucleotide homologous to the JH segment of Xenopus laevis mu chain. One of the clones, JHA/3, corresponded to the complete constant region of the axolotl mu chain, consisting of a 1362-nucleotide sequence coding for a polypeptide of 454 amino acids followed in 3' direction by a 179-nucleotide untranslated region and a polyA+ tail. The axolotl C mu is divided into four typical domains (C mu 1-C mu 4) and can be aligned with the Xenopus C mu with an overall identity of 56% at the nucleotide level. Percent identities were particularly high between C mu 1 (59%) and C mu 4 (71%). The C-terminal 20-amino acid segment which constitutes the secretory part of the mu chain is strongly homologous to the equivalent sequences of chondrichthyans and of other tetrapods, including a conserved N-linked oligosaccharide, the penultimate cysteine and the C-terminal lysine. The four C mu domains of 13 vertebrate species ranging from chondrichthyans to mammals were aligned and compared at the amino acid level. The significant number of mu-specific residues which are conserved into each of the four C mu domains argues for a continuous line of evolution of the vertebrate mu chain. This notion was confirmed by the ability to reconstitute a consistent vertebrate evolution tree based on the phylogenic parsimony analysis of the C mu 4 sequences. PMID:1382992

  3. Identification and mapping of DNA binding proteins target sequences in long genomic regions by two-dimensional EMSA.

    PubMed

    Chernov, Igor P; Akopov, Sergey B; Nikolaev, Lev G; Sverdlov, Eugene D

    2006-07-01

    Specific binding of nuclear proteins, in particular transcription factors, to target DNA sequences is a major mechanism of genome functioning and gene expression regulation in eukaryotes. Therefore, identification and mapping specific protein target sites (PTS) is necessary for understanding genomic regulation. Here we used a novel two-dimensional electrophoretic mobility shift assay (2D-EMSA) procedure for identification and mapping of 52 PTS within a 563-kb human genome region located between the FXYD5 and TZFP genes. The PTS occurred with approximately equal frequency within unique and repetitive genomic regions. PTS belonging to unique sequences tended to group together within gene introns and close to their 5' and 3' ends, whereas PTS located within repeats were evenly distributed between transcribed and intragenic regions. PMID:16869519

  4. Full-genome sequences of hepatitis B virus subgenotype D3 isolates from the Brazilian Amazon Region.

    PubMed

    Spitz, Natália; Mello, Francisco C A; Araujo, Natalia Motta

    2015-02-01

    The Brazilian Amazon Region is a highly endemic area for hepatitis B virus (HBV). However, little is known regarding the genetic variability of the strains circulating in this geographical region. Here, we describe the first full-length genomes of HBV isolated in the Brazilian Amazon Region; these genomes are also the first complete HBV subgenotype D3 genomes reported for Brazil. The genomes of the five Brazilian isolates were all 3,182 base pairs in length and the isolates were classified as belonging to subgenotype D3, subtypes ayw2 (n = 3) and ayw3 (n = 2). Phylogenetic analysis suggested that the Brazilian sequences are not likely to be closely related to European D3 sequences. Such results will contribute to further epidemiological and evolutionary studies of HBV. PMID:25742278

  5. Detection of spurious interruptions of protein-coding regions in cloned cDNA sequences by GeneMark analysis.

    PubMed

    Hirosawa, M; Ishikawa, K; Nagase, T; Ohara, O

    2000-09-01

    cDNA is an artificial copy of mRNA and, therefore, no cDNA can be completely free from suspicion of cloning errors. Because overlooking these cloning errors results in serious misinterpretation of cDNA sequences, development of an alerting system targeting spurious sequences in cloned cDNAs is an urgent requirement for massive cDNA sequence analysis. We describe here the application of a modified GeneMark program, originally designed for prokaryotic gene finding, for detection of artifacts in cDNA clones. This program serves to provide a warning when any spurious split of protein-coding regions is detected through statistical analysis of cDNA sequences based on Markov models. In this study, 817 cDNA sequences deposited in public databases by us were subjected to analysis using this alerting system to assess its sensitivity and specificity. The results indicated that any spurious split of protein-coding regions in cloned cDNAs could be sensitively detected and systematically revised by means of this system after the experimental validation of the alerts. Furthermore, this study offered us, for the first time, statistical data regarding the rates and types of errors causing protein-coding splits in cloned cDNAs obtained by conventional cloning methods. PMID:10984451

  6. Whole-genome sequencing reveals small genomic regions of introgression in an introduced crater lake population of threespine stickleback.

    PubMed

    Yoshida, Kohta; Miyagi, Ryutaro; Mori, Seiichi; Takahashi, Aya; Makino, Takashi; Toyoda, Atsushi; Fujiyama, Asao; Kitano, Jun

    2016-04-01

    Invasive species pose a major threat to biological diversity. Although introduced populations often experience population bottlenecks, some invasive species are thought to be originated from hybridization between multiple populations or species, which can contribute to the maintenance of high genetic diversity. Recent advances in genome sequencing enable us to trace the evolutionary history of invasive species even at whole-genome level and may help to identify the history of past hybridization that may be overlooked by traditional marker-based analysis. Here, we conducted whole-genome sequencing of eight threespine stickleback (Gasterosteus aculeatus) individuals, four from a recently introduced crater lake population and four of the putative source population. We found that both populations have several small genomic regions with high genetic diversity, which resulted from introgression from a closely related species (Gasterosteus nipponicus). The sizes of the regions were too small to be detected with traditional marker-based analysis or even some reduced-representation sequencing methods. Further amplicon sequencing revealed linkage disequilibrium around an introgression site, which suggests the possibility of selective sweep at the introgression site. Thus, interspecies introgression might predate introduction and increase genetic variation in the source population. Whole-genome sequencing of even a small number of individuals can therefore provide higher resolution inference of history of introduced populations. PMID:27069575

  7. Phylogenetic relationship of Turkish Apis mellifera subspecies based on sequencing of mitochondrial cytochrome C oxidase I region.

    PubMed

    Özdil, F; İlhan, F

    2012-01-01

    Mitochondrial DNA sequence variation can be used to infer honey bee evolutionary relationships. We examined DNA sequence diversity in the cytochrome C oxidase I (COI or Cox1) gene segment of the mitochondrial genome in 112 samples of Apis mellifera from 15 different populations in Turkey. Six novel haplotypes were found for the COI gene segment. There were eight variable sites in the COI gene, although only three were parsimony-informative sites. The mean pairwise genetic distance was 0.3% for the COI gene segment. Neighbor-joining (NJ) trees of the COI gene segment were constructed with the published sequences of A. mellifera haplotypes that are available in GenBank; the genetic variation was compared among the different honeybee haplotypes. The NJ dendogram based on the COI sequences available in GenBank showed that Eastern European races were clustered together, whereas the Mellifera and Iberian haplotypes were clustered far apart. The haplotypes found in this study were clustered together with A. mellifera ligustica and some of the Greek honey bees (accession Nos. GU056169 and GU056170) found in NCBI GenBank database. This study expands the knowledge about the mitochondrial COI region and presents the first comprehensive sequence analysis of this region in Turkish honeybees. PMID:22614282

  8. Phylogenetic relations of humans and African apes from DNA sequences in the Psi eta-globin region

    SciTech Connect

    Miyamoto, M.M.; Slightom, J.L.; Goodman, M.

    1987-10-16

    Sequences from the upstream and downstream flanking DNA regions of the Psi eta-globin locus in Pan troglodytes (common chimpanzee), Gorilla gorilla (gorilla), and Pongo pygmaeus (orangutan, the closest living relative to Homo, Pan, and Gorilla) provided further data for evaluating the phylogenetic relations of humans and African apes. These newly sequenced orthologs (an additional 4.9 kilobase pairs (kbp) for each species) were combined with published Psi eta-gene sequences and then compared to the same orthologous stretch (a continuous 7.1-kbp region) available for humans. Phylogenetic analysis of these nucleotide sequences by the parsimony method indicated (i) that human and chimpanzee are more closely related to each other than either is to gorilla and (ii) that the slowdown in the rate of sequence evolution evident in higher primates is especially pronounced in humans. These results indicate that features unique to African apes (but not to humans) are primitive and that even local molecular clocks should be applied with caution.

  9. 40 CFR 81.77 - Puerto Rico Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Puerto Rico Air Quality Control Region... Control Regions § 81.77 Puerto Rico Air Quality Control Region. The Puerto Rico Air Quality Control Region... delimited): The entire Commonwealth of Puerto Rico: Puerto Rico and surrounding islands, Vieques...

  10. 40 CFR 81.51 - Portland Interstate Air Quality Control Region.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Control Region. 81.51 Section 81.51 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... Quality Control Regions § 81.51 Portland Interstate Air Quality Control Region. The Portland Interstate Air Quality Control Region (Oregon-Washington) has been revised to consist of the territorial...

  11. 40 CFR 81.97 - Southwest Florida Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.97 Section 81.97 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.97 Southwest Florida Intrastate Air Quality Control Region. The Southwest Florida Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  12. 40 CFR 81.30 - Southeastern Wisconsin Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.30 Section 81.30 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.30 Southeastern Wisconsin Intrastate Air Quality Control Region. The Metropolitan Milwaukee Intrastate Air Quality Control Region (Wisconsin) has been renamed the...

  13. 40 CFR 81.44 - Metropolitan Memphis Interstate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.44 Section 81.44 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.44 Metropolitan Memphis Interstate Air Quality Control Region. The Metropolitan Memphis Interstate Air Quality Control Region (Arkansas-Mississippi-Tennessee) consists of...

  14. 40 CFR 81.41 - Metropolitan Birmingham Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.41 Section 81.41 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.41 Metropolitan Birmingham Intrastate Air Quality Control Region. The Metropolitan Birmingham Intrastate Air Quality Control Region (Alabama) has been revised to consist of...

  15. 40 CFR 81.120 - Middle Tennessee Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.120 Section 81.120 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.120 Middle Tennessee Intrastate Air Quality Control Region. The Middle Tennessee Intrastate Air Quality Control Region consists of the territorial area encompassed...

  16. 40 CFR 81.24 - Niagara Frontier Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.24 Section 81.24 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.24 Niagara Frontier Intrastate Air Quality Control Region. The Niagara Frontier Intrastate Air Quality Control Region (New York) consists of the territorial...

  17. 40 CFR 81.16 - Metropolitan Denver Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.16 Section 81.16 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.16 Metropolitan Denver Intrastate Air Quality Control Region. The Metropolitan Denver Intrastate Air Quality Control Region (Colorado) consists of the territorial...

  18. 40 CFR 81.23 - Southwest Pennsylvania Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.23 Section 81.23 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.23 Southwest Pennsylvania Intrastate Air Quality Control Region. The Southwest Pennsylvania Intrastate Air Quality Control Region is redesignated to consist of the...

  19. 40 CFR 81.20 - Metropolitan Cincinnati Interstate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.20 Section 81.20 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.20 Metropolitan Cincinnati Interstate Air Quality Control Region. The Metropolitan Cincinnati Interstate Air Quality Control Region (Ohio-Kentucky-Indiana) is revised to consist...

  20. 40 CFR 81.89 - Metropolitan Cheyenne Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.89 Section 81.89 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.89 Metropolitan Cheyenne Intrastate Air Quality Control Region. The Metropolitan Cheyenne Intrastate Air Quality Control Region (Wyoming) consists of the territorial...

  1. 40 CFR 81.48 - Champlain Valley Interstate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.48 Section 81.48 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.48 Champlain Valley Interstate Air Quality Control Region. The Champlain Valley Interstate Air Quality Control Region (Vermont-New York) has been revised to consist of...

  2. 40 CFR 81.29 - Metropolitan Indianapolis Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Air Quality Control Region. 81.29 Section 81.29 Protection of Environment ENVIRONMENTAL PROTECTION... Designation of Air Quality Control Regions § 81.29 Metropolitan Indianapolis Intrastate Air Quality Control Region. The Metropolitan Indianapolis Intrastate Air Quality Control Region consists of the...

  3. 40 CFR 81.62 - Northeast Mississippi Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.62 Section 81.62 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.62 Northeast Mississippi Intrastate Air Quality Control Region. The Alabama-Mississippi-Tennessee Interstate Air Quality Control Region has been renamed the...

  4. 40 CFR 81.29 - Metropolitan Indianapolis Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Air Quality Control Region. 81.29 Section 81.29 Protection of Environment ENVIRONMENTAL PROTECTION... Designation of Air Quality Control Regions § 81.29 Metropolitan Indianapolis Intrastate Air Quality Control Region. The Metropolitan Indianapolis Intrastate Air Quality Control Region consists of the...

  5. 40 CFR 81.43 - Metropolitan Toledo Interstate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.43 Section 81.43 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.43 Metropolitan Toledo Interstate Air Quality Control Region. The Metropolitan Toledo Interstate Air Quality Control Region (Ohio-Michigan) consists of the territorial...

  6. 40 CFR 81.98 - Burlington-Keokuk Interstate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.98 Section 81.98 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.98 Burlington-Keokuk Interstate Air Quality Control Region. The Burlington-Keokuk Interstate Air Quality Control Region (Illinois-Iowa) is revised to consist of...

  7. 40 CFR 81.116 - Northern Missouri Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.116 Section 81.116 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.116 Northern Missouri Intrastate Air Quality Control Region. The Northern Missouri Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  8. 40 CFR 81.75 - Metropolitan Charlotte Interstate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.75 Section 81.75 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.75 Metropolitan Charlotte Interstate Air Quality Control Region. The Metropolitan Charlotte Interstate Air Quality Control Region (North Carolina-South Carolina) has been...

  9. 40 CFR 81.43 - Metropolitan Toledo Interstate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.43 Section 81.43 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.43 Metropolitan Toledo Interstate Air Quality Control Region. The Metropolitan Toledo Interstate Air Quality Control Region (Ohio-Michigan) consists of the territorial...

  10. 40 CFR 81.36 - Maricopa Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Regions § 81.36 Maricopa Intrastate Air Quality Control Region. The Phoenix-Tucson Intrastate Air Quality Control Region has been renamed the Maricopa Intrastate Air Quality Control Region... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Maricopa Intrastate Air...

  11. 40 CFR 81.34 - Metropolitan Dayton Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.34 Section 81.34 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.34 Metropolitan Dayton Intrastate Air Quality Control Region. The Metropolitan Dayton Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  12. 40 CFR 81.87 - Metropolitan Boise Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.87 Section 81.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.87 Metropolitan Boise Intrastate Air Quality Control Region. The Metropolitan Boise Intrastate Air Quality Control Region (Idaho) consists of the territorial area...

  13. 40 CFR 81.16 - Metropolitan Denver Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.16 Section 81.16 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.16 Metropolitan Denver Intrastate Air Quality Control Region. The Metropolitan Denver Intrastate Air Quality Control Region (Colorado) consists of the territorial...

  14. 40 CFR 81.75 - Metropolitan Charlotte Interstate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.75 Section 81.75 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.75 Metropolitan Charlotte Interstate Air Quality Control Region. The Metropolitan Charlotte Interstate Air Quality Control Region (North Carolina-South Carolina) has been...

  15. 40 CFR 81.36 - Maricopa Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Regions § 81.36 Maricopa Intrastate Air Quality Control Region. The Phoenix-Tucson Intrastate Air Quality Control Region has been renamed the Maricopa Intrastate Air Quality Control Region... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Maricopa Intrastate Air...

  16. 40 CFR 81.89 - Metropolitan Cheyenne Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.89 Section 81.89 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.89 Metropolitan Cheyenne Intrastate Air Quality Control Region. The Metropolitan Cheyenne Intrastate Air Quality Control Region (Wyoming) consists of the territorial...

  17. 40 CFR 81.104 - Central Pennsylvania Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.104 Section 81.104 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.104 Central Pennsylvania Intrastate Air Quality Control Region. The Central Pennsylvania Intrastate Air Quality Control Region consists of the territorial area encompassed...

  18. 40 CFR 81.98 - Burlington-Keokuk Interstate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.98 Section 81.98 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.98 Burlington-Keokuk Interstate Air Quality Control Region. The Burlington-Keokuk Interstate Air Quality Control Region (Illinois-Iowa) is revised to consist of...

  19. 40 CFR 81.101 - Metropolitan Dubuque Interstate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.101 Section 81.101 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.101 Metropolitan Dubuque Interstate Air Quality Control Region. The Metropolitan Dubuque Interstate Air Quality Control Region (Illinois-Iowa-Wisconsin) consists of...

  20. 40 CFR 81.106 - Greenville-Spartanburg Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.106 Section 81.106 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.106 Greenville-Spartanburg Intrastate Air Quality Control Region. The Greenville-Spartanburg Intrastate Air Quality Control Region (South Carolina) consists of the...

  1. 40 CFR 81.117 - Southeast Missouri Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.117 Section 81.117 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.117 Southeast Missouri Intrastate Air Quality Control Region. The Southeast Missouri Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  2. 40 CFR 81.118 - Southwest Missouri Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.118 Section 81.118 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.118 Southwest Missouri Intrastate Air Quality Control Region. The Southwest Missouri Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  3. 40 CFR 81.51 - Portland Interstate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Regions § 81.51 Portland Interstate Air Quality Control Region. The Portland Interstate Air Quality Control Region (Oregon-Washington) has been revised to consist of the territorial area... Portland Interstate Air Quality Control Region (Oregon-Washington) will be referred to by...

  4. 40 CFR 81.41 - Metropolitan Birmingham Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.41 Section 81.41 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.41 Metropolitan Birmingham Intrastate Air Quality Control Region. The Metropolitan Birmingham Intrastate Air Quality Control Region (Alabama) has been revised to consist of...

  5. 40 CFR 81.23 - Southwest Pennsylvania Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.23 Section 81.23 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.23 Southwest Pennsylvania Intrastate Air Quality Control Region. The Southwest Pennsylvania Intrastate Air Quality Control Region is redesignated to consist of the...

  6. 40 CFR 81.34 - Metropolitan Dayton Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.34 Section 81.34 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.34 Metropolitan Dayton Intrastate Air Quality Control Region. The Metropolitan Dayton Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  7. 40 CFR 81.30 - Southeastern Wisconsin Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.30 Section 81.30 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.30 Southeastern Wisconsin Intrastate Air Quality Control Region. The Metropolitan Milwaukee Intrastate Air Quality Control Region (Wisconsin) has been renamed the...

  8. 40 CFR 81.62 - Northeast Mississippi Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.62 Section 81.62 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.62 Northeast Mississippi Intrastate Air Quality Control Region. The Alabama-Mississippi-Tennessee Interstate Air Quality Control Region has been renamed the...

  9. 40 CFR 81.87 - Metropolitan Boise Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.87 Section 81.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.87 Metropolitan Boise Intrastate Air Quality Control Region. The Metropolitan Boise Intrastate Air Quality Control Region (Idaho) consists of the territorial area...

  10. 40 CFR 81.49 - Southeast Florida Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.49 Section 81.49 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.49 Southeast Florida Intrastate Air Quality Control Region. The Southeast Florida Intrastate Air Quality Control Region is redesignated to consist of the territorial...

  11. 40 CFR 81.116 - Northern Missouri Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.116 Section 81.116 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.116 Northern Missouri Intrastate Air Quality Control Region. The Northern Missouri Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  12. 40 CFR 81.24 - Niagara Frontier Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.24 Section 81.24 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.24 Niagara Frontier Intrastate Air Quality Control Region. The Niagara Frontier Intrastate Air Quality Control Region (New York) consists of the territorial...

  13. 40 CFR 81.117 - Southeast Missouri Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.117 Section 81.117 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.117 Southeast Missouri Intrastate Air Quality Control Region. The Southeast Missouri Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  14. 40 CFR 81.20 - Metropolitan Cincinnati Interstate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.20 Section 81.20 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.20 Metropolitan Cincinnati Interstate Air Quality Control Region. The Metropolitan Cincinnati Interstate Air Quality Control Region (Ohio-Kentucky-Indiana) is revised to consist...

  15. 40 CFR 81.104 - Central Pennsylvania Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.104 Section 81.104 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.104 Central Pennsylvania Intrastate Air Quality Control Region. The Central Pennsylvania Intrastate Air Quality Control Region consists of the territorial area encompassed...

  16. 40 CFR 81.49 - Southeast Florida Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.49 Section 81.49 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.49 Southeast Florida Intrastate Air Quality Control Region. The Southeast Florida Intrastate Air Quality Control Region is redesignated to consist of the territorial...

  17. 40 CFR 81.44 - Metropolitan Memphis Interstate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.44 Section 81.44 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.44 Metropolitan Memphis Interstate Air Quality Control Region. The Metropolitan Memphis Interstate Air Quality Control Region (Arkansas-Mississippi-Tennessee) consists of...

  18. 40 CFR 81.45 - Metropolitan Atlanta Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.45 Section 81.45 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.45 Metropolitan Atlanta Intrastate Air Quality Control Region. The Metropolitan Atlanta Intrastate Air Quality Control Region (Georgia) has been revised to consist of...

  19. 40 CFR 81.97 - Southwest Florida Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.97 Section 81.97 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.97 Southwest Florida Intrastate Air Quality Control Region. The Southwest Florida Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  20. 40 CFR 81.106 - Greenville-Spartanburg Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.106 Section 81.106 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.106 Greenville-Spartanburg Intrastate Air Quality Control Region. The Greenville-Spartanburg Intrastate Air Quality Control Region (South Carolina) consists of the...

  1. 40 CFR 81.118 - Southwest Missouri Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Quality Control Region. 81.118 Section 81.118 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.118 Southwest Missouri Intrastate Air Quality Control Region. The Southwest Missouri Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  2. 40 CFR 81.101 - Metropolitan Dubuque Interstate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.101 Section 81.101 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.101 Metropolitan Dubuque Interstate Air Quality Control Region. The Metropolitan Dubuque Interstate Air Quality Control Region (Illinois-Iowa-Wisconsin) consists of...

  3. 40 CFR 81.45 - Metropolitan Atlanta Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.45 Section 81.45 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.45 Metropolitan Atlanta Intrastate Air Quality Control Region. The Metropolitan Atlanta Intrastate Air Quality Control Region (Georgia) has been revised to consist of...

  4. 40 CFR 81.48 - Champlain Valley Interstate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Quality Control Region. 81.48 Section 81.48 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.48 Champlain Valley Interstate Air Quality Control Region. The Champlain Valley Interstate Air Quality Control Region (Vermont-New York) has been revised to consist of...

  5. A simple method to control over-alignment in the MAFFT multiple sequence alignment program

    PubMed Central

    Katoh, Kazutaka; Standley, Daron M.

    2016-01-01

    Motivation: We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over-alignment is recently becoming greater, as low-quality or noisy sequences are increasing in protein sequence databases, due, for example, to sequencing errors and difficulty in gene prediction. Results: The proposed method utilizes a variable scoring matrix for different pairs of sequences (or groups) in a single multiple sequence alignment, based on the global similarity of each pair. This method significantly increases the correctly gapped sites in real examples and in simulations under various conditions. Regarding sensitivity, the effect of the proposed method is slightly negative in real protein-based benchmarks, and mostly neutral in simulation-based benchmarks. This approach is based on natural biological reasoning and should be compatible with many methods based on dynamic programming for multiple sequence alignment. Availability and implementation: The new feature is available in MAFFT versions 7.263 and higher. http://mafft.cbrc.jp/alignment/software/ Contact: katoh@ifrec.osaka-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153688

  6. HIV-1 intrapatient sequence diversity in the immunogenic V3 region

    SciTech Connect

    Korber, B.; Myers, G. ); Wolinsky, S.; Kunstman, K.; Levy, R.; Furtado, M.; Otto, P. . Medical School); Haynes, B. . Dept. of Medicine)

    1991-11-12

    The third hypervariable domain (V3) of the human immunodeficiency virus type-1 (HIV-1) envelope protein (env) can serve as an epitope for potent type-specific neutralizing antibodies (NAbs) -- thus short peptides predicted on the most commonly found variants of the antigenic tip of the V3 loop have been considered as potential candidates for an HIV peptide vaccine. To evaluate the extent of intrapatient variation in the immunogenic crest of the V3 loop, sequence sets were analyzed from individuals for whom multiple V3 sequences were available. Several strategies for selecting the best sets of hexapeptides to represent the variable tip of the V3 loop were considered and their effectiveness was evaluated by comparing them with the sequence sets from individuals. Most individuals carried at least one, and frequently many, variants that did not match any of the sequences from among the ten most common hexapeptides. Intrapatient viral sequence variation was increased by including sequences derived from brain biopsy specimens as well as from blood. Additionally, sequences obtained from brain specimens of different individuals had common elements which were not conserved in the corresponding blood samples, suggesting that certain amino acids in the V3 loop may be requisite for viral propagation in the CNS.

  7. New Insertion Sequence Elements in the Upstream Region of cfiA in Imipenem-Resistant Bacteroides fragilis Strains

    PubMed Central

    Kato, Naoki; Yamazoe, Kikuo; Han, Chang-Gyun; Ohtsubo, Eiichi

    2003-01-01

    The 747-bp cfiA gene, which encodes a metallo-β-lactamase, and the regions flanking cfiA in six imipenem-resistant and four imipenem-susceptible Bacteroides fragilis strains isolated in Japan were analyzed by PCR and DNA sequencing. The nucleotide sequences of the cfiA genes (designated cfiA1 to cfiA10) of all 10 strains tested varied from that of the standard cfiA gene from B. fragilis TAL2480. However, putative proteins encoded by the cfiA variants contained conserved amino acid residues important for zinc binding and hairpin loop formation, suggesting that cfiA variants have the capability of producing metallo-β-lactamases with full catalytic activities. PCR assay indicated that six metallo-β-lactamase-producing, imipenem-resistant strains had an insertion mutation in the region immediately upstream of cfiA. Nucleotide sequencing of the PCR-amplified fragments along with the upstream region of cfiA revealed that there were five new kinds of insertion sequence (IS) elements (designated IS612, IS613, IS614, IS615, and IS616, with a size range of 1,594 to 1,691 bp), of which only IS616 was found to be almost identical to IS1188, one of the IS elements previously identified in the upstream region of cfiA. These elements had target site duplications of 4 or 5 bp in length, terminal inverted repeats (14, 15, or 17 bp in size), and a large open reading frame encoding a putative transposase which is required for the transcription of IS elements. Each element was inserted such that the transcriptional direction of the transposase was opposite to that of cfiA. A computer-aided homology search revealed that, based on the homology of their putative transposases, the sizes of their terminal inverted repeat sequences, and their target site duplications, IS612, IS613, IS614, and IS615 belong to the IS4 family, which includes IS942, previously found in some drug-resistant B. fragilis strains, but that IS616 belongs to the IS1380 family. All the IS elements appear to have

  8. Sequence analysis of the breakpoint regions of an X;5 translocation in a female with Duchenne muscular dystrophy

    SciTech Connect

    Bakel, I. van; Holt, S.; Craig, I.

    1995-08-01

    X;autosome translocations in females with Duchenne muscular dystrophy (DMD) provide an opportunity to study the mechanisms responsible for chromosomal rearrangements that occur in the germ line. We describe here a detailed molecular analysis of the translocation breakpoints of an X;autosome reciprocal translocation, t(X;5) (p21;q31.1), in a female with DMD. Cosmid clones that contained the X-chromosome breakpoint region were identified, and subclones that hybridized to the translocation junction fragment in restriction digests of the patient`s DNA were isolated and sequenced. Primers designed from the X-chromosomal sequence were used to obtain the junction fragments on the der(X) and the der(5) by inverse PCR. The resultant clones were also cloned and sequenced, and this information used to isolate the chromosome 5 breakpoint region. Comparison of the DNA sequences of the junction fragments with those of the breakpoint regions on chromosomes X and 5 revealed that the translocation arose by nonhomologous recombination with an imprecise reciprocal exchange. Four and six base pairs of unknown origin are inserted at the exchange points of the der(X) and der(5), respectively, and three nucleotides are deleted from the X-chromosome sequence. Two features were found that may have played a role in the generation of the translocation. These were (1) a repeat motif with an internal homopyrimidine stretch 10 bp upstream from the X-chromosome breakpoint and (2) a 9-bp sequence of 78% homology located near the breakpoints on chromosomes 5 and X. 32 refs., 4 figs., 2 tabs.

  9. Myeloma Ig heavy chain V region sequences reveal prior antigenic selection and marked somatic mutation but no intraclonal diversity

    SciTech Connect

    Vescio, R.A.; Cao, J.; Hong, C.H.

    1995-09-01

    The IgV{sub H} region sequence in 48 patients with multiple myeloma (MM) was analyzed to characterize the malignant cell of origin. The sequences were obtained after amplification of bone marrow cDNA by using V{sub H} family-specific and C{sub H} primers, then compared with either directly sequenced patient germ-line or published V{sub H} gene sequences to assay for somatic mutation. Because somatic hypermutation of the V{sub H} gene occurs late in B cell development, its presence has been helpful in determining the cell of origin in other B cell malignancies. Overall, a median of 8.2% of the nucleotides had evidence of substitution within each V{sub H} gene sequence (range = 2.7% to 16.5%), which is more prevalent than in any other reported tumor type. Strong evidence of prior antigenic selection pressure was also evident. The ratio of nucleotide substitutions that resulted in amino acid replacement was significantly higher in the complementarity-determining region than in the framework region (3.25 vs. 1.56, respectively; p < 0.00005). No V{sub H} gene intraclonal diversity was noted, despite sequencing multiple clones (3-16) from each patient, nor was there evidence of further V{sub H} gene somatic mutation over the course of three patients` disease. These findings strongly imply that the malignant clone in MM evolves from a cell late in B cell development. 63 refs., 4 figs., 2 tabs.

  10. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach

    SciTech Connect

    Uberbacher, E.C.; Mural, R.J. Univ. of Tennessee, Oak Ridge )

    1991-12-15

    Genes in higher eukaryotes may span tens or hundreds of kilobases with the protein-coding regions accounting for only a few percent of the total sequence. Identifying genes within large regions of uncharacterized DNA is a difficult undertaking and is currently the focus of many research efforts. The authors describe a reliable computational approach for locating protein-coding portions of genes in anonymous DNA sequence. Using a concept suggested by robotic environmental sensing, the authors method combines a set of sensor algorithms and a neural network to localize the coding regions. Several algorithms that report local characteristics of the DNA sequence, and therefore act as sensors, are also described. In its current configuration the coding recognition module identifies 90% of coding exons of length 100 bases or greater with less than one false positive coding exon indicated per five coding exons indicated. This is a significantly lower false positive rate than any method of which the authors are aware. This module demonstrates a method with general applicability to sequence-pattern recognition problems and is available for current research efforts.

  11. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach.

    PubMed Central

    Uberbacher, E C; Mural, R J

    1991-01-01

    Genes in higher eukaryotes may span tens or hundreds of kilobases with the protein-coding regions accounting for only a few percent of the total sequence. Identifying genes within large regions of uncharacterized DNA is a difficult undertaking and is currently the focus of many research efforts. We describe a reliable computational approach for locating protein-coding portions of genes in anonymous DNA sequence. Using a concept suggested by robotic environmental sensing, our method combines a set of sensor algorithms and a neural network to localize the coding regions. Several algorithms that report local characteristics of the DNA sequence, and therefore act as sensors, are also described. In its current configuration the "coding recognition module" identifies 90% of coding exons of length 100 bases or greater with less than one false positive coding exon indicated per five coding exons indicated. This is a significantly lower false positive rate than any method of which we are aware. This module demonstrates a method with general applicability to sequence-pattern recognition problems and is available for current research efforts. PMID:1763041

  12. Combined soil treatments and sequence of application in improving the control of soilborne pathogens.

    PubMed

    Eshel, D; Gamliel, A; Grinstein, A; Di Primo, P; Katan, J

    2000-07-01

    ABSTRACT The effects of reduced doses of methyl bromide (MB) or metham sodium, heating, short solarization, and soil microbial activity, alone or in combination, on survival of soilborne fungal pathogens were tested in a controlled-environment system and field plots. Sublethal doses of heating or MB delayed germination of Sclerotium rolfsii sclerotia. Combining MB and heating treatments was more effective than either treatment alone in controlling S. rolfsii and Fusarium oxysporum f. sp. basilici. The application heating followed by fumigation with MB, was significantly more effective in delaying and reducing germination of S. rolfsii sclerotia and in controlling F. oxysporum f. sp. basilici than the opposite sequence. Further, incubation in soil and exposure to microbial activity of previously heated or MB-treated sclerotia increased the mortality rate, indicating a weakening effect. Similarly, incubation of chlamydospores of F. oxysporum f. sp. melonis and F. oxysporum f. sp. radicis-lycopersici in soil in the field after fumigation further reduced their survival, confirming the laboratory results. In field tests, combining MB or metham sodium at reduced doses with short solarization was more effective in controlling fungal pathogens than either treatment alone. Treatment sequence significantly affected pathogen control in the field, similar to its effect under controlled conditions. This study demonstrates a frequent synergistic effect of combining soil treatments and its potential for improving pathogen control and reducing pesticide dose, especially when an appropriate sequence was followed. PMID:18944494

  13. Complete sequence of the Rous sarcoma virus env gene: identification of structural and functional regions of its product.

    PubMed Central

    Hunter, E; Hill, E; Hardwick, M; Bhown, A; Schwartz, D E; Tizard, R

    1983-01-01

    The amino-terminal amino acid sequences of gp85 and gp37, the envelope glycoproteins of Rous sarcoma virus (RSV), were determined. Alignment of these sequences with the amino acid sequence predicted from the complete nucleotide sequence of the Prague strain of RSV, subgroup C (PR-C), has allowed us to delineate the env gene-coding region of this virus. The coding sequences for gp85 and gp37 have been placed in an open reading frame that extends from nucleotide 5045 to nucleotide 6862 and predict sizes of 341 amino acids (36,962 molecular weight) for gp85 and 198 amino acids (21,566 molecular weight) for gp37. Carbohydrate makes a significant contribution to the observed molecular weights of these polypeptides--the amino acid sequence contains 14 potential glycosylation sites (Asn-X-Ser/Thr) in gp85 and two in gp37. Experiments aimed at estimating the number of carbohydrate side chains yielded results consistent with most or all of these sites being occupied. Although an initiation codon is located early (codon 4) in the open reading frame, it is likely that splicing yields an mRNA on which translation initiates at the same AUG as that of the gag gene to produce a nascent polypeptide in which gp85 is preceded by a 62-amino-acid-long leader peptide. This leader contains the hydrophobic sequence (signal sequence) necessary for translocation across the endoplasmic reticulum and is completely removed from the env gene product during translation. The polyprotein precursor, Pr95env, is cleaved to gp85 and gp37 at the carboxyl side of the basic sequence:-Arg-Arg-Lys-Arg-. gp85 is attached through a disulphide linkage to gp37, and although the positions of the cysteines involved in this linkage are not known, the presence of a 27-amino-acid-long hydrophobic region at the carboxy-terminus of gp37 is consistent with its role as a membrane anchor for the viral glycoprotein complex. The location of host range variable regions with respect to the possible tertiary structure of

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

    NASA Astrophysics Data System (ADS)

    Cui, Zhaoxia; Liu, Yuan; Chu, Ka Hou

    2010-07-01

    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.

  15. ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility.

    PubMed

    Otto, T D; Vasconcellos, E A; Gomes, L H F; Moreira, A S; Degrave, W M; Mendonça-Lima, L; Alves-Ferreira, M

    2008-01-01

    Optimizing and monitoring the data flow in high-throughput sequencing facilities is important for data input and output, for tracking the status of results for the users of the facility, and to guarantee a good, high-quality service. In a multi-user system environment with different throughputs, each user wants to access his/her data easily, track his/her sequencing history, analyze sequences and their quality, and apply some basic post-sequencing analysis, without the necessity of installing further software. Recently, Fiocruz established such a core facility as a "technological platform". Infrastructure includes a 48-capillary 3730 DNA Sequence Analyzer (Applied Biosystems) and supporting equipment. The service includes running samples for large-scale users, performing DNA sequencing reactions and runs for medium and small users, and participation in partial or full genome projects. We implemented a workflow that fulfills these requirements for small and high throughput users. Our implementation also includes the monitoring of data for continuous quality improvement (reports by plate, month and user) by the sequencing staff. For the user, different analyses of the chromatograms, such as visualization of good quality regions, as well as processing, such as comparisons or assemblies, are available. So far, 180 users have made use of the service, generating 155,000 sequences, 35% of which were produced for the BCG Moreau-RJ genome project. The pipeline (named ChromaPipe for Chromatogram Pipeline) is available for download by the scientific community at the url http://bioinfo.pdtis.fiocruz.br/ChromaPipe/. The support for assembly is also configured as a web service: http://bioinfo.pdtis.fiocruz.br/Assembly/. PMID:18949705

  16. Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region

    PubMed Central

    Jiang, Zhi J; Castoe, Todd A; Austin, Christopher C; Burbrink, Frank T; Herron, Matthew D; McGuire, Jimmy A; Parkinson, Christopher L; Pollock, David D

    2007-01-01

    Background The mitochondrial genomes of snakes are characterized by an overall evolutionary rate that appears to be one of the most accelerated among vertebrates. They also possess other unusual features, including short tRNAs and other genes, and a duplicated control region that has been stably maintained since it originated more than 70 million years ago. Here, we provide a detailed analysis of evolutionary dynamics in snake mitochondrial genomes to better understand the basis of these extreme characteristics, and to explore the relationship between mitochondrial genome molecular evolution, genome architecture, and molecular function. We sequenced complete mitochondrial genomes from Slowinski's corn snake (Pantherophis slowinskii) and two cottonmouths (Agkistrodon piscivorus) to complement previously existing mitochondrial genomes, and to provide an improved comparative view of how genome architecture affects molecular evolution at contrasting levels of divergence. Results We present a Bayesian genetic approach that suggests that the duplicated control region can function as an additional origin of heavy strand replication. The two control regions also appear to have different intra-specific versus inter-specific evolutionary dynamics that may be associated with complex modes of concerted evolution. We find that different genomic regions have experienced substantial accelerated evolution along early branches in snakes, with different genes having experienced dramatic accelerations along specific branches. Some of these accelerations appear to coincide with, or subsequent to, the shortening of various mitochondrial genes and the duplication of the control region and flanking tRNAs. Conclusion Fluctuations in the strength and pattern of selection during snake evolution have had widely varying gene-specific effects on substitution rates, and these rate accelerations may have been functionally related to unusual changes in genomic architecture. The among-lineage and

  17. Mitochondrial DNA control region analysis of three ethnic groups in the Republic of Macedonia.

    PubMed

    Jankova-Ajanovska, Renata; Zimmermann, Bettina; Huber, Gabriela; Röck, Alexander W; Bodner, Martin; Jakovski, Zlatko; Janeska, Biljana; Duma, Aleksej; Parson, Walther

    2014-11-01

    A total of 444 individuals representing three ethnic groups (Albanians, Turks and Romanies) in the Republic of Macedonia were sequenced in the mitochondrial control region. The mtDNA haplogroup composition differed between the three groups. Our results showed relatively high frequencies of haplogroup H12 in Albanians (8.8%) and less in Turks (3.3%), while haplogroups M5a1 and H7a1a were dominant in Romanies (13.7% and 10.3%, respectively) but rare in the former two. This highlights the importance of regional sampling for forensic mtDNA databasing purposes. These population data will be available on EMPOP under accession numbers EMP00644 (Albanians), EMP00645 (Romanies) and EMP00646 (Turks). PMID:25051224

  18. Mitochondrial DNA control region analysis of three ethnic groups in the Republic of Macedonia

    PubMed Central

    Jankova-Ajanovska, Renata; Zimmermann, Bettina; Huber, Gabriela; Röck, Alexander W.; Bodner, Martin; Jakovski, Zlatko; Janeska, Biljana; Duma, Aleksej; Parson, Walther

    2014-01-01

    A total of 444 individuals representing three ethnic groups (Albanians, Turks and Romanies) in the Republic of Macedonia were sequenced in the mitochondrial control region. The mtDNA haplogroup composition differed between the three groups. Our results showed relatively high frequencies of haplogroup H12 in Albanians (8.8%) and less in Turks (3.3%), while haplogroups M5a1 and H7a1a were dominant in Romanies (13.7% and 10.3%, respectively) but rare in the former two. This highlights the importance of regional sampling for forensic mtDNA databasing purposes. These population data will be available on EMPOP under accession numbers EMP00644 (Albanians), EMP00645 (Romanies) and EMP00646 (Turks). PMID:25051224

  19. Widespread Differential Expression of Coding Region and 3' UTR Sequences in Neurons and Other Tissues.

    PubMed

    Kocabas, Arif; Duarte, Terence; Kumar, Saranya; Hynes, Mary A

    2015-12-16

    Mature messenger RNAs (mRNAs) consist of coding sequence (CDS) and 5' and 3' UTRs, typically expected to show similar abundance within a given neuron. Examining mRNA from defined neurons, we unexpectedly show extremely common unbalanced expression of cognate 3' UTR and CDS sequences; many genes show high 3' UTR relative to CDS, others show high CDS to 3' UTR. In situ hybridization (19 of 19 genes) shows a broad range of 3' UTR-to-CDS expression ratios across neurons and tissues. Ratios may be spatially graded or change with developmental age but are consistent across animals. Further, for two genes examined, a 3' UTR-to-CDS ratio above a particular threshold in any given neuron correlated with reduced or undetectable protein expression. Our findings raise questions about the role of isolated 3' UTR sequences in regulation of protein expression and highlight the importance of separately examining 3' UTR and CDS sequences in gene expression analyses. PMID:26687222

  20. The complete coding region sequence of river buffalo (Bubalus bubalis) SRY gene.

    PubMed

    Parma, Pietro; Feligini, Maria; Greppi, Gianfranco; Enne, Giuseppe

    2004-02-01

    The Y-linked SRY gene is responsible for testis determination in mammals. Mutations in this gene can lead to XY Gonadal Dysgenesis, an abnormal sexual phenotype described in humans, cattle, horses and river buffalo. We report here the complete river buffalo SRY sequence in order to enable the genetic diagnosis of this disease. The SRY sequence was also used to confirm the evolutionary divergence time between cattle and river buffalo 10 million years ago. PMID:15354359

  1. Sequence variation of koala retrovirus transmembrane protein p15E among koalas from different geographic regions.

    PubMed

    Ishida, Yasuko; McCallister, Chelsea; Nikolaidis, Nikolas; Tsangaras, Kyriakos; Helgen, Kristofer M; Greenwood, Alex D; Roca, Alfred L

    2015-01-15

    The koala retrovirus (KoRV), which is transitioning from an exogenous to an endogenous form, has been associated with high mortality in koalas. For other retroviruses, the envelope protein p15E has been considered a candidate for vaccine development. We therefore examined proviral sequence variation of KoRV p15E in a captive Queensland and three wild southern Australian koalas. We generated 163 sequences with intact open reading frames, which grouped into 39 distinct haplotypes. Sixteen distinct haplotypes comprising 139 of the sequences (85%) coded for the same polypeptide. Among the remaining 23 haplotypes, 22 were detected only once among the sequences, and each had 1 or 2 non-synonymous differences from the majority sequence. Several analyses suggested that p15E was under purifying selection. Important epitopes and domains were highly conserved across the p15E sequences and in previously reported exogenous KoRVs. Overall, these results support the potential use of p15E for KoRV vaccine development. PMID:25462343

  2. Sequence variation of koala retrovirus transmembrane protein p15E among koalas from different geographic regions

    PubMed Central

    Ishida, Yasuko; McCallister, Chelsea; Nikolaidis, Nikolas; Tsangaras, Kyriakos; Helgen, Kristofer M.; Greenwood, Alex D.; Roca, Alfred L.

    2014-01-01

    The koala retrovirus (KoRV), which is transitioning from an exogenous to an endogenous form, has been associated with high mortality in koalas. For other retroviruses, the envelope protein p15E has been considered a candidate for vaccine development. We therefore examined proviral sequence variation of KoRV p15E in a captive Queensland and three wild southern Australian koalas. We generated 163 sequences with intact open reading frames, which grouped into 39 distinct haplotypes. Sixteen distinct haplotypes comprising 139 of the sequences (85%) coded for the same polypeptide. Among the remaining 23 haplotypes, 22 were detected only once among the sequences, and each had 1 or 2 non-synonymous differences from the majority sequence. Several analyses suggested that p15E was under purifying selection. Important epitopes and domains were highly conserved across the p15E sequences and in previously reported exogenous KoRVs. Overall, these results support the potential use of p15E for KoRV vaccine development. PMID:25462343

  3. Conserved nucleotide sequences in the open reading frame and 3' untranslated region of selenoprotein P mRNA.

    PubMed Central

    Hill, K E; Lloyd, R S; Burk, R F

    1993-01-01

    Rat liver selenoprotein P contains 10 selenocysteine residues in its primary structure (deduced). It is the only selenoprotein characterized to date that has more than one selenocysteine residue. Selenoprotein P cDNA has been cloned from human liver and heart cDNA libraries and sequenced. The open reading frames are identical and contain a signal peptide, indicating that the protein is secreted by both organs and is therefore not exclusively produced in the liver. Ten selenocysteine residues (deduced) are present. Comparison of the open reading frame of the human cDNA with the rat cDNA reveals a 69% identity of the nucleotide sequence and 72% identity of the deduced amino acid sequence. Two regions in the 3' untranslated portion have high conservation between human and rat. Each of these regions contains a predicted stable stem-loop structure similar to the single stem-loop structures reported in 3' untranslated regions of type I iodothyronine 5'-deiodinase and glutathione peroxidase. The stem-loop structure of type I iodothyronine 5'-deiodinase has been shown to be necessary for incorporation of the selenocysteine residue at the UGA codon. Because only two stem-loop structures are present in the 3' untranslated region of selenoprotein P mRNA, it can be concluded that a separate stem-loop structure is not required for each selenocysteine residue. Images PMID:8421687

  4. Exploring the diploid wheat ancestral A genome through sequence comparison at the high-molecular-weight glutenin locus region.

    PubMed

    Dong, Lingli; Huo, Naxin; Wang, Yi; Deal, Karin; Luo, Ming-Cheng; Wang, Daowen; Anderson, Olin D; Gu, Yong Qiang

    2012-12-01

    The polyploid nature of hexaploid wheat (T. aestivum, AABBDD) often represents a great challenge in various aspects of research including genetic mapping, map-based cloning of important genes, and sequencing and accurately assembly of its genome. To explore the utility of ancestral diploid species of polyploid wheat, sequence variation of T. urartu (A(u)A(u)) was analyzed by comparing its 277-kb large genomic region carrying the important Glu-1 locus with the homologous regions from the A genomes of the diploid T. monococcum (A(m)A(m)), tetraploid T. turgidum (AABB), and hexaploid T. aestivum (AABBDD). Our results revealed that in addition to a high degree of the gene collinearity, nested retroelement structures were also considerably conserved among the A(u) genome and the A genomes in polyploid wheats, suggesting that the majority of the repetitive sequences in the A genomes of polyploid wheats originated from the diploid A(u) genome. The difference in the compared region between A(u) and A is mainly caused by four differential TE insertion and two deletion events between these genomes. The estimated divergence time of A genomes calculated on nucleotide substitution rate in both shared TEs and collinear genes further supports the closer evolutionary relationship of A to A(u) than to A(m). The structure conservation in the repetitive regions promoted us to develop repeat junction markers based on the A(u) sequence for mapping the A genome in hexaploid wheat. Eighty percent of these repeat junction markers were successfully mapped to the corresponding region in hexaploid wheat, suggesting that T. urartu could serve as a useful resource for developing molecular markers for genetic and breeding studies in hexaploid wheat. PMID:23052831

  5. Mitochondrial genome phylogeny among Asiatic black bear Ursus thibetanus subspecies and comprehensive analysis of their control regions.

    PubMed

    Choi, Eun Hwa; Kim, Sang Ki; Ryu, Shi Hyun; Jang, Kuem Hee; Hwang, Ui Wook

    2010-06-01

    The complete mitochondrial genome (16,824 bp) of an Asiatic black bear Ursus thibetanus ussuricus (Mammalia, Carnivora, Ursidae) was newly sequenced and characterized in detail. It is the second mitochondrial genome from this subspecies which has been completely sequenced. The two U. t. ussuricus individuals were compared with each other and then with individuals from the other four U. thibetanus subspecies and the other nine ursid species, focusing especially on the control regions in the 14 mitochondrial genomes. Within these control regions, tandem repeats of basically 10 bp (5'-ACGCACGTGT-3' or its derivatives) were found in Domain II. Plausible secondary structures of the repeat region were compared between the North and South Korean individuals of U. t. ussuricus. According to the maximum likelihood and Bayesian inference trees inferred from the nucleotide sequences of 13 protein-coding and two rRNA genes, the ursine members within the monophyletic ursid clade can be divided into at least three groups: A, B, and C. According to this analysis, U. thibetanus subspecies were found with Ursus americanus and Ursus malayanus within Group A, showing the following relationships with nodal bootstrap values above 91% and Bayesian posterior probabilities of 1.00: ([(U. t. thibetanus, U. t. formosanus), U. t. spp.], U. t. ussuricus), U. t. mupinensis. In addition, we present a hypothetical scenario of the evolution of the major repeat motifs in the control region. PMID:20795781

  6. Intra-regional and inter-regional abnormalities and cognitive control deficits in young adult smokers.

    PubMed

    Feng, Dan; Yuan, Kai; Li, Yangding; Cai, Chenxi; Yin, Junsen; Bi, Yanzhi; Cheng, Jiadong; Guan, Yanyan; Shi, Sha; Yu, Dahua; Jin, Chenwang; Lu, Xiaoqi; Qin, Wei; Tian, Jie

    2016-06-01

    Tobacco use during later adolescence and young adulthood may cause serious neurophysiological changes; rationally, it is extremely important to study the relationship between brain dysfunction and behavioral performances in young adult smokers. Previous resting state studies investigated the neural mechanisms in smokers. Unfortunately, few studies focused on spontaneous activity differences between young adult smokers and nonsmokers from both intra-regional and inter-regional levels, less is known about the association between resting state abnormalities and behavioral deficits. Therefore, we used fractional amplitude of low frequency fluctuation (fALFF) and resting state functional connectivity (RSFC) to investigate the resting state spontaneous activity differences between young adult smokers and nonsmokers. A correlation analysis was carried out to assess the relationship between neuroimaging findings and clinical information (pack-years, cigarette dependence, age of onset and craving score) as well as cognitive control deficits measured by the Stroop task. Consistent with previous addiction findings, our results revealed the resting state abnormalities within frontostriatal circuits, i.e., enhanced spontaneous activity of the caudate and reduced functional strength between the caudate and anterior cingulate cortex (ACC) in young adult smokers. Moreover, the fALFF values of the caudate were correlated with craving and RSFC strength between the caudate and ACC was associated with the cognitive control impairments in young adult smokers. Our findings could lead to a better understanding of intrinsic functional architecture of baseline brain activity in young smokers by providing regional and brain circuit spontaneous neuronal activity properties as well as their association with cognitive control impairments. PMID:26164168

  7. Cloning of human transketolase cDNAs and comparison of the nucleotide sequence of the coding region in Wernicke-Korsakoff and non-Wernicke-Korsakoff individuals.

    PubMed

    McCool, B A; Plonk, S G; Martin, P R; Singleton, C K

    1993-01-15

    Variants of the enzyme transketolase which possess reduced affinity for its cofactor thiamine pyrophosphate (high apparent Km) have been described in chronic alcoholic patients with Wernicke-Korsakoff syndrome. Since the syndrome has been shown to be directly related to thiamine deficiency, it has been hypothesized that such transketolase variants may represent a genetic predisposition to the development of this syndrome. To test this hypothesis, human transketolase cDNA clones were isolated, and their nucleotide and predicted amino acid sequence were determined. Transketolase was found to be a single copy gene which produces a single mRNA of approximately 2100 nucleotides. Additionally, the nucleotide sequence of the transketolase coding region in fibroblasts derived from two Wernicke-Korsakoff (WK) patients was compared to that of two nonalcoholic controls. Although nucleotide and predicted amino acid differences were detected between fibroblast cultures and the original cDNAs and among the cultures themselves, no specific nucleotide variations, which would encode a variant amino acid sequence, were associated exclusively with the coding region from WK patients. Thus, allelic variants of the transketolase gene cannot account for the biochemically distinct forms of the enzyme found in these patients nor be considered as a mechanism for genetic predisposition to the development of Wernicke-Korsakoff syndrome. Instead, the underlying mechanism must be extragenic and may be a result of differences in post-translational processing/modification of the transketolase polypeptide. PMID:8419340

  8. Heat shock factor 1 binds to and transcribes satellite II and III sequences at several pericentromeric regions in heat-shocked cells

    SciTech Connect

    Eymery, Angeline; INSERM Institut Albert Bonniot U823, La Tronche, F-38700 ; Souchier, Catherine; INSERM Institut Albert Bonniot U823, La Tronche, F-38700 ; Vourc'h, Claire; INSERM Institut Albert Bonniot U823, La Tronche, F-38700 ; Jolly, Caroline; INSERM Institut Albert Bonniot U823, La Tronche, F-38700

    2010-07-01

    Cells respond to stress by activating the synthesis of heat shock proteins (HSPs) which protect the cells against the deleterious effects of stress. This mechanism is controlled by the heat shock factor 1 (HSF1). In parallel to HSP gene transcription, in human cells, HSF1 also binds to and transcribes satellite III repeated sequences present in numerous copies in the 9q12 pericentromeric region of chromosome 9. These HSF1 accumulation sites are termed nuclear stress bodies (nSBs). In tumor cells, however, the number of nSBs is higher than the number of 9q12 copies, suggesting the existence of other HSF1 targets. In this paper, we were interested in characterizing these other HSF1 binding sites. We show that HSF1 indeed binds to the pericentromeric region of 14 chromosomes, thereby directing the formation of 'secondary nSBs'. The appearance of secondary nSBs depends on the number of satellite sequences present in the target locus, and on the cellular amount of HSF1 protein. Moreover, secondary nSBs also correspond to transcription sites, thus demonstrating that heat shock induces a genome-wide transcription of satellite sequences. Finally, by analyzing published transcriptomic data, we show that the derepression of these large heterochromatic blocks does not significantly affect the transcription of neighboring genes.

  9. UTRdb and UTRsite: specialized databases of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs

    PubMed Central

    Pesole, Graziano; Liuni, Sabino; Grillo, Giorgio; Licciulli, Flavio; Larizza, Alessandra; Makalowski, Wojciech; Saccone, Cecilia

    2000-01-01

    The 5′ and 3′ untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this reason we developed UTRdb, a specialized database of 5′ and 3′ untranslated sequences of eukaryotic mRNAs cleaned from redundancy. UTRdb entries are enriched with specialized information not present in the primary databases including the presence of nucleotide sequence patterns already demonstrated by experimental analysis to have some functional role. All these patterns have been collected in the UTRsite database so that it is possible to search any input sequence for the presence of annotated functional motifs. Furthermore, UTRdb entries have been annotated for the presence of repetitive elements. All internet resources implemented for retrieval and functional analysis of 5′ and 3′ untranslated regions of eukaryotic mRNAs are accessible at http://bigarea.area.ba.cnr.it:8000/EmbIT/UTRHome/ PMID:10592223

  10. Mitochondrial DNA variation and phylogenetic relationships among five tuna species based on sequencing of D-loop region.

    PubMed

    Kumar, Girish; Kocour, Martin; Kunal, Swaraj Priyaranjan

    2016-05-01

    In order to assess the DNA sequence variation and phylogenetic relationship among five tuna species (Auxis thazard, Euthynnus affinis, Katsuwonus pelamis, Thunnus tonggol, and T. albacares) out of all four tuna genera, partial sequences of the mitochondrial DNA (mtDNA) D-loop region were analyzed. The estimate of intra-specific sequence variation in studied species was low, ranging from 0.027 to 0.080 [Kimura's two parameter distance (K2P)], whereas values of inter-specific variation ranged from 0.049 to 0.491. The longtail tuna (T. tonggol) and yellowfin tuna (T. albacares) were found to share a close relationship (K2P = 0.049) while skipjack tuna (K. pelamis) was most divergent studied species. Phylogenetic analysis using Maximum-Likelihood (ML) and Neighbor-Joining (NJ) methods supported the monophyletic origin of Thunnus species. Similarly, phylogeny of Auxis and Euthynnus species substantiate the monophyly. However, results showed a distinct origin of K. pelamis from genus Thunnus as well as Auxis and Euthynnus. Thus, the mtDNA D-loop region sequence data supports the polyphyletic origin of tuna species. PMID:25329285

  11. Specific binding of a HeLa cell nuclear protein to RNA sequences in the human immunodeficiency virus transactivating region.

    PubMed Central

    Gaynor, R; Soultanakis, E; Kuwabara, M; Garcia, J; Sigman, D S

    1989-01-01

    The transactivator protein, tat, encoded by the human immunodeficiency virus is a key regulator of viral transcription. Activation by the tat protein requires sequences downstream of the transcription initiation site called the transactivating region (TAR). RNA derived from the TAR is capable of forming a stable stem-loop structure and the maintenance of both the stem structure and the loop sequences located between +19 and +44 is required for complete in vivo activation by tat. Gel retardation assays with RNA from both wild-type and mutant TAR constructs generated in vitro with SP6 polymerase indicated specific binding of HeLa nuclear proteins to the TAR. To characterize this RNA-protein interaction, a method of chemical "imprinting" has been developed using photoactivated uranyl acetate as the nucleolytic agent. This reagent nicks RNA under physiological conditions at all four nucleotides in a reaction that is independent of sequence and secondary structure. Specific interaction of cellular proteins with TAR RNA could be detected by enhanced cleavages or imprints surrounding the loop region. Mutations that either disrupted stem base-pairing or extensively changed the primary sequence resulted in alterations in the cleavage pattern of the TAR RNA. Structural features of the TAR RNA stem-loop essential for tat activation are also required for specific binding of the HeLa cell nuclear protein. Images PMID:2544877

  12. A Systems Approach towards an Intelligent and Self-Controlling Platform for Integrated Continuous Reaction Sequences**

    PubMed Central

    Ingham, Richard J; Battilocchio, Claudio; Fitzpatrick, Daniel E; Sliwinski, Eric; Hawkins, Joel M; Ley, Steven V

    2015-01-01

    Performing reactions in flow can offer major advantages over batch methods. However, laboratory flow chemistry processes are currently often limited to single steps or short sequences due to the complexity involved with operating a multi-step process. Using new modular components for downstream processing, coupled with control technologies, more advanced multi-step flow sequences can be realized. These tools are applied to the synthesis of 2-aminoadamantane-2-carboxylic acid. A system comprising three chemistry steps and three workup steps was developed, having sufficient autonomy and self-regulation to be managed by a single operator. PMID:25377747

  13. Pulse-controlled quantum gate sequences on a strongly coupled qubit chain

    NASA Astrophysics Data System (ADS)

    Frydrych, Holger; Marthaler, Michael; Alber, Gernot

    2015-12-01

    We propose a selective dynamical decoupling scheme on a chain of permanently coupled qubits with XX-type interactions, which is capable of dynamically suppressing any coupling in the chain by applying sequences of local pulses to the individual qubits. We demonstrate that high-fidelity single- and two-qubit gates can be achieved by this procedure and that sequences of gates can be implemented by this pulse control alone. We discuss the applicability and physical limitations of our model specifically for strongly coupled superconducting flux qubits. Since dynamically modifying the couplings between flux qubits is challenging, they are a natural candidate for our approach.

  14. Challenges in DNA motion control and sequence readout using nanopore devices

    PubMed Central

    Carson, Spencer; Wanunu, Meni

    2016-01-01

    Nanopores are being hailed as a potential next-generation DNA sequencer that could provide cheap, high-throughput DNA analysis. In this review we present a detailed summary of the various sensing techniques being investigated for use in DNA sequencing and mapping applications. A crucial impasse to the success of nanopores as a reliable DNA analysis tool is the fast and stochastic nature of DNA translocation. We discuss the incorporation of biological motors to step DNA through a pore base-by-base, as well as the many experimental modifications attempted for the purpose of slowing and controlling DNA transport. PMID:25642629

  15. Global control and regional elimination of measles, 2000-2012.

    PubMed

    Perry, Robert T; Gacic-Dobo, Marta; Dabbagh, Alya; Mulders, Mick N; Strebel, Peter M; Okwo-Bele, Jean-Marie; Rota, Paul A; Goodson, James L

    2014-02-01

    In 2010, the World Health Assembly established three milestones toward global measles eradication to be reached by 2015: 1) increase routine coverage with the first dose of measles-containing vaccine (MCV1) for children aged 1 year to ≥90% nationally and ≥80% in every district, 2) reduce and maintain annual measles incidence at <5 cases per million, and 3) reduce measles mortality by 95% from the 2000 estimate. After the adoption by member states of the South-East Asia Region (SEAR) of the goal of measles elimination by 2020, elimination goals have been set by member states of all six World Health Organization (WHO) regions, and reaching measles elimination in four WHO regions by 2015 is an objective of the Global Vaccine Action Plan (GVAP). This report updates the previous report for 2000-2011 and describes progress toward global control and regional elimination of measles during 2000-2012. During this period, increases in routine MCV coverage, plus supplementary immunization activities (SIAs) reaching 145 million children in 2012, led to a 77% decrease worldwide in reported measles annual incidence, from 146 to 33 per million population, and a 78% decline in estimated annual measles deaths, from 562,400 to 122,000. Compared with a scenario of no vaccination, an estimated 13.8 million deaths were prevented by measles vaccination during 2000-2012. Achieving the 2015 targets and elimination goals will require countries and their partners to raise the visibility of measles elimination and make substantial and sustained additional investments in strengthening health systems. PMID:24500289

  16. Essential and nonessential sequences in malPp, a positively controlled promoter in Escherichia coli.

    PubMed

    Raibaud, O; Gutierrez, C; Schwartz, M

    1985-03-01

    A plasmid bearing the malPp promoter was digested with Bal31 to obtain a set of deletions with closely spaced endpoints in the upstream region of this promoter. Some of these deletions were sequenced, and their effect on malPQ expression was determined after having transferred them onto the chromosome. We found that a site which binds the cyclic AMP receptor protein in vitro and which is centered at position -93 with respect to the site of transcription initiation could be deleted without affecting malPQ expression. In contrast, the activity of the malPp promoter decreased abruptly when the deletions reached position -72. The downstream region of the promoter was analyzed by using a technique of "sequence replacement" which involved the selection of Mal+ pseudorevertants from strains which carried small deletions in the -25 region. The pseudorevertants, which expressed the malPQ operon in a manner indistinguishable from wild type, had grossly different sequences downstream from position -38, except for a few positions, some of which must be important for promoter function. By combining all presently available information, it is suggested that the malPp promoter contains three binding sites for its activator, the product of gene malT. These sites are defined by three quasi-identical hexanucleotides present in one orientation around position -37 and twice in the other orientation around positions -60 and -73. PMID:3156124

  17. Evidence on primate phylogeny from epsilon-globin gene sequences and flanking regions.

    PubMed

    Porter, C A; Sampaio, I; Schneider, H; Schneider, M P; Czelusniak, J; Goodman, M

    1995-01-01

    Phylogenetic relationships among various primate groups were examined based on sequences of epsilon-globin genes. epsilon-globin genes were sequenced from five species of strepsirhine primates. These sequences were aligned and compared with other known primate epsilon-globin sequences, including data from two additional strepsirhine species, one species of tarsier, 19 species of New World monkeys (representing all extant genera), and five species of catarrhines. In addition, a 2-kb segment upstream of the epsilon-globin gene was sequenced in two of the five strepsirhines examined. This upstream sequence was aligned with five other species of primates for which data are available in this segment. Domestic rabbit and goat were used as outgroups. This analysis supports the monophyly of order Primates but does not support the traditional prosimian grouping of tarsiers, lorisoids, and lemuroids; rather it supports the sister grouping of tarsiers and anthropoids into Haplorhini and the sister grouping of lorisoids and lemuroids into Strepsirhini. The mouse lemur (Microcebus murinus) and dwarf lemur (Cheirogaleus medius) appear to be most closely related to each other, forming a clade with the lemuroids, and are probably not closely related to the lorisoids, as suggested by some morphological studies. Analysis of the epsilon-globin data supports the hypothesis that the aye-aye (Daubentonia madagascariensis) shares a sister-group relationship with other Malagasy strepsirhines (all being classified as lemuroids). Relationships among ceboids agree with findings from a previous epsilon-globin study in which fewer outgroup taxa were employed. Rates of molecular evolution were higher in lorisoids than in lemuroids. PMID:7714911

  18. Internal transcribed spacer region sequence analysis using SmartGene IDNS software for the identification of unusual clinical yeast isolates.

    PubMed

    Slechta, E Susan; Hohmann, Sheri L; Simmon, Keith; Hanson, Kimberly E

    2012-07-01

    Rapid and accurate identification of clinically important yeasts is essential given their inherent differences in antifungal susceptibility. We implemented nucleic acid sequencing for those species that could not be identified by phenotypic methods. Internal Transcribed Spacer region 1 and 2 (ITS1 and ITS2) sequences were investigated using SmartGene IDNS software, an rDNA sequence database and analysis program for microbial identification (ID). Over a 2.5-year period, 2,938 specimens were evaluated. Most (94%) isolates were fully identified by conventional methods, with Candida species accounting for the majority of them. Of the 169 organisms that required molecular analysis, 79% were identified to species level, 19% to genus and 2% remained unresolved. Sequenced isolates encompassed 33 unique species of which approximately half (52%) were common pathogens with atypical biochemical profiles and the remainder were rarer yeast species. A significant proportion (33%) of sequenced organisms displayed elevated MICs to fluconazole. Our experience supports the use of molecular techniques as an adjunct to conventional methods for the identification of medically important yeasts. Susceptibility testing alone may provide valuable treatment information in situations where phenotypic assessments are inconclusive and molecular or proteomic testing is not readily available. PMID:22103344

  19. Localised sequence regions possessing high melting temperatures prevent the amplification of a DNA mimic in competitive PCR.

    PubMed

    McDowell, D G; Burns, N A; Parkes, H C

    1998-07-15

    The polymerase chain reaction is an immensely powerful technique for identification and detection purposes. Increasingly, competitive PCR is being used as the basis for quantification. However, sequence length, melting temperature and primary sequence have all been shown to influence the efficiency of amplification in PCR systems and may therefore compromise the required equivalent co-amplification of target and mimic in competitive PCR. The work discussed here not only illustrates the need to balance length and melting temperature when designing a competitive PCR assay, but also emphasises the importance of careful examination of sequences for GC-rich domains and other sequences giving rise to stable secondary structures which could reduce the efficiency of amplification by serving as pause or termination sites. We present data confirming that under particular circumstances such localised sequence, high melting temperature regions can act as permanent termination sites, and offer an explanation for the severity of this effect which results in prevention of amplification of a DNA mimic in competitive PCR. It is also demonstrated that when Taq DNA polymerase is used in the presence of betaine or a proof reading enzyme, the effect may be reduced or eliminated. PMID:9649616

  20. Characterization of alanine to valine sequence variants in the Fc region of nivolumab biosimilar produced in Chinese hamster ovary cells.

    PubMed

    Li, Yantao; Fu, Tuo; Liu, Tao; Guo, Huaizu; Guo, Qingcheng; Xu, Jin; Zhang, Dapeng; Qian, Weizhu; Dai, Jianxin; Li, Bohua; Guo, Yajun; Hou, Sheng; Wang, Hao

    2016-07-01

    Nivolumab is a therapeutic fully human IgG4 antibody to programmed death 1 (PD-1). In this study, a nivolumab biosimilar, which was produced in our laboratory, was analyzed and characterized. Sequence variants that contain undesired amino acid sequences may cause concern during biosimilar bioprocess development. We found that low levels of sequence variants were detected in the heavy chain of the nivolumab biosimilar by ultra performance liquid chromatography (UPLC) and tandem mass spectrometry. It was further identified with UPLC-MS/MS by IdeS or trypsin digestion. The sequence variant was confirmed through addition of synthetic mutant peptide. Subsequently, the mixing base signal of normal and mutant sequence was detected through DNA sequencing. The relative levels of mutant A424V in the Fc region of the heavy chain have been detected and demonstrated to be 12.25% and 13.54%, via base peak intensity (BPI) and UV chromatography of the tryptic peptide mapping, respectively. A424V variant was also quantified by real-time PCR (RT-PCR) at the DNA and RNA level, which was 19.2% and 16.8%, respectively. The relative content of the mutant was consistent at the DNA, RNA and protein level, indicating that the A424V mutation may have little influence at transcriptional or translational levels. These results demonstrate that orthogonal state-of-the-art techniques such as LC- UV- MS and RT-PCR should be implemented to characterize recombinant proteins and cell lines for development of biosimilars. Our study suggests that it is important to establish an integrated and effective analytical method to monitor and characterize sequence variants during antibody drug development, especially for antibody biosimilar products. PMID:27050807

  1. Gap Closing/Finishing by Targeted Genomic Region Enrichment and Sequencing

    SciTech Connect

    Singh, Kanwar; Froula, Jeff; Trice, Hope; Pennacchio, Len A.; Chen, Feng

    2010-05-27

    Gap Closing/Finishing of draft genome assemblies is a labor and cost intensive process where several rounds of repetitious amplification and sequencing are required. Here we demonstrate a high throughput procedure where custom primers flanking gaps in draft genomes are designed. Primer libraries containing up to 4,000 unique pairs in independent droplets are merged with a fragmented genomic template. From this millions of picoliter scale droplets are formed, each one being the functional equivalent of an individual PCR reaction. The PCR products are concatenated and sequenced by Illumina which is then assembled and used for gap closure. Here we present an overall experimental strategy, primer design algorithm and initial results.

  2. Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation.

    PubMed

    Zhang, Gong; Lukoszek, Radoslaw; Mueller-Roeber, Bernd; Ignatova, Zoya

    2011-04-01

    In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5'-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB-DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5'-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues. PMID:21138970

  3. Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation

    PubMed Central

    Zhang, Gong; Lukoszek, Radoslaw; Mueller-Roeber, Bernd; Ignatova, Zoya

    2011-01-01

    In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5′-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5′-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB–DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5′-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues. PMID:21138970

  4. Interactions of two large antiviral polyamides with the long control region of HPV16.

    PubMed

    Vasilieva, Elena; Niederschulte, Jacquelyn; Song, Yang; Harris, George Davis; Koeller, Kevin J; Liao, Puhong; Bashkin, James K; Dupureur, Cynthia M

    2016-08-01

    PA1 and PA25 are large hairpin polyamides that are effective in nearly eliminating HPV16 episomes (DNA) in cell culture, and PA25 has broad spectrum activity against three cancer-causing forms of HPV (Edwards, T. G., Koeller, K. J., Slomczynska, U., Fok, K., Helmus, M., Bashkin, J. K., Fisher, C., Antiviral Res. 91 (2011) 177-186). Described here are the interactions of these PAs with sequences in the long control region (LCR) of HPV16 (7348-122). Using an FeEDTA conjugate of PA1 (designed to recognize 5'-W2GW7-3'; W = A or T), 34 affinity cleavage (AC) patterns were detected for this fragment. These sites can be rationalized with sequences featuring perfect, single, double, triple and quadruple mismatches. Quantitative DNase I footprinting analysis indicates that perfect sites bind PA1 with Kds between 0.7 and 2.2 nM. Kds for single, double, triple and quadruple mismatch sites range from 1-3 nM-20 nM. Using AC and EDTA conjugates, we report that unlike smaller 8-ring hairpin PAs, introduction of a chiral turn in this large polyamide has no effect on binding orientation (forward vs. reverse). Despite its design to recognize 5'-W2GW5GW4-3' via two Im residues, a motif not represented in this HPV sequence, a PA25-EDTA conjugate yielded 31 affinity cleavage sites on the region. Low nM Kds for PA25 without EDTA indicates a high tolerance for triple and quadruple mismatches. While there is extensive coverage of the sequence examined, AC cleavage patterns for the two PAs show discrete binding events and do not overlap significantly. This indicates that within the context of A/T rich sequences, these PAs do not recognize a simple shared sequence-related feature of the DNA. These insights continue to inform the complex nature of large hairpin PA-DNA interactions and antiviral behavior. PMID:27155361

  5. Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region.

    PubMed

    Lapidus, A; Galleron, N; Sorokin, A; Ehrlich, S D

    1997-11-01

    The 200 kb region of the Bacillus subtilis chromosome spanning from 255 to 275 degrees on the genetic map was sequenced. The strategy applied, based on use of yeast artificial chromosomes and multiplex Long Accurate PCR, proved to be very efficient for sequencing a large bacterial chromosome area. A total of 193 genes of this part of the chromosome was classified by level of knowledge and biological category of their functions. Five levels of gene function understanding are defined. These are: (i) experimental evidence is available of gene product or biological function; (ii) strong homology exists for the putative gene product with proteins from other organisms; (iii) some indication of the function can be derived from homologies with known proteins; (iv) the gene product can be clustered with hypothetical proteins; (v) no indication on the gene function exists. The percentage of detected genes in each category was: 20, 28, 20, 15 and 17, respectively. In the sequenced region, a high percentage of genes are implicated in transport and metabolic linking of glycolysis and the citric acid cycle. A functional connection of several genes from this region and the genes close to 140 degrees in the chromosome was also observed. PMID:9387221

  6. Cytoplasmic protein binding to highly conserved sequences in the 3' untranslated region of mouse protamine 2 mRNA, a translationally regulated transcript of male germ cells.

    PubMed

    Kwon, Y K; Hecht, N B

    1991-05-01

    The expression of the protamines, the predominant nuclear proteins of mammalian spermatozoa, is regulated translationally during male germ-cell development. The 3' untranslated region (UTR) of protamine 1 mRNA has been reported to control its time of translation. To understand the mechanisms controlling translation of the protamine mRNAs, we have sought to identify cis elements of the 3' UTR of protamine 2 mRNA that are recognized by cytoplasmic factors. From gel retardation assays, two sequence elements are shown to form specific RNA-protein complexes. Protein binding sites of the two complexes were determined by RNase T1 mapping, by blocking the putative binding sites with antisense oligonucleotides, and by competition assays. The sequences of these elements, located between nucleotides + 537 and + 572 in protamine 2 mRNA, are highly conserved among postmeiotic translationally regulated nuclear proteins of the mammalian testis. Two closely linked protein binding sites were detected. UV-crosslinking studies revealed that a protein of about 18 kDa binds to one of the conserved sequences. These data demonstrate specific protein binding to a highly conserved 3' UTR of translationally regulated testicular mRNA. PMID:2023906

  7. Whole genome sequence analyses of Xylella fastidiosa PD strains from different geographical regions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome sequences were determined for two Pierce’s disease (PD) causing Xylella fastidiosa (Xf) strains, one from Florida and one from Taiwan. The Florida strain was ATCC 35879, the type of strain used as a standard reference for related taxonomy research. By contrast, the Taiwan strain used was only...

  8. 40 CFR 81.77 - Puerto Rico Air Quality Control Region.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 18 2013-07-01 2013-07-01 false Puerto Rico Air Quality Control Region... PROGRAMS (CONTINUED) DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Designation of Air Quality Control Regions § 81.77 Puerto Rico Air Quality Control Region. The Puerto Rico Air Quality Control...

  9. 40 CFR 81.77 - Puerto Rico Air Quality Control Region.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 18 2012-07-01 2012-07-01 false Puerto Rico Air Quality Control Region... PROGRAMS (CONTINUED) DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Designation of Air Quality Control Regions § 81.77 Puerto Rico Air Quality Control Region. The Puerto Rico Air Quality Control...

  10. 40 CFR 81.77 - Puerto Rico Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Puerto Rico Air Quality Control Region... PROGRAMS (CONTINUED) DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Designation of Air Quality Control Regions § 81.77 Puerto Rico Air Quality Control Region. The Puerto Rico Air Quality Control...

  11. An electrooculogram-based binary saccade sequence classification (BSSC) technique for augmentative communication and control.

    PubMed

    Keegan, Johnalan; Burke, Edward; Condron, James

    2009-01-01

    In the field of assistive technology, the electrooculogram (EOG) can be used as a channel of communication and the basis of a man-machine interface. For many people with severe motor disabilities, simple actions such as changing the TV channel require assistance. This paper describes a method of detecting saccadic eye movements and the use of a saccade sequence classification algorithm to facilitate communication and control. Saccades are fast eye movements that occurs when a person's gaze jumps from one fixation point to another. The classification is based on pre-defined sequences of saccades, guided by a static visual template (e.g. a page or poster). The template, consisting of a table of symbols each having a clearly identifiable fixation point, is situated within view of the user. To execute a particular command, the user moves his or her gaze through a pre-defined path of eye movements. This results in a well-formed sequence of saccades which are translated into a command if a match is found in a library of predefined sequences. A coordinate transformation algorithm is applied to each candidate sequence of recorded saccades to mitigate the effect of changes in the user's position and orientation relative to the visual template. Upon recognition of a saccade sequence from the library, its associated command is executed. A preliminary experiment in which two subjects were instructed to perform a series of command sequences consisting of 8 different commands are presented in the final sections. The system is also shown to be extensible to facilitate convenient text entry via an alphabetic visual template. PMID:19965222

  12. Research on the Quaternary fluvial geomorphological surface sequence of the foreland region in southern Longmen Shan, eastern Tibet

    NASA Astrophysics Data System (ADS)

    Jiang, Dawei; Zhang, Shimin; Li, Wei

    2016-09-01

    Research on the complex structure of the Longmen Shan foreland is of great significance for understanding the tectonism of the eastern Tibetan Plateau. Therefore, using field survey of abandoned alluvial fans that developed during the middle Pleistocene and the terraces of the modern Qingyi River, a geomorphological surface sequence for the foreland region was established to study the tectonic surface processes. We know that the deformations of river terraces can serve as foundations for the study of tectonic activity. Because the Qingyi River ran through the foreland region in the south range of Longmen Shan, it is an appropriate research area and was adopted to solve these problems. However, in the humid temperate region, the terraces are strongly eroded and hardly retain continuous morphological surfaces. In addition, no marker horizons are available that can be utilized to restrain the corresponding relationships among terraces at the same level. To solve these problems, high-precision field measurements of the terraces and alluvial fan were made, and a series of long cross sections were acquired to determine the spatial relationships between the geomorphological surfaces; moreover, based on major element tests and grain size analyses, we found that the sediments of the geomorphological surfaces at all levels had favorable corresponding relationships. Using those specific analyses of geomorphological surfaces and sediments, a geomorphological surface sequence was derived for the foreland region. The surface sequence can be employed to study the tectonism of the foreland region over larger spatial and temporal ranges rather than using the limited modern terraces. In addition, after the ages of the geomorphological surfaces at various levels were further tested, the evolution of Qingyi River especially its two migrations since the middle Pleistocene in the foreland was determined.

  13. NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

    PubMed Central

    Patel, Ravi K.; Jain, Mukesh

    2012-01-01

    Next generation sequencing (NGS) technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC) of sequence data generated from these technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl programming language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis (statistics tools). A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis. PMID:22312429

  14. Habits as action sequences: hierarchical action control and changes in outcome value

    PubMed Central

    Dezfouli, Amir; Lingawi, Nura W.; Balleine, Bernard W.

    2014-01-01

    Goal-directed action involves making high-level choices that are implemented using previously acquired action sequences to attain desired goals. Such a hierarchical schema is necessary for goal-directed actions to be scalable to real-life situations, but results in decision-making that is less flexible than when action sequences are unfolded and the decision-maker deliberates step-by-step over the outcome of each individual action. In particular, from this perspective, the offline revaluation of any outcomes that fall within action sequence boundaries will be invisible to the high-level planner resulting in decisions that are insensitive to such changes. Here, within the context of a two-stage decision-making task, we demonstrate that this property can explain the emergence of habits. Next, we show how this hierarchical account explains the insensitivity of over-trained actions to changes in outcome value. Finally, we provide new data that show that, under extended extinction conditions, habitual behaviour can revert to goal-directed control, presumably as a consequence of decomposing action sequences into single actions. This hierarchical view suggests that the development of action sequences and the insensitivity of actions to changes in outcome value are essentially two sides of the same coin, explaining why these two aspects of automatic behaviour involve a shared neural structure. PMID:25267824

  15. Sediment and Planform Controls on the Spontaneous Formation and Self Maintenance of Pool-Riffle Sequences

    NASA Astrophysics Data System (ADS)

    De Almeida, G. M.; Rodriguez, J. F.

    2011-12-01

    Continuous numerical simulations coupling unsteady-flow, fractional sediment transport, morphodynamics and grain sorting have been carried out to investigate the complex mechanisms and interactions driving the formation of the irregular morphology and sediment sorting patterns found in streams with pool-riffle sequences. We performed a series of experiments based on field data in which we explore the spontaneous formation of pool-riffle sequences from an initially flat bed topography and the resilience of the bedforms to a series of flood events. Firstly, a one-year long unsteady flow simulation remarkably captured the spontaneous formation of both bed profile and longitudinal sediment sorting observed in the reach. Results show a strong correlation between the stream width and the location and height of pools and riffles. We also performed simulations on existing pool-riffle sequences and analysed feedback mechanisms that enhance the bedforms self maintenance including riffle control, armouring and selective transport. The detailed information provided by these simulations has paved the way for a novel hypothesis explaining the dynamics in pool-riffle sequences, which is strongly linked to the disparity in the time scales of sorting and morphodynamic processes, as well as to the variability of the flow regime. Finally, a series of long term steady flow runs were carried out to study the bed and grain sorting evolution both during the formation and degradation of pool-rifle sequences, demonstrating that steady flows cannot maintain or generate the sediment sorting observed in natural streams.

  16. Phylogeographic study of brown trout from Serbia, based on mitochondrial DNA control region analysis

    PubMed Central

    Marić, Saša; Sušnik, Simona; Simonović, Predrag; Snoj, Aleš

    2006-01-01

    In order to illuminate the phylogeography of brown trout (Salmo trutta) populations in the Balkan state of Serbia, the 561 bp 5'-end of mtDNA control region of 101 individuals originating from upland tributaries of the Danubian, Aegean and Adriatic drainages were sequenced and compared to corresponding brown trout sequences obtained in previous studies. Among 15 haplotypes found, 14 were considered native, representing the Danubian and Adriatic lineages of the brown trout, while one haplotype (ATcs1), found only in two individuals originating from two stocked rivers, corresponded to the Atlantic lineage and was considered introduced. Native haplotypes exhibited a strong geographic pattern of distribution: the Danubian haplotypes were strictly confined to the Danubian drainage, while the Adriatic haplotypes dominated in the Aegean and Adriatic drainages; most of the total molecular variance (69%) was attributed to differences among the drainages. Phylogenetic reconstruction, supplemented with seven haplotypes newly described in this study, suggested a sister position of the Atlantic-Danubian and Adriatic-Mediterranean-marmoratus ("southern") phylogenetic group, and pointed to the existence of a distinct clade, detected within the "southern" group. The data obtained confirmed our expectation of the existence of high genetic diversity in Balkan trout populations, and we recommend more widespread surveys covering trout stocks from the region. PMID:16790230

  17. Structural conservation and variation in the mitochondrial control region of fringilline finches (Fringilla spp.) and the greenfinch (Carduelis chloris).

    PubMed

    Marshall, H D; Baker, A J

    1997-02-01

    We sequenced the entire control region and portions of flanking genes (tRNA(Phe), tRNA(Glu), and ND6) in the common chaffinch (Fringilla coelebs), blue chaffinch (F. teydea), brambling (F. montifringilla), and greenfinch (Carduelis chloris). In these finches the control region is similar in length (1,223-1,237 bp) and has the same flanking gene order as in other birds, and contains a putative TAS element and the highly conserved CSB-1 and F, D, and C boxes recognizable in most vertebrates. Cloverleaf-like structures associated with the TAS element at the 5' end and CSB-1 at the 3' end of the control region may be involved with the stop and start of D-loop synthesis, respectively. The pattern of nucleotide and substitution bias is similar to that in other vertebrates, and consequently the finch control region can be subdivided into a central, conserved G-rich domain (domain II) flanked by hypervariable 5'-C-rich (domain I) and 3'-AT-rich (domain III) segments. In pairwise comparisons among finch species, the central domain has unusually low transition/transversion ratios, which suggests that increased G + T content is a functional constraint, possibly for DNA primase efficiency. In finches the relative rates of evolution vary among domains according to a ratio of 4.2 (domain III) to 2.2 (domain I) to 1 (domain II), and extensively among sites within domains I and II. Domain I and III sequences are extremely useful in recovering intraspecific phylogeographic splits between populations in Africa and Europe, Madeira, and a basal lineage in Nefza, Tunisia. Domain II sequences are highly conserved, and are therefore only useful in conjunction with sequences from domains I and III in phylogenetic studies of closely related species. PMID:9029795

  18. Controls on Extreme Droughts and Adaptation Strategies in Semiarid Regions

    NASA Astrophysics Data System (ADS)

    Scanlon, B. R.; Cook, C.; Fernando, D. N.; LeBlanc, M.

    2012-12-01

    Increasing vulnerability to droughts with reduced per capita water storage, particularly in semiarid regions, underscores the need for predictive understanding of drought controls and development of adaptation strategies for water resources management. In this study we evaluate causes of major droughts in southwest and southcentral US (California and Texas) and southeast Australia (Murray Darling Basin). Impacts of climate cycles (ENSO, PDO, AMO, NAO, IOD) and atmospheric circulation on drought initiation and persistence are examined. Effects of drought on surface water reservoir storage, groundwater storage, irrigation, and crop production are compared. Adaptation strategies being evaluated include water transfers among sectors, particularly from irrigated agriculture to other groups, increasing storage using managed aquifer recharge, water reuse, and development of new water sources (e.g. seawater desalination). It is critical to develop a broad portfolio of water sources to increase resilience to future droughts.

  19. Factors controlling the regional distribution of vanadium in ground water

    USGS Publications Warehouse

    Wright, Michael T.; Belitz, Kenneth

    2010-01-01

    Although the ingestion of vanadium (V) in drinking water may have possible adverse health effects, there have been relatively few studies of V in groundwater. Given the importance of groundwater as a source of drinking water in many areas of the world, this study examines the potential sources and geochemical processes that control the distribution of V in groundwater on a regional scale. Potential sources of V to groundwater include dissolution of V rich rocks, and waste streams from industrial processes. Geochemical processes such as adsorption/desorption, precipitation/dissolution, and chemical transformations control V concentrations in groundwater. Based on thermodynamic data and laboratory studies, V concentrations are expected to be highest in samples collected from oxic and alkaline groundwater. However, the extent to which thermodynamic data and laboratory results apply to the actual distribution of V in groundwater is not well understood. More than 8400 groundwater samples collected in California were used in this study. Of these samples, high (> or = 50 μg/L) and moderate (25 to 49 μg/L) V concentrations were most frequently detected in regions where both source rock and favorable geochemical conditions occurred. The distribution of V concentrations in groundwater samples suggests that significant sources of V are mafic and andesitic rock. Anthropogenic activities do not appear to be a significant contributor of V to groundwater in this study. High V concentrations in groundwater samples analyzed in this study were almost always associated with oxic and alkaline groundwater conditions, which is consistent with predictions based on thermodynamic data.

  20. Processes Controlling Water Vapor in the Winter Arctic Tropopause Region

    NASA Technical Reports Server (NTRS)

    Pfister, Leonhard; Selkirk, Henry B.; Jensen, Eric J.; Padolske, James; Sachse, Glen; Avery, Melody; Schoeberl, Mark R.; Mahoney, Michael J.; Richard, Erik

    2002-01-01

    This work describes transport and thermodynamic processes that control water vapor near the tropopause during the SAGE III-Ozone Loss and Validation Experiment (SOLVE), held during the Arctic 1999/2000 winter season. Aircraft-based water vapor, carbon monoxide, and ozone measurements were analyzed so as to establish how deeply tropospheric air mixes into the Arctic lowermost stratosphere and what the implications are for cloud formation and water vapor removal in this region of the atmosphere. There are three major findings. First, troposphere-to-stratosphere exchange extends into the Arctic stratosphere to about 13 km. Penetration is to similar levels throughout the winter, however, because ozone increases with altitude most rapidly in the early spring, tropospheric air mixes with the highest values of ozone in that season. The effect of this upward mixing is to elevate water vapor mixing ratios significantly above their prevailing stratospheric values of above 5ppmv. Second, the potential for cloud formation in the stratosphere is highest during early spring, with about 20% of the parcels which have ozone values of 300-350 ppbv experiencing ice saturation in a given 10 day period. Third, during early spring, temperatures at the troposphere are cold enough so that 5-10% of parcels experience relative humidities above 100%, even if the water content is as low as 5 ppmv. The implication is that during this period, dynamical processes near the Arctic tropopause can dehydrate air and keep the Arctic tropopause region very dry during early spring.

  1. U3 Region in the HIV-1 Genome Adopts a G-Quadruplex Structure in Its RNA and DNA Sequence

    PubMed Central

    2015-01-01

    Genomic regions rich in G residues are prone to adopt G-quadruplex structure. Multiple Sp1-binding motifs arranged in tandem have been suggested to form this structure in promoters of cancer-related genes. Here, we demonstrate that the G-rich proviral DNA sequence of the HIV-1 U3 region, which serves as a promoter of viral transcription, adopts a G-quadruplex structure. The sequence contains three binding elements for transcription factor Sp1, which is involved in the regulation of HIV-1 latency, reactivation, and high-level virus expression. We show that the three Sp1 binding motifs can adopt different forms of G-quadruplex structure and that the Sp1 protein can recognize and bind to its site folded into a G-quadruplex. In addition, a c-kit2 specific antibody, designated hf2, binds to two different G-quadruplexes formed in Sp1 sites. Since U3 is encoded at both viral genomic ends, the G-rich sequence is also present in the RNA genome. We demonstrate that the RNA sequence of U3 forms dimers with characteristics known for intermolecular G-quadruplexes. Together with previous reports showing G-quadruplex dimers in the gag and cPPT regions, these results suggest that integrity of the two viral genomes is maintained through numerous intermolecular G-quadruplexes formed in different RNA genome locations. Reconstituted reverse transcription shows that the potassium-dependent structure formed in U3 RNA facilitates RT template switching, suggesting that the G-quadruplex contributes to recombination in U3. PMID:24735378

  2. Bean yellow mosaic, clover yellow vein, and pea mosaic are distinct potyviruses: evidence from coat protein gene sequences and molecular hybridization involving the 3' non-coding regions.

    PubMed

    Tracy, S L; Frenkel, M J; Gough, K H; Hanna, P J; Shukla, D D

    1992-01-01

    The sequences of the 3' 1019 nucleotides of the genome of an atypical strain of bean yellow mosaic virus (BYMV-S) and of the 3' 1018 nucleotides of the clover yellow vein virus (CYVV-B) genome have been determined. These sequences contain the complete coding region of the viral coat protein followed by a 3' non-coding region of 173 and 178 nucleotides for BYMV-S and CYVV-B, respectively. When the deduced amino acid sequences of the coat protein coding regions were compared, a sequence identity of 77% was found between the two viruses, and optimal alignment of the 3' untranslated regions of BYMV-S and CYVV-B gave a 65% identity. However, the degree of homology of the amino acid sequences of coat proteins of BYMV-S with the published sequences for three other strains of BYMV ranged from 88% to 94%, while the sequence homology of the 3' untranslated regions between the four strains of BYMV ranged between 86% and 95%. Amplified DNA probes corresponding to the 3' non-coding regions of BYMV-S and CYVV-B showed strong hybridization only with the strains of their respective viruses and not with strains of other potyviruses, including pea mosaic virus (PMV). The relatively low sequence identities between the BYMV-S and CYVV-B coat proteins and their 3' non-coding regions, together with the hybridization results, indicate that BYMV, CYVV, and PMV are distinct potyviruses. PMID:1731696

  3. Identification of clustered YY1 binding sites in Imprinting Control Regions

    SciTech Connect

    Kim, J D; Hinz, A; Bergmann, A; Huang, J; Ovcharenko, I; Stubbs, L; Kim, J

    2006-04-19

    Mammalian genomic imprinting is regulated by Imprinting Control Regions (ICRs) that are usually associated with tandem arrays of transcription factor binding sites. In the current study, the sequence features derived from a tandem array of YY1 binding sites of Peg3-DMR (differentially methylated region) led us to identify three additional clustered YY1 binding sites, which are also localized within the DMRs of Xist, Tsix, and Nespas. These regions have been shown to play a critical role as ICRs for the regulation of surrounding genes. These ICRs have maintained a tandem array of YY1 binding sites during mammalian evolution. The in vivo binding of YY1 to these regions is allele-specific and only to the unmethylated active alleles. Promoter/enhancer assays suggest that a tandem array of YY1 binding sites function as a potential orientation-dependent enhancer. Insulator assays revealed that the enhancer-blocking activity is detected only in the YY1 binding sites of Peg3-DMR but not in the YY1 binding sites of other DMRs. Overall, our identification of three additional clustered YY1 binding sites in imprinted domains suggests a significant role for YY1 in mammalian genomic imprinting.

  4. Frequency and pattern of heteroplasmy in the control region of human mitochondrial DNA.

    PubMed

    Santos, Cristina; Sierra, Blanca; Alvarez, Luis; Ramos, Amanda; Fernández, Elisabet; Nogués, Ramón; Aluja, Maria Pilar

    2008-08-01

    In this work, we present the results of the screening of human mitochondrial DNA (mtDNA) heteroplasmy in the control region of mtDNA from 210 unrelated Spanish individuals. Both hypervariable regions of mtDNA were amplified and sequenced in order to identify and quantify point and length heteroplasmy. Of the 210 individuals analyzed, 30% were fully homoplasmic and the remaining presented point and/or length heteroplasmy. The prevalent form of heteroplasmy was length heteroplasmy in the poly(C) tract of the hypervariable region II (HVRII), followed by length heteroplasmy in the poly(C) tract of hypervariable region I (HVRI) and, finally, point heteroplasmy, which was found in 3.81% of the individuals analyzed. Moreover, no significant differences were found in the proportions of the different kinds of heteroplasmy in the population when blood and buccal cell samples were compared. The pattern of heteroplasmy in HVRI and HVRII presents important differences. Moreover, the mutational profile in heteroplasmy seems to be different from the mutational pattern detected in population. The results suggest that a considerable number of mutations and, particularly, transitions that appear in heteroplasmy are probably eliminated by drift and/or by selection acting at different mtDNA levels of organization. Taking as a whole the results reported in this work, it is mandatory to perform a broad-scale screening of heteroplasmy to better establish the heteroplasmy profile which would be important for medical, evolutionary, and forensic proposes. PMID:18618067

  5. Analysis of complex repeat sequences within the spinal muscular atrophy (SMA) candidate region in 5q13

    SciTech Connect

    Davies, K.E.; Morrison, K.E.; Daniels, R.I.

    1994-09-01

    We previously reported that the 400 kb interval flanked the polymorphic loci D5S435 and D5S557 contains blocks of a chromosome 5 specific repeat. This interval also defines the SMA candidate region by genetic analysis of recombinant families. A YAC contig of 2-3 Mb encompassing this area has been constructed and a 5.5 kb conserved fragment, isolated from a YAC end clone within the above interval, was used to obtain cDNAs from both fetal and adult brain libraries. We describe the identification of cDNAs with stretches of high DNA sequence homology to exons of {beta} glucuronidase on human chromosome 7. The cDNAs map both to the candidate region and to an area of 5p using FISH and deletion hybrid analysis. Hybridization to bacteriophage and cosmid clones from the YACs localizes the {beta} glucuronidase related sequences within the 400 kb region of the YAC contig. The cDNAs show a polymorphic pattern on hybridization to genomic BamH1 fragments in the size range of 10-250 kb. Further analysis using YAC fragmentation vectors is being used to determine how these {beta} glucuronidase related cDNAs are distributed within 5q13. Dinucleotide repeats within the region are being investigated to determine linkage disequilibrium with the disease locus.

  6. Population and forensic genetic analyses of mitochondrial DNA control region variation from six major provinces in the Korean population.

    PubMed

    Hong, Seung Beom; Kim, Ki Cheol; Kim, Wook

    2015-07-01

    We generated complete mitochondrial DNA (mtDNA) control region sequences from 704 unrelated individuals residing in six major provinces in Korea. In addition to our earlier survey of the distribution of mtDNA haplogroup variation, a total of 560 different haplotypes characterized by 271 polymorphic sites were identified, of which 473 haplotypes were unique. The gene diversity and random match probability were 0.9989 and 0.0025, respectively. According to the pairwise comparison of the 704 control region sequences, the mean number of pairwise differences between individuals was 13.47±6.06. Based on the result of mtDNA control region sequences, pairwise FST genetic distances revealed genetic homogeneity of the Korean provinces on a peninsular level, except in samples from Jeju Island. This result indicates there may be a need to formulate a local mtDNA database for Jeju Island, to avoid bias in forensic parameter estimates caused by genetic heterogeneity of the population. Thus, the present data may help not only in personal identification but also in determining maternal lineages to provide an expanded and reliable Korean mtDNA database. These data will be available on the EMPOP database via accession number EMP00661. PMID:25900647

  7. Polymorphism of the 5' terminal region of Citrus tristeza virus (CTV) RNA: incidence of three sequence types in isolates of different origin and pathogenicity.

    PubMed

    Ayllón, M A; López, C; Navas-Castillo, J; Garnsey, S M; Guerri, J; Flores, R; Moreno, P

    2001-01-01

    Sequences of the 5' terminal region of the genomic RNA from eight isolates of Citrus tristeza virus (CTV) were previously classified into three types (I, II and III), with intragroup sequence identity higher than 88% and intergroup sequence identity as low as 44%. Sequencing of an additional 58 cDNA clones from 15 virus isolates showed that all sequences could be unequivocally assigned to one of the three types previously established. The relative frequency of each sequence type was assessed in 57 CTV isolates of different geographic origin and pathogenic characteristics by RT-PCR with sets of type-specific primers using CTV dsRNA as template. None of the isolates yielded amplification of the type I or II sequences alone, but in 19 of them type III sequences were the only amplification product detected. Within isolates containing more than one sequence type, eight had type II and III sequences, 11 had type I and III sequences, and 19 had sequences of the three types. Isolates containing only type III sequences caused only mild to moderate symptoms in Mexican lime, an indicator species for most CTV isolates, whereas isolates causing stem pitting in sweet orange an/or grapefruit, generally contained sequences type II. None of the sequence types could be traced to a precise geographic area, as all types were detected in isolates from at least nine of the 12 countries from which samples were taken. PMID:11266215

  8. Controlling the Radiation Parameters of a Resonant Medium Excited by a Sequence of Ultrashort Superluminal Pulses

    NASA Astrophysics Data System (ADS)

    Arkhipov, R. M.; Arkhipov, M. V.; Belov, P. A.; Babushkin, I.; Tolmachev, Yu. A.

    2016-03-01

    We investigate the possibility of controlling the radiation parameters of a spatially periodic one-dimensional medium consisting of classical harmonic oscillators by means of a sequence of ultrashort pulses that propagate through the medium with a superluminal velocity. We show that, in the spectrum of the transient process, in addition to the radiation at a resonant frequency of oscillators, new frequencies arise that depend on the period of the spatial distribution of the oscillator density, the excitation velocity, and the angle of observation. We have examined in detail the case of excitation of the medium by a periodic sequence of ultrashort pulses that travel with a superluminal velocity. We show that it is possible to excite oscillations of complex shapes and to control the radiation parameters of the resonant medium by changing the relationship between the pulse repetition rate, the medium resonant frequency, and the new frequency.

  9. Genome Sequences of 11 Brucella abortus Isolates from Persistently Infected Italian Regions.

    PubMed

    Garofolo, Giuliano; Foster, Jeffrey T; Drees, Kevin; Zilli, Katiuscia; Platone, Ilenia; Ancora, Massimo; Cammà, Cesare; De Massis, Fabrizio; Calistri, Paolo; Di Giannatale, Elisabetta

    2015-01-01

    Bovine brucellosis, typically caused by Brucella abortus, has been eradicated from much of the developed world. However, the disease remains prevalent in southern Italy, persisting as a public and livestock health concern. We report here the whole-genome sequences of 11 isolates from cattle (Bos taurus) and water buffalo (Bubalus bubalis) that are representative of the current genetic diversity of B. abortus lineages circulating in Italy. PMID:26679575

  10. Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions

    PubMed Central

    2012-01-01

    Background Environmentally induced epigenetic transgenerational inheritance of adult onset disease involves a variety of phenotypic changes, suggesting a general alteration in genome activity. Results Investigation of different tissue transcriptomes in male and female F3 generation vinclozolin versus control lineage rats demonstrated all tissues examined had transgenerational transcriptomes. The microarrays from 11 different tissues were compared with a gene bionetwork analysis. Although each tissue transgenerational transcriptome was unique, common cellular pathways and processes were identified between the tissues. A cluster analysis identified gene modules with coordinated gene expression and each had unique gene networks regulating tissue-specific gene expression and function. A large number of statistically significant over-represented clusters of genes were identified in the genome for both males and females. These gene clusters ranged from 2-5 megabases in size, and a number of them corresponded to the epimutations previously identified in sperm that transmit the epigenetic transgenerational inheritance of disease phenotypes. Conclusions Combined observations demonstrate that all tissues derived from the epigenetically altered germ line develop transgenerational transcriptomes unique to the tissue, but common epigenetic control regions in the genome may coordinately regulate these tissue-specific transcriptomes. This systems biology approach provides insight into the molecular mechanisms involved in the epigenetic transgenerational inheritance of a variety of adult onset disease phenotypes. PMID:23034163

  11. Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species.

    PubMed

    Guyot, Romain; Garavito, Andrea; Gavory, Frédérick; Samain, Sylvie; Tohme, Joe; Ghesquière, Alain; Lorieux, Mathias

    2011-01-01

    A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S(1)A, S(1) and S(1)B (called together the S(1) regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S(1) locus (including a putative F-box gene) were proposed, but candidates for S(1)A and S(1)B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S(1) regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S(1)A, S(1) and the majority of the S(1)B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1) a local invasion of transposable elements around a putative F-box gene within S(1), (2) the multiple duplication and subsequent divergence of the same F-box gene within S(1)A, (3) an interspecific chromosomal inversion in S(1)B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S(1) regions. Hence, the S(1) regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM) model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the

  12. Patterns of Sequence Divergence and Evolution of the S1 Orthologous Regions between Asian and African Cultivated Rice Species

    PubMed Central

    Gavory, Frédérick; Samain, Sylvie; Tohme, Joe; Ghesquière, Alain; Lorieux, Mathias

    2011-01-01

    A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S1A, S1 and S1B (called together the S1 regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S1 locus (including a putative F-box gene) were proposed, but candidates for S1A and S1B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S1 regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S1A, S1 and the majority of the S1B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1) a local invasion of transposable elements around a putative F-box gene within S1, (2) the multiple duplication and subsequent divergence of the same F-box gene within S1A, (3) an interspecific chromosomal inversion in S1B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S1 regions. Hence, the S1 regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM) model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the chromosomal inversion might participate to

  13. Tailored Living Block Copolymerization: Multiblock Poly(cyclohexene carbonate)s with Sequence Control

    SciTech Connect

    Kim, Jeung Gon; Cowman, Christina D.; LaPointe, Anne M.; Wiesner, Ulrich; Coates, Geoffrey W.

    2011-03-08

    In this Communication, the living block copolymerization of functionalized cyclohexene oxides and CO{sub 2} is described, yielding multiblock poly(cyclohexene carbonate)s [p(CHC)s] with a diverse range of functionality on the side chains and good control of block sequence and length. Unlike prior systems that contain stable vinyl backbones, the carbonate backbones of polymers reported herein are degradable, allowing possible applications where removable templates are required.

  14. Sequence analysis of the internal transcribed spacer (ITS) region reveals a novel clade of Ichthyophonus sp. from rainbow trout

    USGS Publications Warehouse

    Rasmussen, C.; Purcell, M.K.; Gregg, J.L.; LaPatra, S.E.; Winton, J.R.; Hershberger, P.K.

    2010-01-01

    The mesomycetozoean parasite Ichthyophonus hoferi is most commonly associated with marine fish hosts but also occurs in some components of the freshwater rainbow trout Oncorhynchus mykiss aquaculture industry in Idaho, USA. It is not certain how the parasite was introduced into rainbow trout culture, but it might have been associated with the historical practice of feeding raw, ground common carp Cyprinus carpio that were caught by commercial fisherman. Here, we report a major genetic division between west coast freshwater and marine isolates of Ichthyophonus hoferi. Sequence differences were not detected in 2 regions of the highly conserved small subunit (18S) rDNA gene; however, nucleotide variation was seen in internal transcribed spacer loci (ITS1 and ITS2), both within and among the isolates. Intra-isolate variation ranged from 2.4 to 7.6 nucleotides over a region consisting of ~740 bp. Majority consensus sequences from marine/anadromous hosts differed in only 0 to 3 nucleotides (99.6 to 100% nucleotide identity), while those derived from freshwater rainbow trout had no nucleotide substitutions relative to each other. However, the consensus sequences between isolates from freshwater rainbow trout and those from marine/anadromous hosts differed in 13 to 16 nucleotides (97.8 to 98.2% nucleotide identity).

  15. Comparative In silico Study of Sex-Determining Region Y (SRY) Protein Sequences Involved in Sex-Determining

    PubMed Central

    Vakili Azghandi, Masoume; Nasiri, Mohammadreza; Shamsa, Ali; Jalali, Mohsen; Shariati, Mohammad Mahdi

    2016-01-01

    Background: The SRY gene (SRY) provides instructions for making a transcription factor called the sex-determining region Y protein. The sex-determining region Y protein causes a fetus to develop as a male. In this study, SRY of 15 spices included of human, chimpanzee, dog, pig, rat, cattle, buffalo, goat, sheep, horse, zebra, frog, urial, dolphin and killer whale were used for determine of bioinformatic differences. Methods: Nucleotide sequences of SRY were retrieved from the NCBI databank. Bioinformatic analysis of SRY is done by CLC Main Workbench version 5.5 and ClustalW (http:/www.ebi.ac.uk/clustalw/) and MEGA6 softwares. Results: The multiple sequence alignment results indicated that SRY protein sequences from Orcinus orca (killer whale) and Tursiopsaduncus (dolphin) have least genetic distance of 0.33 in these 15 species and are 99.67% identical at the amino acid level. Homosapiens and Pantroglodytes (chimpanzee) have the next lowest genetic distance of 1.35 and are 98.65% identical at the amino acid level. Conclusion: These findings indicate that the SRY proteins are conserved in the 15 species, and their evolutionary relationships are similar. PMID:27536700

  16. Nucleotide sequence of the 3'-noncoding region of alfalfa mosaic virus RNA 4 and its homology with the genomic RNAs.

    PubMed Central

    Koper-Zwarthoff, E C; Brederode, F T; Walstra, P; Bol, J F

    1979-01-01

    A 226-nucleotide fragment was derived from alfalfa mosaic virus RNA 4 (ALMV RNA 4), the subgenomic messenger for viral coat protein, and its sequence was deduced by in vitro labeling with polynucleotide kinase and application of RNA sequencing techniques. The fragment contains the 3'-terminal 45 nucleotides of the coat protein cistron and the complete 3'-noncoding region of 182 nucleotides. The total length of RNA 4 was calculated to be 881 nucleotides. AlMV RNAs 1, 2 and 3 were elongated with a 3'-terminal poly(A) stretch and subjected to sequence analysis by using a specific primer, reverse transcriptase and chain terminators. This revealed and extensive homology between the 3'-terminal 140 to 150 nucleotides of all four ALMV RNAs. Despite a number of base substitutions, the secondary structure of the homologous region is highly conserved. The observed homology indicates that, as with RNA 4, the sites with a high affinity for the viral coat protein are located at the 3'-termini of the genomic RNAs. Images PMID:537914

  17. Identification of Cistanche species (Orobanchaceae) based on sequences of the plastid psbA-trnH intergenic region.

    PubMed

    Han, Jian-Ping; Song, Jing-Yuan; Liu, Chang; Chen, Jun; Qian, Jun; Zhu, Ying-Jie; Shi, Lin-Chun; Yao, Hui; Chen, Shi-Lin

    2010-01-01

    The dried succulent stems of Cistanche (Cistanche deserticola Y. C. Ma and Cistanche tubulosa Wight.) are one of the most widely used components of traditional Chinese medicines. However, it is often confused and substituted with the roots of Orobanche pycnostachya, Boschniakia rossica (Cham. & Schltdl.) Standl., Cistanche sinensis Beck, and Cistanche salsa (C. A. Mey.) Beck. In this study, we identified psbA-trnH regions from species and tested their suitable for the identification of the above mentioned taxa. The psbA-trnH sequences showed considerable variations between species and thus were revealed as a promising candidate for barcoding of Cistanche species. Additionally, the average genetic distance of psbA-trnH ranging from 0.077% to 0.743%. In contrast, the intra-specific variation among Cistanche species was found to be significantly different from those of other species, with percentages of variation studied ranged from 0% to 0.007%. The sequence difference between the psbA-trnH sequences of Cistanche species and Orobanche pycnostachya ranged from 0.979% to 1.149%. The distance between the Cistanche species and Boschniakia rossica ranged from 1.066% to 1.224%. Our results suggest that the psbA-trnH intergenic spacer region represent a barcode that can be used to identify Cistanche species and other morphologically undistinguishable species. PMID:21348418

  18. Molecular identification of isolated fungi from unopened containers of greek yogurt by DNA sequencing of internal transcribed spacer region.

    PubMed

    Sulaiman, Irshad M; Jacobs, Emily; Simpson, Steven; Kerdahi, Khalil

    2014-01-01

    In our previous study, we described the development of an internal transcribed spacer (ITS)1 sequencing method, and used this protocol in species-identification of isolated fungi collected from the manufacturing areas of a compounding company known to have caused the multistate fungal meningitis outbreak in the United States. In this follow-up study, we have analyzed the unopened vials of Greek yogurt from the recalled batch to determine the possible cause of microbial contamination in the product. A total of 15 unopened vials of Greek yogurt belonging to the recalled batch were examined for the detection of fungi in these samples known to cause foodborne illness following conventional microbiological protocols. Fungi were isolated from all of the 15 Greek yogurt samples analyzed. The isolated fungi were genetically typed by DNA sequencing of PCR-amplified ITS1 region of rRNA gene. Analysis of data confirmed all of the isolated fungal isolates from the Greek yogurt to be Rhizomucor variabilis. The generated ITS1 sequences matched 100% with the published sequences available in GenBank. In addition, these yogurt samples were also tested for the presence of five types of bacteria (Salmonella, Listeria, Staphylococcus, Bacillus and Escherichia coli) causing foodborne disease in humans, and found negative for all of them. PMID:25438008

  19. Molecular Identification of Isolated Fungi from Unopened Containers of Greek Yogurt by DNA Sequencing of Internal Transcribed Spacer Region

    PubMed Central

    Sulaiman, Irshad M.; Jacobs, Emily; Simpson, Steven; Kerdahi, Khalil

    2014-01-01

    In our previous study, we described the development of an internal transcribed spacer (ITS)1 sequencing method, and used this protocol in species-identification of isolated fungi collected from the manufacturing areas of a compounding company known to have caused the multistate fungal meningitis outbreak in the United States. In this follow-up study, we have analyzed the unopened vials of Greek yogurt from the recalled batch to determine the possible cause of microbial contamination in the product. A total of 15 unopened vials of Greek yogurt belonging to the recalled batch were examined for the detection of fungi in these samples known to cause foodborne illness following conventional microbiological protocols. Fungi were isolated from all of the 15 Greek yogurt samples analyzed. The isolated fungi were genetically typed by DNA sequencing of PCR-amplified ITS1 region of rRNA gene. Analysis of data confirmed all of the isolated fungal isolates from the Greek yogurt to be Rhizomucor variabilis. The generated ITS1 sequences matched 100% with the published sequences available in GenBank. In addition, these yogurt samples were also tested for the presence of five types of bacteria (Salmonella, Listeria, Staphylococcus, Bacillus and Escherichia coli) causing foodborne disease in humans, and found negative for all of them. PMID:25438008

  20. Does the Upstream Region Possessing MULE-Like Sequence in Rice Upregulate PsbS1 Gene Expression?

    PubMed Central

    Nuruzzaman, Mohammed; Kanno, Tatsuo; Amada, Rika; Habu, Yoshiki; Kasajima, Ichiro; Ishikawa, Toshiki; Kawai-Yamada, Maki; Uchimiya, Hirofumi

    2014-01-01

    The genomic nucleotide sequences of japonica rice (Sasanishiki and Nipponbare) contained about 2.7-kb unique region at the point of 0.4-kb upstream of the OsPsbS1 gene. In this study, we found that japonica rice with a few exceptions possessing such DNA sequences [denoted to OsMULE-japonica specific sequence (JSS)] is distinct by the presence of Mutator-like-element (MULE). Such sequence was absent in most of indica cultivars and Oryza glaberrima. In OsMULE-JSS1, we noted the presence of possible target site duplication (TSD; CTTTTCCAG) and about 80-bp terminal inverted repeat (TIR) near TSD. We also found the enhancement ofOsPsbS1 mRNA accumulation by intensified light, which was not associated with the DNA methylation status in OsMULE/JSS. In addition, O. rufipogon, possible ancestor of modern rice cultivars was found to compose PsbS gene of either japonica (minor) or indica (major) type. Transient gene expression assay showed that the japonica type promoter elevated a reporter gene activity than indica type. PMID:25259844

  1. Genome-Based Identification of Active Prophage Regions by Next Generation Sequencing in Bacillus licheniformis DSM13

    PubMed Central

    Hertel, Robert; Rodríguez, David Pintor; Hollensteiner, Jacqueline; Dietrich, Sascha; Leimbach, Andreas; Hoppert, Michael; Liesegang, Heiko; Volland, Sonja

    2015-01-01

    Prophages are viruses, which have integrated their genomes into the genome of a bacterial host. The status of the prophage genome can vary from fully intact with the potential to form infective particles to a remnant state where only a few phage genes persist. Prophages have impact on the properties of their host and are therefore of great interest for genomic research and strain design. Here we present a genome- and next generation sequencing (NGS)-based approach for identification and activity evaluation of prophage regions. Seven prophage or prophage-like regions were identified in the genome of Bacillus licheniformis DSM13. Six of these regions show similarity to members of the Siphoviridae phage family. The remaining region encodes the B. licheniformis orthologue of the PBSX prophage from Bacillus subtilis. Analysis of isolated phage particles (induced by mitomycin C) from the wild-type strain and prophage deletion mutant strains revealed activity of the prophage regions BLi_Pp2 (PBSX-like), BLi_Pp3 and BLi_Pp6. In contrast to BLi_Pp2 and BLi_Pp3, neither phage DNA nor phage particles of BLi_Pp6 could be visualized. However, the ability of prophage BLi_Pp6 to generate particles could be confirmed by sequencing of particle-protected DNA mapping to prophage locus BLi_Pp6. The introduced NGS-based approach allows the investigation of prophage regions and their ability to form particles. Our results show that this approach increases the sensitivity of prophage activity analysis and can complement more conventional approaches such as transmission electron microscopy (TEM). PMID:25811873

  2. 40 CFR 81.88 - Billings Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...) AIR PROGRAMS (CONTINUED) DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Designation of Air...: Region II. 481.169Helena Intrastate Air Quality Control Region: Region IV. 481.170Miles City...

  3. 40 CFR 81.88 - Billings Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...) AIR PROGRAMS (CONTINUED) DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Designation of Air...: Region II. 481.169Helena Intrastate Air Quality Control Region: Region IV. 481.170Miles City...

  4. 40 CFR 81.88 - Billings Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...) AIR PROGRAMS (CONTINUED) DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Designation of Air...: Region II. 481.169Helena Intrastate Air Quality Control Region: Region IV. 481.170Miles City...

  5. 40 CFR 81.88 - Billings Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...) AIR PROGRAMS (CONTINUED) DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Designation of Air...: Region II. 481.169Helena Intrastate Air Quality Control Region: Region IV. 481.170Miles City...

  6. Sequence Variability in Viral Genome Non-coding Regions Likely Contribute to Observed Differences in Viral Replication Amongst MARV Strains

    PubMed Central

    ALONSO, JESUS A.; PATTERSON, JEAN L.

    2013-01-01

    The Marburg viruses Musoke (MARV-Mus) and Angola (MARV-Ang) have highly similar genomic sequences. Analysis of viral replication using various assays consistently identified MARV-Ang as the faster replicating virus. Non-coding genomic regions of negative sense RNA viruses are known to play a role in viral gene expression. A comparison of the six non-coding regions using bicistronic minigenomes revealed that the first two non-coding regions (NP / VP35 and VP35 / VP40) differed significantly in their transcriptional regulation. Deletion mutation analysis of the MARV-Mus NP / VP35 region further revealed that the MARV polymerase (L) is able to initiate production of the downstream gene without the presence of highly conserved regulatory signals. Bicistronic minigenome assays also identified the VP30 mRNA 5′ untranslated region as an rZAP-targeted RNA motif. Overall, our studies indicate that the high variation of MARV non-coding regions may play a significant role in observed differences in transcription and/or replication. PMID:23510675

  7. Isolation and characterization of 21 novel expressed DNA sequences from the distal region of human chromosome 4p

    SciTech Connect

    Ishida, Yoshikazu; Hadano, Shinji; Nagayama, Tomiko

    1994-07-15

    The authors have established an approach to the isolation of expressed DNA sequences from a defined region of the human chromosome. The method relies on the direct screening of cDNA libraries using pooled single-copy microclones generated by a laser chromosome microdissection in conjunction with a single unique primer polymerase chain reaction (SUP-PCR) procedure. They applied this method to the distal region of human chromosome 4p (4p15-4pter), which contains the Huntington disease (HD) and the Wolf-Hirschhorn syndrome (WHS) loci. Twenty-one nonoverlapping and region-specific cDNA clones encoding novel genes were isolated in this manner. Ten of 21 clones were subregionally assigned to 4p16.1-4pter, and the remainder mapped to the region proximal to 4p16.1. Northern blot and reverse transcription followed by the PCR (RT-PCR) analysis revealed that 16 of these 21 clones detected transcripts in total RNA from human tissues. The method is applicable to other chromosomal regions and is a powerful approach to the isolation of region-specific cDNA clones. 44 refs., 3 figs., 3 tabs.

  8. Special structure of mitochondrial DNA control region and phylogenetic relationship among individuals of the black rockfish, Sebastes schlegelii.

    PubMed

    Zhang, Hui; Zhang, Yan; Zhang, Xiumei; Song, Na; Gao, Tianxiang

    2013-04-01

    This study deals with the structure of mitochondrial DNA (mtDNA) control region (CR) of the black rockfish, Sebastes schlegelii. Two termination-associated sequences (TASs), two complementary termination-associated sequences (cTASs), and conserved sequence block (CSB), such as CSB-F, CSB-E, CSB-D, CSB1, CSB2, and CSB3, were detected in S. schlegelii. The results indicated that the structures of these blocks are similar to most marine fishes, but it is special that there are two TASs and two cTASs in the CR of S. schlegelii. One conserved region was found from 450 bp to the end of the CR, which is also a special feature of S. schlegelii. All sequences of CSB1, CSB2, and CSB3 blocks are the consensus among different individuals, which is quite different from most vertebrates. In addition, the complete mtDNA CR sequences and the first 449 bp of the CR are used to analyze the phylogenetic relationships of S. schlegelii. The phylogenetic trees show a lack of genetic structure among individuals. This study also indicated a signal that the genetic diversity might be similar between the wild and cultured individuals, which may be helpful to the fisheries management. PMID:23072475

  9. Multiplex genotype determination at a DNA sequence polymorphism cluster in the human immunoglobulin heavy-chain region

    SciTech Connect

    Li, H.; Hood, L.

    1995-03-20

    We have developed a method for multilocus genotype determination. The method involves using restriction fragment length polymorphisms (RFLPs) for allele discrimination. If a polymorphism is not an RFLP, it is converted into an RFLP during the polymerase chain reaction (PCR). After amplification and restriction enzyme digestion, samples are analyzed by sequential gel loading during electrophoresis. The efficiency of this method was demonstrated by determining the genotypes of 108 semen samples at seven DNA sequence polymorphic sites identified in the human immunoglobulin heavy-chain variable region. It was shown that more than 1000 PCR products could be easily analyzed per day per investigator. To show the reliability of this method, some of the typing results were confirmed by DNA sequence analysis. By computer simulation, most (98%) polymorphisms were shown to be natural or convertible (by changing 1 bp close to or next to each polymorphic site) RFLPs for the commercially available 4-base cutters. 47 refs., 4 figs., 3 tabs.

  10. Nucleotide sequence of the P1 region of foot-and-mouth disease virus strain O1 Caseros.

    PubMed

    Tami, C; Kaplan, G; Piccone, M E; Palma, E L

    1997-01-01

    It has been shown that variation of antigenic site I in VP1 of foot-and-mouth disease virus (FMDV) plays an important role in the antigenic diversification of this virus. However, the O1 Campos strain is able to efficiently cross-protect cattle against the O1 Caseros strain, despite having a different sequence in the site I. In this paper we report and compare the P1 coding region for the capsid proteins of FMDV O1 Caseros and O1 Campos. The deduced amino acid sequence showed a total of 31 amino acid differences. Eight of them are located in surface-exposed loops that have been implicated in antigenic sites. This study should help to identify additional sites to be considered in the development of a new generation of FMDV vaccines. PMID:9311571

  11. Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region.

    PubMed Central

    Fujita, N; Mori, H; Yura, T; Ishihama, A

    1994-01-01

    The complete sequence analysis of the E. coli genome was initiated as a collaborative study in Japan. Following the initial analysis of the 0-2.4 min region (Yura, T. et al. (1992) Nucleic Acids Res. 20, 3305-3308), a contiguous sequence of 82,727 bp corresponding to the 2.4-4.1 min region (110,917-193,643 bp as counted from 0 min) was determined. The resulting sequence was found to contain at least 33 known genes and 24 putative genes predicted from protein sequence homology. PMID:8202364

  12. Genetic diversity analysis of mitochondrial DNA control region in artificially propagated Chinese sucker Myxocyprinus asiaticus.

    PubMed

    Wan, Yuan; Zhou, Chun-Hua; Ouyang, Shan; Huang, Xiao-Chen; Zhan, Yang; Zhou, Ping; Rong, Jun; Wu, Xiao-Ping

    2015-08-01

    The genetic diversity of the three major artificially propagated populations of Chinese sucker, an endangered freshwater fish species, was investigated using the sequences of mitochondrial DNA (mtDNA) control regions. Among the 89 individuals tested, 66 variable sites (7.26%) and 10 haplotypes were detected (Haplotype diversity Hd = 0.805, Nucleotide diversity π = 0.0287). In general, genetic diversity was lower in artificially propagated populations than in wild populations. This reduction in genetic diversity may be due to population bottlenecks, genetic drift and human selection. A stepping-stone pattern of gene flow was detected in the populations studied, showing much higher gene flow between neighbouring populations. To increase the genetic diversity, wild lineages should be introduced, and more lineages should be shared among artificially propagated populations. PMID:24409897

  13. Complex magnetization of the Early Cambrian volcano-sedimentary sequence from the Bou Azzer region, Anti Atlas (Morocco)

    NASA Astrophysics Data System (ADS)

    Perrin, M.

    1994-08-01

    The objective of this paper is to highlight the complexity of the magnetic record carried by the Early Cambrian volcano-sedimentary sequence from the Bou Azzer region in the Anti Atlas Mountains of Morocco. Despite an extensive sampling of various types of rocks with various bedding attitudes, the interpretation of the remanent directions in terms of successive paleomagnetic poles remains ambiguous. The comparison of these results with two paleomagnetic analyses previously carried out on the same sequence of rocks, sampled in the same region, does not clarify the interpretation. When all the results are considered together, some directions are easily explained either as a recent chemical remagnetization or as a Late Paleozoic (probably Permian) remagnetization. Other directions which are statistically similar to those used to define the Early Cambrian Bou Azzer pole, usually considered for the construction of the Apparent Polar Wander Path for Africa, can be interpreted either as a recent chemical remagnetization or as older magnetizations the timings of which are unknown but are unlikely to be Early Cambrian in age. Complementary rock magnetic analyses are needed to try to estimate the process, the chronology and possibly the periods of acquisition of these magnetizations. Finally, other directions of magnetization were identified in the Moroccan samples which are specific to a given locality and a given lithology. The meaning of these localized components is not clear (localized remagnetization process or artefact) but they are surely not representative of the sequence and therefore can not be used to constrain the movement of Africa. At this stage, we suggest that the results from the Bou Azzer sequence should not be used for the construction of the Paleozoic Apparent Polar Wander Path for Africa.

  14. Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control.

    PubMed

    Burzynski, Grzegorz M; Reed, Xylena; Taher, Leila; Stine, Zachary E; Matsui, Takeshi; Ovcharenko, Ivan; McCallion, Andrew S

    2012-11-01

    Illuminating the primary sequence encryption of enhancers is central to understanding the regulatory architecture of genomes. We have developed a machine learning approach to decipher motif patterns of hindbrain enhancers and identify 40,000 sequences in the human genome that we predict display regulatory control that includes the hindbrain. Consistent with their roles in hindbrain patterning, MEIS1, NKX6-1, as well as HOX and POU family binding motifs contributed strongly to this enhancer model. Predicted hindbrain enhancers are overrepresented at genes expressed in hindbrain and associated with nervous system development, and primarily reside in the areas of open chromatin. In addition, 77 (0.2%) of these predictions are identified as hindbrain enhancers on the VISTA Enhancer Browser, and 26,000 (60%) overlap enhancer marks (H3K4me1 or H3K27ac). To validate these putative hindbrain enhancers, we selected 55 elements distributed throughout our predictions and six low scoring controls for evaluation in a zebrafish transgenic assay. When assayed in mosaic transgenic embryos, 51/55 elements directed expression in the central nervous system. Furthermore, 30/34 (88%) predicted enhancers analyzed in stable zebrafish transgenic lines directed expression in the larval zebrafish hindbrain. Subsequent analysis of sequence fragments selected based upon motif clustering further confirmed the critical role of the motifs contributing to the classifier. Our results demonstrate the existence of a primary sequence code characteristic to hindbrain enhancers. This code can be accurately extracted using machine-learning approaches and applied successfully for de novo identification of hindbrain enhancers. This study represents a critical step toward the dissection of regulatory control in specific neuronal subtypes. PMID:22759862

  15. Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control

    PubMed Central

    Burzynski, Grzegorz M.; Reed, Xylena; Taher, Leila; Stine, Zachary E.; Matsui, Takeshi; Ovcharenko, Ivan; McCallion, Andrew S.

    2012-01-01

    Illuminating the primary sequence encryption of enhancers is central to understanding the regulatory architecture of genomes. We have developed a machine learning approach to decipher motif patterns of hindbrain enhancers and identify 40,000 sequences in the human genome that we predict display regulatory control that includes the hindbrain. Consistent with their roles in hindbrain patterning, MEIS1, NKX6-1, as well as HOX and POU family binding motifs contributed strongly to this enhancer model. Predicted hindbrain enhancers are overrepresented at genes expressed in hindbrain and associated with nervous system development, and primarily reside in the areas of open chromatin. In addition, 77 (0.2%) of these predictions are identified as hindbrain enhancers on the VISTA Enhancer Browser, and 26,000 (60%) overlap enhancer marks (H3K4me1 or H3K27ac). To validate these putative hindbrain enhancers, we selected 55 elements distributed throughout our predictions and six low scoring controls for evaluation in a zebrafish transgenic assay. When assayed in mosaic transgenic embryos, 51/55 elements directed expression in the central nervous system. Furthermore, 30/34 (88%) predicted enhancers analyzed in stable zebrafish transgenic lines directed expression in the larval zebrafish hindbrain. Subsequent analysis of sequence fragments selected based upon motif clustering further confirmed the critical role of the motifs contributing to the classifier. Our results demonstrate the existence of a primary sequence code characteristic to hindbrain enhancers. This code can be accurately extracted using machine-learning approaches and applied successfully for de novo identification of hindbrain enhancers. This study represents a critical step toward the dissection of regulatory control in specific neuronal subtypes. PMID:22759862

  16. Sequence analysis of the ERCC2 gene regions in human, mouse, and hamster reveals three linked genes.

    PubMed

    Lamerdin, J E; Stilwagen, S A; Ramirez, M H; Stubbs, L; Carrano, A V

    1996-06-15

    The ERCC2 (excision repair cross-complementing rodent repair group 2) gene product is involved in transcription-coupled repair as an integral member of the basal transcription factor BTF2/TFIIH complex. Defects in this gene can result in three distinct human disorders, namely the cancer-prone syndrome xeroderma pigmentosum complementation group D, trichothiodystrophy, and Cockayne syndrome. We report the comparative analysis of 91.6 kb of new sequence including 54.3 kb encompassing the human ERCC2 locus, the syntenic region in the mouse (32.6 kb), and a further 4.7 kb of sequence 3' of the previously reported ERCC2 region in the hamster. In addition to ERCC2, our analysis revealed the presence of two previously undescribed genes in all three species. The first is centromeric (in the human) to ERCC2 and is most similar to the kinesin light chain gene in sea urchin. The second gene is telomeric (in the human) to ERCC2 and contains a motif found in ankyrins, some cell cycle proteins, and transcription factors. Multiple EST matches to this putative new gene indicate that it is expressed in several human tissues, including breast. The identification and description of two new genes provides potential candidate genes for disorders mapping to this region of 19q13.2. PMID:8786141

  17. Molecular characterization and sequence analysis of the 2B region of Aichivirus C strains in Japan and Thailand.

    PubMed

    Okitsu, Shoko; Khamrin, Pattara; Thongprachum, Aksara; Kalesaran, Angela F C; Takanashi, Sayaka; Shimizu, Hiroyuki; Maneekarn, Niwat; Mizuguchi, Masashi; Hayakawa, Satoshi; Ushijima, Hiroshi

    2014-08-01

    Aichivirus C is the third species in the genus Kobuvirus, family Picornaviridae, and the virus is circulating in pigs worldwide. Aichivirus A in humans and Aichivirus B in cows have been shown to associate with diarrheal diseases, however, the pathogenesis of Aichivirus C has not been demonstrated clearly. In this study, the full genome nucleotide sequence of the Thai strain, CMP06/2007/THA collected from stool sample of a diarrheal piglet was analyzed and identified as a variant type with a 90-nt deletion in the 2B-coding region. In addition, molecular characterization of nucleotide sequences of the 2B-coding region of Aichivirus C strains from six diarrheal and six healthy piglets in Thailand, and four strains from healthy pigs in Japan revealed that all of the strains in this study were variant types. These findings indicate that variant strains of Aichivirus C are circulating in Asian countries such as China, Thailand and Japan, and deletion of tandem repeat of 2B-region is unlikely to associate with the pathogenesis of the virus. PMID:24837671

  18. Sequence analysis of the ERCC2 gene regions in human, mouse, and hamster reveals three linked genes

    SciTech Connect

    Lamerdin, J.E.; Stilwagen, S.A.; Ramirez, M.H.

    1996-06-15

    The ERCC2 (excision repair cross-complementing rodent repair group 2) gene product is involved in transcription-coupled repair as an integral member of the basal transcription factor BTF2/TFIIH complex. Defects in this gene can result in three distinct human disorders, namely the cancer-prone syndrome xeroderma pigmentosum complementation group D, trichothiodystrophy, and Cockayne syndrome. We report the comparative analysis of 91.6 kb of new sequence including 54.3 kb encompassing the human ERCC2 locus, the syntenic region in the mouse (32.6 kb), and a further 4.7 kb of sequence 3{prime} of the previously reported ERCC2 region in the hamster. In addition to ERCC2, our analysis revealed the presence of two previously undescribed genes in all three species. The first is centromeric (in the human) to ERCC2 and is most similar to the kinesin light chain gene in sea urchin. The second gene is telomeric (in the human) to ERCC2 and contains a motif found in ankyrins, some cell proteins, and transcription factors. Multiple EST matches to this putative new gene indicate that it is expressed in several human tissues, including breast. The identification and description of two new genes provides potential candidate genes for disorders mapping to this region of 19q13.2. 42 refs., 6 figs., 3 tabs.

  19. 40 CFR 81.187 - Olympic-Northwest Washington Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Olympic-Northwest Washington... Designation of Air Quality Control Regions § 81.187 Olympic-Northwest Washington Intrastate Air Quality Control Region. The Olympic-Northwest Washington Intrastate Air Quality Control Region consists of...

  20. 40 CFR 81.79 - Northeastern Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Northeastern Oklahoma Intrastate Air... Air Quality Control Regions § 81.79 Northeastern Oklahoma Intrastate Air Quality Control Region. The Metropolitan Tulsa Intrastate Air Quality Control Region has been renamed the Northeastern Oklahoma...

  1. 40 CFR 81.123 - Southeastern Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 18 2014-07-01 2014-07-01 false Southeastern Oklahoma Intrastate Air... Air Quality Control Regions § 81.123 Southeastern Oklahoma Intrastate Air Quality Control Region. The Southeastern Oklahoma Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  2. 40 CFR 81.47 - Central Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Central Oklahoma Intrastate Air... Air Quality Control Regions § 81.47 Central Oklahoma Intrastate Air Quality Control Region. The Metropolitan Oklahoma Intrastate Air Quality Control Region has been renamed the Central Oklahoma...

  3. 40 CFR 81.124 - North Central Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 18 2013-07-01 2013-07-01 false North Central Oklahoma Intrastate Air... Air Quality Control Regions § 81.124 North Central Oklahoma Intrastate Air Quality Control Region. The North Central Oklahoma Intrastate Air Quality Control Region consists of the territorial...

  4. 40 CFR 81.123 - Southeastern Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 18 2013-07-01 2013-07-01 false Southeastern Oklahoma Intrastate Air... Air Quality Control Regions § 81.123 Southeastern Oklahoma Intrastate Air Quality Control Region. The Southeastern Oklahoma Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  5. 40 CFR 81.123 - Southeastern Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Southeastern Oklahoma Intrastate Air... Air Quality Control Regions § 81.123 Southeastern Oklahoma Intrastate Air Quality Control Region. The Southeastern Oklahoma Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  6. 40 CFR 81.47 - Central Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 18 2013-07-01 2013-07-01 false Central Oklahoma Intrastate Air... Air Quality Control Regions § 81.47 Central Oklahoma Intrastate Air Quality Control Region. The Metropolitan Oklahoma Intrastate Air Quality Control Region has been renamed the Central Oklahoma...

  7. 40 CFR 81.124 - North Central Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 17 2010-07-01 2010-07-01 false North Central Oklahoma Intrastate Air... Air Quality Control Regions § 81.124 North Central Oklahoma Intrastate Air Quality Control Region. The North Central Oklahoma Intrastate Air Quality Control Region consists of the territorial...

  8. 40 CFR 81.125 - Southwestern Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 18 2012-07-01 2012-07-01 false Southwestern Oklahoma Intrastate Air... Air Quality Control Regions § 81.125 Southwestern Oklahoma Intrastate Air Quality Control Region. The Southwestern Oklahoma Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  9. 40 CFR 81.124 - North Central Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 17 2011-07-01 2011-07-01 false North Central Oklahoma Intrastate Air... Air Quality Control Regions § 81.124 North Central Oklahoma Intrastate Air Quality Control Region. The North Central Oklahoma Intrastate Air Quality Control Region consists of the territorial...

  10. 40 CFR 81.126 - Northwestern Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Northwestern Oklahoma Intrastate Air... Air Quality Control Regions § 81.126 Northwestern Oklahoma Intrastate Air Quality Control Region. The Northwestern Oklahoma Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  11. 40 CFR 81.125 - Southwestern Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 18 2013-07-01 2013-07-01 false Southwestern Oklahoma Intrastate Air... Air Quality Control Regions § 81.125 Southwestern Oklahoma Intrastate Air Quality Control Region. The Southwestern Oklahoma Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  12. 40 CFR 81.65 - Joplin (Missouri)-Northeast Oklahoma Interstate Air Quality Control Region.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 18 2012-07-01 2012-07-01 false Joplin (Missouri)-Northeast Oklahoma... Designation of Air Quality Control Regions § 81.65 Joplin (Missouri)-Northeast Oklahoma Interstate Air Quality Control Region. The Joplin (Missouri)-Northeast Oklahoma Interstate Air Quality Control Region,...

  13. 40 CFR 81.125 - Southwestern Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Southwestern Oklahoma Intrastate Air... Air Quality Control Regions § 81.125 Southwestern Oklahoma Intrastate Air Quality Control Region. The Southwestern Oklahoma Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  14. 40 CFR 81.126 - Northwestern Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Northwestern Oklahoma Intrastate Air... Air Quality Control Regions § 81.126 Northwestern Oklahoma Intrastate Air Quality Control Region. The Northwestern Oklahoma Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  15. 40 CFR 81.47 - Central Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 18 2012-07-01 2012-07-01 false Central Oklahoma Intrastate Air... Air Quality Control Regions § 81.47 Central Oklahoma Intrastate Air Quality Control Region. The Metropolitan Oklahoma Intrastate Air Quality Control Region has been renamed the Central Oklahoma...

  16. 40 CFR 81.65 - Joplin (Missouri)-Northeast Oklahoma Interstate Air Quality Control Region.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 18 2014-07-01 2014-07-01 false Joplin (Missouri)-Northeast Oklahoma... Designation of Air Quality Control Regions § 81.65 Joplin (Missouri)-Northeast Oklahoma Interstate Air Quality Control Region. The Joplin (Missouri)-Northeast Oklahoma Interstate Air Quality Control Region,...

  17. 40 CFR 81.47 - Central Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Central Oklahoma Intrastate Air... Air Quality Control Regions § 81.47 Central Oklahoma Intrastate Air Quality Control Region. The Metropolitan Oklahoma Intrastate Air Quality Control Region has been renamed the Central Oklahoma...

  18. 40 CFR 81.65 - Joplin (Missouri)-Northeast Oklahoma Interstate Air Quality Control Region.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Joplin (Missouri)-Northeast Oklahoma... Designation of Air Quality Control Regions § 81.65 Joplin (Missouri)-Northeast Oklahoma Interstate Air Quality Control Region. The Joplin (Missouri)-Northeast Oklahoma Interstate Air Quality Control Region,...

  19. 40 CFR 81.126 - Northwestern Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 18 2012-07-01 2012-07-01 false Northwestern Oklahoma Intrastate Air... Air Quality Control Regions § 81.126 Northwestern Oklahoma Intrastate Air Quality Control Region. The Northwestern Oklahoma Intrastate Air Quality Control Region consists of the territorial area encompassed by...

  20. 40 CFR 81.123 - Southeastern Oklahoma Intrastate Air Quality Control Region.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 18 2012-07-01 2012-07-01 false Southeastern Oklahoma Intrastate Air... Air Quality Control Regions § 81.123 Southeastern Oklahoma Intrastate Air Quality Control Region. The Southeastern Oklahoma Intrastate Air Quality Control Region consists of the territorial area encompassed by...