CR Sequence Research Articles

Comparison of genetic characteristics between captive and wild giant pandas based on 13 mitochondrial coding genes.

Research on genetic diversity based on mitochondrial DNA of giant pandas mainly focused on a single marker or a few genes. To provide a more comprehensive assessment of the genetic diversity on giant pandas based on 13 mitochondrial protein coding genes. We assembled 13 protein coding genes in the mitochondrial genome of the giant panda based on the whole genome sequencing data, including ND1, ND2, COX1, COX2, ATP8, ATP6, COX3, ND3, ND4L, ND4, ND5, ND6 and Cyt b. We successfully obtained long sequence of 11,416 base pairs with all 13 genes for 110 giant panda individual, accounting for 67.93% in length of the mitochondrial reference genome. Haplotype diversity was 0.9518 ± 0.009 and nucleotide diversity (π) was 0.00157 ± 0.00014. We detected three new haplotypes, including GPC10 and GPC21 for the CR sequence and GPB12 for the Cyt b gene. These multi-gene sequences provided more genetic variable information to compare captive and wild giant panda population.

Disruption of doubly uniparental inheritance of mitochondrial DNA associated with hybridization area of European Mytilus edulis and Mytilus trossulus in Norway

Doubly uniparental inheritance of mitochondria (DUI) is best known in the blue mussel Mytilus. Under this model, two types of mitochondrial DNA exist: female type (F), transmitted from females to offspring of both genders, and male type (M), transmitted exclusively from males to sons. The mitogenomes are usually highly divergent, but an occasional replacement of a typical M genome by a particular F genome has been postulated to explain reduction of this divergence. Disruption of the DUI model has been reported in hybridization areas. Here, we present a new case of DUI disruption in a hybrid M. trossulus/M. edulis population from the North Sea (Norway). No M haplotypes derived from M. trossulus were identified in this population. Typical M haplotypes derived from M. edulis (ME) were rare. Two F-type haplogroups were found: one derived from M. edulis (FE) and the second derived from M. trossulus (FT). Many haplotypes from the FT group were recombinants, with the male CR sequence coming from the M. trossulus genome (FT1 haplogroup) in contrast to M. edulis CR as in the Baltic. FT1 haplotypes were abundant in the studied population, including homoplasmic females. However, males significantly more often carried these haplotypes; therefore, male heteroplasmy involved the original FE and recombinant FT, indicating that the FT genome undergoes masculinization. Structural similarity of FT1 CR with previously reported, masculinized Baltic haplotypes, which were derived from FE/ME recombination, provides further evidence that CR M–F recombination is a prerequisite for masculinization, also in the context of native M. trossulus mtDNA.

Influence of sequence of elemental addition on phase evolution in nanocrystalline AlCoCrFeNi: Novel approach to alloy synthesis using mechanical alloying

The conventional way to form a multicomponent alloy requires mixing individual elements in a single step. Phase formation, therefore, is governed by inherent thermodynamic and kinetic factors of the system. We propose here a new approach for multicomponent alloy synthesis, which involves step by step addition of constituent elements. In the present work, this is illustrated through the formation of nanocrystalline equiatomic AlCoCrFeNi by mechanical alloying. For example, first, binary CoNi is formed by milling elemental Co and Ni powders. In the subsequent steps, Fe, Cr and Al are added to form ternary (CoNiFe), quaternary (CoNiFeCr) and quinary (CoNiFeCrAl) alloy, respectively.Three different classes of binaries have been selected as initial phases, namely, B2 (AlNi, AlCo and AlFe), BCC (FeCr) and FCC (CoNi and FeNi). Remaining constituent elements are added step-wise in varying sequences and equiatomic AlCoCrFeNi is obtained in the concluding step. The final AlCoCrFeNi alloy at the end of each sequence has varied fractions of BCC and FCC phases. For instance, AlNi+Co+Fe+Cr sequence is single phase BCC, whereas the sequence FeNi+Co+Cr+Al results in a mixture of BCC (75%) and FCC (25%) phases. The extent to which a particular element stabilizes a structure (BCC/B2/FCC) has also been elucidated.

A Pathogenic Isolate of Monopartite PepYLCV DNA A-like Genome Differs Significantly in C1 Gene and CR Sequence, but not in their other Genes

A Pathogenic Isolate of Monopartite PepYLCV DNA A-like Genome Differs Significantly in C1 Gene and CR Sequence, but not in their other Genes

Identification of wild tilapia species in the main rivers of south China using mitochondrial control region sequence and morphology

Tilapias are now the most common alien fish in the rivers of South China and the dominant species in many sites. However, wild tilapia species have not been well-characterized or studied systematically. In this study, mitochondrial DNA control regions (mtDNA CR) and morphological characteristics were used to identify invasive tilapia species. Using mtDNA CR sequence, we identified Oreochromis niloticus, Tilapia zillii, Oreochromis aureus, Sarotherodon galilaeus, and hybrids of Oreochromis mossambicus and O. niloticus in the rivers of South China, and characterized their morphological features. Of the 5 species, O. niloticus and T. zillii were the most abundant in the rivers of South China. Furthermore, the distribution of O. niloticus may be related to their large numbers in the aquaculture industry, and the explosion of T. zillii invasion may be related to their strong capacity for environmental adaptation. These findings are beneficial for identifying wild tilapia populations and for the specific control of invasive tilapia species.

Polyamine stimulation of eEF1A synthesis based on the unusual position of a complementary sequence to 18S rRNA in eEF1A mRNA.

It is thought that Shine-Dalgarno-like sequences, which exhibit complementarity to the nucleotide sequences at the 3'-end of 18S rRNA, are not present in eukaryotic mRNAs. However, complementary sequences consisting of more than 5 nucleotides to the 3'-end of 18S rRNA, i.e., a CR sequence, are present at -17 to -32 upstream from the initiation codon AUG in 18 mRNAs involved in protein synthesis except eEF1A mRNA. Thus, effects of the CR sequence in mRNAs and polyamines on protein synthesis were examined using control and polyamine-reduced FM3A and NIH3T3 cells. Polyamines did not stimulate protein synthesis encoded by 18 mRNAs possessing a normal CR sequence. When the CR sequence was deleted, protein synthetic activities decreased to less than 70% of intact mRNAs. In eEF1A mRNA, the CR sequence was located at -33 to -39 upstream from the initiation codon AUG, and polyamines stimulated eEF1A synthesis about threefold. When the CR sequence was shifted to -22 to -28 upstream from the AUG, eEF1A synthesis increased in polyamine-reduced cells and the degree of polyamine stimulation decreased greatly. The results indicate that the CR sequence exists in many eukaryotic mRNAs, and the location of a CR sequence in mRNAs influences polyamine stimulation of protein synthesis.

Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus <i>Orestias</i> (Teleostei: Cyprinodontidae)

Specimens stored in museum collections represent a crucial source of morphological and genetic information, notably for taxonomically problematic groups and extinct taxa. Although fluid-preserved specimens of groups such as teleosts may constitute an almost infinite source of DNA, few ancient DNA protocols have been applied to such material. In this study, we describe a non-invasive Guanidine-based (GuSCN) ancient DNA extraction protocol adapted to fluid-preserved specimens that we use to re-assess the systematics of the genus Orestias (Cyprinodontidae: Teleostei). The latter regroups pupfishes endemic to the inter-Andean basin that have been considered as a 'species flock', and for which the morphology-based taxonomic delimitations have been hotly debated. We extracted DNA from the type specimens of Orestias kept at the Muséum National d'Histoire Naturelle of Paris, France, including the extinct species O. cuvieri. We then built the first molecular (control region [CR] and rhodopsin [RH]) phylogeny including historical and recently collected representatives of all the Orestias complexes as recognized by Parenti (1984a): agassizii, cuvieri, gilsoni and mulleri. Our ancient DNA extraction protocol was validated after PCR amplification through an approach based on fragment-by-fragment chimera detection. After optimization, we were able to amplify < 200 bp fragments from both mitochondrial and nuclear DNA (CR and RH, respectively) from probably formalin-fixed type specimens bathed entirely in the extraction fluid. Most of the individuals exhibited few modifications of their external structures after GuSCN bath. Our approach combining type material and 'fresh' specimens allowed us to taxonomically delineate four clades recovered from the well-resolved CR tree into four redefined complexes: agassizii (sensu stricto, i.e. excluding luteus-like species), luteus, cuvieri and gilsoni. The mulleri complex is polyphyletic. Our phylogenetic analyses based on both mitochondrial and nuclear DNA revealed a main, deep dichotomy within the genus Orestias, separating the agassizii complex from a clade grouped under shallow dichotomies as (luteus, (cuvieri, gilsoni)). This 'deep and shallow' diversification pattern could fit within a scenario of ancient divergence between the agassizii complex and the rest of Orestias, followed by a recent diversification or adaptive radiation within each complex during the Pleistocene, in- and outside the Lake Titicaca. We could not recover the reciprocal monophyly of any of the 15 species or morphotypes that were considered in our analyses, possibly due to incomplete lineage sorting and/or hybridization events. As a consequence, our results starkly question the delineation of a series of diagnostic characters listed in the literature for Orestias. Although not included in our phylogenetic analysis, the syntype of O. jussiei could not be assigned to the agassizii complex as newly defined. The CR sequence of the extinct O. cuvieri was recovered within the cuvieri clade (same haplotype as one representative of O. pentlandii), so the mtDNA of the former species might still be represented in the wild.

Internal Initiation of Translation Directed by the 5′-Untranslated Region of the Tobamovirus Subgenomic RNA I2

Previously we reported that, unlike RNA of typical tobamoviruses, the translation of the coat protein (CP) gene of a crucifer-infecting tobamovirus (crTMV) in vitro occurred by an internal ribosome entry mechanism mediated by the 148-nt region that contained an internal ribosome entry site (IRESCP,148CR). The equivalent 148-nt sequence from TMV U1 RNA (U1CP,148SP) was incapable of promoting internal initiation. In the present work, we have found that the 228-nt region upstream of the movement protein (MP) gene of crTMV RNA (IRESMP,228CR) contained an IRES element that directed in vitro translation of the 3′-proximal reporter genes from chimeric dicistronic transcripts. Surprisingly, the equivalent 228-nt sequence upstream from the MP gene of TMV U1 directed translation of the downstream gene of a dicistronic transcripts as well. Consequently this sequence was termed IRESMP,228U1. It was shown that IRESMP,228CR, IRESMP,228U1, and IRESCP,148CR could mediate expression of the 3′-proximal GUS gene from dicistronic 35S promoter-based constructs in vivo in experiments on transfection of tobacco protoplasts and particle bombardment of Nicotiana benthamiana leaves. The results indicated that an IRES element was located within the 75-nt region upstream of MP gene (IRESMP,75), which corresponded closely to the length of the 5′UTR of TMV subgenomic RNA (sgRNA) I2. The RNA transcripts structurally equivalent to I2 sgRNAs of TMV U1 and crTMV, but containing a hairpin structure (H) immediately upstream of IRESMP,75 (HIRESMP,75CR-MP-CP-3′UTR; HIRESMP,75U1-MP-CP-3′UTR), were able to express the MP gene in vitro. The capacity of HIRESMP,75CR sequence for mediating internal translation of the 3′-proximal GUS gene in vivo, in tobacco protoplasts, was demonstrated. We suggested that expression of the MP gene from I2 sgRNAs might proceed via internal ribosome entry pathway mediated by IRESMP element contained in the 75-nt 5′UTR. Our results admit that a ribosome scanning mechanism of the MP gene expression from I2 sgRNA operates concurrently.

Characterization of Ribonucleoprotein Complexes and Their Binding Sites on the Neurofilament Light Subunit mRNA

Levels of neurofilament (NF) gene expression are important determinants of basic neuronal properties, but overexpression can lead to motoneuron degeneration in transgenic mice. In a companion study (Cañete-Soler, R., Schwartz, M. L., Hua, Y., and Schlaepfer, W. W. (1998) J. Biol. Chem. 273, 12650-12654), we show that levels of NF expression are regulated by altering mRNA stability and that stability determinants are present in the 3'-coding region (3'-CR) and 3'-untranslated region (3'-UTR) of the NF light subunit (NF-L) transcript. This study characterizes the ribonucleoprotein complexes that bind to the NF-L mRNA when cytoplasmic brain extracts are incubated with radioactive probes. Gel retardation assays reveal ribonucleoprotein complexes that are selectively competed with poly(C) or poly(U))/poly(A) homoribopolymers and are referred to as C-binding and U/A-binding complexes, respectively. The C-binding complex forms on the proximal 45 nucleotides of 3'-UTR, but its assembly is markedly enhanced by 23 nucleotides of flanking 3'-CR sequence. U/A-binding complexes form at multiple binding sites in the 3'-CR and 3'-UTR. A pattern of reciprocal binding suggests that the C-binding and U/A-binding complexes interact and may compete for common components or binding sites. Cross-linking studies reveal unique polypeptides in the C-binding and U/A-binding complexes. The findings provide the basis for probing mechanisms regulating NF-L mRNA stability and the relationship between NF overexpression and motoneuron degeneration in transgenic mice.

Sorption and Speciation of Heavy Metals from Incinerator Fly Ash in a Marine Clay

The ever-increasing popularity of waste incineration in the recent past has resulted in increasing environmental concerns on secure land disposal of incinerator fly ash. In this study, the capability of a marine clay to immobilize Zn, Pb, Cd, Cu, and Cr, which are commonly found in fly ash leachates, was investigated in a laboratory under acidic, neutral, and slightly alkaline conditions. The sorption process was carried out in batch sorption experiments in the single species system. A background electrolyte consisting of a NaCl solution was introduced. The heavy metals retained in the soil phases were fractionated into exchangeable, carbonate, reducible, organic, and residual fractions using a sequential extraction technique. The results indicated that the slightly alkaline marine clay could completely retain these heavy metals at its natural soil pH of 8.4. In acidic conditions, the mobility of heavy metals followed the Cd > Zn > Cu > Pb > Cr sequence. The heavy-metal speciation in marine clay depended significantly on soil pH, and changed with the metal elements. Between the slightly acidic and slightly alkaline conditions, metal sorption in carbonate and oxide phases was more important, whereas the exchangeable sorption could be of relatively greater importance in acidic conditions. The portion of heavy metals retained in the residual fraction could also be important, and this fraction was less influenced by soil pH. The organic component in marine clay was of the least importance in metal immobilization. Results of time-dependent sorption tests for a period of up to 65 d indicated that total metal sorption and metal speciation in marine clay changed with time. The degree of changes was dependent on soil pH.

The recognition by RNase P of precursor tRNAs.

We have generated mutants of M1 RNA, the catalytic subunit of Escherichia coli RNaseP, and have analyzed their properties in vitro and in vivo. The mutations, A333----C333, A334----U334, and A333 A334----C333 U334 are within the sequence UGAAU which is complementary to the GT psi CR sequence found in loop IV of all E. coli tRNAs. We have examined: 1) whether the mutant M1 RNAs are active in processing wild type tRNA precursors and 2) whether they can restore the processing defect in mutant tRNA precursors with changes within the GT psi CR sequence. As substrates for in vitro studies we used wild type E. coli SuIII tRNA(Tyr) precursor, and pTyrA54, a mutant tRNA precursor with a base change that could potentially complement the U334 mutation in M1 RNA. The C333 mutation had no effect on activity of M1 RNA on wild type pTyr. The U334 mutant M1 RNA, on the other hand, had a much lower activity on wild type pTyr. However, use of pTyrA54 as substrate instead of wild type pTyr did not restore the activity of the U334 mutant M1 RNA. These results suggest that interactions via base pairing between nucleotides 331-335 of M1 RNA and the GT psi CG of pTyr are probably not essential for cleavage of these tRNA precursors by M1 RNA. For assays of in vivo function, we examined the ability of mutant M1 RNAs to complement a ts mutation in the protein component of RNaseP in FS101, a recA- derivative of E. coli strain A49. In contrast to wild type M1 RNA, which complements the ts mutation when it is overproduced, neither the C333 nor the U334 mutant M1 RNAs was able to do so.

Observed resonance lines of highly ionized titanium, chromium, iron, and nickel in tokamak discharges

view Abstract Citations (26) References (8) Co-Reads Similar Papers Volume Content Graphics Metrics Export Citation NASA/ADS Observed resonance lines of highly ionized titanium, chromium, iron, and nickel in tokamak discharges. Hinnov, E. Abstract Wavelengths and relative intensities were measured in the PLT tokamak discharges for the Ti, Cr, Fe, and Ni ion lithium sequence (2s-2p) and beryllium sequence (2s 2-2s2p 1 P) transitions and some resonance and intercombination lines of Fe XXII and Fe XXIII lines. The discussion is interdisciplinary, covering processes occurring in solar flares as well as tokamak plasmas. Publication: The Astrophysical Journal Pub Date: June 1979 DOI: 10.1086/182992 Bibcode: 1979ApJ...230L.197H Keywords: Atomic Spectra; Gas Discharges; Line Spectra; Plasma Resonance; Solar Flares; Tokamak Devices; Atomic Excitations; Chromium; Energy Technology; Iron; Metal Ions; Nickel; Plasma Spectra; Titanium; Transition Probabilities; Plasma Physics; Iron:Solar Flares; Transition Probabilities full text sources ADS |