Sequence B2 Research Articles

Phase transitions for the long-time behavior of interacting diffusions

Let ({Xi(t)}i∈ℤd)t≥0 be the system of interacting diffusions on [0, ∞) defined by the following collection of coupled stochastic differential equations: $$dX_{i}(t)=\sum\limits_{j\in \mathbb{Z}^{d}}a(i,j)[X_{j}(t)-X_{i}(t)]\,dt+\sqrt{bX_{i}(t)^{2}} dW_{i}(t),\quad i\in \mathbb{Z}^{d}, t\geq 0.$$ Here, a(⋅, ⋅) is an irreducible random walk transition kernel on ℤd×ℤd, b∈(0, ∞) is a diffusion parameter, and ({Wi(t)}i∈ℤd)t≥0 is a collection of independent standard Brownian motions on ℝ. The initial condition is chosen such that {Xi(0)}i∈ℤd is a shift-invariant and shift-ergodic random field on [0, ∞) with mean Θ∈(0, ∞) (the evolution preserves the mean). We show that the long-time behavior of this system is the result of a delicate interplay between a(⋅, ⋅) and b, in contrast to systems where the diffusion function is subquadratic. In particular, let a(i, j)=½[a(i, j)+a(j, i)], i, j∈ℤd, denote the symmetrized transition kernel. We show that: (A) If a(⋅, ⋅) is recurrent, then for any b>0 the system locally dies out. (B) If a(⋅, ⋅) is transient, then there exist b*≥b2>0 such that: (B1) The system converges to an equilibrium νΘ (with mean Θ) if 0 b*. (B3) νΘ has a finite 2nd moment if and only if 0 b2. The equilibrium νΘ is shown to be associated and mixing for all 0 b2. We further conjecture that the system locally dies out at b=b*. For the case where a(⋅, ⋅) is symmetric and transient we further show that: (C) There exists a sequence b2≥b3≥b4≥⋯>0 such that: (C1) νΘ has a finite mth moment if and only if 0 bm. (C3) b2≤(m−1)bm<2. (C4) lim m→∞(m−1)bm=c=sup m≥2(m−1)bm. The proof of these results is based on self-duality and on a representation formula through which the moments of the components are related to exponential moments of the collision local time of random walks. Via large deviation theory, the latter lead to variational expressions for b* and the bm’s, from which sharp bounds are deduced. The critical value b* arises from a stochastic representation of the Palm distribution of the system. The special case where a(⋅, ⋅) is simple random walk is commonly referred to as the parabolic Anderson model with Brownian noise. This case was studied in the memoir by Carmona and Molchanov [Parabolic Anderson Problem and Intermittency (1994) Amer. Math. Soc., Providence, RI], where part of our results were already established.

Mid-Turonian–early Campanian sequence stratigraphy of northeast Iraq

ABSTRACT A sequence stratigraphic and tectonic model for the mid-Turonian-early Campanian carbonate sequence in North Iraq was constructed based on subsurface lithologic, thin-section and well-log analyses of ten boreholes. The studied sequence is represented by the Gulneri, Kometan and Mushorah formations in the eastern sector (seven wells) and their correlative Khasib, Tanuma, Sa’adi and lower part of the Hartha formations in the western sector of the study area (three wells). Three second-order sequences (from oldest to youngest A, B and C) were identified. Sequence A consists of two third-order sequences (A1 and A2) and is represented by the mid-Turonian Gulneri Formation. Sequence B consists of three third-order sequences: B1 corresponds to the late Turonian-early Coniacian Khasib Formation and correlative lower part of Kometan Formation. Sequences B2 and B3 are exclusive to the late Coniacian-early Santonian Tanuma Formation and correlative middle part of the Kometan Formation. Sequence C is comprised of three third-order sequences of which C1 and C2 encompass the late Santonian Sa’adi Formation and correlative upper part of the Kometan Formation, while C3 corresponds to the early Campanian Mushorah Formation and correlative lower part of the Hartha Formation. Each of the third-order sequences is comprised of transgressive and highstand systems tracts, while the lowstand systems tract is restricted to sequences B2, B3, C1 and C2. These systems tracts are, in turn, comprised of vertically stacked parasequences of shallowing upward packages. The tectono-depositional model that was deduced from the sequence analysis is characterised by two flat-topped ramps that formed as a consequence of extensional tectonism. Three NW-trending normal faults are interpreted to separate the ramps whose inclined apex was continuously being eroded. The eroded detritus from the apex consists of shallow-marine carbonates that were deposited in basinal sites. Within this structural framework, the ten boreholes are placed within their appropriate depositional sites within the ramp system. Facies analysis demonstrated an array of facies associations, which generally accumulate in basins that are fed by an influx of eroded shallow-water derivatives. The depositional architecture developed in an open-marine, low-energy, middle- to outer-ramp setting in the case of Gulneri and Kometan formations. A middle–inner ramp setting is attributed to the Khasib, Tanuma and the lower part of the Hartha formations. A transition to a slope setting is suggested during the deposition of the Mushorah Formation; whereas slope-apron facies are common to all formations in the well Quwair-2. Diagenetic modification overprinted the carbonates and its effect on reservoir properties is considered. Recognition of third-order cycles demonstrates the utility of using genetic units and sequence stratigraphy to discern the depositional architecture of these formations. Local tectonic influences, which control sedimentation patterns, eustasy and sedimentation rates are additional determinants for the final stratigraphic framework.

Evidence for a polar biaxial SmA phase (CPA) in the sequence SmA–CPA–B2

The isobaric phase diagram of a binary system is presented where one mixing component is an achiral five-ring bent-core mesogen and the other is the electron acceptor compound 2,4,7-trinitrofluorenone (TNF). In the mixed phase region a SmA phase as well as a polar (antiferroelectric) biaxial SmA phase (CPA) are induced. Depending on the concentration the unusual phase sequences B2–SmA, CPA–SmA and B2–CPA–SmA could be observed. The mesophases occurring in this system have been characterised by their optical textures, by X-ray investigations and by electro-optical measurements.

SmA-SmC-B2 polymorphism in an achiral cyano substituted banana-shaped mesogen

A new achiral five-ring banana-shaped mesogen is presented which has a cyano substituent in the 4-position of the central core. Microscopical, X-ray, dielectric and electro-optical investigations give evidence for the unusual phase sequence B2, SmC, SmA. The B2 phase shows an antiferroelectric switching behaviour; the spontaneous polarization was found to be 330 nCcm-2.

A study on the nickel-rich ternary Ti–Ni–Al shape memory alloys

The transformation sequence and hardening effects of 400 °C aged Ti47.5Ni50.65Al1.85 and Ti49.5Ni50.13Al0.37 shape memory alloys have been investigated by electrical resistivity tests, internal friction measurements, hardness tests and TEM observations. Both solution hardening and precipitation hardening are found to occur in these alloys. The hardening effects of Ti47.5Ni50.65Al1.85 alloy are obvious and much higher than those of Ti49.5Ni50.13Al0.37 alloy due to the former having the larger Ni/Ti ratio and a higher Al solute content in its matrix. The transformation sequence of 400 °C aged Ti47.5Ni50.65Al1.85 alloy shows B2↔R-phase only for an ageing time of more than 10 h and that of 400°C aged Ti49.5Ni50.13Al0.37 alloy shows the sequence B2↔R-phase↔B19′ or B2↔R-phase with different ageing times. All of these characteristics are associated with Ti11Ni14 precipitates during the ageing process. These aged Ti–Ni–Al alloys exhibit very good shape memory effects, in which the maximal shape recovery occurs at the peak of hardness.

The Protein Import System of Mitochondria

The Protein Import System of Mitochondria

Transcriptional Regulation of NF-κB2: Evidence for κB-Mediated Positive and Negative Autoregulation

NF-kappa B is an inducible transcription factor complex which regulates the expression of a variety of genes which are involved in the immune, inflammatory, and acute-phase responses. The maintenance of NF-kappa B activity in stimulated cells requires ongoing protein synthesis, suggesting several modes of regulation. In this report, we have characterized the transcriptional regulation of one family member, NF-kappa B2. The genomic structure and sequence of NF-kappa B2 revealed the presence of two promoters and at least four kappa B regulatory elements, which mediate responsiveness to phorbol myristate acetate and tumor necrosis factor alpha. Similar to other NF-kappa B family members, NF-kappa B2 is positively autoregulated. In contrast to other family members, we find that kappa B elements in the NFKB2 promoter can also mediate transcriptional repression in the absence of NF-kappa B. We identified a nuclear complex which binds specifically to a subset of kappa B-related sites but not to the canonical kappa B element. Because of its putative inhibitory or repressive effect, this binding activity has been termed Rep-kappa B. This mechanism of repressing basal NF-kappa B2 transcription in an inactivated state enables the cell to tightly control NF-kappa B2 activity. These data demonstrate that a novel mode of kappa B-dependent regulation is mediated by specific kappa B sites in the NFKB2 promoter.

Transcriptional regulation of NF-kappa B2: evidence for kappa B-mediated positive and negative autoregulation.

NF-kappa B is an inducible transcription factor complex which regulates the expression of a variety of genes which are involved in the immune, inflammatory, and acute-phase responses. The maintenance of NF-kappa B activity in stimulated cells requires ongoing protein synthesis, suggesting several modes of regulation. In this report, we have characterized the transcriptional regulation of one family member, NF-kappa B2. The genomic structure and sequence of NF-kappa B2 revealed the presence of two promoters and at least four kappa B regulatory elements, which mediate responsiveness to phorbol myristate acetate and tumor necrosis factor alpha. Similar to other NF-kappa B family members, NF-kappa B2 is positively autoregulated. In contrast to other family members, we find that kappa B elements in the NFKB2 promoter can also mediate transcriptional repression in the absence of NF-kappa B. We identified a nuclear complex which binds specifically to a subset of kappa B-related sites but not to the canonical kappa B element. Because of its putative inhibitory or repressive effect, this binding activity has been termed Rep-kappa B. This mechanism of repressing basal NF-kappa B2 transcription in an inactivated state enables the cell to tightly control NF-kappa B2 activity. These data demonstrate that a novel mode of kappa B-dependent regulation is mediated by specific kappa B sites in the NFKB2 promoter.

Characterization of the mitochondrial processing peptidase of Neurospora crassa.

The mitochondrial processing peptidase (MPP) of Neurospora crassa is constituted by an alpha- and a beta-subunit. We have purified alpha-MPP after expression in Escherichia coli while beta-MPP was purified from mitochondria. A fusion protein between precytochrome b2 and mouse dihydrofolate reductase was expressed in E. coli, and the purified protein was used as substrate for MPP. Both subunits of MPP are required for processing. MPP removes the matrix targeting signal of cytochrome b2 by a single cut, and the resulting presequence peptide is 31 amino acid residues in length. It acts as a competitive inhibitor of processing but has a approximately 30-fold lower affinity for MPP than the preprotein. Competition assays show that MPP recognizes the COOH-terminal portion of the presequence of cytochrome b2 rather than the NH2-terminal part which has the potential to form an amphiphilic helix. Substitution of arginine in position -2 of the matrix targeting sequence of cytochrome b2 prevents processing but not import of a chimeric precursor. Substitution of the tyrosyl residue in position +1 also prevents processing, indicating that MPP interacts with sequences COOH-terminal to the cleavage site. Non-cleavable preprotein is still recognized by MPP. Our data suggest that processing peptidase and import machinery recognize distinct structural elements in preproteins which, however, can be overlapping.

Molecular cloning of a putative plant endomembrane protein resembling vertebrate protein disulfide-isomerase and a phosphatidylinositol-specific phospholipase C.

cDNA clones containing sequence similarity to the multifunctional vertebrate protein disulfide-isomerase (PDI, EC 5.3.4.1) were isolated from an alfalfa (Medicago sativa L.) cDNA library by screening with a cDNA sequence encoding human PDI. The polypeptide encoded by a clone designated B2 consisted of 512 amino acids and was characterized by a 24-amino acid hydrophobic leader sequence, two regions with absolute identity to the vertebrate PDI active site (Ala-Pro-Trp-Cys-Gly-His-Cys-Lys), and a C-terminal endoplasmic reticulum retention signal (Lys-Asp-Glu-Leu). The overall identity of the B2 sequence to that of human PDI was 35% at the amino acid level (79% when conservative substitutions were included) and 39% at the nucleotide level; this included homology between B2 and the region of human PDI believed to be involved in binding estrogens. The deduced amino acid sequence of B2 was also 35% identical to that of a rat form I phosphatidylinositol-specific phospholipase C. Lysates from Escherichia coli cells harboring an expression plasmid bearing the B2 sequence contained significantly elevated levels of PDI activity. Southern analysis indicated the presence of a small PDI-related gene family in alfalfa, of which B2 appeared to correspond to a single gene. An approximately 2-kilobase B2 transcript was expressed in all alfalfa organs tested. In alfalfa cell suspension cultures, B2 transcripts were strongly induced by tunicamycin but not by exposure to fungal elicitor.

Deletion mutation in an eye lens beta-crystallin. An animal model for inherited cataracts.

The most prevalent proteins in the lens of the eye are called crystallins, and it is thought that aberrant crystallins may cause opacification of lens tissue. The Philly mouse, a strain with an inherited cataract, has an abnormal beta B2-crystallin, the principal beta-crystallin in the mouse. The cDNA that codes for the beta B2-crystallin protein has been cloned and sequenced from both the normal and the cataractous Philly mouse. The normal mouse beta B2 cDNA is 756 nucleotides in length with 618 nucleotides of open reading frame. An in-frame deletion of 12 nucleotides has occurred in the Philly mouse cDNA, which results in the loss of 4 amino acids. The sequence of the mutant beta B2 was analyzed against the reported structure of the normal bovine beta B2-crystallin determined by x-ray crystallography. The region, in which the deletion of the amino acids occurs near the COOH terminus, is essential for the formation of the tertiary structure of the beta B2-crystallin. The loss of these residues could explain the alterations that are seen with the Philly beta B2 protein and may account for the instability of the Philly beta B2 protein. This abnormal beta B2-crystallin may be the cause of the cataract in this animal.

Effect of thermal cycling on as-quenched and aged nickel-rich Ni-Ti alloy

The effect of Ni4Ti3 precipitates on the structure and transformation sequences in Ni-49%Ti alloy has been investigated using internal friction, electrical resistivity and electron microscopy studies. It has been confirmed that in the alloy without precipitates the transformation occurs following the sequence B2 → R → M on cooling and M → B2 on heating with easily distinguished peaks on the internal friction curves and typical behaviour of the electrical resistivity, while the presence of the precipitates brings about complicated internal friction curves indicating either the appearance of two types of martensite or the transformation sequence: B2 ® B2 + R → B2 + M → M.

A study of electrical resistivity, internal friction and shear modulus on an aged Ti 49Ni 51 alloy

The 400°C aged Ti 49Ni 51 alloy can exhibit the transformation sequence of B2 →r premartensite R-phase →r martensite. In the early aging stage, only the premartensitic transformation is observed due to the M s point being deeply depressed by the coherent stress of Ti 11Ni 14 precipitates. In the later aging stage, internal friction peaks associated with premartensitic and martensitic transformations are all observed on both heating and cooling. The sharp peaks associated premartensitic transformation on heating is believed to be related to the “bias” effect of the coherent stress induced by the Ti 11Ni 14 precipitates. The serrations of internal friction appearing significantly in the temperature around −30 to −80°C are found to be caused by the stress induced accomodation of R-phase or martensite variants, and are not associated with the transformation. The Ti 11Ni 14 precipitates can enhance the amount of martensite formed by unit of temperature or time during the martensitic transformation.

Analysis of the Bovine Herpesvirus Type 1 Thymidine Kinase (TK) Gene from Wild-type Virus and TK-deficient Mutants

Five thymidine kinase (TK)-deficient mutants (B1 to B5) of bovine herpesvirus type 1 (BHV-1) were isolated by selection for resistance to the nucleotide analogue bromovinyldeoxyuridine. The genetic lesion in mutant B1 was localized in a 2.7 kb SalI-SalI subfragment (fTK2.7) which maps between 0.456 and 0.475 within the HindIII A fragment of the BHV-1 genome. The tk genes from wild-type and the TK-mutants B1 to B5 were cloned and sequenced using eight unique synthetic primers designed from a published sequence. The BHV-1 tk gene sequence for the strain 6660 contained some differences compared with that published previously for strain LA. Alignment of the predicted amino acid sequence of the BHV-1 TK polypeptide with different herpesvirus TKs revealed five strongly conserved regions and also identified putative functional relationships with other enzymes. Several interesting features were apparent in the tk gene sequences from the TK- mutants. The TK mutant B1 was a typical frameshift and chain termination mutant due to the deletion of a single base. The tk gene sequence of mutant B2 revealed the deletion of three bases resulting in the loss of valine at amino acid residue 174 of the TK polypeptide. The tk genes of mutants B3 to B5 contained an identical change of a single base addition resulting in frameshift and premature chain termination. In contrast to wild-type BHV-1, the TK-defective mutants were incapable of adsorbing TK-neutralizing antibodies from serum.

Molecular cloning andin vitrotranscription of rat 4.5S RNAHgenes

4.5S RNAH (4.5S RNA associated with poly A containing RNA) has extensive homology to major interspersed repeat B1 in rodent genomes. We developed a new cloning technique for screening genomic library that eliminates the signal produced by repeated sequences or pseudogenes and applied it to cloning of 4.5S RNAH genes. Six phage clones (2, 3, 6, 9, 10 and 15) which hybridize with 4.5S RNAH were isolated from a rat gene library by this method. The restriction fragments containing the 4.5S RNAH locus were subcloned into plasmids and sequenced. Clones 2, 3, 9 and 15 contained one to five base substitutions in the coding region for 4.5S RNAH and were probably pseudogenes. In clone 2, the 4.5S RNAH locus was linked directly with the identifier sequence. Clone 6 contained three copies of the 4.5S RNAH gene (6a, b and c) which were clustered in the same direction within 455 base pairs. 6b was linked directly with 6c and ubiquitous repetitive DNA sequences B2 were inserted immediately after 6a and 6c. These three sequences as well as the sequence in clone 10 were colinear with rat 4.5S RNAH. In an in vitro transcription system, only clone 10 gave intact 4.5S RNAH.

Complete amino acid sequence of flavocytochrome b2 from baker's yeast

Complete amino acid sequence of flavocytochrome b2 from baker's yeast

Complete amino acid sequence of flavocytochrome b2 from baker's yeast

Each subunit of baker's yeast flavocytochrome b2 can be selectively cleaved by proteases into two fragments, amino-terminal fragment alpha and carboxy-terminal fragment beta. The primary structure of the former has been reported before [Ghrir, B., Becam, A. M. & Lederer, F. (1984) Eur. J. Biochem. 139, 59-74]. The amino acid sequence of the 197-residue fragment beta has now been established. The fragment was cleaved with cyanogen bromide; the three peptides thus obtained were submitted to digestions with Staphylococcus aureus V8 protease, chymotrypsin and trypsin, sometimes after succinylation. The complete fragment was also submitted to tryptic cleavage after citraconylation. Peptides were separated by thin-layer finger-printing or high-pressure liquid chromatography. They were mostly sequenced in a liquid-phase sequenator. The 511-residue amino acid sequence of the mature protein is thus completely established. Secondary structure predictions indicate an alternation of helical and extended structure, with a higher percentage of the former. Comparisons with other flavoproteins do not detect any significant sequence similarity.

Titanium nickelide. Crystalline structure and phase transformations

In conclusion, we turn attention to the following aspects of the structural investigations of the Ti-Ni system near the equiatom composition, which have not yet received development in practice up to this time. 1. Existing experimental data indicate that the high-temperature TiNi phase has a B2 structure with ordered atom location of CsCl type. Meanwhile, up to now there are no purposeful investigations (firstly by the neutron diffraction method) of the change in the degree of long-range order in TiNi as a function of the temperature and concentration. These investigations are important not only for the setting up of the atomic distribution in the high-temperature phase, they have a direct relationship to the comprehension of the nature of the change in MT temperature and sequence, as well as to the formation of noncommensurate structures in the TiNi system. 2. The passage from the MT sequence B2 → B19′ to B2 → R → B19′ is of great value for the realization of the superelasticity effect and the achievement of large reversible strains in TiNi alloys. Investigations existing at this time indicate that redistribution of the Ti and Ni atoms precedes this passage. However, what changes occur here in the crystalline or electronic structure of the high-temperature phase is not known here. 3. For intermetallides with B2 structure, a high concentration of structural vacancies (especially for deviations from the stoichiometric composition) that can exert noticeable influence on the phase transformations is not unusual. However, up to now there are no investigations of the change in vacancy concentration in TiNi alloys as a function of the temperature and concentration of the Ti and Ni atoms.

Nucleotide sequence of small polyadenylated B2 RNA

Small poly(A)-containing RNA molecules which hybridize to the ubiquitous short repetitive sequence B2 and which are transcribed by RNA polymerase III have been identified in the cytoplasm of mouse cells. Here, we describe the structure of this small B2 RNA. A cDNA library was prepared from low-molecular-weight cytoplasmic poly(A)+RNA isolated from Ehrlich carcinoma cells and the clones which hybridized to B2 sequence were selected. The clones were sequenced and shown to contain B2 sequences followed by a poly(A) tract. The sequences of the cloned B2 RNAs different from each other by 3-10%, being similar in this respect to genomic B2 copies. Thus, B2 RNA is transcribed from many different B2 sequences in the genome. The 5'-ends of B2 RNA at least in most molecules coincide with the beginning of B2 genomic sequence. The poly(A) segments located at the 3'-end of small B2 RNA are the same size as in mRNA molecules, suggesting posttranscriptional formation. In some clones, additional sequences were detected between the 3'-end of B2 sequence and the poly(A) stretch. They seem to result from a lesion in the RNA polymerase III terminator in the corresponding B2 sequences. The possible significance of B2 sequences and small B2 RNA is discussed.

Nucleotide sequence involved in the replication of cloned yeast mitochondrial DNA.

A fragment of yeast mitochondrial DNA, Alu B, has two subfragments, Alu B1 and Alu B2. They were each cloned and sequenced. The autonomously replicating function of the curtailed Alu B1 (342 bp) was defined within 186 bp. A GC-rich sequence identical to the oris sequence in the curtailed Alu B1 was unnecessary for its autonomously replicating function. The 186 bp sequence had an ATATAAAT sequence and the stem and loop structures. The base sequence of Alu B2 also contained the same octanucleotides, the stem and loop structures, one oris sequence and one unique GC cluster. Yeast transformants with cloned Alu B2 grew slowly. The cloned Alu B2 was enlarged in the yeast host concomitantly with compensation of the slow growth of the transformants.