Why Shot Noise Does Not Generally Detect Pairing in Mesoscopic Superconducting Tunnel Junctions

The shot noise in tunneling experiments reflects the Poissonian nature of the tunneling process. The shot-noise power is proportional to both the magnitude of the current and the effective charge of the carrier. Shot-noise spectroscopy thus enables us, in principle, to determine the effective charge q of the charge carriers of that tunnel. This can be used to detect electron pairing in superconductors: In the normal state, the noise corresponds to single electron tunneling (q=1e), while in the paired state, the noise corresponds to q=2e. Here, we use a newly developed amplifier to reveal that in typical mesoscopic superconducting junctions, the shot noise does not reflect the signatures of pairing and instead stays at a level corresponding to q=1e. We show that transparency can control the shot noise, and this q=1e is due to the large number of tunneling channels with each having very low transparency. Our results indicate that in typical mesoscopic superconducting junctions, one should expect q=1e noise and lead to design guidelines for junctions that allow the detection of electron pairing.

Nernst Sign Reversal in the Hexatic Vortex Phase of Weakly Disordered a-MoGe Thin Films

The hexatic phase is an intermediate stage in the melting process of a 2D crystal due to topological defects. Recently, this exotic phase was experimentally identified in the vortex lattice of 2D weakly disordered superconducting MoGe by scanning tunneling microscopic measurements. Here, we study this vortex state by the Nernst effect, which is an effective and sensitive tool to detect vortex motion, especially in the superconducting fluctuation regime. We find a surprising Nernst sign reversal at the melting transition of the hexatic phase. We propose that they are a consequence of vortex dislocations in the hexatic state which diffuse preferably from the cold to hot.

Superfluid density in conventional superconductors: from clean to strongly disordered

The highly convergent form of superfluid density in disordered conventional superconductors available in the literature and independently obtained by us following the approach of an earlier paper (Mandal and Ramakrishnan 2020Phys. Rev.B102024514) has been reformulated to separate out the generally used so-called 'dirty-limit' term and an additional term. We use this new expression for making an extensive comparison with previously published experimental data and show that the former, generally used, term isnotsufficient for analyzing these results. We point out that consequently, there is a large regime (disordered superconductors with moderate to no disorder) where theoretical predictions need to be confronted with experiment.

Phase fluctuations in conventional superconductors

Within the Bardeen-Cooper-Schrieffer (BCS) theory, superconductivity is entirely governed by the pairing energy scale, which gives rise to the superconducting energy gap, Δ. However, another important energy scale, the superfluid phase stiffness,J, which determines the resilience of the superconductor to phase-fluctuations is normally ignored. The spectacular success of BCS theory owes to the fact that in conventional superconductorsJis normally several orders of magnitude larger than Δ and thus an irrelevant energy scale. However, in certain situations such as in the presence of low carrier density, strong disorder, at low-dimensions or in granular superconductors,Jcan drastically come down and even become smaller than Δ. In such situations, the temperature and magnetic field evolution of superconducting properties is governed by phase fluctuations, which gives rise to novel electronic states where signatures of electronic pairing continue to exist even when the zero resistance state is destroyed. In this article, we will review the recent experimental developments on the study of phase fluctuations in conventional superconductors.

Andreev Reflections in NbN/Graphene Junctions under Large Magnetic Fields

Hybrid superconductor/graphene (SC/g) junctions are excellent candidates for investigating correlations between Cooper pairs and quantum Hall (QH) edge modes. Experimental studies are challenging as Andreev reflections are extremely sensitive to junction disorder, and high magnetic fields are required to form QH edge states. We fabricated low-resistance SC/g interfaces, composed of graphene edge contacted with NbN with a barrier strength of Z ≈ 0.4, that remain superconducting under magnetic fields larger than 18 T. We establish the role of graphene's Dirac band structure on zero-field Andreev reflections and demonstrate dynamic tunability of the Andreev reflection spectrum by moving the boundary between specular and retro Andreev reflections with parallel magnetic fields. Through the application of perpendicular magnetic fields, we observe an oscillatory suppression of the 2-probe conductance in the ν = 4 Landau level attributed to the reduced efficiency of Andreev processes at the NbN/g interface, consistent with theoretical predictions.

Collective flux pinning in hexatic vortex fluid in a-MoGe thin film

We investigate the magnetic field variation of the thermally activated flux flow resistivity, ρ _TAFF and flux flow critical current density, J _c, in a weakly pinned thin film of the amorphous superconductor a-MoGe, where vortices are in a fluid state over a large range of magnetic fields. We show that both quantities can be understood within the framework of collective pinning theory. In particular, our results demonstrate that a 'peak effect' can arise at the order-disorder transition of the vortex lattice even when both the ordered and disordered states are vortex fluids, such as the boundary between a hexatic vortex fluid and an isotropic vortex liquid.

Melting of the Vortex Lattice through Intermediate Hexatic Fluid in an a-MoGe Thin Film

The hexatic fluid refers to a phase in between a solid and a liquid that has short-range positional order but quasi-long-range orientational order. In the celebrated theory of Berezinskii, Kosterlitz, and Thouless and subsequently refined by Halperin, Nelson, and Young, it was predicted that a two-dimensional hexagonal solid can melt in two steps: first, through a transformation from a solid to a hexatic fluid, which retains quasi-long-range orientational order; and then from a hexatic fluid to an isotropic liquid. In this Letter, using a combination of real space imaging and transport measurements, we show that the two-dimensional vortex lattice in an a-MoGe thin film follows this sequence of melting as the magnetic field is increased. Identifying the signatures of various transitions on the bulk transport properties of the superconductor, we construct a vortex phase diagram for a two-dimensional superconductor.

Inter-Landau-level Andreev Reflection at the Dirac Point in a Graphene Quantum Hall State Coupled to a NbSe_{2} Superconductor

Superconductivity and the quantum Hall effect are distinct states of matter occurring in apparently incompatible physical conditions. Recent theoretical developments suggest that the coupling of the quantum Hall effect with a superconductor can provide fertile ground for realizing exotic topological excitations such as non-Abelian Majorana fermions or Fibonacci particles. As a step toward that goal, we report observation of Andreev reflection at the junction of a quantum Hall edge state in a single layer graphene and a quasi-two-dimensional niobium diselenide (NbSe_{2}) superconductor. Our principal finding is the observation of an anomalous finite-temperature conductance peak located precisely at the Dirac point, providing a definitive evidence for inter-Landau-level Andreev reflection in a quantum Hall system. Our observations are well supported by detailed numerical simulations, which offer additional insight into the role of the edge states in Andreev physics. This study paves the way for investigating analogous Andreev reflection in a fractional quantum Hall system coupled to a superconductor to realize exotic quasiparticles.

Quantum Phase Transition in Few-Layer NbSe_{2} Probed through Quantized Conductance Fluctuations

We present the first observation of dynamically modulated quantum phase transition between two distinct charge density wave (CDW) phases in two-dimensional 2H-NbSe_{2}. There is recent spectroscopic evidence for the presence of these two quantum phases, but its evidence in bulk measurements remained elusive. We studied suspended, ultrathin 2H-NbSe_{2} devices fabricated on piezoelectric substrates-with tunable flakes thickness, disorder level, and strain. We find a surprising evolution of the conductance fluctuation spectra across the CDW temperature: the conductance fluctuates between two precise values, separated by a quantum of conductance. These quantized fluctuations disappear for disordered and on-substrate devices. With the help of mean-field calculations, these observations can be explained as to arise from dynamical phase transition between the two CDW states. To affirm this idea, we vary the lateral strain across the device via piezoelectric medium and map out the phase diagram near the quantum critical point. The results resolve a long-standing mystery of the anomalously large spectroscopic gap in NbSe_{2}.

Orientational coupling between the vortex lattice and the crystalline lattice in a weakly pinned Co(0.0075)NbSe2 single crystal

We report experimental evidence of strong orientational coupling between the crystal lattice and the vortex lattice in a weakly pinned Co-doped NbSe2 single crystal through direct imaging using low temperature scanning tunneling microscopy/spectroscopy. When the magnetic field is applied along the six-fold symmetric c-axis of the NbSe2 crystal, the basis vectors of the vortex lattice are preferentially aligned along the basis vectors of the crystal lattice. The orientational coupling between the vortex lattice and crystal lattice becomes more pronounced as the magnetic field is increased. This orientational coupling enhances the stability of the orientational order of the vortex lattice, which persists even in the disordered state at high fields where dislocations and disclinations have destroyed the topological order. Our results underpin the importance of crystal lattice symmetry on the vortex state phase diagram of weakly pinned type II superconductors.

Disordering of the vortex lattice through successive destruction of positional and orientational order in a weakly pinned Co0.0075NbSe2 single crystal

The vortex lattice in a Type II superconductor provides a versatile model system to investigate the order-disorder transition in a periodic medium in the presence of random pinning. Here, using scanning tunnelling spectroscopy in a weakly pinned Co(0.0075)NbSe(2) single crystal, we show that the vortex lattice in a 3-dimensional superconductor disorders through successive destruction of positional and orientational order, as the magnetic field is increased across the peak effect. At the onset of the peak effect, the equilibrium quasi-long range ordered state transforms into an orientational glass through the proliferation of dislocations. At a higher field, the dislocations dissociate into isolated disclination giving rise to an amorphous vortex glass. We also show the existence of a variety of additional non-equilibrium metastable states, which can be accessed through different thermomagnetic cycling.

A 350 mK, 9 T scanning tunneling microscope for the study of superconducting thin films on insulating substrates and single crystals

We report the construction and performance of a low temperature, high field scanning tunneling microscope (STM) operating down to 350 mK and in magnetic fields up to 9 T, with thin film deposition and in situ single crystal cleaving capabilities. The main focus lies on the simple design of STM head and a sample holder design that allows us to get spectroscopic data on superconducting thin films grown in situ on insulating substrates. Other design details on sample transport, sample preparation chamber, and vibration isolation schemes are also described. We demonstrate the capability of our instrument through the atomic resolution imaging and spectroscopy on NbSe2 single crystal and spectroscopic maps obtained on homogeneously disordered NbN thin film.

Correlated conductance fluctuations close to the Berezinskii-Kosterlitz-Thouless transition in ultrathin NbN films

We probe the presence of long-range correlations in phase fluctuations by analyzing the higher-order spectrum of resistance fluctuations in ultrathin NbN superconducting films. The non-Gaussian component of resistance fluctuations is found to be sensitive to film thickness close to the transition, which allows us to distinguish between mean field and Berezinskii-Kosterlitz-Thouless (BKT) type superconducting transitions. The extent of non-Gaussianity was found to be bounded by the BKT and mean field transition temperatures and depends strongly on the roughness and structural inhomogeneity of the superconducting films. Our experiment outlines a novel fluctuation-based kinetic probe in detecting the nature of superconductivity in disordered low-dimensional materials.

Emergence of nanoscale inhomogeneity in the superconducting state of a homogeneously disordered conventional superconductor

The notion of spontaneous formation of an inhomogeneous superconducting state is at the heart of most theories attempting to understand the superconducting state in the presence of strong disorder. Using scanning tunneling spectroscopy and high resolution scanning transmission electron microscopy, we experimentally demonstrate that under the competing effects of strong homogeneous disorder and superconducting correlations, the superconducting state of a conventional superconductor, NbN, spontaneously segregates into domains. Tracking these domains as a function of temperature we observe that the superconducting domains persist across the bulk superconducting transition, T_c, and disappear close to the pseudogap temperature, T*, where signatures of superconducting correlations disappear from the tunneling spectrum and the superfluid response of the system.

Enhancement of the finite-frequency superfluid response in the pseudogap regime of strongly disordered superconducting films

The persistence of a soft gap in the density of states above the superconducting transition temperature Tc, the pseudogap, has long been thought to be a hallmark of unconventional high-temperature superconductors. However, in the last few years this paradigm has been strongly revised by increasing experimental evidence for the emergence of a pseudogap state in strongly-disordered conventional superconductors. Nonetheless, the nature of this state, probed primarily through scanning tunneling spectroscopy (STS) measurements, remains partly elusive. Here we show that the dynamic response above Tc, obtained from the complex ac conductivity, is highly modified in the pseudogap regime of strongly disordered NbN films. Below the pseudogap temperature, T*, the superfluid stiffness acquires a strong frequency dependence associated with a marked slowing down of critical fluctuations. When translated into the length-scale of fluctuations, our results suggest a scenario of thermal phase fluctuations between superconducting domains in a strongly disordered s-wave superconductor.

Role of the vortex-core energy on the Berezinskii-Kosterlitz-Thouless transition in thin films of NbN

We analyze the occurrence of the Berezinskii-Kosterlitz-Thouless (BKT) transition in thin films of NbN at various film thickness, by probing the effect of vortex fluctuations on the temperature dependence of the superfluid density below T(BKT) and of the resistivity above T(BKT). By direct comparison between the experimental data and the theory, we show the crucial role played by the vortex-core energy in determining the characteristic signatures of the BKT physics, and we estimate its dependence on the disorder level. Our work provides a paradigmatic example of BKT physics in a quasi-two-dimensional superconductor.

Prospective study of antenatally diagnosed congenital cystic adenomatoid malformations

PURPOSE

Congenital cystic adenomatoid malformations (CCAMs) are increasingly diagnosed in recent years due to the routine usage of antenatal ultrasound. The aim of this study was to present the natural course and outcome of antenatally diagnosed cystic lung diseases, which were prospectively studied.

METHODS

Between the period June 2004 and June 2010, 25 fetuses with suspected CCAMs were seen in a single tertiary maternal fetal unit. One child was excluded as the fetal MRI suggested congenital diaphragmatic hernia. Data were prospectively entered into a database including antenatal and postnatal findings which were then analyzed.

RESULTS

Mean gestational age at the time of diagnosis was 20.8 weeks (range 17-29). Fetal interventions included amnioreduction (n = 2) and fetal thoracocentesis (n = 3) in one child. The mean gestational age at delivery was 38.5 weeks (range 31.6-40.6). None of the mothers underwent termination of pregnancy or spontaneous abortion. All patients underwent postnatal radiological assessment. Of the 24 cases, 5 children were symptomatic in the immediate neonatal period and 19 were asymptomatic. Anatomical surgical resection was undertaken in all symptomatic cases. There was one death in this group due to severe pre-existing pulmonary hypoplasia. Among the 19 asymptomatic cases, 5 children were managed conservatively as the lesions were not significant and the remaining 14 (73%) underwent surgical resection. The mean age at surgery was 11.1 months (range 3.3-34 months). Postnatal pathology confirmed CCAM in all operated cases, except one who had pulmonary sequestration.

CONCLUSION

Antenatally diagnosed CCAMs have an excellent prognosis except in children with a large lesion and associated with lung hypoplasia. Postnatal investigations are required in all cases to confirm the diagnosis. Symptomatic CCAMs require immediate surgery in the neonatal period with a good outcome. Asymptomatic CCAMs can be safely operated between 9 and 12 months of age.

Phase fluctuations in a strongly disordered s-wave NbN superconductor close to the metal-insulator transition

We explore the role of phase fluctuations in a three-dimensional s-wave superconductor, NbN, as we approach the critical disorder for destruction of the superconducting state. Close to critical disorder, we observe a finite gap in the electronic spectrum which persists at temperatures well above T(c). The superfluid density is strongly suppressed at low temperatures and evolves towards a linear-T variation at higher temperatures. These observations provide strong evidence that phase fluctuations play a central role in the formation of a pseudogap state in a disordered s-wave superconductor.

Approaches in type 1 diabetes research: A status report

Type 1 diabetes is a multifactorial disease with an early age of onset, in which the insulin producing beta cell of the pancreas are destroyed because of autoimmunity. It is the second most common chronic disease in children and account for 5% to 10% of all diagnosed cases of diabetes. India is having an incidence of 10.6 cases/year/100,000, and recent studies indicate that the prevalence of type 1 diabetes in India is increasing. However in view of poor health care network, there is no monitoring system in the country. Of the 18 genomic intervals implicated for the risk to develop type 1 diabetes, the major histocompatibility complex (MHC) region on chromosome 6p21.31 has been the major contributor estimated to account for 40-50%, followed by 10% frequency of INS-VNTR at 5' flanking region of the insulin gene on chromosome 11p15.5. However, population studies suggest that > 95% of type 1 diabetes have HLA-DR3 or DR4, or both, and in family studies, sibling pairs affected with type 1 diabetes have a non-random distribution of shared HLA haplotypes. As predisposing genetic factors such as HLA alleles are known, immunological interventions to prevent type 1 diabetes are of great interest. In the present study we have reviewed the status of molecular genetics of the disease and the approaches that need to be adopted in terms of developing patient and suitable control cohorts in the country.

Competing effects of surface phonon softening and quantum size effects on the superconducting properties of nanostructured Pb

The superconducting transition temperature (T(C)) in nanostructured Pb decreases from 7.24 to 6.4 K as the particle size is reduced from 65 to 7 nm, below which superconductivity is lost rather abruptly. In contrast, there is a large enhancement in the upper critical field (H(C2)) in the same size regime. We explore the origin of the unusual robustness of T(C) over such a large particle size range in nanostructured Pb by measuring the temperature dependence of the superconducting energy gap in planar tunnel junctions of Al/Al(2)O(3)/nano-Pb. We show that below 22 nm, the electron-phonon coupling strength increases monotonically with decreasing particle size, and almost exactly compensates for the quantum size effect, which is expected to suppress T(C).

Proliferation defects and genome instability in cells lacking Cul4A

The Cul4A gene, which encodes a core component of a cullin-based E3 ubiquitin ligase complex, is over-expressed in breast and hepatocellular cancers. In breast cancers, over-expression of Cul4A strongly correlates with poor prognosis. Also, Cul4A is required for early embryonic development. Early lethality of mouse embryos prevented a detailed analysis of the functions of Cul4A. Here, we used a strain of mice carrying floxed alleles of Cul4A to study its role in cell division, in vitro and in vivo. Embryonic fibroblasts exhibit a severe deficiency in cell proliferation following deletion of Cul4A. We observed that the Cul4A protein is abundantly expressed in brain, liver and in the mammary tissue of pregnant mice. Deletion of Cul4A in liver impairs hepatocyte proliferation during regeneration following carbon tetrachloride induced injury. The Cul4A-deleted cells are slow in entering S phase, and are deficient in progressing through early M phase. Several cell cycle regulators, including p53 and p27Kip1, are de-regulated in the Cul4A-deleted cells. Expression of a dominant negative mutant of p53 causes significant reversal of the proliferation defects in Cul4A-deleted cells. The Cul4A-deleted cells exhibit aberrant number of centrosome, multipolar spindles and micronuclei formation. Furthermore, those cells are sensitive to UV irradiation and exhibit reduced levels of unscheduled DNA synthesis. Together, our observations indicate that Cul4A is required for efficient cell proliferation, control of the centrosome amplification and genome stability.

Synthesis of nanodimensional TiO2 thin films

Nanodimensional TiO2 has wide application in the field of photocatalysis, photovoltaic and photochromic devices. In present investigation TiO2 thin films deposited by pulsed laser deposition method are irradiated by 100 MeV Ag ion beam to achieve growth of nanophases. The nanostructure evolution is characterized by atomic force microscopy (AFM). The phases of TiO2 formed after irradiation are identified by glancing angle X-ray diffraction and Raman spectroscopy. The particle radius estimated by AFM varies from 10-13 nm. Anatase phase of TiO2 is formed after irradiation. The blue shift observed in UV-VIS absorption spectra indicates the nanostructure formation. The shape and size of nanoparticles formed due to high electronic excitation depend upon thickness of the film.

An N-terminal inhibitory domain modulates activity of FoxM1 during cell cycle

The FoxM1 transcription factor plays critical roles in the expression of genes that are essential for cell proliferation. FoxM1 null or depleted cells fail to progress through mitosis, as expression of several mitotic genes depends upon FoxM1. The transcriptional activity of FoxM1 is stimulated by cyclin-cdk-mediated phosphorylation at a site within the transcriptional activation domain. Here, we characterize the role of an N-terminal inhibitory domain in the transcriptional activity of FoxM1. Deletion of the N-terminal 232 amino-acid residues increases the transcriptional and transforming activities of FoxM1. Moreover, while the activity of the full-length FoxM1 is stimulated by growth factors, the activity of the N-terminal deletion mutant is constitutively high in all phases of the cell cycle. The N-terminal deletion also eliminates the requirement for cyclin-cdk to activate FoxM1. We provide evidence that the N-terminal domain interacts with the C-terminal half of the transcription factor to attenuate its transcriptional activity. Moreover, the N-terminal fragment inhibits the transcriptional activity of FoxM1 in G1/S cells, but not in G2/M cells. Our results suggest that cyclin-cdk phosphorylates FoxM1 to counteract the inhibition by the N-terminal domain to fully activate FoxM1 in G2/M phase.

Mechanism of the size dependence of the superconducting transition of nanostructured Nb

A direct measurement of the superconducting energy gap by point contact spectroscopy in nanostructured Nb films shows that the gap decreases with a reduction in the average particle size. The superconducting T(c), obtained from transport and magnetic measurements, also decreases with size and scales with the energy gap. The size dependence of the superconducting properties in this intermediate coupling type II superconductor is therefore governed by changes in the electronic density of states rather than by phonon softening. Consistent with the Anderson criterion, no T(c) was observed for sizes below 8 nm.

Evidence of gap anisotropy in superconducting YNi2B2C using directional point-contact spectroscopy

We present a study of the anisotropy in the superconducting energy gap in a single crystal of YNi2B2C (T(c) approximately 14.6 K) using directional point-contact spectroscopy. The superconducting energy gap at 2.7 K, when measured for I||c, is 4.5 times larger than that for I||a. The energy gaps in the two directions also have different temperature dependences. Our results support a scenario with s + g like symmetry.

Observation of minority spin character of the new electron doped manganite La0.7Ce0.3MnO3 from tunneling magnetoresistance

We report the magnetotransport characteristics of a trilayer ferromagnetic tunnel junction built of an electron doped manganite (La0.7Ce0.3MnO3) and a hole doped manganite (La0.7Ca0.3MnO3). At low temperatures the junction exhibits a large positive tunneling magnetoresistance (TMR), irrespective of the bias voltage. At intermediate temperatures below T(C) the sign of the TMR is dependent on the bias voltage across the junction. The magnetoresistive characteristics of the junction strongly suggest that La0.7Ce0.3MnO3 is a minority spin carrier ferromagnet with a high degree of spin polarization, i.e., a transport half-metal.

Sensitivity to disorder of the metallic state in the ruthenates

We report the results of transport measurements on SrRuO3, Sr3Ru2O7, and CaRuO3. In SrRuO3 and Sr3Ru2O7, our findings are consistent with the predictions of Fermi liquid theory, in contrast to previous reports based on samples with much shorter mean free paths. In CaRuO3, however, a T1.5 power law is seen in the resistivity in the high purity samples studied here. Our work gives concrete evidence that even the metallic state of the ruthenates is highly sensitive to disorder.

DDB2 induces nuclear accumulation of the hepatitis B virus X protein independently of binding to DDB1

The hepatitis B virus (HBV) X protein (HBx) is critical for the life cycle of the virus. HBx associates with several host cell proteins including the DDB1 subunit of the damaged-DNA binding protein DDB. Recent studies on the X protein encoded by the woodchuck hepadnavirus have provided correlative evidence indicating that the interaction with DDB1 is important for establishment of infection by the virus. In addition, the interaction with DDB1 has been implicated in the nuclear localization of HBx. Because the DDB2 subunit of DDB is required for the nuclear accumulation of DDB1, we investigated the role of DDB2 in the nuclear accumulation of HBx. Here we show that expression of DDB2 increases the nuclear levels of HBx. Several C-terminal deletion mutants of DDB2 that fail to bind DDB1 are able to associate with HBx, suggesting that DDB2 may associate with HBx independently of binding to DDB1. We also show that DDB2 enhances the nuclear accumulation of HBx independently of binding to DDB1, since a mutant that does not bind DDB1 is able to enhance the nuclear accumulation of HBx. HBV infection is associated with liver pathogenesis. We show that the nuclear levels of DDB1 and DDB2 are tightly regulated in hepatocytes. Studies with regenerating mouse liver indicate that during late G1 phase the nuclear levels of both subunits of DDB are transiently increased, followed by a sharp decrease in S phase. Taken together, these results suggest that DDB1 and DDB2 would participate in the nuclear functions of HBx effectively only during the late-G1 phase of the cell cycle.

The xeroderma pigmentosum group E gene product DDB2 is a specific target of cullin 4A in mammalian cells

The damaged-DNA binding protein DDB consists of two subunits, DDB1 (127 kDa) and DDB2 (48 kDa). Mutations in the DDB2 subunit have been detected in patients suffering from the repair deficiency disease xeroderma pigmentosum (group E). In addition, recent studies suggested a role for DDB2 in global genomic repair. DDB2 also exhibits transcriptional activity. We showed that expression of DDB1 and DDB2 stimulated the activity of the cell cycle regulatory transcription factor E2F1. Here we show that DDB2 is a cell cycle-regulated protein. It is present at a low level in growth-arrested primary fibroblasts, and after release the level peaks at the G(1)/S boundary. The cell cycle regulation of DDB2 involves posttranscriptional mechanisms. Moreover, we find that an inhibitor of 26S proteasome increases the level of DDB2, suggesting that it is regulated by the ubiquitin-proteasome pathway. Our previous study indicated that the cullin family protein Cul-4A associates with the DDB2 subunit. Because cullins are involved in the ubiquitin-proteasome pathway, we investigated the role of Cul-4A in regulating DDB2. Here we show that DDB2 is a specific target of Cul-4A. Coexpression of Cul-4A, but not Cul-1 or other highly related cullins, increases the ubiquitination and the decay rate of DDB2. A naturally occurring mutant of DDB2 (2RO), which does not bind Cul-4A, is not affected by coexpression of Cul-4A. Studies presented here identify a specific function of the Cul-4A gene, which is amplified and overexpressed in breast cancers.

Mechanism of melphalan-induced B7-1 gene expression in P815 tumor cells

We have previously shown that exposure of P815 tumor cells to melphalan (L-phenylalanine mustard; L-PAM) leads to up-regulation of B7-1 surface expression, and this L-PAM-induced up-regulation requires de novo RNA synthesis and is associated with accumulation of B7-1 mRNA. Here we show that the effect of L-PAM on B7-1 surface expression can be mimicked by exposing P815 tumor cells to oxidative stress but not to heat shock. Moreover, the antioxidant N-acetyl-L-cysteine prevented the L-PAM-induced accumulation of B7-1 mRNA in P815 tumor cells, suggesting that reactive oxygen species are involved in the transcriptional regulation of L-PAM-induced B7-1 gene expression. Although AP-1 and NF-kappaB are regarded as redox-sensitive transcription factors and the promoter/enhancer region of the B7-1 gene contains an AP-1 and an NF-kappaB binding site, exposure of P815 tumor cells to L-PAM led to rapid and transient activation only of NF-kappaB, but not AP-1, that bound specifically to a probe containing the respective binding site in the murine or human B7-1 gene. Moreover, exposure of P815 tumor cells to a cell-permeable peptide that selectively inhibits NF-kappaB activation by blocking the activation of the IkappaB-kinase complex was found to inhibit the L-PAM-induced B7-1 mRNA accumulation, indicating that NF-kappaB activation is essential for the L-PAM-induced B7-1 gene expression. Taken together, these results indicate that L-PAM leads to activation of B7-1 gene expression by activating NF-kappaB via a pathway that involves reactive oxygen species.

Both Rb and E7 are regulated by the ubiquitin proteasome pathway in HPV-containing cervical tumor cells

High-risk human papillomaviruses (HPVs) are etiologically linked to human cervical and oral cancers. The E6 and E7 oncoproteins encoded by HPV target host cell tumor suppressor proteins. E6 induces proteolysis of p53 through the ubiquitin-proteasome pathway. Recent studies showed that overexpression of E7 caused proteolytic degradation of the tumor suppressor Rb. However, unlike p53, Rb is not regulated by proteolysis in normal cells. In addition, it was unclear whether in its natural context E7 regulates Rb through the ubiquitin-proteasome pathway. Therefore, we sought to determine whether Rb is regulated by the ubiquitin-proteasome pathway in HPV-containing tumor cells. We carried out a detailed analysis in Caski cells, that are derived from HPV-containing cervical cancer tissues. Studies with various protease inhibitors revealed that Rb is regulated specifically by the ubiquitin-proteasome pathway in HPV-containing cervical tumor cells. Several inhibitors of the 26S proteasome significantly increased the level of Rb in the Caski cells. Rb controls cell growth by forming complexes with the E2F-family transcription factors. Surprisingly, in spite of a significant accumulation of the hypophosphorylated form of Rb, no Rb/E2F complex was detectable in the proteasome inhibitor treated cells. Further analysis revealed that there was an increased accumulation of the E7 oncoprotein. We showed that the proteasome inhibitors simultaneously blocked the proteolysis of E7 and Rb, suggesting that E7 is also regulated by the ubiquitin-dependent proteolysis in cervical cancer cells. Taken together, this study suggests that targeted inhibition of Rb proteolysis will be required for restoring Rb function in HPV-containing cervical cancer cells.

The p48 subunit of the damaged-DNA binding protein DDB associates with the CBP/p300 family of histone acetyltransferase

DDB has been implicated in DNA repair as well as transcription. Mutations in DDB have been correlated with the repair-deficiency disease, xeroderma pigmentosum group E (XP-E). The XP-E cells exhibit deficiencies in global genomic repair, suggesting a role for DDB in that process. DDB also possesses a transcription stimulatory activity. We showed that DDB could function as a transcriptional partner of E2F1. But the mechanism by which DDB stimulates E2F-regulated transcription or carry out its DNA repair function is not understood. To investigate the mechanisms, we looked for nuclear proteins that interact with DDB. Here we show that DDB associates with the CBP/p300 family of proteins, in vivo and in vitro. We suggest that DDB participates in global genomic repair by recruiting CBP/p300 to the damaged-chromatin. It is possible that the histone acetyltransferase activities of the CBP/p300 proteins induce chromatin remodeling at the damaged-sites to allow recruitment of the repair complexes. The observation offers insights into both transcription and repair functions of DDB.

Cullin 4A associates with the UV-damaged DNA-binding protein DDB

The damaged DNA-binding protein (DDB) is believed to be involved in DNA repair, and it has been linked to the repair deficiency disease xeroderma pigmentosum. DDB also exhibits transcriptional activities. DDB binds to the activation domain of E2F1 and stimulates E2F1-activated transcription. Here we provide evidence that DDB or DDB-associated proteins are targets of cullin 4A (CUL-4A). CUL-4A is a member of the cullin family of proteins, which are believed to be ubiquitin-protein isopeptide ligases (type E3). The CUL-4A gene has been shown to be amplified and up-regulated in breast carcinomas. In this study, we identify CUL-4A as one of the DDB-associated proteins. CUL-4A co-immunoprecipitates with DDB, but not with a naturally occurring mutant of DDB. Moreover, CUL-4A in HeLa nuclear extracts co-purifies with DDB, suggesting they are parts of the same complex. The observation provides insights how CUL-4A, through an interaction with DDB, might be playing a role in the development of breast carcinomas.

Functional interaction between human topoisomerase IIalpha and retinoblastoma protein

DNA topoisomerase II-an essential nuclear enzyme in DNA replication and transcription, chromatin segregation, and cell cycle progression-is also a target of clinically useful anticancer drugs. Preliminary observations of a positive correlation between the expression of topoisomerase (topo) IIalpha and the retinoblastoma protein (Rb) in a series of rhabdomyosarcoma cells prompted us to ask whether these two proteins interact in vivo. Using human rhabdomyosarcoma and leukemic cell lines, we found a physical association between topo IIalpha and Rb protein by reciprocal immunoprecipitation and immunoblotting, in which topo IIalpha appeared to interact primarily with the underphosphorylated form of Rb. Experiments with truncated glutathione S-transferase-Rb fusion proteins and nuclear extracts of Rh1 rhabdomyosarcoma cells indicated that topo IIalpha binds avidly to the A/B pocket domain of Rb, which contains the intact spacer amino acid sequence. To determine whether this interaction has functional consequences in vivo, we expressed wild-type and mutant Rb in human cervical carcinoma cells lacking functional Rb. Wild-type, but not mutant, Rb inhibited topo II activity in nuclear extracts of these transfected cells. Moreover, purified wild-type Rb inhibited the activity of purified human topo IIalpha, indicating a direct interaction between these two proteins. We conclude that topo IIalpha associates physically with Rb in interactions that appear to have functional significance.

The naturally occurring mutants of DDB are impaired in stimulating nuclear import of the p125 subunit and E2F1-activated transcription

The human UV-damaged-DNA binding protein DDB has been linked to the repair deficiency disease xeroderma pigmentosum group E (XP-E), because a subset of XP-E patients lack the damaged-DNA binding function of DDB. Moreover, the microinjection of purified DDB complements the repair deficiency in XP-E cells lacking DDB. Two naturally occurring XP-E mutations of DDB, 82TO and 2RO, have been characterized. They have single amino acid substitutions (K244E and R273H) within the WD motif of the p48 subunit of DDB, and the mutated proteins lack the damaged-DNA binding activity. In this report, we describe a new function of the p48 subunit of DDB, which reveals additional defects in the function of the XP-E mutants. We show that when the subunits of DDB were expressed individually, p48 localized in the nucleus and p125 localized in the cytoplasm. The coexpression of p125 with p48 resulted in an increased accumulation of p125 in the nucleus, indicating that p48 plays a critical role in the nuclear localization of p125. The mutant forms of p48, 2RO and 82TO, are deficient in stimulating the nuclear accumulation of the p125 subunit of DDB. In addition, the mutant 2RO fails to form a stable complex with the p125 subunit of DDB. Our previous studies indicated that DDB can associate with the transcription factor E2F1 and can function as a transcriptional partner of E2F1. Here we show that the two mutants, while they associate with E2F1 as efficiently as wild-type p48, are severely impaired in stimulating E2F1-activated transcription. This is consistent with our observation that both subunits of DDB are required to stimulate E2F1-activated transcription. The results provide insights into the functions of the subunits of DDB and suggest a possible link between the role of DDB in E2F1-activated transcription and the repair deficiency disease XP-E.

Site-directed mutant p21 proteins defective in both inhibition of E2F-regulated transcription and disruption of E2F-p130-cyclin-cdk2 complexes

P21 is a regulatory protein that can contribute to cell cycle arrest by inhibiting the cyclin-dependent-kinases (cdks). However, the mechanism that links the inhibition of the cdk activities and the cell cycle arrest is not well established. To investigate this, we studied a purified endogenous cellular complex which contained E2F (in the form of E2F-4), p130, cyclin, and cdk2. This complex of E2F-p130-cyclin-cdk2 is found mainly in cycling cells and is postulated to be an intermediate that leads to the activation of E2F. We previously showed that p21 could disrupt this complex leading to the accumulation of an E2F-p130 complex and the inhibition of E2F-regulated transcription. We analyzed a group of p21 mutants including those that harbored changes in cyclin- and cdk2-binding motifs. We show that both the cyclin and cdk2 binding motifs of p21 are crucial for the disruption of this endogenous complex of E2F-p130-cyclin-cdk2. This suggests a model where the ability of p21 to inhibit the function of this complex is dependent on interactions with both cyclin and cdk2 molecules. This was substantiated by studies with intact cells. P21 mutants that are impaired in their ability to disrupt the cellular E2F-p130-cyclin-cdk2 complex are also shown to be maximally impaired in the ability to repress E2F-regulated transcription.

DDB, a putative DNA repair protein, can function as a transcriptional partner of E2F1

The transcription factor E2F1 is believed to be involved in the regulated expression of the DNA replication genes. To gain insights into the transcriptional activation function of E2F1, we looked for proteins in HeLa nuclear extracts that bind to the activation domain of E2F1. Here we show that DDB, a putative DNA repair protein, associates with the activation domain of E2F1. DDB was identified as a heterodimeric protein (48 and 127 kDa) that binds to UV-damaged DNA. We show that the UV-damaged-DNA binding activity from HeLa nuclear extracts can associate with the activation domain of E2F1. Moreover, the 48-kDa subunit of DDB, synthesized in vitro, binds to a fusion protein of E2F1 depending on the C-terminal activation domain. The interaction between DDB and E2F1 can also be detected by coimmunoprecipitation experiments. Immunoprecipitation of an epitope-tagged DDB from cell extracts resulted in the coprecipitation of E2F1. In a reciprocal experiment, immunoprecipitates of E2F1 were found to contain DDB. Fractionation of HeLa nuclear extracts also revealed a significant overlap in the elution profiles of E2F1 and DDB. For instance, DDB, which does not bind to the E2F sites, was enriched in the high-salt fractions containing E2F1 during chromatography through an E2F-specific DNA affinity column. We also observed evidence for a functional interaction between DDB and E2F1 in living cells. For instance, expression of DDB specifically stimulated E2F1-activated transcription. In addition, the transcriptional activation function of a heterologous transcription factor containing the activation domain of E2F1 was stimulated by coexpression of DDB. Moreover, DDB expression could overcome the retinoblastoma protein (Rb)-mediated inhibition of E2F1-activated transcription. The results suggest that this damaged-DNA binding protein can function as a transcriptional partner of E2F1. We speculate that the damaged-DNA binding function of DDB, besides repair, might serve as a negative regulator of E2F1-activated transcription, as damaged DNA will sequester DDB and make it unavailable for E2F1. Furthermore, the binding of DDB to damaged DNA might be involved in downregulating the replication genes during growth arrest induced by damaged DNA.

Differential regulation of the pocket domains of the retinoblastoma family proteins by the HPV16 E7 oncoprotein

The human papillomavirus E7 oncoprotein binds to the retinoblastoma (Rb) tumor suppressor protein, and the binding to Rb correlates with the oncogenic potential of E7. Recent studies from several laboratories indicated that the half-life of the Rb protein is reduced in cells that are stably transformed with E7, suggesting that E7 could induce the proteolytic degradation of Rb. To investigate whether the Rb degradation is a primary effect of E7 or a result of altered cell phenotype, we sought to develop assays that can distinguish between the two possibilities. Using recombinant adenovirus expressing the human papillomavirus type 16 E7 protein, we show that the expression of E7 leads to an increased rate of decay of the Rb protein. Moreover, Rb degradation immediately follows the expression of E7 suggesting that it is an early and primary effect. Consistent with a previous study, we observed that the E7-induced degradation of Rb can be blocked by the inhibitors of the 26S proteasome. We have also developed a transient transfection assay for the E7-induced degradation of Rb. Using this assay, we show that the pocket domain of Rb is necessary and sufficient for the E7-induced degradation. However, the proteolysis is relatively specific for Rb because the level of p107 or p130 was not significantly altered by the expression of E7. Thus, although E7 binds to all three members of the Rb family of proteins, the proteolysis is much more efficient in the case of Rb. In the transient transfection assays, adenovirus E1A and SV40 large T antigen failed to induce degradation of Rb, suggesting that the Rb degradation is a unique property of the E7 oncoprotein.

p27Kip1 induces an accumulation of the repressor complexes of E2F and inhibits expression of the E2F-regulated genes

p27Kip1 is an inhibitor of the cyclin-dependent kinases and it plays an inhibitory role in the progression of cell cycle through G1 phase. To investigate the mechanism of cell cycle inhibition by p27Kip1, we constructed a cell line that inducibly expresses p27Kip1 upon addition of isopropyl-1-thio-beta-D-galactopyranoside in the culture medium. Isopropyl-1-thio-beta-D-galactopyranoside-induced expression of p27Kip1 in these cells causes a specific reduction in the expression of the E2F-regulated genes such as cyclin E, cyclin A, and dihydrofolate reductase. The reduction in the expression of these genes correlates with the p27Kip1-induced accumulation of the repressor complexes of the E2F family of factors (E2Fs). Our previous studies indicated that p21WAF1 could disrupt the interaction between cyclin/cyclin-dependent kinase 2 (cdk2) and the E2F repressor complexes E2F-p130 and E2F-p107. We show that p27Kip1, like p21WAF1, disrupts cyclin/cdk2-containing complexes of E2F-p130 leading to the accumulation of the E2F-p130 complexes, which is found in growth-arrested cells. In transient transfection assays, expression of p27Kip1 specifically inhibits transcription of a promoter containing E2F-binding sites. Mutants of p27Kip1 harboring changes in the cyclin- and cdk2-binding motifs are deficient in inhibiting transcription from the E2F sites containing reporter gene. Moreover, these mutants of p27Kip1 are also impaired in disrupting the interaction between cyclin/cdk2 and the repressor complexes of E2Fs. Taken together, these observations suggest that p27Kip1 reduces expression of the E2F-regulated genes by generating repressor complexes of E2Fs. Furthermore, the results also demonstrate that p27Kip1 inhibits expression of cyclin A and cyclin E, which are critical for progression through the G1-S phases.

Accumulation of human papillomavirus type 16 E7 protein bypasses G1 arrest induced by serum deprivation and by the cell cycle inhibitor p21

The E7 oncoproteins encoded by the high-risk type of human papillomaviruses (HPVs) interact with the Rb family proteins Rb, p107, and p130. The Rb family proteins associate with the factors of the E2F family to form transcription repressor complexes, which control expression of several genes essential for S-phase entry and DNA replication. The E7 oncoproteins, by interacting with the Rb family proteins, dissociate the repressor complexes involving the factors of the E2F and Rb families, leading to a release of the E2F factors in their activator forms. In this study, we have addressed the mechanism by which the HPV type 16 (HPV16) E7 stimulates the cell cycle. Using a cell line that inducibly expresses the HPV16 E7 protein, we show that an accumulation of E7 induces quiescent cells to enter S phase and that this function of E7 depends on retention of the motif involved in binding to the Rb family proteins. To study the effects of E7 on normal human cells, we generated a recombinant adenovirus that expresses the HPV16 E7 protein. Infection of normal human fibroblasts, which were arrested in G1 phase by serum deprivation, with the E7-expressing virus induced the cells to enter S phase. The E7-induced S phase entry was accompanied by an increase in the activator form of E2F, but no increase in the cyclin-dependent kinase (cdk) activity was detected. Infection of serum-stimulated fibroblasts with a recombinant adenovirus expressing the cdk inhibitor p21 inhibited progression into S phase. Coinfection with the E7-expressing virus abrogated the p21 inhibition of progression into S phase without increasing the cdk activity. These results are consistent with the notion that E7 stimulates entry into S phase through targets downstream of the cdks such as the proteins of the E2F and Rb families.

p21 Disrupts the interaction between cdk2 and the E2F-p130 complex

In nonproliferating or growth-arrested cells, the transcription factor E2F remains bound to the retinoblastoma-related protein p130. Accumulation of this E2F-p130 complex correlates with an arrest of the cell cycle progression. Progression through G1 phase is associated with a cyclin-dependent binding of the cyclin-dependent kinase cdk2 to the E2F-p130 complex. By fractionating mouse L-cell extracts, we have obtained a partially purified preparation of the E2F-p130 complex that also contains cdk2. Incubation of this complex with recombinant p21 results in a disruption of the interaction between cdk2 and the E2F-p130 complex in extracts of a cell line that expresses a temperature-sensitive mutant of p53. Incubation at the permissive temperature (32 degrees C) results in an induction of p21 synthesis. An increase in the level of p21 in these cells correlates with a loss of cdk2 from the cdk2-containing E2F-p130 complex. We also show that the expression of a reporter gene containing E2F sites in the promoter region is reduced by the coexpression of p21. Since p21 is believed to be a mediator of p53, we speculated that the p21-mediated disruption of the cdk2-containing E2F-p130 complex plays a role in the growth suppression function of p53.

trans-Activation by the hnRNP K protein involves an increase in RNA synthesis from the reporter genes

The function of many of the pre-mRNA-binding proteins in mRNA biogenesis is unclear. We have analyzed the biochemical function of the hnRNP K protein by using a mouse cDNA clone. A previous study indicated that the expression of hnRNP K activates c-myc promoter in transient transfection assays. We show that the expression of hnRNP K results in a trans-activation of a variety of RNA polymerase II promoters. The trans-activation function depends on the sequences of hnRNP K that are also necessary for RNA binding. However, the RNA binding motifs are not sufficient for trans-activation. We could identify a mutant that bound RNA in vitro but was impaired in its ability to trans-activate the reporter genes. The trans-activation was not a result of the stabilization of the reporter mRNA, because hnRNP K increased the steady-state level of the reporter mRNA without altering its decay rate. By doing nuclear run-on assays, we provide evidence that the hnRNP K protein trans-activates the reporter genes by increasing the level of transcription.

Association of p107 with Sp1: genetically separable regions of p107 are involved in regulation of E2F- and Sp1-dependent transcription

The retinoblastoma-related protein p107 has been shown to be a regulator of the transcription factor E2F. p107 associates with E2F via its pocket region and represses E2F-dependent transcription. In this study, we provide evidence for a novel interaction between p107 and the transcription factor Sp1. We show that p107 can be found endogenously associated with Sp1 in the extracts of several different cell lines. Moreover, in transient transfection assays, expression of p107 represses Sp1-dependent transcription. This repression of Sp1-dependent transcription does not require the DNA-binding domain of Sp1. Transcription driven by a chimeric protein containing the Ga14 DNA-binding domain and the Sp1 activation domains is inhibited by p107. Interestingly, unlike the repression of E2F-dependent transcription, the repression of Sp1-dependent transcription does not depend on an intact pocket region. We show that distinct regions of p107 are involved in the control of Sp1 and E2F.

HPV16 E7 oncoprotein induces expression of a 110 kDa heat shock protein

Heat shock protein genes are induced by various kinds of stress. Besides stress, the heat shock family gene hsp70 has been shown to be induced by growth-stimulating agents such as the DNA virus oncoproteins and serum. Here, we report cloning of a novel cDNA that encodes a 100 kDa heat shock protein-related polypeptide as a human papillomavirus oncoprotein E7-inducible gene. E7 induces expression of this heat shock protein at the level of RNA synthesis. Moreover, the induction of this heat shock protein-mRNA was dependent on the conserved region 2 of the E7 protein, which is essential for binding to the proteins of the retinoblastoma family.

Activation of the c-fos gene by the HPV16 oncoproteins depends upon the cAMP-response element at -60

The E6 and the E7 genes of the high-risk types of human papillomavirus (types 16 and 18) are associated with the induction or maintenance of malignant growth. The molecular mechanism by which these oncogenes contribute to the malignant phenotype is not clear. To study the effects of E7 on cellular processes, we constructed a stable cell line that inducibly expressed the E7 gene of HPV16. By using this cell line, we provide evidence that expression of E7 of HPV16 stimulates c-fos gene expression. Also, by doing transient transfection experiments, we show that the expression of either E6 or E7 induces transcription from the c-fos promoter. Analysis of a series of c-fos promoter mutants indicates that the activation by both E6 and E7 is dependent on the cyclic AMP response element. To further investigate the mechanism(s) of the activation of the c-fos gene and their relation to the oncogenic properties of E6 and E7, several mutants of the E6 and E7 genes were analyzed. The results of these studies indicate that the CR1 and CR2 regions in the E7 protein, and sequences distinct from the p53-binding region in the E6 protein, are critical for activation of the c-fos promoter.

Association of the human papillomavirus type 16 E7 protein with the S-phase-specific E2F-cyclin A complex

The transcription factor E2F has been shown to be involved in the expression of several cell cycle-regulated genes, and the activity of this factor is controlled by cellular proteins such as pRB and p107. E2F is also a target of the DNA virus oncoproteins (adenovirus E1A, simian virus 40 T antigen, and human papillomavirus [HPV] E7) (see the review by J. R. Nevins [Science 258: 424-429, 1992]). These viral oncoproteins dissociate an inactive complex between E2F and the retinoblastoma tumor suppressor protein (pRB), and this dissociation of the E2F-pRB complex correlates with a stimulation of the E2F-dependent transcription. In the S phase of the cell cycle, E2F forms a complex with p107, cyclin A, and the cdk2 kinase (E2F-cyclin A complex). The cellular function of this S-phase-specific complex is unclear. The adenovirus E1A protein dissociates the E2F-cyclin A complex. The HPV type 16 (HPV-16) E7 protein, which possesses significant sequence homology with E1A, does not dissociate the E2F-cyclin A complex. We find that the HPV-16 E7 protein associates very efficiently with the E2F-cyclin A complex. This association is dependent on the sequences that are also necessary for the transforming activity of E7. Moreover, the E7 protein of a low-risk HPV (type 6b) is much less efficient in binding to the E2F-cyclin A complex compared with that of the high-risk type. We also find that the E2F-cyclin A complex remains endogenously associated with the E7 protein in extracts of Caski cells, which express high levels of HPV-16 E7 protein. Finally, we have extensively purified the E2F-cyclin A complex from mouse L-cell extracts and show that, in cell extracts, the E2F-cyclin A complex remains associated with other cellular proteins.