BRD7 suppresses tumor chemosensitivity to CHK1 inhibitors by inhibiting USP1-mediated deubiquitination of CHK1.

Checkpoint kinase 1 (CHK1), a key effector in the cellular response to DNA lesions, is a crucial component of all cell cycle checkpoints. Recent reports have revealed that CHK1 is highly expressed in numerous cancer types in the clinical settings. However, the mechanisms underlying the regulation of CHK1 expression in tumor cells remain unclear. Here, we report that CHK1 is negatively regulated by the bromodomain-containing protein 7 (BRD7). Specifically, BRD7 silencing increased CHK1 (but not CHK2) expression at both mRNA and protein levels, in a p53-independent manner in multiple tumor cell lines. Furthermore, BRD7 silencing stabilized CHK1 via reducing its ubiquitination. Mechanistically, BRD7 knockdown not only increased the levels of USP1, a deubiquitinase for CHK1, but also promoted the interaction between CHK1 and USP1, subsequently enhancing the de-ubiquitination of CHK1. USP1 knockdown abrogated BRD7 silencing-induced CHK1 induction. Biologically, the increased expression of CHK1 in tumor cells caused by BRD7 silencing significantly increased cell sensitivity to CHK1 inhibitors by enhancing tumor cell apoptosis, and this effect was reversed by the simultaneous knockdown of CHK1 or USP1. Taken together, our findings suggest that BRD7 is a potential genetic or drug target that may help to improve the efficacy of chemotherapeutic drugs targeting CHK1 in combinatorial therapy.

Deubiquitinase USP33 is negatively regulated by ß-TrCP through ubiquitin-dependent proteolysis.

Ubiquitin-mediated proteolysis regulates cellular levels of various proteins, and therefore plays important roles in controlling cell signaling and disease progression. The Skp1-Cul1-F-box ubiquitin ligase ß-TrCP is recognized as an important negative regulator for numerous key signaling proteins. Recently, the deubiquitinases (DUBs) have turned out to be essential to regulate signaling pathways related to human diseases. However, whether ß-TrCP is able to regulate the deubiquitinase family members remains largely unexplored. Here, we found that ß-TrCP downregulated cellular levels of endogenous USP33. We also revealed that ß-TrCP interacted with USP33 independently of the classic binding motif for ß-TrCP, and mediated USP33 degradation via the ubiquitin proteasome pathway. Furthermore, we found that the WD40 motif of ß-TrCP and 201-400 amino acid motif of USP33 are required for the interaction between ß-TrCP and USP33. Consequently, ß-TrCP attenuated USP33-mediated inhibition of cell proliferation and cell invasion. Taken together, our study clarified that the E3 ligase ß-TrCP regulates cellular USP33 levels by the ubiquitin-proteasomal proteolysis.

Ultralow-power near-infrared excited neodymium-doped nanoparticles for long-term in vivo bioimaging.

Lanthanide-doped luminescent nanoparticles with both emission and excitation in the near-infrared (NIR-to-NIR) region hold great promise for bioimaging. Herein, core@shell structured LiLuF4:Nd@LiLuF4 (named as Nd@Lu) nanoparticles (NPs) with highly efficient NIR emission were developed for high-performance in vivo bioimaging. Strikingly, the absolute quantum yield of Nd@Lu NPs reached as high as 32%. After coating with polyethylene glycol (PEG), the water-dispersible Nd@Lu NPs showed good bio-compatibility and low toxicity. With efficient NIR emission, the Nd@Lu NPs were clearly detectable in tissues at depths of up to 20 mm. In addition, long-term in vivo biodistribution with a high signal-to-noise ratio of 25.1 was distinctly tracked upon an ultralow-power-density excitation (10 mW cm-2) of 732 nm for the first time.

Ubiquitin-dependent Turnover of Adenosine Deaminase Acting on RNA 1 (ADAR1) Is Required for Efficient Antiviral Activity of Type I Interferon.

Adenosine deaminase acting on RNA 1 (ADAR1) catalyzes RNA editing of cellular and viral RNAs. Besides RNA editing, ADAR1 has recently been shown to play important roles in maintaining the body balance, including tissue homoeostasis, organ development, and autoimmune regulations, by inhibiting both IFN production and subsequent IFN-activated pathways. Accordingly, the question was raised how IFN signaling induced by viral infections overcomes the inhibitory effect of constitutively expressed ADAR1 (ADAR1-P110) to execute efficient antiviral activity. Here we unexpectedly found that IFN signaling promoted Lys48-linked ubiquitination and degradation of ADAR1-P110. Furthermore, we identified the E3 ligase ß transducin repeat-containing protein responsible for IFN-mediated ADAR1-P110 down-regulation. IFN signaling promoted the interaction between ß transducin repeat-containing protein and ADAR1-P110 as well as protein turnover of ADAR1-P110. Moreover, we found that both lysine 574 and 576 are essential for ADAR1-P110 ubiquitination. Critically, we demonstrated that down-regulation of ADAR1-P110 is required for IFN signaling to execute efficient antiviral activity during viral infections. These findings renew the understanding of the mechanisms by which IFN signaling acts to achieve antiviral functions and may provide potential targets for IFN-based antiviral therapy.

Deubiquitinase USP2a Sustains Interferons Antiviral Activity by Restricting Ubiquitination of Activated STAT1 in the Nucleus.

STAT1 is a critical transcription factor for regulating host antiviral defenses. STAT1 activation is largely dependent on phosphorylation at tyrosine 701 site of STAT1 (pY701-STAT1). Understanding how pY701-STAT1 is regulated by intracellular signaling remains a major challenge. Here we find that pY701-STAT1 is the major form of ubiquitinated-STAT1 induced by interferons (IFNs). While total STAT1 remains relatively stable during the early stages of IFNs signaling, pY701-STAT1 can be rapidly downregulated by the ubiquitin-proteasome system. Moreover, ubiquitinated pY701-STAT1 is located predominantly in the nucleus, and inhibiting nuclear import of pY701-STAT1 significantly blocks ubiquitination and downregulation of pY701-STAT1. Furthermore, we reveal that the deubiquitinase USP2a translocates into the nucleus and binds to pY701-STAT1, and inhibits K48-linked ubiquitination and degradation of pY701-STAT1. Importantly, USP2a sustains IFNs-induced pY701-STAT1 levels, and enhances all three classes of IFNs- mediated signaling and antiviral activity. To our knowledge, this is the first identified deubiquitinase that targets activated pY701-STAT1. These findings uncover a positive mechanism by which IFNs execute efficient antiviral signaling and function, and may provide potential targets for improving IFNs-based antiviral therapy.

A Scheme to Optimize Flow Routing and Polling Switch Selection of Software Defined Networks.

This paper aims at minimizing the communication cost for collecting flow information in Software Defined Networks (SDN). Since flow-based information collecting method requires too much communication cost, and switch-based method proposed recently cannot benefit from controlling flow routing, jointly optimize flow routing and polling switch selection is proposed to reduce the communication cost. To this end, joint optimization problem is formulated as an Integer Linear Programming (ILP) model firstly. Since the ILP model is intractable in large size network, we also design an optimal algorithm for the multi-rooted tree topology and an efficient heuristic algorithm for general topology. According to extensive simulations, it is found that our method can save up to 55.76% communication cost compared with the state-of-the-art switch-based scheme.

Photonic radio-frequency phase shifter based on polarization interference.

An rf photonic phase shifter based on polarization interference is presented, and the theoretical fundamentals of the design are explained. This phase shifter provides broad operational bandwidth and a full 360 degrees phase-shift tuning range with a single external electrical control. A prototype of the rf photonic phase shifter with a frequency of 26.75 GHz and 360 degrees tuning range is experimentally demonstrated.

Hydrogen-bond network and local structure of liquid water: An atoms-in-molecules perspective.

The nearly linear relationship between hydrogen-bond strength at the CCSD(T)/Aug-cc-pVTZ level and the electron density at the bond critical point in the atoms-in-molecules theory provides a practical means of calculating the hydrogen-bond strength in liquid water. A statistical analysis of the hydrogen-bonds obtained from Car-Parrinello molecular dynamics simulations shows that the strengths of hydrogen bonds in liquid water conform to a Gaussian distribution. Considering supercooled (250 K) water to have a fully coordinated (icelike) local tetrahedral configuration, we show that the local structure of liquid water is partly distorted tetrahedral in normal liquid water and even in superheated water.

Atomic orbitals in molecules: general electronegativity and improvement of Mulliken population analysis.

An approach of atomic orbitals in molecules (AOIM) has been developed to study the atomic properties in molecules, in which the molecular orbitals are expressed in terms of the optimized minimal atomic orbitals. The atomic electronegativities are calculated using Pauling's electronegativity of free atom and are employed to find the electronegativity equilibrium in molecules and to describe the amphoteric properties of the transition metals from the groups 4 to 10. AOIM can also improve the numerical stability and accuracy of the original Mulliken population analysis.

A new heuristic algorithm with shared segment-backup paths for trap avoidance in survivable optical networks.

This paper proposes a new heuristic algorithm, called Quick Method with Shared Protection (QMSP), to protect the single-link failure in survivable WDM optical networks. QMSP first computes one primary path for each connection request. If the primary path is a trap path, QMSP will compute two segment-backup paths to avoid the trap problem based on the routing policy. Compared to previous algorithms, QMSP not only has better time complexity but also can obtain higher resource utilization ratio and lower blocking probability.

Analysis of the effect of spin-orbit coupling on the electronic structure and excitation spectrum of the Bi2(2-) anion in (K-crypt)2Bi2 on the basis of relativistic electronic structure calculations.

The Bi2(2-) anions that have been characterized in (K-crypt)2Bi2 are isoelectronic with O2 but are diamagnetic and EPR-silent, unlike O2. The UV-vis spectrum measured for (K-crypt)2Bi2 shows two broad absorption peaks located at 2.05 and 2.85 eV, but no absorption at lower energies down to 0.62 eV. To account for these observations, the electronic structures of the isoelectronic diatomic dianions Q2(2-) (Q = N, P, As, Sb, Bi) were compared on the basis of relativistic density functional theory calculations, and the electronic excitations of Bi2(2-) were analyzed on the basis of relativistic configuration interaction calculations. The extent of spin-orbit coupling, brought about by the relativistic effect, increases steadily in the order N < P < As < Sb < Bi such that the "closed-shell" state is more stable than the "open-shell" state for Bi2(2-), while the opposite is the case for N2(2-), P2(2-), As2(2-), and Sb2(2-). The nature of the electronic excitations of Bi2(2-) was assigned and discussed from the viewpoint of molecular orbitals in the absence of spin-orbit coupling.

Dynamic segment shared protection algorithm for reliable wavelength-division-multiplexing mesh networks.

With the maturation of the technology of Wavelength-Division-Multiplexing (WDM) in optical networks, the survivable design has become a key issue. In this paper, we propose a Segment Shared Protection Algorithm (SSPA), which is based on the reliability of the networks and the different levels of the fault tolerance requested by the users, to protect the single-link failure in WDM optical networks. The main idea of the SSPA is to provide a backup path for a segment, which is divided in accordance with the policy of the Differentiated Reliability (DiR), on the primary path of each connection request. Under the guarantee of the blocking probability and the connection's reliability, the SSPA has higher resource utilization ratio and faster recovery time than the previous algorithm PSPA-DiR. We evaluate the effectiveness of the SSPA and the results are found to be promising.

Parallelization of MRCI based on hole-particle symmetry.

The parallel implementation of multireference configuration interaction program based on the hole-particle symmetry is described. The platform to implement the parallelization is an Intel-Architectural cluster consisting of 12 nodes, each of which is equipped with two 2.4-G XEON processors, 3-GB memory, and 36-GB disk, and are connected by a Gigabit Ethernet Switch. The dependence of speedup on molecular symmetries and task granularities is discussed. Test calculations show that the scaling with the number of nodes is about 1.9 (for C1 and Cs), 1.65 (for C2v), and 1.55 (for D2h) when the number of nodes is doubled. The largest calculation performed on this cluster involves 5.6 x 10(8) CSFs.

An efficient method for constructing nonorthogonal localized molecular orbitals.

A new method for constructing nonorthogonal localized molecular orbitals (NOLMOs) is presented. The set of highly localized NOLMOs is obtained by minimization of the spread functional starting from an initial set of canonical orthogonal molecular orbitals. To enhance the stability and efficiency, the centroids of the NOLMOs are constrained to be those of the corresponding orthogonal localized molecular orbitals (OLMOs), which are obtained with the Boys criterion in advance. In particular, these centroid constraints make the optimization for each NOLMO independent of the others, which is an attractive feature for application to large systems. The minimization with the constraints incorporated through the multiplier-penalty function method is stable and efficient in convergence. While exhibiting the classical bonding pattern in chemistry and sharing a spatial distribution similar to that of the corresponding OLMOs, the obtained NOLMOs are more compact than the corresponding OLMOs with about 10%-28% reduction in the value of the spread functional and devoid of the troublesome "orthogonalization tails."

Numerical examination of performance of some exchange-correlation functionals for molecules containing heavy elements.

The performance of 17 exchange-correlation functionals for molecules containing heavy elements are numerically examined through four-component relativistic density DFT calculations. The examined functionals show the similar accuracy as they do for the molecules containing light elements only except for bond lengths. LDA and OP86 produce good results for bond lengths and frequencies but bad bond energies. Different functionals do not show much different performance for bond energies except LDA. BP86 and GP86 produce results with average accuracy while LYP does not perform well. Although encouraging results are obtained with functional B97GGA-1, other heavily parameterized and meta-GGA functionals do not produce impressive results.

Joint routing-selection algorithm for a shared path with differentiated reliability in survivable wavelength-division-multiplexing mesh networks.

A routing-selection algorithm is important in survivable wavelength-division networks. A sound algorithm should carefully consider the efficiency of resource utilization and the protection-switching time. Under shared-risk link group constraints with differentiated reliability (DiR), a novel algorithm for a shared path, called a joint routing-selection algorithm (JRSA) with DiR, is proposed. The simulation results show that a JRSA with DiR not only can efficiently satisfy the specific requirements of users but also can produce nearly optimal performance and determine the appropriatetrade-offs between the resource utilization ratio and the protection-switching time.

Path protection algorithm with trade-off ability for survivable wavelength-division-multiplexing mesh networks.

We present a new path protection algorithm, called resource sharing degree constraints (RSDCs), for survivable wavelength-divisionmultiplexing mesh networks. We define a parameter k to adjust the resource sharing degree (RSD). When we compute the reserved backup wavelengths, if the RSD is larger than the value of k, more wavelengths are assigned until the RSD is not greater than the value of k. With respect to previous work, RSDCs, adds a valuable elasticity in resource assignment and is able to determine the appropriate trade-offs between the resource utilization ratio and the protection ability.

Burst segmentation for void-filling scheduling and its performance evaluation in optical burst switching.

As a promising solution for the next generation optical Internet, optical burst switching still has much to be improved, especially the design of core routers. This paper mainly focuses on channel scheduling algorithms of core routers and proposes a new practical scheduling algorithm. In the new algorithm, burst segmentation, one of the contention resolution schemes that are another major concern in core router design, is introduced. The proposed algorithm is analyzed theoretically and evaluated by computer simulations. The results show that the new algorithm, compared with existing traditional scheduling algorithms, can lower the packet loss probability and enhance the link utilization and network performance.

Analytical energy gradient evaluation in relativistic and nonrelativistic density functional calculations.

The expressions of analytical energy gradients in density functional theory and their implementation in programs are reported. The evaluation of analytical energy gradients can be carried out in the fully 4-component relativistic, approximate relativistic, and nonrelativistic density functional calculations under local density approximation or general gradient approximation with or without frozen core approximation using different basis sets in our programs. The translational invariance condition and the fact that the one-center terms do not contribute to the energy gradients are utilized to improve the calculation accuracy and to reduce the computational effort. The calculated results of energy gradients and optimized geometry as well as atomization energies of some molecules by the analytical gradient method are in very good agreement with results obtained by the numerical derivative method.