bluuebunny/crossref_metadata_2025 huggingface dataset:
Raptinal bypasses BAX, BAK, and BOK for mitochondrial outer membrane permeabilization and intrinsic apoptosis
Authors: Heimer Sina , Knoll Gertrud , Schulze-Osthoff Klaus , Ehrenschwender Martin
Published: July 2019

Most antineoplastic chemotherapies eliminate cancer cells through activation of the mitochondria-controlled intrinsic apoptotic pathway. Therein, BAX, BAK, and/or BOK function as the essential pore-forming executioners of mitochondrial outer membrane permeabilization (MOMP). The activation threshold of BAX and BAK also correlates inversely with the required strength of an apoptotic stimulus to induce MOMP and thereby effectively determines a cell’s readiness to undergo apoptosis. Consequently, the ‘gatekeepers’ BAX and BAK emerged as therapeutic targets, but functional or genetic loss renders BAX/BAK-targeting strategies prone to fail. Here, we show that the small molecule Raptinal overcomes this limitation by triggering cytochrome c release in a BAX/BAK/BOK-independent manner. Raptinal exerts a dual cytotoxic effect on cancer cells by rapid activation of the intrinsic apoptotic pathway and simultaneous shutdown of mitochondrial function. Together with its efficacy to eliminate cancer cells in vivo, Raptinal could be useful in difficult-to-treat cancer entities harboring defects in the intrinsic apoptosis pathway.
Author Correction: Variation of a major facilitator superfamily gene contributes to differential cadmium accumulation between rice subspecies
Authors: Yan Huili , Xu Wenxiu , Xie Jianyin , Gao Yiwei , Wu Lulu , Sun Liang , Feng Lu , Chen Xu , Zhang Tian , Dai Changhua , Li Ting , Lin Xiuni , Zhang Zhanying , Wang Xueqiang , Li Fengmei , Zhu Xiaoyang , Li Jinjie , Li Zichao , Chen Caiyan , Ma Mi , Zhang Hongliang , He Zhenyan
Published: July 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Pptc7 is an essential phosphatase for promoting mammalian mitochondrial metabolism and biogenesis
Authors: Niemi Natalie M. , Wilson Gary M. , Overmyer Katherine A. , Vögtle F.-Nora , Myketin Lisa , Lohman Danielle C. , Schueler Kathryn L. , Attie Alan D. , Meisinger Chris , Coon Joshua J. , Pagliarini David J.
Published: July 2019

Mitochondrial proteins are replete with phosphorylation, yet its functional relevance remains largely unclear. The presence of multiple resident mitochondrial phosphatases, however, suggests that protein dephosphorylation may be broadly important for calibrating mitochondrial activities. To explore this, we deleted the poorly characterized matrix phosphatase Pptc7 from mice using CRISPR-Cas9 technology. Strikingly, Pptc7−/− mice exhibit hypoketotic hypoglycemia, elevated acylcarnitines and serum lactate, and die soon after birth. Pptc7−/− tissues have markedly diminished mitochondrial size and protein content despite normal transcript levels, and aberrantly elevated phosphorylation on select mitochondrial proteins. Among these, we identify the protein translocase complex subunit Timm50 as a putative Pptc7 substrate whose phosphorylation reduces import activity. We further find that phosphorylation within or near the mitochondrial targeting sequences of multiple proteins could disrupt their import rates and matrix processing. Overall, our data define Pptc7 as a protein phosphatase essential for proper mitochondrial function and biogenesis during the extrauterine transition.
Alternative splicing regulates stochastic NLRP3 activity
Authors: Hoss Florian , Mueller James L. , Rojas Ringeling Francisca , Rodriguez-Alcazar Juan F. , Brinkschulte Rebecca , Seifert Gerald , Stahl Rainer , Broderick Lori , Putnam Chris D. , Kolodner Richard D. , Canzar Stefan , Geyer Matthias , Hoffman Hal M. , Latz Eicke
Published: July 2019

Leucine-rich repeat (LRR) domains are evolutionarily conserved in proteins that function in development and immunity. Here we report strict exonic modularity of LRR domains of several human gene families, which is a precondition for alternative splicing (AS). We provide evidence for AS of LRR domain within several Nod-like receptors, most prominently the inflammasome sensor NLRP3. Human NLRP3, but not mouse NLRP3, is expressed as two major isoforms, the full-length variant and a variant lacking exon 5. Moreover, NLRP3 AS is stochastically regulated, with NLRP3 ∆ exon 5 lacking the interaction surface for NEK7 and hence loss of activity. Our data thus reveals unexpected regulatory roles of AS through differential utilization of LRRs modules in vertebrate innate immunity.
Boosting NAD+ with a small molecule that activates NAMPT
Authors: Gardell Stephen J. , Hopf Meghan , Khan Asima , Dispagna Mauro , Hampton Sessions E. , Falter Rebecca , Kapoor Nidhi , Brooks Jeanne , Culver Jeffrey , Petucci Chris , Ma Chen-Ting , Cohen Steven E. , Tanaka Jun , Burgos Emmanuel S. , Hirschi Jennifer S. , Smith Steven R. , Sergienko Eduard , Pinkerton Anthony B.
Published: July 2019

Pharmacological strategies that boost intracellular NAD+ are highly coveted for their therapeutic potential. One approach is activation of nicotinamide phosphoribosyltransferase (NAMPT) to increase production of nicotinamide mononucleotide (NMN), the predominant NAD+ precursor in mammalian cells. A high-throughput screen for NAMPT activators and hit-to-lead campaign yielded SBI-797812, a compound that is structurally similar to active-site directed NAMPT inhibitors and blocks binding of these inhibitors to NAMPT. SBI-797812 shifts the NAMPT reaction equilibrium towards NMN formation, increases NAMPT affinity for ATP, stabilizes phosphorylated NAMPT at His247, promotes consumption of the pyrophosphate by-product, and blunts feedback inhibition by NAD+. These effects of SBI-797812 turn NAMPT into a “super catalyst” that more efficiently generates NMN. Treatment of cultured cells with SBI-797812 increases intracellular NMN and NAD+. Dosing of mice with SBI-797812 elevates liver NAD+. Small molecule NAMPT activators such as SBI-797812 are a pioneering approach to raise intracellular NAD+ and realize its associated salutary effects.
Nonlinear wavefront shaping with optically induced three-dimensional nonlinear photonic crystals
Authors: Liu Shan , Switkowski Krzysztof , Xu Chenglong , Tian Jie , Wang Bingxia , Lu Peixiang , Krolikowski Wieslaw , Sheng Yan
Published: July 2019

Generation of coherent light with desirable amplitude and phase profiles throughout the optical spectrum is a key issue in optical technologies. Nonlinear wavefront shaping offers an exceptional way to achieve this goal by converting an incident light beam into the beam (or beams) of different frequency with spatially modulated amplitude and phase. The realization of such frequency conversion and shaping processes critically depends on the matching of phase velocities of interacting waves, for which nonlinear photonic crystals (NPCs) with spatially modulated quadratic nonlinearity have shown great potential. Here, we present the first experimental demonstration of nonlinear wavefront shaping with three-dimensional (3D) NPCs formed by ultrafast-light-induced ferroelectric domain inversion approach. Compared with those previously used low-dimensional structures, 3D NPCs provide all spatial degrees of freedom for the compensation of phase mismatch in nonlinear interactions and thereby constitute an unprecedented system for the generation and control of coherent light at new frequencies.
Reduced marine phytoplankton sulphur emissions in the Southern Ocean during the past seven glacials
Authors: Goto-Azuma K. , Hirabayashi M. , Motoyama H. , Miyake T. , Kuramoto T. , Uemura R. , Igarashi M. , Iizuka Y. , Sakurai T. , Horikawa S. , Suzuki K. , Suzuki T. , Fujita K. , Kondo Y. , Hattori S. , Fujii Y.
Published: July 2019

Marine biogenic sulphur affects Earth’s radiation budget and may be an indicator of primary productivity in the Southern Ocean, which is closely related to atmospheric CO2 variability through the biological pump. Previous ice-core studies in Antarctica show little climate dependence of marine biogenic sulphur emissions and hence primary productivity, contradictory to marine sediment records. Here we present new 720,000-year ice core records from Dome Fuji in East Antarctica and show that a large portion of non-sea-salt sulphate, which was traditionally used as a proxy for marine biogenic sulphate, likely originates from terrestrial dust during glacials. By correcting for this, we make a revised calculation of biogenic sulphate and find that its flux is reduced in glacial periods. Our results suggest reduced dimethylsulphide emissions in the Antarctic Zone of the Southern Ocean during glacials and provide new evidence for the coupling between climate and the Southern Ocean sulphur cycle.
Strong coupling of collective intermolecular vibrations in organic materials at terahertz frequencies
Authors: Damari Ran , Weinberg Omri , Krotkov Daniel , Demina Natalia , Akulov Katherine , Golombek Adina , Schwartz Tal , Fleischer Sharly
Published: July 2019

Several years ago, strong coupling between electronic molecular transitions and photonic structures was shown to modify the electronic landscape of the molecules and affect their chemical behavior. Since then, this concept has evolved into a new field known as polaritonic chemistry. An important ingredient in the progress of this field was the demonstration of strong coupling with intra-molecular vibrations, which enabled the modification of processes occurring at the electronic ground-state. Here we demonstrate strong coupling with collective, inter-molecular vibrations occurring in organic materials in the low-terahertz region ($$\lesssim$$
≲
1012 Hz). Using a cavity filled with α-lactose molecules, we measure the temporal evolution and observe coherent Rabi oscillations, corresponding to a splitting of 68 GHz. These results take strong coupling into a new class of materials and processes, including skeletal polymer motions, protein dynamics, metal organic frameworks and other materials, in which collective, spatially extended degrees of freedom participate in the dynamics.
Inflammation triggers immediate rather than progressive changes in monocyte differentiation in the small intestine
Authors: Desalegn Girmay , Pabst Oliver
Published: July 2019

Bone marrow-derived circulating monocytes contribute to the replenishment and maintenance of the intestinal macrophage population. Intestinal monocytes undergo context-dependent phenotypic and functional adaptations to either maintain local immune balance or support intestinal inflammation. Here we use monocyte adoptive transfer to dissect the dynamics of monocyte-to-macrophage differentiation in normal and inflamed small intestine. We find that during homeostasis CCR2 and β7-integrin mediate constitutive homing of monocytes to the gut. By contrast, intestinal inflammation increases monocyte recruitment via CCR2, but not β7-integrin. In the non-inflamed intestine, monocytes gradually differentiate to express genes typically associated with tolerogenic macrophage functions. Conversely, immediately upon entry into the inflamed intestine, monocytes adapt a different expression pattern in a partly Trem-1-dependent manner. Our observations suggest that inflammation fundamentally changes the kinetics and modalities of monocyte differentiation in tissues.
Hydrophobic recognition allows the glycosyltransferase UGT76G1 to catalyze its substrate in two orientations
Authors: Yang Ting , Zhang Jinzhu , Ke Dan , Yang Wenxian , Tang Minghai , Jiang Jian , Cheng Guo , Li Jianshu , Cheng Wei , Wei Yuquan , Li Qintong , Naismith James H. , Zhu Xiaofeng
Published: July 2019

Diets high in sugar are recognized as a serious health problem, and there is a drive to reduce their consumption. Steviol glycosides are natural zero-calorie sweeteners, but the most desirable ones are biosynthesized with low yields. UGT76G1 catalyzes the β (1–3) addition of glucose to steviol glycosides, which gives them the preferred taste. UGT76G1 is able to transfer glucose to multiple steviol substrates yet remains highly specific in the glycosidic linkage it creates. Here, we report multiple complex structures of the enzyme combined with biochemical data, which reveal that the enzyme utilizes hydrophobic interactions for substrate recognition. The lack of a strict three-dimensional recognition arrangement, typical of hydrogen bonds, permits two different orientations for β (1–3) sugar addition. The use of hydrophobic recognition is unusual in a regio- and stereo-specific catalysis. Harnessing such non-specific hydrophobic interactions could have wide applications in the synthesis of complex glycoconjugates.
Artificial cysteine-lipases with high activity and altered catalytic mechanism created by laboratory evolution
Authors: Cen Yixin , Singh Warispreet , Arkin Mamatjan , Moody Thomas S. , Huang Meilan , Zhou Jiahai , Wu Qi , Reetz Manfred T.
Published: July 2019

Engineering artificial enzymes with high activity and catalytic mechanism different from naturally occurring enzymes is a challenge in protein design. For example, many attempts have been made to obtain active hydrolases by introducing a Ser → Cys exchange at the respective catalytic triads, but this generally induced a breakdown of activity. We now report that this long-standing dogma no longer pertains, provided additional mutations are introduced by directed evolution. By employing Candida antarctica lipase B (CALB) as the model enzyme with the Ser-His-Asp catalytic triad, a highly active cysteine-lipase having a Cys-His-Asp catalytic triad and additional mutations W104V/A281Y/A282Y/V149G can be evolved, showing a 40-fold higher catalytic efficiency than wild-type CALB in the hydrolysis of 4-nitrophenyl benzoate, and tolerating bulky substrates. Crystal structures, kinetics, MD simulations and QM/MM calculations reveal dynamic features and explain all results, including the preference of a two-step mechanism involving the zwitterionic pair Cys105−/His224+ rather than a concerted process.
circTP63 functions as a ceRNA to promote lung squamous cell carcinoma progression by upregulating FOXM1
Authors: Cheng Zhuoan , Yu Chengtao , Cui Shaohua , Wang Hui , Jin Haojie , Wang Cun , Li Botai , Qin Meilin , Yang Chen , He Jia , Zuo Qiaozhu , Wang Siying , Liu Jun , Ye Weidong , Lv Yuanyuan , Zhao Fangyu , Yao Ming , Jiang Liyan , Qin Wenxin
Published: July 2019

Circular RNAs (circRNAs) are identified as vital regulators in a variety of cancers. However, the role of circRNA in lung squamous cell carcinoma (LUSC) remains largely unknown. Herein, we explore the expression profiles of circRNA and mRNA in 5 paired samples of LUSC. By analyzing the co-expression network of differentially expressed circRNAs and dysregulated mRNAs, we identify that a cell cycle-related circRNA, circTP63, is upregulated in LUSC tissues and its upregulation is correlated with larger tumor size and higher TNM stage in LUSC patients. Elevated circTP63 promotes cell proliferation both in vitro and in vivo. Mechanistically, circTP63 shares miRNA response elements with FOXM1. circTP63 competitively binds to miR-873-3p and prevents miR-873-3p to decrease the level of FOXM1, which upregulates CENPA and CENPB, and finally facilitates cell cycle progression.
Activation of NIX-mediated mitophagy by an interferon regulatory factor homologue of human herpesvirus
Authors: Vo Mai Tram , Smith Barbara J. , Nicholas John , Choi Young Bong
Published: July 2019

Viral control of mitochondrial quality and content has emerged as an important mechanism for counteracting the host response to virus infection. Despite the knowledge of this crucial function of some viruses, little is known about how herpesviruses regulate mitochondrial homeostasis during infection. Human herpesvirus 8 (HHV-8) is an oncogenic virus causally related to AIDS-associated malignancies. Here, we show that HHV-8-encoded viral interferon regulatory factor 1 (vIRF-1) promotes mitochondrial clearance by activating mitophagy to support virus replication. Genetic interference with vIRF-1 expression or targeting to the mitochondria inhibits HHV-8 replication-induced mitophagy and leads to an accumulation of mitochondria. Moreover, vIRF-1 binds directly to a mitophagy receptor, NIX, on the mitochondria and activates NIX-mediated mitophagy to promote mitochondrial clearance. Genetic and pharmacological interruption of vIRF-1/NIX-activated mitophagy inhibits HHV-8 productive replication. Our findings uncover an essential role of vIRF-1 in mitophagy activation and promotion of HHV-8 lytic replication via this mechanism.
Evidence for the weakly coupled electron mechanism in an Anderson-Blount polar metal
Authors: Laurita N. J. , Ron A. , Shan Jun-Yi , Puggioni D. , Koocher N. Z. , Yamaura K. , Shi Y. , Rondinelli J. M. , Hsieh D.
Published: July 2019

Over 50 years ago, Anderson and Blount proposed that ferroelectric-like structural phase transitions may occur in metals, despite the expected screening of the Coulomb interactions that often drive polar transitions. Recently, theoretical treatments have suggested that such transitions require the itinerant electrons be decoupled from the soft transverse optical phonons responsible for polar order. However, this decoupled electron mechanism (DEM) has yet to be experimentally observed. Here we utilize ultrafast spectroscopy to uncover evidence of the DEM in LiOsO3, the first known band metal to undergo a thermally driven polar phase transition (Tc ≈ 140 K). We demonstrate that intra-band photo-carriers relax by selectively coupling to only a subset of the phonon spectrum, leaving as much as 60% of the lattice heat capacity decoupled. This decoupled heat capacity is shown to be consistent with a previously undetected and partially displacive TO polar mode, indicating the DEM in LiOsO3.
Structural and functional analyses of hepatitis B virus X protein BH3-like domain and Bcl-xL interaction
Authors: Zhang Tian-Ying , Chen Hong-Ying , Cao Jia-Li , Xiong Hua-Long , Mo Xiao-Bing , Li Tian-Liang , Kang Xiao-Zhen , Zhao Jing-Hua , Yin Bo , Zhao Xiang , Huang Cheng-Hao , Yuan Quan , Xue Ding , Xia Ning-Shao , Yuan Y. Adam
Published: July 2019

Hepatitis B virus (HBV) X protein, HBx, interacts with anti-apoptotic Bcl-2 and Bcl-xL proteins through its BH3-like motif to promote HBV replication and cytotoxicity. Here we report the crystal structure of HBx BH3-like motif in complex with Bcl-xL where the BH3-like motif adopts a short α-helix to snuggle into a hydrophobic pocket in Bcl-xL via its noncanonical Trp120 residue and conserved Leu123 residue. This binding pocket is ~2 Å away from the canonical BH3-only binding pocket in structures of Bcl-xL with proapoptotic BH3-only proteins. Mutations altering Trp120 and Leu123 in HBx impair its binding to Bcl-xL in vitro and HBV replication in vivo, confirming the importance of this motif to HBV. A HBx BH3-like peptide, HBx-aa113-135, restores HBV replication from a HBx-null HBV replicon, while a shorter peptide, HBx-aa118-127, inhibits HBV replication. These results provide crucial structural and functional insights into drug designs for inhibiting HBV replication and treating HBV patients.
Probing the impact of sulfur/selenium/carbon linkages on prodrug nanoassemblies for cancer therapy
Authors: Sun Bingjun , Luo Cong , Zhang Xuanbo , Guo Mengran , Sun Mengchi , Yu Han , Chen Qin , Yang Wenqian , Wang Menglin , Zuo Shiyi , Chen Pengyu , Kan Qiming , Zhang Haotian , Wang Yongjun , He Zhonggui , Sun Jin
Published: July 2019

Tumor cells are characterized as redox-heterogeneous intracellular microenvironment due to the simultaneous overproduction of reactive oxygen species and glutathione. Rational design of redox-responsive drug delivery systems is a promising prospect for efficient cancer therapy. Herein, six paclitaxel-citronellol conjugates are synthesized using either thioether bond, disulfide bond, selenoether bond, diselenide bond, carbon bond or carbon-carbon bond as linkages. These prodrugs can self-assemble into uniform nanoparticles with ultrahigh drug-loading capacity. Interestingly, sulfur/selenium/carbon bonds significantly affect the efficiency of prodrug nanoassemblies. The bond angles/dihedral angles impact the self-assembly, stability and pharmacokinetics. The redox-responsivity of sulfur/selenium/carbon bonds has remarkable influence on drug release and cytotoxicity. Moreover, selenoether/diselenide bond possess unique ability to produce reactive oxygen species, which further improve the cytotoxicity of these prodrugs. Our findings give deep insight into the impact of chemical linkages on prodrug nanoassemblies and provide strategies to the rational design of redox-responsive drug delivery systems for cancer therapy.
Quantum biological tunnel junction for electron transfer imaging in live cells
Authors: Xin Hongbao , Sim Wen Jing , Namgung Bumseok , Choi Yeonho , Li Baojun , Lee Luke P.
Published: July 2019

Quantum biological electron transfer (ET) essentially involves in virtually all important biological processes such as photosynthesis, cellular respiration, DNA repair, cellular homeostasis, and cell death. However, there is no real-time imaging method to capture biological electron tunnelling in live cells to date. Here, we report a quantum biological electron tunnelling (QBET) junction and its application in real-time optical detection of QBET and the dynamics of ET in mitochondrial cytochrome c during cell life and death process. QBET junctions permit to see the behaviours of electron tunnelling through barrier molecules with different barrier widths. Using QBET spectroscopy, we optically capture real-time ET in cytochrome c redox dynamics during cellular apoptosis and necrosis in living cells. The non-invasive real-time QBET spectroscopic imaging of ET in live cell open a new era in life sciences and medicine by providing a way to capture spatiotemporal ET dynamics and to reveal the quantum biological mechanisms.
Acetylation regulates ribonucleotide reductase activity and cancer cell growth
Authors: Chen Guo , Luo Yin , Warncke Kurt , Sun Youwei , Yu David S. , Fu Haian , Behera Madhusmita , Ramalingam Suresh S. , Doetsch Paul W. , Duong Duc M. , Lammers Michael , Curran Walter J. , Deng Xingming
Published: July 2019

Ribonucleotide reductase (RNR) catalyzes the de novo synthesis of deoxyribonucleoside diphosphates (dNDPs) to provide dNTP precursors for DNA synthesis. Here, we report that acetylation and deacetylation of the RRM2 subunit of RNR acts as a molecular switch that impacts RNR activity, dNTP synthesis, and DNA replication fork progression. Acetylation of RRM2 at K95 abrogates RNR activity by disrupting its homodimer assembly. RRM2 is directly acetylated by KAT7, and deacetylated by Sirt2, respectively. Sirt2, which level peak in S phase, sustains RNR activity at or above a threshold level required for dNTPs synthesis. We also find that radiation or camptothecin-induced DNA damage promotes RRM2 deacetylation by enhancing Sirt2–RRM2 interaction. Acetylation of RRM2 at K95 results in the reduction of the dNTP pool, DNA replication fork stalling, and the suppression of tumor cell growth in vitro and in vivo. This study therefore identifies acetylation as a regulatory mechanism governing RNR activity.
Reversible intercalation of methyl viologen as a dicationic charge carrier in aqueous batteries
Authors: Wei Zhixuan , Shin Woochul , Jiang Heng , Wu Xianyong , Stickle William F. , Chen Gang , Lu Jun , Alex Greaney P. , Du Fei , Ji Xiulei
Published: July 2019

The interactions between charge carriers and electrode structures represent one of the most important considerations in the search for new energy storage devices. Currently, ionic bonding dominates the battery chemistry. Here we report the reversible insertion of a large molecular dication, methyl viologen, into the crystal structure of an aromatic solid electrode, 3,4,9,10-perylenetetracarboxylic dianhydride. This is the largest insertion charge carrier when non-solvated ever reported for batteries; surprisingly, the kinetic properties of the (de)insertion of methyl viologen are excellent with 60% of capacity retained when the current rate is increased from 100 mA g−1 to 2000 mA g−1. Characterization reveals that the insertion of methyl viologen causes phase transformation of the organic host, and embodies guest-host chemical bonding. First-principles density functional theory calculations suggest strong guest-host interaction beyond the pure ionic bonding, where a large extent of covalency may exist. This study extends the boundary of battery chemistry to large molecular ions as charge carriers and also highlights the electrochemical assembly of a supramolecular system.
RNA is a critical element for the sizing and the composition of phase-separated RNA–protein condensates
Authors: Garcia-Jove Navarro Marina , Kashida Shunnichi , Chouaib Racha , Souquere Sylvie , Pierron Gérard , Weil Dominique , Gueroui Zoher
Published: July 2019

Liquid–liquid phase separation is thought to be a key organizing principle in eukaryotic cells to generate highly concentrated dynamic assemblies, such as the RNP granules. Numerous in vitro approaches have validated this model, yet a missing aspect is to take into consideration the complex molecular mixture and promiscuous interactions found in vivo. Here we report the versatile scaffold ArtiG to generate concentration-dependent RNA–protein condensates within living cells, as a bottom-up approach to study the impact of co-segregated endogenous components on phase separation. We demonstrate that intracellular RNA seeds the nucleation of the condensates, as it provides molecular cues to locally coordinate the formation of endogenous high-order RNP assemblies. Interestingly, the co-segregation of intracellular components ultimately impacts the size of the phase-separated condensates. Thus, RNA arises as an architectural element that can influence the composition and the morphological outcome of the condensate phases in an intracellular context.
Determining the rotation direction in pulsars
Authors: Gueroult Renaud , Shi Yuan , Rax Jean-Marcel , Fisch Nathaniel J.
Published: July 2019

Pulsars are rotating neutron stars emitting lighthouse-like beams. Owing to their unique properties, pulsars are a unique astrophysical tool to test general relativity, inform on matter in extreme conditions, and probe galactic magnetic fields. Understanding pulsar physics and emission mechanisms is critical to these applications. Here we show that mechanical-optical rotation in the pulsar magnetosphere affects polarisation in a way which is indiscernible from Faraday rotation in the interstellar medium for typical GHz observations frequency, but which can be distinguished in the sub-GHz band. Besides being essential to correct for possible systematic errors in interstellar magnetic field estimates, this result offers a unique means to determine the rotation direction of pulsars, providing additional constraints on magnetospheric physics. With the ongoing development of sub-GHz observation capabilities, our finding promises discoveries, such as the spatial distribution of pulsars rotation directions, which could exhibit potentially interesting, but presently invisible, correlations or features.
Stereoselective synthesis of medium lactams enabled by metal-free hydroalkoxylation/stereospecific [1,3]-rearrangement
Authors: Zhou Bo , Zhang Ying-Qi , Zhang Kairui , Yang Ming-Yang , Chen Yang-Bo , Li You , Peng Qian , Zhu Shou-Fei , Zhou Qi-Lin , Ye Long-Wu
Published: July 2019

Rearrangement reactions have attracted considerable interest over the past decades due to their high bond-forming efficiency and atom economy in the construction of complex organic architectures. In contrast to the well-established [3,3]-rearrangement, [1,3] O-to-C rearrangement has been far less vigorously investigated, and stereospecific [1,3]-rearrangement is extremely rare. Here, we report a metal-free intramolecular hydroalkoxylation/[1,3]-rearrangement, leading to the practical and atom-economical assembly of various valuable medium-sized lactams with wide substrate scope and excellent diastereoselectivity. Moreover, such an asymmetric cascade cyclization has also been realized by chiral Brønsted acid-catalyzed kinetic resolution. In addition, biological tests reveal that some of these medium-sized lactams displayed their bioactivity as antitumor agents against melanoma cells, esophageal cancer cells and breast cancer cells. A mechanistic rationale for the reaction is further supported by control experiments and theoretical calculations.
Phosphorylation of MAVS/VISA by Nemo-like kinase (NLK) for degradation regulates the antiviral innate immune response
Authors: Li Shang-Ze , Shu Qi-Peng , Song Yang , Zhang Hui-Hui , Liu Yi , Jin Bing-Xue , Liuyu Tian-Zi , Li Chao , Huang Xi-Chen , Du Run-Lei , Song Wei , Zhong Bo , Zhang Xiao-Dong
Published: July 2019

MAVS is essential for antiviral immunity, but the molecular mechanisms responsible for its tight regulation remain poorly understood. Here, we show that NLK inhibits the antiviral immune response during viral infection by targeting MAVS for degradation. NLK depletion promotes virus-induced antiviral cytokine production and decreases viral replication, which is potently rescued by the reintroduction of NLK. Moreover, the depletion of NLK promotes antiviral effects and increases the survival times of mice after infection with VSV. NLK interacts with and phosphorylates MAVS at multiple sites on mitochondria or peroxisomes, thereby inducing the degradation of MAVS and subsequent inactivation of IRF3. Most importantly, a peptide derived from MAVS promotes viral-induced IFN-β production and antagonizes viral replication in vitro and in vivo. These findings provide direct insights into the molecular mechanisms by which phosphorylation of MAVS regulates its degradation and influences its activation and identify an important peptide target for propagating antiviral responses.
Stochastic search and joint fine-mapping increases accuracy and identifies previously unreported associations in immune-mediated diseases
Authors: Asimit Jennifer L. , Rainbow Daniel B. , Fortune Mary D. , Grinberg Nastasiya F. , Wicker Linda S. , Wallace Chris
Published: July 2019

Thousands of genetic variants are associated with human disease risk, but linkage disequilibrium (LD) hinders fine-mapping the causal variants. Both lack of power, and joint tagging of two or more distinct causal variants by a single non-causal SNP, lead to inaccuracies in fine-mapping, with stochastic search more robust than stepwise. We develop a computationally efficient multinomial fine-mapping (MFM) approach that borrows information between diseases in a Bayesian framework. We show that MFM has greater accuracy than single disease analysis when shared causal variants exist, and negligible loss of precision otherwise. MFM analysis of six immune-mediated diseases reveals causal variants undetected in individual disease analysis, including in IL2RA where we confirm functional effects of multiple causal variants using allele-specific expression in sorted CD4+ T cells from genotype-selected individuals. MFM has the potential to increase fine-mapping resolution in related diseases enabling the identification of associated cellular and molecular phenotypes.
A ZEB1/p53 signaling axis in stromal fibroblasts promotes mammary epithelial tumours
Authors: Fu Rong , Han Chen-Feng , Ni Ting , Di Lei , Liu Li-Juan , Lv Wen-Cong , Bi Yan-Ran , Jiang Nan , He Yin , Li Hong-Mei , Wang Shui , Xie Hui , Chen Bao-An , Wang Xiao-Sheng , Weiss Stephen J. , Lu Tao , Guo Qing-Long , Wu Zhao-Qiu
Published: July 2019

Accumulating evidence indicates that the zinc-finger transcription factor ZEB1 is predominantly expressed in the stroma of several tumours. However, the role of stromal ZEB1 in tumour progression remains unexplored. In this study, while interrogating human databases, we uncover a remarkable decrease in relapse-free survival of breast cancer patients expressing high ZEB1 levels in the stroma. Using a mouse model of breast cancer, we show that ZEB1 inactivation in stromal fibroblasts suppresses tumour initiation, progression and metastasis. We associate this with reduced extracellular matrix remodeling, immune cell infiltration and decreased angiogenesis. ZEB1 deletion in stromal fibroblasts increases acetylation, expression and recruitment of p53 to FGF2/7, VEGF and IL6 promoters, thereby reducing their production and secretion into the surrounding stroma. Importantly, p53 ablation in ZEB1 stroma-deleted mammary tumours sufficiently recovers the impaired cancer growth and progression. Our findings identify the ZEB1/p53 axis as a stroma-specific signaling pathway that promotes mammary epithelial tumours.
Controlled open-cell two-dimensional liquid foam generation for micro- and nanoscale patterning of materials
Authors: Bae Juyeol , Lee Kyunghun , Seo Sangjin , Park Jun Gyu , Zhou Qitao , Kim Taesung
Published: July 2019

Liquid foam consists of liquid film networks. The films can be thinned to the nanoscale via evaporation and have potential in bottom-up material structuring applications. However, their use has been limited due to their dynamic fluidity, complex topological changes, and physical characteristics of the closed system. Here, we present a simple and versatile microfluidic approach for controlling two-dimensional liquid foam, designing not only evaporative microholes for directed drainage to generate desired film networks without topological changes for the first time, but also microposts to pin the generated films at set positions. Patterning materials in liquid is achievable using the thin films as nanoscale molds, which has additional potential through repeatable patterning on a substrate and combination with a lithographic technique. By enabling direct-writable multi-integrated patterning of various heterogeneous materials in two-dimensional or three-dimensional networked nanostructures, this technique provides novel means of nanofabrication superior to both lithographic and bottom-up state-of-the-art techniques.
Repeated evolution of cytochrome P450-mediated spiroketal steroid biosynthesis in plants
Authors: Christ Bastien , Xu Chengchao , Xu Menglong , Li Fu-Shuang , Wada Naoki , Mitchell Andrew J. , Han Xiu-Lin , Wen Meng-Liang , Fujita Makoto , Weng Jing-Ke
Published: July 2019

Diosgenin is a spiroketal steroidal natural product extracted from plants and used as the single most important precursor for the world steroid hormone industry. The sporadic occurrences of diosgenin in distantly related plants imply possible independent biosynthetic origins. The characteristic 5,6-spiroketal moiety in diosgenin is reminiscent of the spiroketal moiety present in anthelmintic avermectins isolated from actinomycete bacteria. How plants gained the ability to biosynthesize spiroketal natural products is unknown. Here, we report the diosgenin-biosynthetic pathways in himalayan paris (Paris polyphylla), a monocot medicinal plant with hemostatic and antibacterial properties, and fenugreek (Trigonella foenum–graecum), an eudicot culinary herb plant commonly used as a galactagogue. Both plants have independently recruited pairs of cytochromes P450 that catalyze oxidative 5,6-spiroketalization of cholesterol to produce diosgenin, with evolutionary progenitors traced to conserved phytohormone metabolism. This study paves the way for engineering the production of diosgenin and derived analogs in heterologous hosts.
A mosaic hemagglutinin-based influenza virus vaccine candidate protects mice from challenge with divergent H3N2 strains
Authors: Broecker Felix , Liu Sean T. H. , Suntronwong Nungruthai , Sun Weina , Bailey Mark J. , Nachbagauer Raffael , Krammer Florian , Palese Peter
Published: July 2019

Current seasonal influenza virus vaccines only provide limited, short-lived protection, and antigenic drift in the hemagglutinin surface glycoprotein necessitates their annual re-formulation and re-administration. To overcome these limitations, universal vaccine strategies that aim at eliciting broadly protective antibodies to conserved epitopes of the hemagglutinin show promise for protecting against diverse and drifted influenza viruses. Here a vaccination strategy that focuses antibody responses to conserved epitopes of the H3 hemagglutinin is described. The approach is based on antigenic silencing of the immunodominant major antigenic sites of an H3 protein from 2014 by replacing them with corresponding sequences of exotic avian hemagglutinins, yielding “mosaic” hemagglutinins. In mice, vaccination with inactivated viruses expressing mosaic hemagglutinins induced highly cross-reactive antibodies against the H3 stalk domain that elicited Fc-mediated effector functions in vitro. In addition, the mosaic viruses elicited head-specific antibodies with neutralizing and hemagglutination-inhibiting activity against recent H3N2 viruses in vitro. Immune sera protected mice from heterologous challenge with viruses carrying H3 proteins from 1968 and 1982, whereas immune sera generated with a seasonal vaccine did not protect. Consequently, the mosaic vaccination approach provides a promising avenue toward a universal influenza virus vaccine.
De novo phased assembly of the Vitis riparia grape genome
Authors: Girollet Nabil , Rubio Bernadette , Lopez-Roques Céline , Valière Sophie , Ollat Nathalie , Bert Pierre-François
Published: July 2019

Grapevine is one of the most important fruit species in the world. In order to better understand genetic basis of traits variation and facilitate the breeding of new genotypes, we sequenced, assembled, and annotated the genome of the American nativeVitis riparia, one of the main species used worldwide for rootstock and scion breeding. A total of 164 Gb raw DNA reads were obtained fromVitis ripariaresulting in a 225X depth of coverage. We generated a genome assembly of theV.ripariagrapede novousing the PacBio long-reads that was phased with the 10x Genomics Chromium linked-reads. At the chromosome level, a 500 Mb genome was generated with a scaffold N50 size of 1 Mb. More than 34% of the whole genome were identified as repeat sequences, and 37,207 protein-coding genes were predicted. This genome assembly sets the stage for comparative genomic analysis of the diversification and adaptation of grapevine and will provide a solid resource for further genetic analysis and breeding of this economically important species.
Tradeoffs and Compatibilities of Chemical Properties in CpHqFrOs System
Authors: Okamoto Yasuharu
Published: July 2019

To comply with the Kigali amendment to the Montreal Protocol in 2016, development of new refrigerants with low global warming potential is urgently required in addition to satisfying the conventional requirements of cooling performance, safety, and non-destructiveness to the ozone layer. Because these requirements closely correlated, the proper control of various chemical properties is necessary to fulfill the requirements. However, simultaneous satisfaction of all the requirements is extremely difficult because of the tradeoffs among the chemical properties. Hence, we must correctly recognize how chemical properties behave when the composition of molecules is changed. We performed an in-silico screening that combines quantum chemical calculations, machine learning, and database search, where 10,163 molecules were investigated exhaustively within the properly imposed constraints; subsequently we found a few candidates.
Mechanism of rift flank uplift and escarpment formation evidenced by Western Ghats, India
Authors: T. Radhakrishna , R. Mohamed Asanulla , M. Venkateshwarlu , G. S. Soumya , P. K. Prachiti
Published: July 2019

The Western Ghats is one of the largest escarpments on earth, containing Reunion plume derived Deccan Traps, it is an excellent example to probe epeirogenic uplift, extension and subsidence in volcanic continental margins. The most continuous unbiased stratigraphic section of basalt down to the basement within a 1250 m drill hole of the Continental Scientific Deep Drilling Project is a valuable resource to investigate the above aspects. The flows across the entire drill core are geologically subaerial in character with basement exposed ~300 m below the mean sea level; they clearly display more evolved compositions from primary melts of mantle in terms of petrology, and only a single geomagnetic polarity transition in palaeomagnetic data. These results, combined with existing geological and geophysical data, constitute a multi-method approach that demonstrates (a) igneous underplating caused uplift prior to frequently suggested flexural isostasy (b) plume impact and eruption are near-simultaneous and extension/rifting essentially followed soon after volcanism and (c) lithosphere beneath the continental margin, while returning to normal temperatures following the Seychelles-India breakup, experienced thermal collapse and subsidence causing slumping of basalt basement below sea level.
Structures of N-terminally processed KRAS provide insight into the role of N-acetylation
Authors: Dharmaiah Srisathiyanarayanan , Tran Timothy H. , Messing Simon , Agamasu Constance , Gillette William K. , Yan Wupeng , Waybright Timothy , Alexander Patrick , Esposito Dominic , Nissley Dwight V. , McCormick Frank , Stephen Andrew G. , Simanshu Dhirendra K.
Published: July 2019

Although post-translational modification of the C-terminus of RAS has been studied extensively, little is known about N-terminal processing. Mass spectrometric characterization of KRAS expressed in mammalian cells showed cleavage of the initiator methionine (iMet) and N-acetylation of the nascent N-terminus. Interestingly, structural studies on GDP- and GMPPNP-bound KRAS lacking the iMet and N-acetylation resulted in Mg2+-free structures of KRAS with flexible N-termini. In the Mg2+-free KRAS-GDP structure, the flexible N-terminus causes conformational changes in the interswitch region resulting in a fully open conformation of switch I. In the Mg2+-free KRAS-GMPPNP structure, the flexible N-terminus causes conformational changes around residue A59 resulting in the loss of Mg2+ and switch I in the inactive state 1 conformation. Structural studies on N-acetylated KRAS-GDP lacking the iMet revealed the presence of Mg2+ and a conformation of switch regions also observed in the structure of GDP-bound unprocessed KRAS with the iMet. In the absence of the iMet, the N-acetyl group interacts with the central beta-sheet and stabilizes the N-terminus and the switch regions. These results suggest there is crosstalk between the N-terminus and the Mg2+ binding site, and that N-acetylation plays an important role by stabilizing the N-terminus of RAS upon excision of the iMet.
The effect of regular dental cast artifacts on the 3D superimposition of serial digital maxillary dental models
Authors: Henninger Eva , Vasilakos Georgios , Halazonetis Demetrios , Gkantidis Nikolaos
Published: July 2019

Superimpositions of serial 3D dental surface models comprise a powerful tool to assess morphological changes due to growth, treatment, or pathology. In this study, we evaluated the effect of artifacts on the superimposition outcome, using standard model acquisition and superimposition techniques. Ten pre- and post-orthodontic treatment plaster models were scanned with an intraoral scanner and superimposed using the iterative closest point algorithm. We repeated the whole process after manual removal of plaster artifacts, according to the current practice, as well as after re-scanning the cleaned models, to assess the effect of the model acquisition process derived artifacts on the superimposition outcome. Non-parametric multivariate models showed no mean effect on accuracy and precision by software settings, cleaning status (artifact removal), or time point. The choice of the superimposition reference area was the only factor that affected the measurements. However, assessment of individual cases revealed significant differences on the detected tooth movement, depending on artifact removal and on the model acquisition process. The effects of all factors tended to decrease with an increase in the size of the superimposition reference area. The present findings highlight the importance of accurate, artifact-free models, for valid assessment of morphological changes through serial 3D model superimpositions.
Contrasting Roles of Cannabidiol as an Insecticide and Rescuing Agent for Ethanol–induced Death in the Tobacco Hornworm Manduca sexta
Authors: Park Sang-Hyuck , Staples S. Kyle , Gostin Eric L. , Smith Jeffrey P. , Vigil Jose J. , Seifried Dustin , Kinney Chad , Pauli Christopher S. , Heuvel Brian D. Vanden
Published: July 2019

Cannabis sativa, also known as marijuana or hemp, produces a non-psychoactive compound cannabidiol (CBD). To investigate the defensive role of CBD, a feeding preference assay was performed with tobacco hornworm Manduca sexta. The larvae clearly show feeding preference towards the Cannabis tissue containing low CBD over high CBD. While the larva avoided the high CBD diet, we investigated detrimental effects of CBD in the insects’ diet. Contrasted to the performance on low CBD-infused artificial diet (AD), larvae reared on the high CBD diet suffer significantly reduced growth and increased mortality. Through testing different carriers, we found that the increase of EtOH in the diet is negatively correlated with insect development and behaviors. Notably, CBD treatment significantly improved ethanol-intoxicated larval survival rate by 40% and also improved diet searching activity, resulting in increased diet consumption. Electrophysiology results revealed that the CBD-treated ganglia had delayed but much larger response with electric stimuli in comparison to the larvae reared on AD only and EtOH-added diet. Our results show CBDs’ defensive role against pest insects, which suggests its possible use as an insecticide. We also provide evidence that CBD alleviates alcohol-induced stress; consequently, improving the performance and viability of M. sexta larvae.
Development of a quantitative method to measure EV uptake
Authors: Toribio Víctor , Morales Sara , López-Martín Soraya , Cardeñes Beatriz , Cabañas Carlos , Yáñez-Mó María
Published: July 2019

The outstanding potential of Extracellular Vesicles (EVs) in medicine, deserves a detailed study of the molecular aspects regulating their incorporation into target cells. However, because EV size lies below the limit of resolution of optical techniques, quantification together with discrimination between EV binding to the target cell and uptake is usually not completely achieved with current techniques. Human tetraspanins CD9 and CD63 were fused to a dual EGFP-Renilla-split tag. Subcellular localization and incorporation of these fusion proteins into EVs was assessed by western-blot and fluorescence microscopy. EV binding and uptake was measured using either a classical Renilla substrate or a cytopermeable one. Incubation of target cells expressing DSP2 with EVs containing the complementary DSP1 portion could not recover fluorescence or luciferase activity. However, using EVs carrying the fully reconstituted Dual-EGFP-Renilla protein and the cytopermeable Renilla luciferase substrate, we could distinguish EV binding from uptake. We provide proof of concept of the system by analysing the effect of different chemical inhibitors, demonstrating that this method is highly sensitive and quantitative, allowing a dynamic follow-up in a high-throughput scheme to unravel the molecular mechanisms of EV uptake in different biological systems.