Ballistic thermophoresis of adsorbates on free-standing graphene
Emanuele Panizon, Roberto Guerra, and Erio Tosatti
In thermophoresis, temperature gradients in a fluid cause a proportional force on a body. Reasonably, a small physisorbed cluster on a membrane-like system such as a graphene sheet suspended between temperatures ΔT apart should do just that—except it doesn't. Simulations show for submicrometer sheet length a phoretic force proportional to ΔT but independent of length and thus of gradient, disclosing a regime of ballistic thermophoresis. The soft flexural phonons, ballistic in this regime, are responsible. The anharmonic mechanism by which they carry real momentum, some of which is given to the adsorbate, involves longitudinal phonons that permit a mass accumulation moving with the flexural group velocity. The distance independence of ballistic thermophoretic force could be important in nanomanipulations. (See pp. E7035–E7044.)
Janus dendrimersomes coassembled from fluorinated, hydrogenated, and hybrid Janus dendrimers as models for cell fusion and fission
Qi Xiao, Samuel E. Sherman, Samantha E. Wilner, Xuhao Zhou, Cody Dazen, Tobias Baumgart, Ellen H. Reed, Daniel A. Hammer, Wataru Shinoda, Michael L. Klein, and Virgil Percec
Janus particles (JPs) are structures with two distinct faces. This study reports the discovery of an unprecedented class of JPs denoted Janus dendrimersomes (JDSs) coassembled from amphiphilic Janus dendrimers (JDs) with fluorinated, hydrogenated, and hybrid fluorinated–hydrogenated hydrophobic chains. JDSs consist of fluorinated and hydrogenated vesicles connected in a dumbbell-like shape. They appear as one structure in a broader fission-like pathway, which is revealed by varying the ratios of the three JD components. This pathway implies that non–protein-mediated fission and fusion is a likely mechanism by which similar structures form in synthetic and biological systems. These results highlight the potential importance of non–protein-mediated fusion and fission for biology and medicine. (See pp. E7045–E7053.)
Inkjet-printed point-of-care immunoassay on a nanoscale polymer brush enables subpicomolar detection of analytes in blood
Daniel Y. Joh, Angus M. Hucknall, Qingshan Wei, Kelly A. Mason, Margaret L. Lund, Cassio M. Fontes, Ryan T. Hill, Rebecca Blair, Zackary Zimmers, Rohan K. Achar, Derek Tseng, Raluca Gordan, Michael Freemark, Aydogan Ozcan, and Ashutosh Chilkoti
Sensitive quantitation of protein biomarkers plays an important role in modern clinical decision making. This work introduces an inkjet-printed assay platform built on a nonfouling, nanoscale polymer brush, which eliminates nonspecific binding, the largest source of noise in surface-based assays. The assay goes to completion after adding a drop of blood (with no additional reagents or mixing), and the assay can be read with a smartphone-based detector. This technology is significant because it enables high-performance diagnostic testing in blood with minimal infrastructural requirements. Furthermore, its fully printed nature makes it highly customizable and thus broadly applicable to a wide range of diagnostic targets. (See pp. E7054–E7062.)
A study of problems encountered in Granger causality analysis from a neuroscience perspective
Patrick A. Stokes and Patrick L. Purdon
Granger causality analysis is a statistical method for investigating the flow of information between time series. Granger causality has become more widely applied in neuroscience, due to its ability to characterize oscillatory and multivariate data. However, there are ongoing concerns regarding its applicability in neuroscience. When are these methods appropriate? How reliably do they recover the functional structure of the system? Also, what do they tell us about oscillations in neural systems? In this paper, we analyze fundamental properties of Granger causality and illustrate statistical and conceptual problems that make Granger causality difficult to apply and interpret in neuroscience studies. This work provides important conceptual clarification of Granger causality methods and suggests ways to improve analyses of neuroscience data in the future. (See pp. E7063–E7072.)
Near-atomic resolution cryoelectron microscopy structure of the 30-fold homooligomeric SpoIIIAG channel essential to spore formation in Bacillus subtilis
Natalie Zeytuni, Chuan Hong, Kelly A. Flanagan, Liam J. Worrall, Kate A. Theiltges, Marija Vuckovic, Rick K. Huang, Shawn C. Massoni, Amy H. Camp, Zhiheng Yu, and Natalie C. Strynadka
Bacteria use sophisticated nanomachines to transport proteins across membranes. Although these secretion systems are typically associated with bacterial pathogenicity, a specialized variant has been proposed to play a central role in bacterial sporulation. Sporulation is a primitive protective process that allows starving cells to form spores that can survive in extreme environments. Following an asymmetric cellular division, the mother cell engulfs the forespore, with a “feeding-tube” channel creating a direct conduit between them. Here, using near-atomic resolution cryoelectron microscopy, we show that a central component of the feeding tube channel self-assembles into an unprecedented 30-fold symmetrical complex with unique architectural features and dimensions. We discuss the similarities and diverse features of the feeding tube relative to other bacterial secretion nanomachines. (See pp. E7073–E7081.)
Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis
Liang Xu, Wei Wang, Jiabin Wu, Ji Hyun Shin, Pengcheng Wang, Ilona Christy Unarta, Jenny Chong, Yinsheng Wang, and Dong Wang
DNA alkylation represents a major form of DNA damage that is of high clinical and human health relevance; however, the molecular mechanisms of transcriptional lesion recognition, stalling, and bypass remain unknown. Herein, we carried out a comprehensive investigation to compare the effects of three regioisomeric EtdT lesions on transcription. Intriguingly, we found that the location of alkyl group dictates transcriptional stalling profile and lesion bypass routes, and we identified a novel minor-groove–sensing motif, termed Pro-Gate, which plays an important role in detecting the minor-groove lesion. This work provides important mechanistic insights into DNA alkylation-induced transcriptional stalling and mutagenesis. Our study also provides knowledge about cancer etiology and for the future design of effective cancer chemotherapeutic agents. (See pp. E7082–E7091.)
Histone phosphorylation by TRPM6’s cleaved kinase attenuates adjacent arginine methylation to regulate gene expression
Grigory Krapivinsky, Luba Krapivinsky, Nora E. Renthal, Ana Santa-Cruz, Yunona Manasian, and David E. Clapham
Ion channels are proteins that span the cell’s membrane and affect the rapid transfer of ions. Kinases are proteins that transfer a phosphate from ATP to specific substrates. In mammals, there are two unusual proteins, melastatin-related transient receptor potential (TRPM)6 and TRPM7, that have both functions. Here we show that TRPM6’s kinase and channel domains are functionally connected: The kinase is cleaved from the channel domain, and this cleavage depends on the channel being operational. The freed kinase moves to the nucleus and phosphorylates specific histone residues. This results in a dramatic decrease in methylation of adjacent arginine amino acids shown to be critical epigenetic marks for cell differentiation and embryonic development. TRPM6’s kinase-dependent histone posttranslational modifications change the transcription of hundreds of genes. (See pp. E7092–E7100.)
Self-organization process in newborn skin organoid formation inspires strategy to restore hair regeneration of adult cells
Mingxing Lei, Linus J. Schumacher, Yung-Chih Lai, Wen-Tau Juan, Chao-Yuan Yeh, Ping Wu, Ting-Xin Jiang, Ruth E. Baker, Randall Bruce Widelitz, Li Yang, and Cheng-Ming Chuong
This study opens avenues to improve the ability of adult skin cells to form a fully functional skin, with clinical applications. Our investigation elucidates a relay of molecular events and biophysical processes at the core of the self-organization process during tissue morphogenesis. Molecules key to the multistage morphological transition are identified and can be added or inhibited to restore the stalled process in adult cells. The principles uncovered here are likely to function in other organ systems and will inspire us to view organoid morphogenesis, embryogenesis, and regeneration differently. The application of these findings will enable rescue of robust hair formation in adult skin cells, thus eventually helping patients in the context of regenerative medicine. (See pp. E7101–E7110.)
Zbtb7b engages the long noncoding RNA Blnc1 to drive brown and beige fat development and thermogenesis
Siming Li, Lin Mi, Lei Yu, Qi Yu, Tongyu Liu, Guo-Xiao Wang, Xu-Yun Zhao, Jun Wu, and Jiandie D. Lin
Brown and beige fat function has important implications for metabolic physiology and the treatment of metabolic disorders. How transcription factors interface with long noncoding RNAs (lncRNAs), an emerging class of regulatory factors, to drive development and thermogenesis of brown/beige fat remains essentially unknown. Here we identified Zbtb7b as an activator of the thermogenic gene program through a genome-wide functional screen and showed that it plays an essential role in cold-induced thermogenesis and beige fat formation. Mechanistically, Zbtb7b forms a ribonucleoprotein transcriptional complex with the lncRNA Blnc1 and drives thermogenic gene expression via a feedforward loop. This work illustrates the emerging concept of a protein–lncRNA regulatory network in the control of adipose tissue biology and energy metabolism. (See pp. E7111–E7120.)
Protein kinase C delta phosphorylates ecdysone receptor B1 to promote gene expression and apoptosis under 20-hydroxyecdysone regulation
Cai-Hua Chen, Jing Pan, Yu-Qin Di, Wen Liu, Li Hou, Jin-Xing Wang, and Xiao-Fan Zhao
The steroid hormone 20-hydroxyecdysone (20E) promotes apoptosis during larval-to-adult metamorphosis in insects. However, the mechanisms governing this process are unclear. This work reveals that 20E up-regulates the expression of the protein kinase PKCδ isoform E. Overexpression of the catalytic domain of PKCδ is sufficient to increase caspase-3 activity and apoptosis. PKCδ directly phosphorylates a threonine residue at position 468 of the amino acid sequence of nuclear receptor EcRB1. The phosphorylation of EcRB1 is essential for apoptotic gene transcription. These results demonstrate the mechanism by which the steroid hormone 20E promotes PKCδ expression to regulate apoptosis. (See pp. E7121–E7130.)
Genetic background-dependent role of Egr1 for eyelid development
Jangsuk Oh, Yujuan Wang, Shida Chen, Peng Li, Ning Du, Zu-Xi Yu, Donna Butcher, Tesfay Gebregiorgis, Erin Strachan, Ordan J. Lehmann, Brian P. Brooks, Chi-Chao Chan, and Warren J. Leonard
Eyelid formation begins at approximately day E15.5 in mice. Over the next 24 h, the epidermis of both upper and lower eyelids rapidly grows and merges to cover the cornea. Here, we demonstrate that Egr1−/− mice on the C57BL/6 background have normal eyelid development, but back-crossing to BALB/c background for four or five generations resulted in defective eyelid development by embryonic day E15.5. This defective eyelid formation was then further associated with profound ocular anomalies evident by postnatal days 1-4. The BALB/c albino phenotype associated with the Tyrc tyrosinase mutation also appeared to contribute to the phenotype. Thus EGR1 in a genetic background-dependent manner plays a critical role in mammalian eyelid development, with subsequent impact on ocular integrity. (See pp. E7131–E7139.)
miR-146a–Traf6 regulatory axis controls autoimmunity and myelopoiesis, but is dispensable for hematopoietic stem cell homeostasis and tumor suppression
Nathaniel Magilnick, Estefany Y. Reyes, Wei-Le Wang, Steven L. Vonderfecht, Jin Gohda, Jun-ichiro Inoue, and Mark P. Boldin
Aberrant inflammation is the root cause of numerous human diseases, from autoimmunity to cancer. microRNA-146a (miR-146a), a member of a large class of small regulatory RNAs, functions as a critical molecular brake on inflammation and malignant transformation. However, the molecular mechanism through which miR-146a exerts its regulatory activity in immune cells is unclear. Using mouse genetics, we have examined the role of the miR-146a–Traf6 signaling axis and found that although this miRNA–target interaction is responsible for regulating normal myeloid cell development and autoimmunity, it is dispensable for hematopoietic stem cell homeostasis and tumor suppression. (See pp. E7140–E7149.)
Cytokine signature associated with disease severity in chronic fatigue syndrome patients
Jose G. Montoya, Tyson H. Holmes, Jill N. Anderson, Holden T. Maecker, Yael Rosenberg-Hasson, Ian J. Valencia, Lily Chu, Jarred W. Younger, Cristina M. Tato, and Mark M. Davis
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) devastates the lives of millions of people and has remained a mystery illness despite decades of research. It has long been suspected that inflammation is central to its pathogenesis. Although only two cytokines were found to be different (TGF-β higher and resistin lower) in ME/CFS patients compared with controls, 17 cytokines correlated with ME/CFS severity. Thirteen of these cytokines are proinflammatory and may contribute to many of the symptoms these patients experience for several years. Only CXCL9 (MIG) inversely correlated with fatigue duration. (See pp. E7150–E7158.)
Stress-inducible gene Atf3 in the noncancer host cells contributes to chemotherapy-exacerbated breast cancer metastasis
Yi Seok Chang, Swati P. Jalgaonkar, Justin D. Middleton, and Tsonwin Hai
Chemotherapy is a double-edged sword. It is anticancer because of its cytotoxicity. Paradoxically, by increasing chemoresistance and cancer metastasis, it is also pro-cancer. However, the mechanisms underlying chemotherapy-induced procancer activities are not well understood. Here we present data that provide mechanistic explanations for the ability of paclitaxel (PTX), a frontline chemotherapeutic agent, to exacerbate metastasis in mouse models of breast cancer. Importantly, Atf3, a stress-inducible gene, in the noncancer host cells is necessary for this PTX effect. Analyses of publicly available datasets suggest that our data from mouse models have relevance to human cancers. Thus, ATF3 links a chemotherapeutic agent—a stressor—to pro-metastatic changes in the host cells. Dampening the effect of ATF3 may improve the efficacy of chemotherapy. (See pp. E7159–E7168.)
Early cytoplasmic uncoating is associated with infectivity of HIV-1
João I. Mamede, Gianguido C. Cianci, Meegan R. Anderson, and Thomas J. Hope
After fusion, HIV delivers its capsid formed of CA proteins into the cytoplasm. The regulated disassembly of the capsid (uncoating) is critical to the timely exposure of the viral genome and infection. The timing of this process is controversial. Utilizing an intravirion GFP fluid phase marker with a live-cell imaging approach, where we use less than one virion per cell, we demonstrate that the uncoating of HIV-1 particles is an early cytoplasmic process taking place ∼30 minutes after fusion, and dependent on ongoing reverse transcription. Early uncoating is observed in culture cells, primary T cells, and macrophages with either HIV or pseudotyped envelope. Partial CA retention with the viral complex facilitates late CA functions, including nuclear import and integration site selection. (See pp. E7169–E7178.)
Glycine receptor α3 and α2 subunits mediate tonic and exogenous agonist-induced currents in forebrain
Lindsay M. McCracken, Daniel C. Lowes, Michael C. Salling, Cyndel Carreau-Vollmer, Naomi N. Odean, Yuri A. Blednov, Heinrich Betz, R. Adron Harris, and Neil L. Harrison
Neuronal inhibition in the CNS occurs via two mechanisms. Synaptic inhibition is transient and localized; extrasynaptic inhibition is continuous and diffuse. Glycine receptor (GlyR)-mediated synaptic inhibition in spinal cord was established decades ago; however, GlyR physiology in higher brain regions remains obscure. We show that functional GlyRs are expressed in forebrain structures and mediate tonic and exogenous glycine-induced currents. Unlike synaptic α1β GlyRs in the spinal cord, forebrain GlyRs are primarily composed of α2 or α3 subunits. We identified distinct roles for these subunits by showing that α3 subunits mediate tonic GlyR currents, whereas α2 subunits mediate exogenously activated GlyR currents. Our findings demonstrate mechanisms of neuronal modulation by glycine in the forebrain due to subunit-specific contributions of GlyRs. (See pp. E7179–E7186.)
Adiponectin protects against development of metabolic disturbances in a PCOS mouse model
Anna Benrick, Belén Chanclón, Peter Micallef, Yanling Wu, Laila Hadi, John M. Shelton, Elisabet Stener-Victorin, and Ingrid Wernstedt Asterholm
Women with polycystic ovary syndrome (PCOS) have reduced fertility and increased risk of developing type 2 diabetes. Adiponectin, an adipocyte-derived hormone, together with adipocyte size, is the strongest factor associated with insulin resistance in PCOS. The potential causal relationship among adiponectin levels, infertility, and metabolic dysfunction in PCOS is, however, unknown. Exploiting mouse models, we found that adiponectin is indeed involved in PCOS-related insulin resistance, and, albeit to a much smaller extent, is also involved in the development of reproductive dysfunction. Thus, increased levels of adiponectin can prevent prepubertal androgen-induced metabolic dysfunction in dihydrotestosterone-exposed mice with PCOS-like traits. Collectively, our findings support the notion that altered adipose tissue functionality is a key mediator of metabolic dysfunction in women with PCOS. (See pp. E7187–E7196.)
Arabidopsis SH3P2 is an ubiquitin-binding protein that functions together with ESCRT-I and the deubiquitylating enzyme AMSH3
Marie-Kristin Nagel, Kamila Kalinowska, Karin Vogel, Gregory D. Reynolds, Zhixiang Wu, Franziska Anzenberger, Mie Ichikawa, Chie Tsutsumi, Masa H. Sato, Bernhard Kuster, Sebastian Y. Bednarek, and Erika Isono
The endosomal sorting of integral proteins is essential for controlling signaling pathways at the plasma membrane. Posttranslational modification by ubiquitin is key to proper degradation of plasma membrane proteins as the ubiquitylated transmembrane proteins are recognized by multiple ubiquitin adaptor proteins and trafficked to the vacuole for degradation. Although plants lack orthologs of the yeast and metazoan endosomal sorting complex required for transport-0 heterodimer that functions as an ubiquitin adaptor, plants appear to have evolved other strategies to recognize and concentrate ubiquitylated proteins that have been endocytosed. Here, we report the SH3P2 protein as a yet-unknown ubiquitin adaptor protein in Arabidopsis and its molecular function in regulating the endocytic transport and degradation. (See pp. E7197–E7204.)
Flower-specific jasmonate signaling regulates constitutive floral defenses in wild tobacco
Ran Li, Ming Wang, Yang Wang, Meredith C. Schuman, Arne Weinhold, Martin Schäfer, Guillermo H. Jiménez-Alemán, Andrea Barthel, and Ian T. Baldwin
Plants are at the base of most food chains and hence are frequently attacked by herbivores. Leaves are the dominant aboveground tissues of most plants and their defense responses against folivores are well studied and known to be regulated by jasmonate (JA) phytohormone signaling. As the most fitness-valuable and frequently the most nutritious tissues, flowers are also commonly attacked by florivores. However floral defense, compared with leaf defense, is rarely studied, and the signaling systems that regulate these defenses are unknown. Here we show that flowers of the wild tobacco, Nicotiana attenuata, constitutively accumulate large amounts of defensive compounds, trypsin proteinase inhibitors, (E)-α-bergamotene and defensins, and that a flower-specific sector of JA signaling regulates these constitutively expressed floral defenses. (See pp. E7205–E7214.)