Shape control and compartmentalization in active colloidal cells
Matthew Spellings, Michael Engel, Daphne Klotsa, Syeda Sabrina, Aaron M. Drews, Nguyen H. P. Nguyen, Kyle J. M. Bishop, and Sharon C. Glotzer
Advances in simulation and synthesis of nanoparticles and colloids are leading to a new class of active colloidal systems where self-propelled and self-rotated particles convert energy to motion. Such systems hold promise for the possibility of colloidal machines–integrated systems of colloids able to carry out functions. An important step in this direction is appropriately confining colloids within cells whose shape can be controlled and within which activity can be compartmentalized. This paper uses theory and computer simulation to propose active colloidal cells and investigates their behavior. Our findings provide motivation and design rules for the fabrication of primitive colloidal machines. (See pp. E4642–E4650.)
Key bioactive reaction products of the NO/H2S interaction are S/N-hybrid species, polysulfides, and nitroxyl
Miriam M. Cortese-Krott, Gunter G. C. Kuhnle, Alex Dyson, Bernadette O. Fernandez, Marian Grman, Jenna F. DuMond, Mark P. Barrow, George McLeod, Hidehiko Nakagawa, Karol Ondrias, Péter Nagy, S. Bruce King, Joseph E. Saavedra, Larry K. Keefer, Mervyn Singer, Malte Kelm, Anthony R. Butler, and Martin Feelisch
Reactions of sulfur-centered nucleophiles with nitrogenous species have been studied independently for more than a century for synthetic/industrial purposes; to understand geochemical, atmospheric, and biological processes; and to explain the origins of life. Various products and reaction mechanisms were proposed. We here identify a singular process comprising a network of cascading chemical reactions that form three main bioactive products at physiological pH: nitrosopersulfide, polysulfides, and dinitrososulfite. These anionic products scavenge, transport, and release NO/HNO or sulfide/sulfane sulfur, each displaying distinct chemistries and bioactivities. Our observations provide a chemical foundation for the cross-talk between the NO and H2S signaling pathways in biology and suggest that the biological actions of these entities can be neither considered nor studied in isolation. (See pp. E4651–E4660.)
Results of a large-scale randomized behavior change intervention on road safety in Kenya
James Habyarimana and William Jack
Road accidents kill 1.3 million people each year, most in the developing world. Evocative messages inside Kenyan matatus, or mini-buses, that promote passenger agency and legitimize complaints against dangerous driving are found to reduce average maximum speeds and average moving speeds by 1–2 km/h and insurance claims by between one-quarter and one-third. The cost-effectiveness of the most impactful stickers is between $10 and $45 per disability-adjusted life-year saved. (See pp. E4661–E4670.)
Quantifying the impact of weak, strong, and super ties in scientific careers
Alexander Michael Petersen
A scientist will encounter many potential collaborators throughout his/her career. As such, the choice to start or terminate a collaboration can be an important strategic consideration with long-term implications. While previous studies have focused primarily on aggregate cross-sectional collaboration patterns, here we analyze the collaboration network from a researcher’s local perspective along his/her career. Our longitudinal approach reveals that scientific collaboration is characterized by a high turnover rate juxtaposed with surprisingly frequent “life partners.” We show that these extremely strong collaborations have a significant positive impact on productivity and citations—the apostle effect—representing the advantage of “super” social ties characterized by trust, conviction, and commitment. (See pp. E4671–E4680.)
Measuring and mitigating agricultural greenhouse gas production in the US Great Plains, 1870–2000
William J. Parton, Myron P. Gutmann, Emily R. Merchant, Melannie D. Hartman, Paul R. Adler, Frederick M. McNeal, and Susan M. Lutz
The US Great Plains is an agricultural production center for the global market and a source of greenhouse gas (GHG) emissions. This article uses historical data and ecosystem models to estimate the magnitude of annual GHG fluxes from all agricultural sources (cropping, livestock, irrigation, fertilizer production, and tractor use) from 1870 to 2000. Carbon (C) emissions from plow-out of native grasslands peaked in the 1930s and were the largest agricultural source of GHG emissions at the time. Soil C emissions subsequently declined, whereas GHG fluxes from other activities increased. The results inform knowledge about the relationship between agriculture and its environmental setting and show that available alternative management practices could substantially mitigate the environmental consequences of agricultural activities without reducing food production. (See pp. E4681–E4688.)
Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast
Mingtao Huang, Yunpeng Bai, Staffan L. Sjostrom, Björn M. Hallström, Zihe Liu, Dina Petranovic, Mathias Uhlén, Haakan N. Joensson, Helene Andersson-Svahn, and Jens Nielsen
Increasing demand for recombinant proteins leads to continuous attempts for improving the protein secretion capacity of host cells. In this study, we show that by combining high-throughput microfluidic screening with whole-genome sequencing of the selected clones from yeast libraries we can identify and map the mutations associated with significantly improved protein production. These identified mutations can be used as reverse metabolic engineering target genes in design of efficient cell factories for protein secretion. The mutations that we identified will also help in improving our understanding of the protein secretory mechanisms in yeast. (See pp. E4689–E4696.)
Fmr1 deficiency promotes age-dependent alterations in the cortical synaptic proteome
Bin Tang, Tingting Wang, Huida Wan, Li Han, Xiaoyan Qin, Yaoyang Zhang, Jian Wang, Chunlei Yu, Fulvia Berton, Walter Francesconi, John R. Yates III, Peter W. Vanderklish, and Lujian Liao
Fragile X syndrome (FXS) is a frequent mental disorder characterized by intellectual disability and other symptoms including autism. The disease gene-encoded protein FMRP regulates activity-dependent translation of a large number of mRNAs in neurons. We used quantitative mass spectrometry to systematically compare protein expression in neocortical synaptic fractions between Fmr1 (fragile X mental retardation 1) knockout (KO) and wild-type mice during adolescence and adulthood. We discovered an upregulation of a large number of synaptic proteins in young KO mice but not in adult ones. Many of the upregulated proteins are correlated with an increased protein synthesis in KO neurons. This study provides a greatly expanded view of protein-level changes in FXS and identifies a previously unrecognized developmental dynamics in FXS pathogenesis. (See pp. E4697–E4706.)
Single methylation of 23S rRNA triggers late steps of 50S ribosomal subunit assembly
Taiga Arai, Kensuke Ishiguro, Satoshi Kimura, Yuriko Sakaguchi, Takeo Suzuki, and Tsutomu Suzuki
Ribosome biogenesis requires a number of assembly factors. However, the exact mechanism of this process remains largely unknown. We could successfully reconstitute the 50S subunit from the 45S precursor by a 2′-O-methylation of U2552 (Um2552) mediated by rRNA methyltransferase RlmE, in the presence of the wash fraction from crude ribosomes. To our knowledge, this experiment is the first demonstration of enzymatic formation of a ribosomal subunit in vitro from its precursor via the action of an assembly factor. Mechanistic studies revealed that RlmE-mediated Um2552 formation promotes interdomain interactions of 23S rRNA, in concert with the incorporation of L36, triggering late steps of 50S subunit assembly. RlmE and Um2552 are conserved in other organisms, including human, indicating the functional importance of this process in ribosome biogenesis. (See pp. E4707–E4716.)
Biologically active LIL proteins built with minimal chemical diversity
Erin N. Heim, Jez L. Marston, Ross S. Federman, Anne P. B. Edwards, Alexander G. Karabadzhak, Lisa M. Petti, Donald M. Engelman, and Daniel DiMaio
Most proteins are long polymers of amino acids with 20 or more chemically distinct side-chains, whereas transmembrane domains are short membrane-spanning protein segments with mainly hydrophobic amino acids. Here, we have defined the minimal chemical diversity sufficient for a protein to display specific biological activity by isolating artificial 26-aa-long transmembrane proteins consisting of random sequences of only two hydrophobic amino acids, leucine and isoleucine. A small fraction of proteins with this composition interact with the transmembrane domain of a growth factor receptor to specifically activate the receptor, resulting in growth transformation. These findings change our view of what can constitute an active protein and have important implications for protein evolution, protein engineering, and synthetic biology. (See pp. E4717–E4725.)
Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities
Jian Zhang, Yen K. Lieu, Abdullah M. Ali, Alex Penson, Kathryn S. Reggio, Raul Rabadan, Azra Raza, Siddhartha Mukherjee, and James L. Manley
Mutations in genes encoding proteins that function in splicing of mRNA precursors occur frequently in myelodysplastic syndromes (MDS) and certain leukemias. However, the mechanism by which the mutated splicing factors function has begun to be elucidated only recently. Here we use genome-editing techniques to introduce a common MDS mutation in the gene Serine/arginine-rich splicing factor 2 (SRSF2), which encodes an RNA-binding splicing regulator, in cultured blood cells. We show that splicing of several hundred transcripts, including some with possible relevance to disease, is altered. We further show that mutant SRSF2 is sufficient to induce these changes and does so by binding to RNA sequence elements in the misregulated mRNAs with altered specificity. (See pp. E4726–E4734.)
Quantitative genomic analysis of RecA protein binding during DNA double-strand break repair reveals RecBCD action in vivo
Charlotte A. Cockram, Milana Filatenkova, Vincent Danos, Meriem El Karoui, and David R. F. Leach
Maintaining genomic integrity is crucial for cell survival. In Escherichia coli, RecA-mediated homologous recombination plays an essential role in the repair of DNA double-strand breaks (DSBs). A greater understanding of the mechanism of homologous recombination requires quantitative analysis of genomic studies in live cells. We have developed a novel method that is able to capture these interactions on a genome-wide scale by combining ChIP-seq and mathematical modeling to interpret the patterns of RecA–DNA interaction during DSB repair (DSBR). This genomic analysis has also revealed unexpected RecA binding in the terminus region of the chromosome, consistent with a second DSBR event (at a distance of 1 Mb) that is indirectly caused by the first DSBR event induced at the lacZ. (See pp. E4735–E4742.)
Cryptic infection of a broad taxonomic and geographic diversity of tadpoles by Perkinsea protists
Aurélie Chambouvet, David J. Gower, Miloslav Jirků, Michael J. Yabsley, Andrew K. Davis, Guy Leonard, Finlay Maguire, Thomas M. Doherty-Bone, Gabriela Bueno Bittencourt-Silva, Mark Wilkinson, and Thomas A. Richards
Amphibians are among the most threatened animal groups. Population declines and extinctions have been linked, in part, to emerging infectious diseases. One such emerging disease has been attributed to Perkinsea-like protists causing mass mortality events in the United States. Using molecular methods, we evaluated the diversity of Perkinsea parasites in livers sampled from a wide taxonomic collection of tadpoles from six countries across three continents. We discovered a previously unidentified phylogenetically distinct infectious agent of tadpole livers present in a broad range of frogs from both tropical and temperate sites and across all sampled continents. These data demonstrate the high prevalence and global distribution of this infectious protist. (See pp. E4743–E4751.)
Coexistence of Y, W, and Z sex chromosomes in Xenopus tropicalis
Álvaro S. Roco, Allen W. Olmstead, Sigmund J. Degitz, Tosikazu Amano, Lyle B. Zimmerman, and Mónica Bullejos
As in most amphibians, sex chromosomes of the model species Xenopus tropicalis are homomorphic, complicating identification of the heterogametic sex. Using genetic approaches, we have proved the existence of three types of sex chromosomes (Y, W, and Z), defining three kinds of males (YZ, YW, and ZZ) and two kinds of females (ZW and WW). The existence of both male and female heterogametic individuals in one species is an extremely rare situation in nature, because some sex chromosome combinations produce offspring with sex ratios different from 1:1. Thus, parental sex chromosomes must be taken into account when X. tropicalis is used in multigeneration genetic studies or in ecotoxicological assays of endocrine disruptors with gender effects. (See pp. E4752–E4761.)
Epigenetic mechanisms, T-cell activation, and CCR5 genetics interact to regulate T-cell expression of CCR5, the major HIV-1 coreceptor
German G. Gornalusse, Srinivas Mummidi, Alvaro A. Gaitan, Fabio Jimenez, Veron Ramsuran, Anabela Picton, Kristen Rogers, Muthu Saravanan Manoharan, Nymisha Avadhanam, Krishna K. Murthy, Hernan Martinez, Angela Molano Murillo, Zoya A. Chykarenko, Richard Hutt, Demetre Daskalakis, Ludmila Shostakovich-Koretskaya, Salim Abdool Karim, Jeffrey N. Martin, Steven G. Deeks, Frederick Hecht, Elizabeth Sinclair, Robert A. Clark, Jason Okulicz, Fred T. Valentine, Neil Martinson, Caroline Tanya Tiemessen, Thumbi Ndung’u, Peter W. Hunt, Weijing He, and Sunil K. Ahuja
Levels of CC chemokine receptor 5 (CCR5) on T cells are a critical factor influencing HIV/AIDS susceptibility. DNA methylation is an epigenetic feature associated with lower gene expression. Here we show that the DNA methylation status of CCR5 cis-regulatory regions (cis-regions) correlates inversely with CCR5 levels on T cells. T-cell activation induces demethylation of CCR5 cis-regions, upregulating CCR5 expression. Higher vs. lower sensitivity of CCR5 cis-regions to undergoing T-cell activation-induced demethylation is associated with increased vs. decreased CCR5 levels. Polymorphisms in CCR5 cis-regions that are associated with increased vs. decreased HIV/AIDS susceptibility are also associated with increased vs. decreased sensitivity to activation-induced demethylation. Thus, interactions among T-cell activation, CCR5 epigenetics, and genetics influence CCR5 levels on T cells and, by extension, HIV/AIDS susceptibility. (See pp. E4762–E4771.)
Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella
Kai Papenfort, Elena Espinosa, Josep Casadesús, and Jörg Vogel
Horizontal gene transfer is a major force in bacterial evolution, and a widespread mechanism involves conjugative plasmids. Albeit potentially beneficial at the population level, plasmid transfer is a burden for individual cells. Therefore, assembly of the conjugation machinery is strictly controlled, especially under stress. Here, we describe an RNA-based regulatory circuit in host–plasmid communication where a regulatory RNA (RprA) inhibits plasmid transfer through posttranscriptional activation of two genes. Because one of the activated factors (σS) is necessary for transcription of the other (RicI), RprA forms the centerpiece of a posttranscriptional feedforward loop with AND-gate logic for gene activation. We also show that the synthesis of RicI, a membrane protein, inhibits plasmid transfer, presumably by interference with pilus assembly. (See pp. E4772–E4781.)
MeCP2 regulates the timing of critical period plasticity that shapes functional connectivity in primary visual cortex
Keerthi Krishnan, Bor-Shuen Wang, Jiangteng Lu, Lang Wang, Arianna Maffei, Jianhua Cang, and Z. Josh Huang
Rett syndrome is a neurodevelopmental disorder caused by mutations in methyl-CpG-binding protein 2 (MeCP2). It is thought to result from altered neuronal connectivity and/or plasticity, possibly through abnormal experience-dependent synapse development, but the underlying mechanisms remain obscure. Using MeCP2-null mice, we examined experience-dependent development of neural circuits in the primary visual cortex where GABAergic interneurons regulate a critical period of neural plasticity. We provide evidence that a precocious maturation of parvalbumin+ GABAergic interneurons correlates with the altered timing of the critical period and deficient visual function in the absence of MECP2. Our study begins to establish a link from specific molecular changes in GABAergic neurons to critical period of circuit development and to functional alterations in a mouse model of Rett syndrome. (See pp. E4782–E4791.)
STIM1 enhances SR Ca2+ content through binding phospholamban in rat ventricular myocytes
Guiling Zhao, Tianyu Li, Didier X. P. Brochet, Paul B. Rosenberg, and W. J. Lederer
Calcium ions play a central role in controlling contraction in heart muscle cells. We have investigated the function of a calcium ion signaling protein found in the heart called STIM1 (stromal interaction molecule 1) that has a known function in many other cells. We discovered, however, that in the heart STIM1 works completely differently. Instead of enabling Ca2+ entry into the cell, STIM1 enhances the rate and amount of Ca2+ stored and released from intracellular organelles in the steady state. Hence, more STIM1 expression increases the magnitude of the calcium signal, and this increases contraction. STIM1 thus may play an important and novel role in ventricular myocytes under physiological conditions by regulating the [Ca2+]i transient and contraction. (See pp. E4792–E4801.)
Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis
Dawn H. Nagel, Colleen J. Doherty, Jose L. Pruneda-Paz, Robert J. Schmitz, Joseph R. Ecker, and Steve A. Kay
The circadian clock, an endogenous time-keeping mechanism common to most species, allows organisms to coordinate biological processes with specific times of day. In plants, the role of the clock extends to almost every aspect of growth and development, including responses to biotic and abiotic stresses. The core molecular components and circuits of the clock have been well studied in the model organism Arabidopsis thaliana; however, how this mechanism connects to clock-controlled outputs remains poorly understood. Here, we performed a genome-wide characterization of the direct targets of a key clock component in Arabidopsis. Our results emphasize the broad role of the plant clock in regulating multiple biological functions and provide direct links between the oscillator and clock-regulated outputs. (See pp. E4802–E4810.)