bluuebunny/crossref_metadata_2025 huggingface dataset:
Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome
c
oxidase
Authors: Sharma Vivek , Enkavi Giray , Vattulainen Ilpo , Róg Tomasz , Wikström Mårten
Published: February 2015

Significance

Classical atomistic molecular dynamics simulations and free-energy calculations performed on cytochrome
c
oxidase in an explicit membrane–solvent environment show that the water molecules in the nonpolar cavity near the active site of oxygen reduction reorientate according to the redox state of the enzyme, guiding the path of proton transfer and thereby effectively preventing short-circuit of the proton pump. The results highlight the important role of protein-bound water molecules in biological energy conversion––a notion shared with bacteriorhodopsin, the light-driven proton pump.
Archaeal replicative primases can perform translesion DNA synthesis
Authors: Jozwiakowski Stanislaw K. , Borazjani Gholami Farimah , Doherty Aidan J.
Published: February 2015

Significance

DNA replicases stall at lesions during replication, potentially leading to genome instability. However, cells use specialized lesion bypass polymerases to restart stalled replisomes. Although most organisms possess these damage tolerance polymerases, capable of traversing blocking DNA lesions, many appear to lack these enzymes. We have discovered that replicative primases from archaea, previously considered to be solely involved in priming replication, are also capable of performing translesion DNA synthesis. This discovery has major implications for our understanding of additional roles of DNA primases during replication and the subsequent evolution of related lesion bypass pathways in eukaryotic organisms.
PTEN regulates natural killer cell trafficking in vivo
Authors: Leong Jeffrey W. , Schneider Stephanie E. , Sullivan Ryan P. , Parikh Bijal A. , Anthony Bryan A. , Singh Anvita , Jewell Brea A. , Schappe Timothy , Wagner Julia A. , Link Daniel C. , Yokoyama Wayne M. , Fehniger Todd A.
Published: February 2015

Significance

Natural killer (NK) cells are critical players in the response to viruses and transformed cells, but the molecular mechanisms controlling their functions are incompletely understood. A major pathway leading to NK cell activation is the phosphoinositide 3-kinase pathway. However, the impact of phosphatase and tensin homolog (PTEN), a key phosphatase opposing this pathway, on NK cells has not been reported. We generated a previously unreported NK cell-intrinsic PTEN-deletion mouse model to evaluate its role in NK cell biology. In contrast to other lymphocytes, we demonstrate that the primary effects of PTEN loss are marked perturbation in NK cell trafficking and distribution during both homeostasis and malignancy. These findings indicate that PTEN plays an essential role in NK cell localization in vivo.
Residue-level resolution of alphavirus envelope protein interactions in pH-dependent fusion
Authors: Zeng Xiancheng , Mukhopadhyay Suchetana , Brooks Charles L.
Published: February 2015

Significance

Alphaviruses infect human cells through endocytosis and low pH-triggered membrane fusion. Because of the recent epidemics and lack of specific treatment for alphaviral infections, numerous investigations have aimed to deduce the mechanism of the alphaviral infection pathway. Building on previous structural models of the viral envelope proteins, we identify critical histidine protonation-state changes responsible for pH-triggered conformational transitions between key fusion intermediates through quantitative calculation of pK
a
and free energies and further show that the key contributions arise from the His residues having conserved sequences and chemical environments. Our study provides insight into the mechanistic roles of these residues and suggests hotspots for targeting inhibitors that could shift the pH profile of membrane fusion and thus, interfere with infectivity.
Elucidation of synaptonemal complex organization by super-resolution imaging with isotropic resolution
Authors: Schücker Katharina , Holm Thorge , Franke Christian , Sauer Markus , Benavente Ricardo
Published: February 2015

Significance

Synaptonemal complexes (SCs) are meiosis-specific, 200-nm-wide, ladder-like structures that are essential for synapsis, recombination, and segregation of homologous chromosomes. Despite its importance for the spatial organization of individual components during meiosis, the molecular architecture of the SC is still unknown. We used super-resolution imaging by
direct
stochastic optical reconstruction microscopy (
d
STORM), which provides subdiffraction resolution for structural investigation of the SC. The helical ladder-like structure allowed us to reconstruct the 3D molecular organization of the mammalian SC from 2D “frontal” and “lateral” views with isotropic resolution. In combination with particle averaging, we managed to elucidate the molecular organization of the mammalian SC with nanometer precision and unraveled previously unknown details of its molecular architecture.
Distinct activation of an E2 ubiquitin-conjugating enzyme by its cognate E3 ligases
Authors: Cohen Itamar , Wiener Reuven , Reiss Yuval , Ravid Tommer
Published: February 2015

Significance

Ubiquitin (Ub) conjugation triggers protein degradation by the proteasome. Here we describe an unexplored feature of the Ub conjugation system that entails differential activation of an E2-conjugating enzyme by its cognate E3 Ub ligases. In vitro and in vivo analyses of activity-reducing mutants of the yeast Ub-conjugating (Ubc) enzyme, Ubc7, demonstrated selective activation by one of its two cognate E3 ligases, Hrd1, but not by the other, Doa10. Supported by structural modeling of the RING:Ubc7∼Ub complex, these findings are consistent with a model whereby the E2∼Ub transition state depends on noncovalent interactions between helix α2 of Ubc7 and Ub that are differentially stabilized by the two E3 RING domains. This differential activation represents a previously unidentified mechanism for regulating protein ubiquitylation.
Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin
Authors: Dailey Harry A. , Gerdes Svetlana , Dailey Tamara A. , Burch Joseph S. , Phillips John D.
Published: February 2015

Significance

It has been accepted dogma that eukaryotes and heme-synthesizing bacteria use the same metabolic intermediates in their heme synthesis pathways, where protoporphyrin is the final intermediate into which iron is inserted to make protoheme. Herein, we present data demonstrating that Gram-positive bacteria do not use protoporphyrin as an intermediate but, instead, have an altered set of terminal reactions that oxidize coproporphyrinogen to coproporphyrin and insert ferrous iron into coproporphyrin, resulting in the formation of coproheme. A newly characterized enzyme, HemQ, decarboxylates coproheme to generate protoheme. Because some organisms that possess this coproporphyrin-dependent branch are major causes of human disease, HemQ is a novel pharmacological target of significant therapeutic relevance, particularly given high rates of antimicrobial resistance among these pathogens.
Behavioral training reverses global cortical network dysfunction induced by perinatal antidepressant exposure
Authors: Zhou Xiaoming , Lu Jordan Y.-F. , Darling Ryan D. , Simpson Kimberly L. , Zhu Xiaoqing , Wang Fang , Yu Liping , Sun Xinde , Merzenich Michael M. , Lin Rick C. S.
Published: February 2015

Significance

Cortical circuit miswiring underlying dysfunctional networks and aberrant behavior and distortions in modulatory control nuclei contributing to the regulation of learning, memory, and mood are hallmarks of autism. No available treatment effectively addresses these different dimensions of neurological distortion expressed in this disorder. Here, we show that a simple form of intensive auditory behavioral training in young adult rats resulted in a reversal of autistic-like neurological distortions expressed in the primary auditory cortex arising in an early postnatal epoch and also broadly improved the status of modulatory control processes expressing serotonin, dopamine, and noradrenaline.
Validating vignette and conjoint survey experiments against real-world behavior
Authors: Hainmueller Jens , Hangartner Dominik , Yamamoto Teppei
Published: February 2015

Significance

Little evidence exists on whether preferences about hypothetical choices measured in a survey experiment are driven by the same structural determinants of the actual choices made in the real world. This study answers this question using a natural experiment as a behavioral benchmark. Comparing the results from conjoint and vignette experiments on which attributes of hypothetical immigrants generate support for naturalization with the outcomes of closely corresponding referendums in Switzerland, we find that the effects estimated from the surveys match the effects of the same attributes in the behavioral benchmark remarkably well. We also find that seemingly subtle differences in survey designs can produce significant differences in performance. Overall, the paired conjoint design performs the best.
Genome-wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I
Authors: Peña-Hernández Rodrigo , Marques Maud , Hilmi Khalid , Zhao Teijun , Saad Amine , Alaoui-Jamali Moulay A. , del Rincon Sonia V. , Ashworth Todd , Roy Ananda L. , Emerson Beverly M. , Witcher Michael
Published: February 2015

Significance

CCCTC-binding factor (CTCF) is an epigenetic regulatory protein that is not only functionally diverse, but is also targeted to highly diverse DNA binding sites. CTCF cooperates with accessory proteins to achieve various functional outputs. Further evidence in
Drosophila
shows that CTCF may also be targeted to chromatin via accessory proteins. The identity of such mammalian proteins remains elusive. Herein, we describe evidence that the transcription factor general transcription factor II-I (TFII-I) targets CTCF binding to metabolism-related genes across the genome. We find that TFII-I regulates the transcription of genes within this network on the level of initiation via RNA polymerase II phosphorylation. These results provide a starting point for understanding a biological network communicating information between chromatin architecture, transcription, and metabolism.
Role of the motor system in language knowledge
Authors: Berent Iris , Brem Anna-Katharine , Zhao Xu , Seligson Erica , Pan Hong , Epstein Jane , Stern Emily , Galaburda Albert M. , Pascual-Leone Alvaro
Published: February 2015

Significance

All spoken languages express words by sound patterns, and certain sound patterns (e.g.,blog) are systematically preferred to others (e.g.,lbog). However, whether those preferences reflect abstract rules or the motor difficulties associated with speech production is unknown. We address this question using transcranial magnetic stimulation and functional MRI. Results show that speech perception automatically engages the articulatory motor system, but linguistic preferences persist even when the motor system is disrupted. These findings suggest that, despite their intimate links, the language and motor systems are distinct. Language is designed to optimize motor action, but its knowledge includes principles that are disembodied and potentially abstract.
IL-4 abrogates T
H
17 cell-mediated inflammation by selective silencing of IL-23 in antigen-presenting cells
Authors: Guenova Emmanuella , Skabytska Yuliya , Hoetzenecker Wolfram , Weindl Günther , Sauer Karin , Tham Manuela , Kim Kyu-Won , Park Ji-Hyeon , Seo Ji Hae , Ignatova Desislava , Cozzio Antonio , Levesque Mitchell P. , Volz Thomas , Köberle Martin , Kaesler Susanne , Thomas Peter , Mailhammer Reinhard , Ghoreschi Kamran , Schäkel Knut , Amarov Boyko , Eichner Martin , Schaller Martin , Clark Rachael A. , Röcken Martin , Biedermann Tilo
Published: February 2015

Significance

Interleukin 4 (IL-4) has been shown to be highly protective against delayed type hypersensitivity and organ-specific autoimmune and autoinflammatory reactions in mice and humans, but its mode of action has remained controversial and has failed to be explained solely by redirection of T
H
1/T
H
17 toward a T
H
2-type immune response. Here we uncovered that IL-4 selectively suppresses IL-23 transcription and secretion by cells of the innate immune system. We further describe a previously unidentified therapeutic mode of action of IL-4 in T
H
17-mediated inflammation, and a physiologically highly relevant approach to selectively target IL-23/T
H
17-dependent inflammation while sparing IL-12 and T
H
1 immune responses.
Autoinhibition and relief mechanism for Polo-like kinase 4
Authors: Klebba Joseph E. , Buster Daniel W. , McLamarrah Tiffany A. , Rusan Nasser M. , Rogers Gregory C.
Published: February 2015

Significance

Polo-like kinases (Plks) are a conserved family of enzymes that function as master regulators for the process of cell division. Among their duties, Plks control the assembly of centrosomes, tiny organelles that facilitate mitotic spindle assembly and maintain the fidelity of chromosome inheritance. Plks are overexpressed in cancer, and therefore it is critical to unravel the normal regulation of these kinases. Here, we studied Plk4 regulation whose activity controls centrosome number. We showed that, as do other Plks, Plk4 autoinhibits its kinase activity. However, Plk4 is unique in its ability to relieve autoinhibition through a third Polo box domain not present in other Plk family members. Moreover, autoinhibition controls Plk4 oligomerization, which ultimately governs its stability and thus centrosome duplication.
Single liposome analysis of peptide translocation by the ABC transporter TAPL
Authors: Zollmann Tina , Moiset Gemma , Tumulka Franz , Tampé Robert , Poolman Bert , Abele Rupert
Published: February 2015

Significance

The human lysosomal polypeptide transporter TAPL belongs to the ATP-binding cassette (ABC) superfamily. Transport studies of ABC exporters are rare, and, most often, function is inferred from ATP hydrolysis rather than translocation measurements. For mechanistic understanding of solute transport, the proteins have to be purified and incorporated into lipid vesicles. Macroscopic measurements with ensembles of molecules are often problematic due to inhomogeneities in reconstitution. Therefore, we developed a method called dual-color fluorescence-burst analysis to analyze peptide transport into single liposomes with, on average, one to three TAPL complexes per vesicle. We show that the turnover number is in a physiologically meaningful range and that TAPL is indeed an active transporter accumulating peptides against a concentration gradient.
The SWI/SNF chromatin remodeling complex regulates germinal center formation by repressing Blimp-1 expression
Authors: Choi Jinwook , Jeon Shin , Choi Seungjin , Park Kyungsoo , Seong Rho Hyun
Published: February 2015

Significance

Germinal center (GC) response is central for generation of memory B cells and plasma cells that produce high-affinity antibodies, which are crucial for protective immunity against various foreign antigens. Even though key genetic factors for the GC formation are known, it is largely unknown how this process is controlled by epigenetic factors. Here we have demonstrated that the activity of SWI/SNF chromatin remodeling complex is required for the development of both GC B cells and follicular helper T cells. The SWI/SNF complex modulates Bcl-6–mediated Blimp-1 repression, and thus plays as a key mediator in the GC response. Our results provide fundamental insights into the epigenetic regulation in the GC reaction.
Haploinsufficiency screen highlights two distinct groups of ribosomal protein genes essential for embryonic stem cell fate
Authors: Fortier Simon , MacRae Tara , Bilodeau Mélanie , Sargeant Tobias , Sauvageau Guy
Published: February 2015

Significance

Stem cells hold great promise in the field of regenerative medicine because of their capability both to self-renew and to differentiate. Regulation of these processes by molecular players is crucial to maintain stem cells' unique functions. We previously reported the generation of a library of embryonic stem cells (ESCs) with engineered chromosomal deletions, in an effort to identify novel genes or elements essential for ESC differentiation. We now reveal that ESCs heterozygous for ribosomal protein (RP)-coding genes show strong defects in embryoid body (EB) differentiation but not in self-renewal. We also identify p53-dependent and -independent mechanisms that mediate the defects in EB formation of RP-deleted clones. Together, our results highlight previously unidentified roles for RP genes in ESC fate regulation.
TCF1 and LEF1 act as T-cell intrinsic HTLV-1 antagonists by targeting Tax
Authors: Ma Guangyong , Yasunaga Jun-ichirou , Akari Hirofumi , Matsuoka Masao
Published: February 2015

Significance

HTLV-1 is a peripheral T-cell tropic virus and induces proliferation of CD4+ T cells, resulting in T-cell malignancy and inflammatory diseases. Recent studies demonstrated that several restriction factors inhibiting HIV are also inhibitory to HTLV-1. We identified two T-cell–specific proteins, TCF1 and LEF1, as HTLV-1 restriction factors that determine the peripheral T-cell tropism of this virus by targeting Tax. They are highly expressed in immature thymocytes and thereby become a natural intrinsic barrier for HTLV-1 replication in the thymus. However, their expression can be down-regulated by Tax, as well as by activation and differentiation of T cells. These findings provide a mechanistic understanding of how HTLV-1 induces T-cell malignancies in the periphery but never in the thymus.
Breakdown of coral colonial form under reduced pH conditions is initiated in polyps and mediated through apoptosis
Authors: Kvitt Hagit , Kramarsky-Winter Esti , Maor-Landaw Keren , Zandbank Keren , Kushmaro Ariel , Rosenfeld Hanna , Fine Maoz , Tchernov Dan
Published: February 2015

Significance

Stony corals have survived through geologic timescale periods of unfavorable calcification conditions, including low-pH regimes, possibly by alternating between a calcifying colonial form and noncalcifying soft body solitary polyps. Although experimentally supported, the mechanisms enabling this biological plasticity are unidentified. We show that incubating two coral species under reduced pH conditions induced tissue-specific apoptosis that leads to loss of coloniality because of the dissociation of polyps (the basic modular units of the colony) from their connective tissue (coenosarc). Apoptosis was initiated in the polyps and subsided once the dissociation between polyps and coenosarc terminated. When conditions returned to normal, these solitary polyps initiated calcification and regenerated coenosarcs. These results indicate that regulation of coloniality is under the control of the polyp.
A CaMKII/PDE4D negative feedback regulates cAMP signaling
Authors: Mika Delphine , Richter Wito , Conti Marco
Published: February 2015

Significance

Cardiovascular disease is the leading cause of death worldwide. A better understanding of the pathophysiological mechanisms governing such disease states as heart failure is essential to the identification of novel therapeutic targets. We have discovered a regulatory loop that coordinates the function of proteins and secondary messengers involved in cardiac contractility and the development of heart failure. This regulatory loop may be a novel target for pharmacologic intervention to restore cardiac homeostasis.
CryoEM and mutagenesis reveal that the smallest capsid protein cements and stabilizes Kaposi's sarcoma-associated herpesvirus capsid
Authors: Dai Xinghong , Gong Danyang , Xiao Yuchen , Wu Ting-Ting , Sun Ren , Zhou Z. Hong
Published: February 2015

Significance

Kaposi's sarcoma-associated herpesvirus (KSHV) and EBV are cancer-causing human herpesviruses. Their smallest capsid proteins (SCPs) were shown to be required for capsid assembly and are potential drug targets for curbing viral infections, but how they work is unclear. By cryoEM and genetic engineering, we determine the structures of KSHV capsids bearing full-length or truncated SCPs and localize regions of SCP that are important for capsid assembly. We show that a long kinked helix of SCP cross-links neighboring subunits of the major capsid protein of hexons to stabilize the capsid. Our results explain how SCP, acting like a cementing protein found in bacterial viruses, facilitates tumor herpesvirus capsid assembly and viral maturation.
Bacterial proteins pinpoint a single eukaryotic root
Authors: Derelle Romain , Torruella Guifré , Klimeš Vladimír , Brinkmann Henner , Kim Eunsoo , Vlček Čestmír , Lang B. Franz , Eliáš Marek
Published: February 2015

Significance

The root of eukaryote phylogeny formally represents the last eukaryotic common ancestor (LECA), but its position has remained controversial. Using new genome sequences, we revised and expanded two datasets of eukaryotic proteins of bacterial origin, which previously yielded conflicting views on the eukaryotic root. Analyses using state-of-the-art phylogenomic methodology revealed that both expanded datasets now support the same root position. Our results justify a new nomenclature for the two main eukaryotic groups and provide a robust phylogenetic framework to investigate the early evolution of the eukaryotic cell.
Building coral reef resilience through assisted evolution
Authors: van Oppen Madeleine J. H. , Oliver James K. , Putnam Hollie M. , Gates Ruth D.
Published: February 2015

The genetic enhancement of wild animals and plants for characteristics that benefit human populations has been practiced for thousands of years, resulting in impressive improvements in commercially valuable species. Despite these benefits, genetic manipulations are rarely considered for noncommercial purposes, such as conservation and restoration initiatives. Over the last century, humans have driven global climate change through industrialization and the release of increasing amounts of CO
2
, resulting in shifts in ocean temperature, ocean chemistry, and sea level, as well as increasing frequency of storms, all of which can profoundly impact marine ecosystems. Coral reefs are highly diverse ecosystems that have suffered massive declines in health and abundance as a result of these and other direct anthropogenic disturbances. There is great concern that the high rates, magnitudes, and complexity of environmental change are overwhelming the intrinsic capacity of corals to adapt and survive. Although it is important to address the root causes of changing climate, it is also prudent to explore the potential to augment the capacity of reef organisms to tolerate stress and to facilitate recovery after disturbances. Here, we review the risks and benefits of the improvement of natural and commercial stocks in noncoral reef systems and advocate a series of experiments to determine the feasibility of developing coral stocks with enhanced stress tolerance through the acceleration of naturally occurring processes, an approach known as (human)-assisted evolution, while at the same time initiating a public dialogue on the risks and benefits of this approach.
The autophagic machinery ensures nonlytic transmission of mycobacteria
Authors: Gerstenmaier Lilli , Pilla Rachel , Herrmann Lydia , Herrmann Hendrik , Prado Monica , Villafano Geno J. , Kolonko Margot , Reimer Rudolph , Soldati Thierry , King Jason S. , Hagedorn Monica
Published: February 2015

Significance

Pathogenic mycobacteria can be transmitted by direct ejection from one host cell to another. However, the mechanism of ejection, and how lysing the host cell is prevented are unknown. This study explains how the host cell remains intact and alive while
Mycobacterium marinum
breaks through its plasma membrane during ejection. We show that a membraneous cup is specifically recruited to the distal pole of ejecting
M. marinum
. We demonstrate that these membranes are formed by the canonical autophagic pathway, though they do not mature to autophagolysosomes. Disruption of autophagy causes the host cells to become leaky and die during ejection. This dramatically reduces cell-to-cell transmission of the infection, demonstrating an important and unexpected role for autophagy in maintaining plasma membrane integrity during mycobacterial infection.
Physical detection of influenza A epitopes identifies a stealth subset on human lung epithelium evading natural CD8 immunity
Authors: Keskin Derin B. , Reinhold Bruce B. , Zhang Guang Lan , Ivanov Alexander R. , Karger Barry L. , Reinherz Ellis L.
Published: February 2015

Significance

Influenza A viruses (IAVs) are a cause of major morbidity in the human population. Being RNA viruses, replication is error prone, and proteins such as viral envelope hemagglutinin rapidly mutate. Current vaccines stimulate antibodies targeting exposed virion proteins but require annual reformation due to constant sequence variation. In contrast, vaccines that stimulate CD8 T cells directed at conserved peptides from internal proteins would offer stable immunity if these peptides are displayed by HLA proteins on infected cells. Currently, functional readouts infer the IAV peptides displayed. Using new MS technology, epitopes on infected human HLA-A2
+
lung epithelium are identified and abundances characterized. The data show interconnections between viral evasion, immunodominance, and stealth responses that will aid in developing cellular vaccines against influenza.
An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin
Authors: Wade Kristin R. , Hotze Eileen M. , Kuiper Michael J. , Morton Craig J. , Parker Michael W. , Tweten Rodney K.
Published: February 2015

Significance

Bacterial pathogens produce pore-forming toxins that damage eukaryotic membranes, whereas the pore-forming immune defense proteins produced by vertebrates can damage bacterial membranes. Despite the opposite functions of these proteins in pathogenesis or protection, many use a common pore-forming mechanism whereby membrane-bound monomers oligomerize into a circular structure, termed the prepore, which then assembles a β-barrel structure that punches a hole in the membrane. Here we show that once the prepore is assembled, an intermolecular electrostatic interaction is established that drives the formation of the pore. This mechanism is likely to be used by toxins and other pore-forming proteins that span the biological domains of life.
Age-related immune clearance of hepatitis B virus infection requires the establishment of gut microbiota
Authors: Chou Han-Hsuan , Chien Wei-Hung , Wu Li-Ling , Cheng Chi-Hung , Chung Chen-Han , Horng Jau-Haw , Ni Yen-Hsuan , Tseng Hong-Tai , Wu Dafei , Lu Xuemei , Wang Hurng-Yi , Chen Pei-Jer , Chen Ding-Shinn
Published: February 2015

Significance

Ninety-five percent of adult-acquired infections lead to spontaneous clearance, whereas >90% of exposed neonates and ∼30% of children aged 1–5 y fail to resolve hepatitis B virus (HBV) and develop chronic infection. A strong, diverse, adaptive immune response is considered essential for HBV clearance, but the mechanisms to generate a favorable response remain elusive. Here, we show that, while 12-wk-old C3H/HeN mice cleared HBV within 6 wk postinjection (wpi), their 6-wk-old counterparts remained HBV-positive at 26 wpi. Sterilization of gut microbiota from 6 to 12 wk of age using antibiotics prevented mice from rapidly clearing HBV. This model is valuable to the study of liver tolerance and enables the investigation of the mechanisms involved in effective control of HBV.
DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity
Authors: Leray Matthieu , Knowlton Nancy
Published: February 2015

Significance

High-throughput DNA sequencing methods are revolutionizing our ability to census communities, but most analyses have focused on microbes. Using an environmental DNA sequencing approach based on cytochrome
c
oxidase subunit 1 primers, we document the enormous diversity and fine-scale geographic structuring of the cryptic animals living on oyster reefs, many of which are rare and very small. Sequence data reflected both the presence and relative abundance of organisms, but only 10.9% of the sequences could be matched to reference barcodes in public databases. These results highlight the enormous numbers of marine animal species that remain genetically unanchored to conventional taxonomy and the importance of standardized, genetically based biodiversity surveys to monitor global change.
Differential RNA-seq of
Vibrio cholerae
identifies the VqmR small RNA as a regulator of biofilm formation
Authors: Papenfort Kai , Förstner Konrad U. , Cong Jian-Ping , Sharma Cynthia M. , Bassler Bonnie L.
Published: February 2015

Significance

To our knowledge, this work describes the first genome-wide annotation of transcriptional start sites in
Vibrio cholerae
and the discovery and characterization of a regulatory RNA, named VqmR, which controls collective behaviors in this major human pathogen. We show that VqmR is activated by the VqmA transcriptional regulator. VqmR represses expression of multiple mRNA targets including those encoding the Rtx (repeats in toxin) toxin and VpsT, which is required for biofilm formation. Indeed, we show that VqmR controls biofilm formation through repression of
vpsT
.
Enhanced poly(3-hydroxybutyrate) production in transgenic tobacco BY-2 cells using engineered acetoacetyl-CoA reductase
Authors: Yokoo Toshinori , Matsumoto Ken'ichiro , Ooba Takashi , Morimoto Kenjiro , Taguchi Seiichi
Published: February 2015

Highly active mutant of NADPH-dependent acetoacetyl-CoA reductase (PhaB) was expressed in Nicotiana tabacum cv. Bright Yellow-2 cultured cells to produce poly(3-hydroxybutyrate) [P(3HB)]. The mutated PhaB increased P(3HB) content by three-fold over the control, indicating that the mutant was a versatile tool for P(3HB) production. Additionally, the PhaB-catalyzed reaction was suggested to be a rate-limiting step of P(3HB) biosynthesis in tobacco BY-2 cells.
Phosphorothioate backbone modifications of nucleotide-based drugs are potent platelet activators
Authors: Flierl Ulrike , Nero Tracy L. , Lim Bock , Arthur Jane F. , Yao Yu , Jung Stephanie M. , Gitz Eelo , Pollitt Alice Y. , Zaldivia Maria T.K. , Jandrot-Perrus Martine , Schäfer Andreas , Nieswandt Bernhard , Andrews Robert K. , Parker Michael W. , Gardiner Elizabeth E. , Peter Karlheinz
Published: February 2015

Nucleotide-based drug candidates such as antisense oligonucleotides, aptamers, immunoreceptor-activating nucleotides, or (anti)microRNAs hold great therapeutic promise for many human diseases. Phosphorothioate (PS) backbone modification of nucleotide-based drugs is common practice to protect these promising drug candidates from rapid degradation by plasma and intracellular nucleases. Effects of the changes in physicochemical properties associated with PS modification on platelets have not been elucidated so far. Here we report the unexpected binding of PS-modified oligonucleotides to platelets eliciting strong platelet activation, signaling, reactive oxygen species generation, adhesion, spreading, aggregation, and thrombus formation in vitro and in vivo. Mechanistically, the platelet-specific receptor glycoprotein VI (GPVI) mediates these platelet-activating effects. Notably, platelets from GPVI function–deficient patients do not exhibit binding of PS-modified oligonucleotides, and platelet activation is fully abolished. Our data demonstrate a novel, unexpected, PS backbone–dependent, platelet-activating effect of nucleotide-based drug candidates mediated by GPVI. This unforeseen effect should be considered in the ongoing development programs for the broad range of upcoming and promising DNA/RNA therapeutics.
Neonatal Oxygenation, Pulmonary Hypertension, and Evolutionary Adaptation to High Altitude (2013 Grover Conference series)
Authors: Niermeyer Susan , Andrade‐M Mario Patricio , Vargas Enrique , Moore Lorna G.
Published: February 2015

Andeans and Tibetans have less altitude reduction in birth weight than do shorter‐resident groups, but only Tibetans are protected from pulmonary hypertension and chronic mountain sickness (CMS). We hypothesized that differences in neonatal oxygenation were involved, with arterial O2 saturation (SaO2) being highest in Tibetans, intermediate in Andeans, and lowest in Han or Europeans, and that improved oxygenation in Andeans relative to Europeans was accompanied by a greater postnatal decline in systolic pulmonary arterial pressures (). We studied 41 healthy (36 Andeans, 5 Europeans) and 9 sick infants at 3,600 m in Bolivia. The SaO2 in healthy babies was highest at 6–24 hours of postnatal age and then declined, whereas sick babies showed the opposite pattern. Compared to that of 30 Tibetan or Han infants studied previously at 3,600 m, SaO2 was higher in Tibetans than in Han or Andeans during wakefulness and active or quiet sleep. Tibetans, as well as Andeans, had higher values than Han while feeding. The SaO2's of healthy Andeans and Europeans were similar and, like those of Tibetans, remained at 85% or above, whereas Han values dipped below 70%. Andean and European values were above sea‐level norms and higher in sick than in healthy babies, but right heart pressure decreased across 4–6 months in all groups. We concluded that Tibetans had better neonatal oxygenation than Andeans at 3,600 m but that, counter to our hypothesis, neither was SaO2 higher nor Ppa lower in Andean than in European infants. Further, longitudinal studies in these 4 groups are warranted to determine whether neonatal oxygenation influences susceptibility to high‐altitude pulmonary hypertension and CMS later in life.
Poset limits can be totally ordered
Authors: Hladký Jan , Máthé András , Patel Viresh , Pikhurko Oleg
Published: February 2015

S. Janson [Poset limits and exchangeable random posets, Combinatorica 31 (2011), 529–563] defined limits of finite posets in parallel to the emerging theory of limits of dense graphs.

We prove that each poset limit can be represented as a kernel on the unit interval with the standard order, thus answering an open question of Janson. We provide two proofs: real-analytic and combinatorial. The combinatorial proof is based on a Szemerédi-type Regularity Lemma for posets which may be of independent interest.

Also, as a by-product of the analytic proof, we show that every atomless ordered probability space admits a measure-preserving and almost order-preserving map to the unit interval.
The Marchenko representation of reflectionless Jacobi and Schrödinger operators
Authors: Hur Injo , McBride Matt , Remling Christian
Published: February 2015

We consider Jacobi matrices and Schrödinger operators that are reflectionless on an interval. We give a systematic development of a certain parametrization of this class, in terms of suitable spectral data, that is due to Marchenko. Then some applications of these ideas are discussed.
Approximation of dynamic and quasi-static evolution problems in elasto-plasticity by cap models
Authors: Babadjian Jean-François , Mora Maria
Published: February 2015

This work is devoted to the analysis of elasto-plasticity models arising in soil mechanics. Contrary to the typical models mainly used for metals, it is required here to take into account plastic dilatancy due to the sensitivity of granular materials to hydrostatic pressure. The yield criterion thus depends on the mean stress, and the elasticity domain is unbounded and not invariant in the direction of hydrostatic matrices. In the mechanical literature, so-calledcap modelshave been introduced, where the elasticity domain is cut in the direction of hydrostatic stresses by means of a strain-hardening yield surface, called a cap. The purpose of this article is to study the well-posedness of plasticity models with unbounded elasticity sets in dynamical and quasi-static regimes. An asymptotic analysis as the cap is moved to infinity is also performed, which enables one to recover solutions to the uncapped model of perfect elasto-plasticity.
High Prevalence of Anal Human Papillomavirus–Associated Cancer Precursors in a Contemporary Cohort of Asymptomatic HIV-Infected Women
Authors: Heard Isabelle , Etienney Isabelle , Potard Valérie , Poizot-Martin Isabelle , Moore Catherine , Lesage Anne-Carole , Ressiot Emmanuelle , Crenn-Hebert Catherine , Fléjou Jean-François , Cubie Heather , Costagliola Dominique , Darragh Teresa M. ,   for the ANRS-C017 VIHGY Study Group, Franceschi S. , Palefsky J. , Heard I. , Costagliola D. , Cubie H. , Bergeron C. , Carcelain G. , Foulot H. , Crenn-Hébert C. , Tubiana R. , Poizot-Martin I. , Isabelle Richet A. , Lefebvre B. , Rousset Jablonski C. , Viard J. P. , Sastre Garau X. , Tubiana R. , Bonmarchand M. , Cuccu L. , Lefebvre B. , Richet A. , Torchin D. , Carbonne B. , Fléjou J. F. , Hoyeau N. , Poizot I. , Ducassou M.J. , Ressiot E. , Figarella-Branger D. , Meier F. , Crenn-Hébert C. , Gorbatchev C. , Rousset-Jablonski C. , Viard J. P. , Etienney I. , Lesage A. , Potard V. , Taibi S. , Costagliola D. , Cubie Virology: H. , Moore C. , Bergeron C.
Published: February 2015

Background.  Although human immunodeficiency virus (HIV)-infected women are at high risk for anal cancer, few data have been published on prevalence of and risk factors for anal precancer and potential screening strategies in this risk group.

Methods.  A cross-sectional anal screening study was nested in a gynecological cohort of HIV-infected women. Anal swab specimens were collected for cytology and human papillomavirus (HPV) testing. High-resolution anoscopy, with biopsy when indicated, was systematically performed.

Results.  Among the 171 enrolled women, median age was 47.3 years and 98% were receiving combination antiretroviral therapy. Median CD4+ count was 655 cells/µL and HIV load was <50 copies/mL in 89% of subjects. High-grade anal intraepithelial neoplasia or worse (HG-AIN+) was diagnosed in 12.9% (n = 21). In multivariable analysis, a history of cervical squamous intraepithelial lesion (odds ratio [OR], 4.2; 95% confidence interval [CI], 1.1–16.4) and anal HPV-16 infection (OR, 16.1; 95% CI, 5.4–48.3) was associated with increased risk of HG-AIN+. Abnormal anal cytology and HPV-16 infection performed best as a screening strategy for HG-AIN+ histology, with positive likelihood ratios of 3.4 (95% CI, 2.3–5.1) and 4.7 (95% CI, 2.5–8.7) and negative likelihood ratios of 0.2 (95% CI, .07–.8) and 0.4 (95% CI, .2–.9), respectively.

Conclusions.  HIV-infected women with a history of HPV-associated cervical disease are at increased risk for HG-AIN+ and should be offered anal cancer screening. Anal cytology and HPV-16 genotyping had the best screening performance. Anal cytology is easy to perform routinely; it may be the best candidate for screening for HG-AIN among HIV-infected women.
Novel gentamicin resistance genes in Campylobacter isolated from humans and retail meats in the USA
Authors: Zhao Shaohua , Mukherjee Sampa , Chen Yuansha , Li Cong , Young Shenia , Warren Melissa , Abbott Jason , Friedman Sharon , Kabera Claudine , Karlsson Maria , McDermott Patrick F.
Published: February 2015

Objectives

To understand the molecular epidemiology of gentamicin-resistant Campylobacter and investigate aminoglycoside resistance mechanisms.

Methods

One-hundred-and-fifty-one gentamicin-resistant Campylobacter isolates from humans (n = 38 Campylobacter jejuni; n = 41, Campylobacter coli) and retail chickens (n = 72 C. coli), were screened for the presence of gentamicin resistance genes by PCR and subtyped using PFGE. A subset of the isolates (n = 41) was analysed using WGS.

Results

Nine variants of gentamicin resistance genes were identified: aph(2″)-Ib, Ic, Ig, If, If1, If3, Ih, aac(6′)-Ie/aph(2″)-Ia and aac(6′)-Ie/aph(2″)-If2. The aph(2″)-Ib, Ic, If1, If3, Ih and aac(6′)-Ie/aph(2″)-If2 variants were identified for the first time in Campylobacter. Human isolates showed more diverse aminoglycoside resistance genes than did retail chicken isolates, in which only aph(2″)-Ic and -Ig were identified. The aph(2″)-Ig gene was only gene shared by C. coli isolates from human (n = 27) and retail chicken (n = 69). These isolates displayed the same resistance profile and similar PFGE patterns, suggesting that contaminated retail chicken was probably the source of human C. coli infections. Human isolates were genetically diverse and generally more resistant than the retail chicken isolates. The most frequent co-resistance was to tetracycline (78/79, 98.7%), followed by ciprofloxacin/nalidixic acid (46/79, 58.2%), erythromycin and azithromycin (36/79, 45.6%), telithromycin (32/79, 40.5%) and clindamycin (18/79, 22.8%). All human and retail meat isolates were susceptible to florfenicol.

Conclusions

This study demonstrated that several new aminoglycoside resistance genes underlie the recent emergence of gentamicin-resistant Campylobacter, and that, in addition to contaminated retail chicken, other sources have also contributed to gentamicin-resistant Campylobacter infections in humans.
Selection and molecular characterization of ceftazidime/avibactam-resistant mutants in Pseudomonas aeruginosa strains containing derepressed AmpC
Authors: Lahiri Sushmita D. , Walkup Grant K. , Whiteaker James D. , Palmer Tiffany , McCormack Kathy , Tanudra M. Angela , Nash Tory J. , Thresher Jason , Johnstone Michele R. , Hajec Laurie , Livchak Stephania , McLaughlin Robert E. , Alm Richard A.
Published: February 2015

Objectives

Pseudomonas aeruginosa is an important nosocomial pathogen that can cause a wide range of infections resulting in significant morbidity and mortality. Avibactam, a novel non-β-lactam β-lactamase inhibitor, is being developed in combination with ceftazidime and has the potential to be a valuable addition to the treatment options for the infectious diseases practitioner. We compared the frequency of resistance development to ceftazidime/avibactam in three P. aeruginosa strains that carried derepressed ampC alleles.

Methods

The strains were incubated in the presence of increasing concentrations of ceftazidime with a fixed concentration (4 mg/L) of avibactam to calculate the frequency of spontaneous resistance. The mutants were characterized by WGS to identify the underlying mechanism of resistance. A representative mutant protein was characterized biochemically.

Results

The resistance frequency was very low in all strains. The resistant variants isolated exhibited ceftazidime/avibactam MIC values that ranged from 64 to 256 mg/L. All of the mutants exhibited changes in the chromosomal ampC gene, the majority of which were deletions of various sizes in the Ω-loop region of AmpC. The mutant enzyme that carried the smallest Ω-loop deletion, which formed a part of the avibactam-binding pocket, was characterized biochemically and found to be less effectively inhibited by avibactam as well as exhibiting increased hydrolysis of ceftazidime.

Conclusions

The development of high-level resistance to ceftazidime/avibactam appears to occur at low frequency, but structural modifications in AmpC can occur that impact the ability of avibactam to inhibit the enzyme and thereby protect ceftazidime from hydrolysis.
The progenitors of the Milky Way stellar halo: big bricks favoured over little bricks
Authors: Deason A. J. , Belokurov V. , Weisz D. R.
Published: February 2015

We present a census of blue horizontal branch (BHB) and blue straggler (BS) stars belonging to dwarf galaxies and globular clusters, and compare these counts to that of the Milky Way stellar halo. We find, in agreement with earlier studies, that the ratio of BS-to-BHB stars in these satellite populations is dependent on stellar mass. Dwarf galaxies show an increasing BS-to-BHB ratio with luminosity. In contrast, globular clusters display the reverse trend, with NBS/NBHB (≲ 1) decreasing with luminosity. The faintest (L < 105 Lȯ) dwarfs have similar numbers of BS and BHB stars (NBS/NBHB ∼ 1), whereas more-massive dwarfs tend to be dominated by BS stars (NBS/NBHB ∼ 2–40). We find that the BS-to-BHB ratio in the stellar halo is relatively high (NBS/NBHB ∼ 5–6), and thus inconsistent with the low ratios found in both ultra-faint dwarfs and globular clusters. Our results favour more-massive dwarfs as the dominant ‘building blocks’ of the stellar halo, in good agreement with current predictions from Λ cold dark matter models.
Further evidence for a time-dependent initial mass function in massive early-type galaxies
Authors: Ferreras Ignacio , Weidner Carsten , Vazdekis Alexandre , La Barbera Francesco
Published: February 2015

Spectroscopic analyses of gravity-sensitive line strengths give growing evidence towards an excess of low-mass stars in massive early-type galaxies (ETGs). Such a scenario requires a bottom-heavy initial mass function (IMF). However, strong constraints can be imposed if we take into account galactic chemical enrichment. We extend the analysis of Weidner et al. and consider the functional form of bottom-heavy IMFs used in recent works, where the high-mass end slope is kept fixed to the Salpeter value, and a free parameter is introduced to describe the slope at stellar masses below some pivot mass scale (M < MP = 0.5 Mȯ). We find that no such time-independent parametrization is capable to reproduce the full set of constraints in the stellar populations of massive ETGs – resting on the assumption that the analysis of gravity-sensitive line strengths leads to a mass fraction at birth in stars with mass M < 0.5 Mȯ above 60 per cent. Most notably, the large amount of metal-poor gas locked in low-mass stars during the early, strong phases of star formation results in average stellar metallicities [M/H] ≲ −0.6, well below the solar value. The conclusions are unchanged if either the low-mass end cutoff, or the pivot mass are left as free parameters, strengthening the case for a time-dependent IMF.
Immanuel Kant: Aesthetics and Teleology
Authors: Guyer Paul
Published: February 2015

The Critique of the Power of Judgment (Kritik der Urteilskraft), published in 1790, was the last of the three critiques by Immanuel Kant (b. 1724–d. 1804). In the Introduction to the work, Kant argues that the gulf between the realms of the laws of nature and of freedom, or between theoretical and practical philosophy, needs to be bridged, and that the “reflecting” use of the faculty of judgment can do this while also taking us from the most general principles of natural science to empirical concepts and laws of nature. In the first main part of the work, the critique of the aesthetic power of judgment, Kant analyzes and defends our responses to, and judgments of, the beautiful in both nature and art and the sublime in nature; in the second main part, the critique of the teleological power of judgment, Kant defends our “regulative” rather than “constitutive” judgments of organisms as purposive systems within nature and of nature as a whole as a purposive system that has as its “final goal” (Endzweck) the development of the discipline necessary for the realization of human morality—although as a product of human freedom, morality can never, in Kant’s view, be achieved by merely natural means, only by an act of choice. Kant had been interested in reconciling a teleological outlook with the development of modern science since such early works as the Universal Natural History and Theory of the Heavens of 1755 and The Only Possible Basis for a Demonstration of the Existence of God of 1763. He had likewise long been interested in issues in aesthetics, having published a popular work of Observations on the Feeling of the Beautiful and Sublime in 1764. In addition, following the example of the textbooks by Alexander Gottlieb Baumgarten and Georg Friedrich Meier that he used for his courses on logic, metaphysics, and, beginning in 1772–1773, anthropology, he had touched upon aesthetics in all of those courses. But the idea of addressing aesthetics and teleology in a single book does not seem to have occurred to Kant before the end of 1787, after he had finished writing the Critique of Practical Reason, and he then wrote the third critique very quickly. His deepest reason for having written this book seems to have been his realization that both aesthetic and teleological judgment could support the human effort to be moral without sacrificing what is distinctive to them.