bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular mechanism of the dual regulation of bacterial iron sulfur cluster biogenesis by CyaY and IscX
Authors: Adinolfi Salvatore , Puglisi Rita , Crack Jason C. , Iannuzzi Clara , Dal Piaz Fabrizio , Konarev Petr V. , Svergun Dmitri I. , Martin Stephen , Le Brun Nick E. , Pastore Annalisa 
Published: November 2017

AbstractIscX (or YfhJ) is a protein of unknown function which takes part in the iron-sulfur cluster assembly machinery, a highly specialised and essential metabolic pathway. IscX binds to iron with low affinity and interacts with IscS, the desulfurase central to cluster assembly. Previous studies have suggested a competition between IscX and CyaY, the bacterial ortholog of frataxin, for the same binding surface of IscS. This competition could suggest a link between the two proteins with a functional significance. Using a hybrid approach, we show here that IscX is a modulator of the inhibitory properties of CyaY: by competing for the same site on IscS, the presence of IscX rescues the rates of enzymatic cluster formation which are inhibited by CyaY. The effect is stronger at low iron concentrations, whereas it becomes negligible at high iron concentrations. These results strongly suggest that iron-sulfur cluster assembly is an exquisite example of an enzymatic process which requires a double regulation under the control of iron as the effector.
The ventral disc is a flexible microtubule organelle that depends on domed ultrastructure for functional attachment ofGiardia lamblia
Authors: Nosala Christopher , Dawson Scott C. 
Published: November 2017

AbstractThe parasiteGiardia lambliainteracts with its host by directly attaching the lumen of the small intestine. Attachment is mediated by a cytoskeletal structure termed the ventral disc and proceeds in four distinct stages: skimming, seal formation, cell body contacts, and bare area contacts. The precise mechanism of disc-mediated attachment is unclear and attachment models rely heavily on whether or not the ventral disc is a dynamic structure. We sought to investigate the second stage of attachment in which a seal is formed beneath the ventral disc. Three-dimensional, live imaging ofGiardiaexpressing specific ventral disc markers to the lateral crest, ventral groove, and disc body indicate dynamic movement in all of these regions. We observe seal formation by the lateral crest and determine that movement of the ventral groove region aids lateral crest seal formation. We also report the discovery of a new protein that is necessary for ventral disc formation and functional attachment (DAP_7268). Lastly, we observed that attachment largely depends on ventral disc ultrastructure as flattened discs display hindered attachment proficiency whether or not they retain the ability to form a seal. We propose a synthesized mechanism for attachment that includes flagellar hydrodynamic flow to help generate suction as well as disc conformational dynamics to aid in both hydrodynamic flow and the maintenance of negative pressure.
Molecular genetic diversity of donkey (Equus asinus) in South Korea
Authors: Yun Sungwook , Cho Giljae 
Published: November 2017

AbstractThe research on domestic donkey has little information and criteria comparing to other livestock, companion animal in South Korea. We analyzed genetic database of domestic donkey using microsatellite marker to clarify domestic donkey identification and paternity test. It is the first microsatellite marker analysis on domestic donkey in South Korea. We studied 179 horse samples from 50 Thoroughbred, 50 Jeju Halla horse, including 79 donkeys then analyzed 15 microsatellite marker (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3 and VHL20). We observed genetic diversity from biostatic analysis of them.The number of alleles on total average is 6.08 observed from 1 (ASB17), 2 (HMS1) to 14 (AHT5). The observed heterozygosity (OHet) is from 0.0000 (ASB17, HMS1) to 0.8608 (ASB23) which is mean value of 0.4861, the expected heterozygosity (EHet) is from 0.0000 (CA425) to 0.9104 (AHT5) with mean value of 0.5915, and the Polymorphism Information Content (PIC) on each group of microsatellite marker is from 0.0000 (ASB17) to 0.8968 (AHT5) observed as a mean value of 0.5374. Among 15 markers AHT4, AHT5, ASB23, CA425, HMS2, HMS3, HTG4, HTG10, LEX3 is observed above 5.000.The results on 15 microsatellite marker analysis of 3 horse groups is that the donkey had 0.5915 EHet, 0.4861 OHet on average, Thoroughbred had 0.6721 EHet, 0.6587 OHet on average, and the Jeju halla horse had 0.7898 EHet, 0.7093 OHet on average observed. Furthermore the mean alleles value is observed as 6.08, 4.83, 8.00 in donkey, Thoroughbred, Jeju halla horse breed in each.
Multi-state design of kinetically-controlled RNA aptamer ribosensors
Authors: Burke Cassandra R. , Sparkman-Yager David , Carothers James M. 
Published: November 2017

ABSTRACTMetabolite-responsive RNA regulators with kinetically-controlled responses are widespread in nature. By comparison, very limited success has been achieved creating kinetic control mechanisms for synthetic RNA aptamer devices. Here, we show that kinetically-controlled RNA aptamer ribosensors can be engineered using a novel approach for multi-state, co-transcriptional folding design. The design approach was developed through investigation of 29 candidatep-aminophenylalanine-responsive ribosensors. We show that ribosensors can be transcribedin situand used to analyze metabolic production directly from engineered microbial cultures, establishing a new class of cell-free biosensors. We found that kinetically-controlled ribosensors exhibited 5-10 fold greater ligand sensitivity than a thermodynamically-controlled device. And, we further demonstrated that a second aptamer, promiscuous for aromatic amino acid binding, could be assembled into kinetic ribosensors with 45-fold improvements in ligand selectivity. These results have broad implications for engineering RNA aptamer devices and overcoming thermodynamic constraints on molecular recognition through the design of kinetically-controlled responses.
Smad9 is a key player of follicular selection in goose via keeping the balance of LHR transcription
Authors: Yu Daolun , Chen Fanghui , Zhang Li , Wang Hejian , Chen Jie , Zhang Zongmeng , Li Jie , Xing Chaofeng , Li Honglin , Li Jun , Cai Yafei 
Published: November 2017

ABSTRACTThe egg production of poultry depends on follicular development and selection. However, the mechanism of selecting the priority of hierarchical follicles is completely unknown. Smad9 is one of the important transcription factors in BMP/Smads pathway and involved in goose follicular initiation. To explore its potential role in goose follicle hierarchy determination, we first blocked Smad9 expression using BMP typeⅠreceptor inhibitor LDN–193189 bothin vivoandin vitro. Unexpectedly, LDN–193189 administration could dramatically suppress Smad9 level and elevate egg production (7.08 eggs / bird,P< 0.05) of animals, and the estradiol (E2) and luteinizing hormone receptor (LHR) level were significantly increased (P< 0.05), but the progesterone (P4) and follicle stimulating hormone receptor (FSHR) mRNA remain unchanged. Surprisingly, Smad9 knockdown notably attenuated (P< 0.05) in E2, P4, FSHR and LHR level in goose granulosa cells (gGCs). Further chromatin immunoprecipitation (ChIP) assay of gGCs revealed that Smad9, served as a sensor of balance, bound to the LHR promoter regulating its transcription. These findings demonstrated that Smad9 is differentially expressed in goose follicles, and acts as a key player in controlling goose follicular selection.SUMMARY STATEMENTTo study the hierarchical development mechanism of avian follicle, new strategies can be found to improve the egg production of low-yielding poultry, such as geese.
Stochastic dynamics of an epidemics with recurrent spillovers from an endemic reservoir
Authors: Voinson Marina , Alvergne Alexandra , Billiard Sylvain , Smadi Charline 
Published: November 2017

AbstractMost emerging human infectious diseases have an animal origin. Yet, while zoonotic diseases originate from a primary reservoir, most theoretical studies have principally focused on single-host processes, either exclusively humans or exclusively animals, without considering the importance of animal to human transmission for understanding the dynamics of emerging infectious diseases. Here we aim to investigate the importance of spillover transmission for explaining the number and the size of outbreaks. We propose a simple stochastic Susceptible-Infected-Recovered model with a recurrent infection of an incidental host from a reservoir (e.g. humans by a zoonotic species), considering two modes of transmission, (1) animal-to-human and (2) human-to-human. The model assumes that (i) epidemiological processes are faster than other processes such as demographics or pathogen evolution and (ii) that an epidemic occurs until there are no susceptible individuals left. The results show that during an epidemic, even when the pathogens are barely contagious, multiple outbreaks are observed due to spillover transmission. Overall, the findings demonstrate that the only consideration of direct transmission between individuals is not sufficient to explain the dynamics of zoonotic pathogens in an incidental host.
Evidence for loss and adaptive reacquisition of alcoholic fermentation in an early-derived fructophilic yeast lineage
Authors: Gonçalves Carla , Wisecaver Jennifer H. , Salema-Oom Madalena , Leandro Maria José , Shen Xing-Xing , Peris David , Hittinger Chris Todd , Rokas Antonis , Gonçalves Paula 
Published: November 2017

AbstractFructophily is a rare trait that consists in the preference for fructose over other carbon sources. Here we show that in a yeast lineage (theWickerhamiella/Starmerella, W/S clade) formed by fructophilic species thriving in the floral niche, the acquisition of fructophily is part of a wider process of adaptation of central carbon metabolism to the high sugar environment. Coupling comparative genomics with biochemical and genetic approaches, we show that the alcoholic fermentation pathway was profoundly remodeled in the W/S clade, as genes required for alcoholic fermentation were lost and subsequently re-acquired from bacteria through horizontal gene transfer. We further show that the reinstated fermentative pathway is functional and that an enzyme required for sucrose assimilation is also of bacterial origin, reinforcing the adaptive nature of the genetic novelties identified in the W/S clade. This work shows how even central carbon metabolism can be remodeled by a surge of HGT events.
The Hallucination Machine: A Deep-Dream VR platform for Studying the Phenomenology of Visual Hallucinations
Authors: Suzuki Keisuke , Roseboom Warrick , Schwartzman David J. , Seth Anil K. 
Published: November 2017

AbstractAltered states of consciousness, such as psychotic or pharmacologically-induced hallucinations, provide a unique opportunity to examine the mechanisms underlying conscious perception. However, the phenomenological properties of these states are difficult to isolate experimentally from other, more general physiological and cognitive effects of psychoactive substances or psychopathological conditions. Thus, simulating phenomenological aspects of altered states in the absence of these other more general effects provides an important experimental tool for consciousness science and psychiatry. Here we describe such a tool, theHallucination Machine. It comprises a novel combination of two powerful technologies: deep convolutional neural networks (DCNNs) and panoramic videos of natural scenes, viewed immersively through a head-mounted display (panoramic VR). By doing this, we are able to simulate visual hallucinatory experiences in a biologically plausible and ecologically valid way. Two experiments illustrate potential applications of theHallucination Machine. First, we show that the system induces visual phenomenology qualitatively similar to classical psychedelics. In a second experiment, we find that simulated hallucinations do not evoke the temporal distortion commonly associated with altered states. Overall, theHallucination Machineoffers a valuable new technique for simulating altered phenomenology without directly altering the underlying neurophysiology.
A proposed chaperone of the bacterial type VI secretion system functions to constrain a self-identity protein
Authors: Zepeda-Rivera Martha A. , Saak Christina C. , Gibbs Karine A. 
Published: November 2017

AbstractThe opportunistic bacterial uropathogenProteus mirabiliscan communicate identity through the export of the self-identity protein, IdsD, via the type VI secretion (T6S) system. Expression of theidsgenes provides a fitness advantage during polymicrobial infections in a mouse infection model. Here we provide an answer to the unresolved question of how the activity of a T6S substrate, such as IdsD, is regulated before export. We demonstrate that IdsD is found in clusters that form independently of the T6S machinery and activity. We show that the protein IdsC, which is a member of the proposed DUF4123 chaperone family, is essential for the stability of these clusters as well as the IdsD protein itself. And we provide evidence that amino acid disruptions in IdsC are sufficient to disrupt IdsD export but not IdsD localization into stable subcellular clusters, strongly supporting that IdsC functions in at least two different ways: IdsD stabilization and IdsD export. We propose that IdsC, and likely other DUF4123-containing proteins, function to regulate T6S substrates before export by both stabilizing the protein and mediating export at the T6S machinery.
Conductive particles enable syntrophic acetate oxidation between Geobacter and Methanosarcina from coastal sediments
Authors: Rotaru Amelia-Elena , Stryhanyuk Hryhoriy , Calabrese Federica , Musat Florin , Shrestha Pravin Malla , Weber Hannah Sophia , Snoeyenbos-West Oona L.O. , Hall Per O.J. , Richnow Hans H. , Musat Niculina , Thamdrup Bo 
Published: November 2017

AbstractCoastal sediments are rich in conductive minerals, which could impact microbial processes for which acetate is a central intermediate. In the methanogenic zone, acetate is consumed by methanogens and/or syntrophic acetate oxidizing (SAO) consortia. SAO consortia live under extreme thermodynamic pressure and their survival depends on successful partnership. Here we demonstrate that conductive minerals facilitate a SAO partnership betweenGeobacterandMethanosarcinafrom the coastal sediments of the Bothnian Bay, Baltic Sea. Bothnian methanogenic sediments showed a high apparent isotopic fractionation (αc1.07) characteristic of CO2-reductive methanogenesis. The native community was represented by electrogens such asGeobacterand methanogens likeMethanosarcina. Upon the addition of conductive particles (activated carbon and magnetite) methanogenesis from acetate increased four fold.Geobacter(96% related toG. psychrophilus) andMethanosarcina(99% related toM. subterranea) dominated the conductive particle-spiked SAO communities. Using NanoSIMS we demonstrated that during SAO,Geobacterincorporated 82% of the labeled acetate as compared to only 18% byMethanosarcina. At the same timeGeobacterconverted 27% of the13C-acetate to13CO2as detected by IRMS. Indigenous soluble shuttles were not involved in SAO, since spiking fresh cultures with spent-media filtrate had no effect on methanogenic rates. Our results demonstrate thatGeobacteroxidizes acetate to CO2while transferring electrons extracellularly via conductive particles toMethanosarcina, which utilizes them for CO2reduction to methane. In natural environments, mediation of SAO by conductive particles between electrogens and methanogens could impact the iron and methane cycles.SignificanceAcetate oxidizing bacteria are known to thrive in mutualistic consortia in which H2or formate is shuttled to a methane-producingArchaeapartner. Here we discovered that they could instead transfer electrons via conductive minerals. Mineral-SAO (syntrophic acetate oxidation) could be a vital pathway for CO2-reductive methanogenesis in the environment, especially in sediments rich in conductive minerals. Mineral-SAO is therefore of potential importance for both iron and methane cycles in sediments and soils. Additionally, our observations imply that agricultural runoff or amendments with conductive chars could trigger a significant increase in methane emissions.
An eutherian intronic sequence gave rise to a major satellite DNA in Platyrrhini
Authors: Valeri Mirela Pelizaro , Dias Guilherme Borges , Socorro Pereira Valéria do , Kuhn Gustavo Campos Silva , Svartman Marta 
Published: November 2017

AbstractSatellite DNAs (satDNAs) are major components of eukaryote genomes. However, because of their quick divergence, the evolutionary origin of a given satDNA family can rarely be determined. Herein we took advantage of available primate sequenced genomes to determine the origin of the CapA satDNA (~1,500 bp long monomers), first described in Sapajus apella. We show that CapA is an abundant satDNA in Platyrrhini, whereas in the genomes of most eutherian mammals, including humans, this sequence is present only as a single copy located within a large intron of the NOS1AP (nitric oxid synthase 1 adaptor protein) Gene. Our data suggest that this intronic CapA-like sequence gave rise to the CapA satDNA and we discuss possible mechanisms implicated in this event. This is the first report of a single copy intronic sequence giving origin to a satDNA that reaches up to 100,000 copies in some genomes.
Chromatin accessibility changes betweenArabidopsisstem cells and mesophyll cells illuminate cell type-specific transcription factor networks
Authors: Sijacic Paja , Bajic Marko , McKinney Elizabeth C. , Meagher Richard B. , Deal Roger B. 
Published: November 2017

AbstractBackgroundCell differentiation is driven by changes in transcription factor (TF) activity and subsequent alterations in transcription. To study this process, differences in TF binding between cell types can be deduced by methods that probe chromatin accessibility. We used cell type-specific nuclei purification followed by the Assay for Transposase Accessible Chromatin (ATAC-seq) to delineate differences in chromatin accessibility and TF regulatory networks between stem cells of the shoot apical meristem (SAM) and differentiated leaf mesophyll cells ofArabidopsis thaliana.ResultsChromatin accessibility profiles of SAM stem cells and leaf mesophyll cells were highly similar at a qualitative level, yet thousands of regions of quantitatively different chromatin accessibility were also identified. We found that chromatin regions preferentially accessible in mesophyll cells tended to also be substantially accessible in the stem cells as compared to the genome-wide average, whereas the converse was not true. Analysis of genomic regions preferentially accessible in each cell type identified hundreds of overrepresented TF binding motifs, highlighting a set of TFs that are likely important for each cell type. Among these, we found evidence for extensive co-regulation of target genes by multiple TFs that are preferentially expressed in one cell type or the other. For example, a set of zinc-finger TFs appear to control a suite of growth-and development-related genes specifically in stem cells, while another TF set co-regulates genes involved in light responses and photosynthesis specifically in mesophyll cells. Interestingly, the TFs within both of these sets also show evidence of extensively co-regulating each other.ConclusionsQuantitative analysis of chromatin accessibility differences between stem cells and differentiated mesophyll cells allowed us to identify TF regulatory networks and downstream target genes that are likely to be functionally important in each cell type. Our findings that mesophyll cell-enriched accessible sites tend to already be substantially accessible in stem cells, but not vice versa, suggests that widespread regulatory element accessibility may be important for the developmental plasticity of stem cells. This work also demonstrates the utility of cell type-specific chromatin accessibility profiling in quickly developing testable models of regulatory control differences between cell types.
DO CELLMATES MATTER? A CAUSAL TEST OF THE SCHOOLS OF CRIME HYPOTHESIS WITH IMPLICATIONS FOR DIFFERENTIAL ASSOCIATION AND DETERRENCE THEORIES
Authors: HARRIS HEATHER M. , NAKAMURA KIMINORI , BUCKLEN KRISTOFER BRET 
Published: November 2017

AbstractIn the schools of crime hypothesis, social interactions between inmates are assumed to produce criminogenic rather than deterrent prison peer effects, thus implicating them in the persistence of high recidivism rates and null or criminogenic prison effects. We assess the validity of the schools of crime hypothesis by estimating prison peer effects that result from differential cellmate associations in a male, first‐time release cohort from the Pennsylvania Department of Corrections. To isolate causal prison peer effects in the presence of essential heterogeneity, we use a semiparametric local instrumental variables estimation strategy. Our results do not support the school of crime hypothesis. In our sample, prison peer effects produced in interaction with more criminally experienced cellmates are always null or deterrent rather than criminogenic. Although we do not explicitly test for the operant conditioning mechanisms theorized to underlie social influence in the context of differential association, we argue that, under the assumption that the differential association context relates positively to the direction of peer influence, our universally noncriminogenic estimates exclude direct reinforcement, vicarious reinforcement, and direct punishment as potential drivers of prison peer effects produced in interaction with more criminally experienced cellmates. Our results support the assertion that operant conditioning mechanisms connect differential association and deterrence theories.
AGE, PERIOD, AND COHORT EFFECTS ON DEATH PENALTY ATTITUDES IN THE UNITED STATES, 1974–2014
Authors: ANDERSON AMY L. , LYTLE ROBERT , SCHWADEL PHILIP 
Published: November 2017

AbstractIn this article, we further the understanding of both changes in public opinion on capital punishment in the United States and changes in the factors associated with public opinion on the death penalty. Support for the death penalty may be motivated by events happening during specific time periods, and it can vary across birth cohorts as a result of cohort‐specific socialization processes, demographic changes, and formative events that are specific to each generation. An explication of the sources of and variation in death penalty attitudes over time would benefit from the accounting for the age of the respondent, the year of the survey response, and the birth cohort of the respondent. We improve on previous research by using multiple approaches including hierarchical age–period–cohort models and data from the General Social Survey (N = 41,474) to examine changes in death penalty attitudes over time and across birth cohorts. The results showed curvilinear age effects, strong period effects, and weak cohort effects on death penalty support. The violent crime rate explained much of the variation in support for the death penalty across periods. The examination of subgroup differences suggests that support for the death penalty is becoming concentrated among Whites, Protestants, and Republicans.