bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system
Authors: Osterholz Helena , Singer Gabriel , Wemheuer Bernd , Daniel Rolf , Simon Meinhard , Niggemann Jutta , Dittmar Thorsten 
Published: January 2016

Abstract
Dissolved organic matter (DOM) is the main substrate and energy source for heterotrophic bacterioplankton. To understand the interactions between DOM and the bacterial community (BC), it is important to identify the key factors on both sides in detail, chemically distinct moieties in DOM and the various bacterial taxa. Next-generation sequencing facilitates the classification of millions of reads of environmental DNA and RNA amplicons and ultrahigh-resolution mass spectrometry yields up to 10 000 DOM molecular formulae in a marine water sample. Linking this detailed biological and chemical information is a crucial first step toward a mechanistic understanding of the role of microorganisms in the marine carbon cycle. In this study, we interpreted the complex microbiological and molecular information via a novel combination of multivariate statistics. We were able to reveal distinct relationships between the key factors of organic matter cycling along a latitudinal transect across the North Sea. Total BC and DOM composition were mainly driven by mixing of distinct water masses and presumably retain their respective terrigenous imprint on similar timescales on their way through the North Sea. The active microbial community, however, was rather influenced by local events and correlated with specific DOM molecular formulae indicative of compounds that are easily degradable. These trends were most pronounced on the highest resolved level, that is, operationally defined ‘species’, reflecting the functional diversity of microorganisms at high taxonomic resolution.
Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific
Authors: Larkin Alyse A , Blinebry Sara K , Howes Caroline , Lin Yajuan , Loftus Sarah E , Schmaus Carrie A , Zinser Erik R , Johnson Zackary I 
Published: January 2016

Abstract
The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We examined high light (HL) adapted Prochlorococcus communities across spatial and temporal environmental gradients in the Pacific Ocean to determine the ecological drivers of population structure and diversity across taxonomic ranks. We show that the Prochlorococcus community has the highest diversity at low latitudes, but seasonality driven by temperature, day length and nutrients adds complexity. At finer taxonomic resolution, some ‘sub-ecotype’ clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Intriguingly, biogeographies of the HL-I sub-ecotypes are driven by unique combinations of environmental traits, rather than through trait hierarchy, while the HL-II sub-ecotypes appear ecologically similar, thus demonstrating differences among these dominant HL ecotypes. Examining biodiversity across taxonomic ranks reveals high-resolution dynamics of Prochlorococcus evolution and ecology that are masked at phylogenetically coarse resolution. Spatial and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function.
Comparative genomics reveals new evolutionary and ecological patterns of selenium utilization in bacteria
Authors: Peng Ting , Lin Jie , Xu Yin-Zhen , Zhang Yan 
Published: January 2016

Abstract
Selenium (Se) is an important micronutrient for many organisms, which is required for the biosynthesis of selenocysteine, selenouridine and Se-containing cofactor. Several key genes involved in different Se utilization traits have been characterized; however, systematic studies on the evolution and ecological niches of Se utilization are very limited. Here, we analyzed more than 5200 sequenced organisms to examine the occurrence patterns of all Se traits in bacteria. A global species map of all Se utilization pathways has been generated, which demonstrates the most detailed understanding of Se utilization in bacteria so far. In addition, the selenophosphate synthetase gene, which is used to define the overall Se utilization, was also detected in some organisms that do not have any of the known Se traits, implying the presence of a novel Se form in this domain. Phylogenetic analyses of components of different Se utilization traits revealed new horizontal gene transfer events for each of them. Moreover, by characterizing the selenoproteomes of all organisms, we found a new selenoprotein-rich phylum and additional selenoprotein-rich species. Finally, the relationship between ecological environments and Se utilization was investigated and further verified by metagenomic analysis of environmental samples, which indicates new macroevolutionary trends of each Se utilization trait in bacteria. Our data provide insights into the general features of Se utilization in bacteria and should be useful for a further understanding of the evolutionary dynamics of Se utilization in nature.
Unexpected seasonality in quantity and composition of Amazon rainforest air reactivity
Authors: Nölscher A. C. , Yañez-Serrano A. M. , Wolff S. , de Araujo A. Carioca , Lavrič J. V. , Kesselmeier J. , Williams J. 
Published: January 2016

AbstractThe hydroxyl radical (OH) removes most atmospheric pollutants from air. The loss frequency of OH radicals due to the combined effect of all gas-phase OH reactive species is a measureable quantity termed total OH reactivity. Here we present total OH reactivity observations in pristine Amazon rainforest air, as a function of season, time-of-day and height (0–80 m). Total OH reactivity is low during wet (10 s−1) and high during dry season (62 s−1). Comparison to individually measured trace gases reveals strong variation in unaccounted for OH reactivity, from 5 to 15% missing in wet-season afternoons to mostly unknown (average 79%) during dry season. During dry-season afternoons isoprene, considered the dominant reagent with OH in rainforests, only accounts for ∼20% of the total OH reactivity. Vertical profiles of OH reactivity are shaped by biogenic emissions, photochemistry and turbulent mixing. The rainforest floor was identified as a significant but poorly characterized source of OH reactivity.
Broadband single-molecule excitation spectroscopy
Authors: Piatkowski Lukasz , Gellings Esther , van Hulst Niek F. 
Published: January 2016

AbstractOver the past 25 years, single-molecule spectroscopy has developed into a widely used tool in multiple disciplines of science. The diversity of routinely recorded emission spectra does underpin the strength of the single-molecule approach in resolving the heterogeneity and dynamics, otherwise hidden in the ensemble. In early cryogenic studies single molecules were identified by their distinct excitation spectra, yet measuring excitation spectra at room temperature remains challenging. Here we present a broadband Fourier approach that allows rapid recording of excitation spectra of individual molecules under ambient conditions and that is robust against blinking and bleaching. Applying the method we show that the excitation spectra of individual molecules exhibit an extreme distribution of solvatochromic shifts and distinct spectral shapes. Importantly, we demonstrate that the sensitivity and speed of the broadband technique is comparable to that of emission spectroscopy putting both techniques side-by-side in single-molecule spectroscopy.
Producing air-stable monolayers of phosphorene and their defect engineering
Authors: Pei Jiajie , Gai Xin , Yang Jiong , Wang Xibin , Yu Zongfu , Choi Duk-Yong , Luther-Davies Barry , Lu Yuerui 
Published: January 2016

AbstractIt has been a long-standing challenge to produce air-stable few- or monolayer samples of phosphorene because thin phosphorene films degrade rapidly in ambient conditions. Here we demonstrate a new highly controllable method for fabricating high quality, air-stable phosphorene films with a designated number of layers ranging from a few down to monolayer. Our approach involves the use of oxygen plasma dry etching to thin down thick-exfoliated phosphorene flakes, layer by layer with atomic precision. Moreover, in a stabilized phosphorene monolayer, we were able to precisely engineer defects for the first time, which led to efficient emission of photons at new frequencies in the near infrared at room temperature. In addition, we demonstrate the use of an electrostatic gate to tune the photon emission from the defects in a monolayer phosphorene. This could lead to new electronic and optoelectronic devices, such as electrically tunable, broadband near infrared lighting devices operating at room temperature.
Nanoscale manipulation of the Mott insulating state coupled to charge order in 1T-TaS2
Authors: Cho Doohee , Cheon Sangmo , Kim Ki-Seok , Lee Sung-Hoon , Cho Yong-Heum , Cheong Sang-Wook , Yeom Han Woong 
Published: January 2016

AbstractThe controllability over strongly correlated electronic states promises unique electronic devices. A recent example is an optically induced ultrafast switching device based on the transition between the correlated Mott insulating state and a metallic state of a transition metal dichalcogenide 1T-TaS2. However, the electronic switching has been challenging and the nature of the transition has been veiled. Here we demonstrate the nanoscale electronic manipulation of the Mott state of 1T-TaS2. The voltage pulse from a scanning tunnelling microscope switches the insulating phase locally into a metallic phase with irregularly textured domain walls in the charge density wave order inherent to this Mott state. The metallic state is revealed as a correlated phase, which is induced by the moderate reduction of electron correlation due to the charge density wave decoherence.
The lack of the Celf2a splicing factor converts a Duchenne genotype into a Becker phenotype
Authors: Martone J. , Briganti F. , Legnini I. , Morlando M. , Picillo E. , Sthandier O. , Politano L. , Bozzoni I. 
Published: January 2016

AbstractSubstitutions, deletions and duplications in the dystrophin gene lead to either the severe Duchenne muscular dystrophy (DMD) or mild Becker muscular dystrophy depending on whether out-of-frame or in-frame transcripts are produced. We identified a DMD case (GSΔ44) where the correlation between genotype and phenotype is not respected, even if carrying a typical Duchenne mutation (exon 44 deletion) a Becker-like phenotype was observed. Here we report that in this patient, partial restoration of an in-frame transcript occurs by natural skipping of exon 45 and that this is due to the lack of Celf2a, a splicing factor that interacts with exon 45 in the dystrophin pre-mRNA. Several experiments are presented that demonstrate the central role of Celf2a in controlling exon 45 splicing; our data point to this factor as a potential target for the improvement of those DMD therapeutic treatments, which requires exon 45 skipping.
A simple and novel way of maintaining constant wall temperature in microdevices
Authors: Duryodhan V. S. , Singh Abhimanyu , Singh Shiv Govind , Agrawal Amit 
Published: January 2016

AbstractConstant wall temperature /homogeneity in wall temperature is the need of various lab-on-chip devices employed in biological and chemical investigations. However method to maintain this condition does not seem to be available. In this work, a novel and simple way of maintaining constant wall temperature is proposed. A diverging microchannel along with conjugate effects is utilized towards this end. Both measurements and three dimensional numerical simulations are undertaken to prove the design. The investigation has been carried out over a large parameter range (divergence angle: 1–8°; length: 10–30 mm; depth: 86–200 μm; solid-to-fluid thickness ratio: 1.5–4.0 and solid-to-fluid thermal conductivity ratio: 27–646) and input conditions (mass flow rate: 4.17 × 10−5 −9.17 × 10−5 kg/s, heat flux: 2.4–9.6 W/cm2) which helped in establishing the finding. It is observed that a nearly constant wall temperature condition can be achieved over a large parameter range investigated. A model to arrive at the design parameter values is also proposed. The method is further demonstrated for series of microchannels where we successfully maintain each station at different temperature within ±1 °C. The finding is therefore significant and can be employed in both single and multi-stage processes such as PCR requiring different constant wall temperature with a fine resolution.
Ratchet transport powered by chiral active particles
Authors: Ai Bao-quan 
Published: January 2016

AbstractWe numerically investigate the ratchet transport of mixtures of active and passive particles in a transversal asymmetric channel. A big passive particle is immersed in a ‘sea’ of active particles. Due to the chirality of active particles, the longitudinal directed transport is induced by the transversal asymmetry. For the active particles, the chirality completely determines the direction of the ratchet transport, the counterclockwise and clockwise particles move to the opposite directions and can be separated. However, for the passive particle, the transport behavior becomes complicated, the direction is determined by competitions among the chirality, the self-propulsion speed and the packing fraction. Interestingly, within certain parameters, the passive particle moves to the left, while active particles move to the right. In addition, there exist optimal parameters (the chirality, the height of the barrier, the self-propulsion speed and the packing fraction) at which the rectified efficiency takes its maximal value. Our findings could be used for the experimental pursuit of the ratchet transport powered by chiral active particles.
Controlling condensation and frost growth with chemical micropatterns
Authors: Boreyko Jonathan B. , Hansen Ryan R. , Murphy Kevin R. , Nath Saurabh , Retterer Scott T. , Collier C. Patrick 
Published: January 2016

AbstractIn-plane frost growth on chilled hydrophobic surfaces is an inter-droplet phenomenon, where frozen droplets harvest water from neighboring supercooled liquid droplets to grow ice bridges that propagate across the surface in a chain reaction. To date, no surface has been able to passively prevent the in-plane growth of ice bridges across the population of supercooled condensate. Here, we demonstrate that when the separation between adjacent nucleation sites for supercooled condensate is properly controlled with chemical micropatterns prior to freezing, inter-droplet ice bridging can be slowed and even halted entirely. Since the edge-to-edge separation between adjacent supercooled droplets decreases with growth time, deliberately triggering an early freezing event to minimize the size of nascent condensation was also necessary. These findings reveal that inter-droplet frost growth can be passively suppressed by designing surfaces to spatially control nucleation sites and by temporally controlling the onset of freezing events.
An endometrial gene expression signature accurately predicts recurrent implantation failure after IVF
Authors: Koot Yvonne E. M. , van Hooff Sander R. , Boomsma Carolien M. , van Leenen Dik , Groot Koerkamp Marian J. A. , Goddijn Mariëtte , Eijkemans Marinus J. C. , Fauser Bart C. J. M. , Holstege Frank C. P. , Macklon Nick S. 
Published: January 2016

AbstractThe primary limiting factor for effective IVF treatment is successful embryo implantation. Recurrent implantation failure (RIF) is a condition whereby couples fail to achieve pregnancy despite consecutive embryo transfers. Here we describe the collection of gene expression profiles from mid-luteal phase endometrial biopsies (n = 115) from women experiencing RIF and healthy controls. Using a signature discovery set (n = 81) we identify a signature containing 303 genes predictive of RIF. Independent validation in 34 samples shows that the gene signature predicts RIF with 100% positive predictive value (PPV). The strength of the RIF associated expression signature also stratifies RIF patients into distinct groups with different subsequent implantation success rates. Exploration of the expression changes suggests that RIF is primarily associated with reduced cellular proliferation. The gene signature will be of value in counselling and guiding further treatment of women who fail to conceive upon IVF and suggests new avenues for developing intervention.
CRMAGE: CRISPR Optimized MAGE Recombineering
Authors: Ronda Carlotta , Pedersen Lasse Ebdrup , Sommer Morten O. A. , Nielsen Alex Toftgaard 
Published: January 2016

AbstractA bottleneck in metabolic engineering and systems biology approaches is the lack of efficient genome engineering technologies. Here, we combine CRISPR/Cas9 and λ Red recombineering based MAGE technology (CRMAGE) to create a highly efficient and fast method for genome engineering of Escherichia coli. Using CRMAGE, the recombineering efficiency was between 96.5% and 99.7% for gene recoding of three genomic targets, compared to between 0.68% and 5.4% using traditional recombineering. For modulation of protein synthesis (small insertion/RBS substitution) the efficiency was increased from 6% to 70%. CRMAGE can be multiplexed and enables introduction of at least two mutations in a single round of recombineering with similar efficiencies. PAM-independent loci were targeted using degenerate codons, thereby making it possible to modify any site in the genome. CRMAGE is based on two plasmids that are assembled by a USER-cloning approach enabling quick and cost efficient gRNA replacement. CRMAGE furthermore utilizes CRISPR/Cas9 for efficient plasmid curing, thereby enabling multiple engineering rounds per day. To facilitate the design process, a web-based tool was developed to predict both the λ Red oligos and the gRNAs. The CRMAGE platform enables highly efficient and fast genome editing and may open up promising prospective for automation of genome-scale engineering.
Lactate Chemical Exchange Saturation Transfer (LATEST) Imaging in vivo: A Biomarker for LDH Activity
Authors: DeBrosse Catherine , Nanga Ravi Prakash Reddy , Bagga Puneet , Nath Kavindra , Haris Mohammad , Marincola Francesco , Schnall Mitchell D. , Hariharan Hari , Reddy Ravinder 
Published: January 2016

AbstractNon-invasive imaging of lactate is of enormous significance in cancer and metabolic disorders where glycolysis dominates. Here, for the first time, we describe a chemical exchange saturation transfer (CEST) magnetic resonance imaging (MRI) method (LATEST), based on the exchange between lactate hydroxyl proton and bulk water protons to image lactate with high spatial resolution. We demonstrate the feasibility of imaging lactate with LATEST in lactate phantoms under physiological conditions, in a mouse model of lymphoma tumors and in skeletal muscle of healthy human subjects pre- and post-exercise. The method is validated by measuring LATEST changes in lymphoma tumors pre- and post-infusion of pyruvate and correlating them with lactate determined from multiple quantum filtered proton magnetic resonance spectroscopy (SEL-MQC 1H-MRS). Similarly, dynamic LATEST changes in exercising human skeletal muscle are correlated with lactate determined from SEL-MQC 1H-MRS. The LATEST method does not involve injection of radioactive isotopes or labeled metabolites. It has over two orders of magnitude higher sensitivity compared to conventional 1H-MRS. It is anticipated that this technique will have a wide range of applications including diagnosis and evaluation of therapeutic response of cancer, diabetes, cardiac and musculoskeletal diseases. The advantages of LATEST over existing methods and its potential challenges are discussed.
Divergent targets of glycolysis and oxidative phosphorylation result in additive effects of metformin and starvation in colon and breast cancer
Authors: Marini Cecilia , Bianchi Giovanna , Buschiazzo Ambra , Ravera Silvia , Martella Roberto , Bottoni Gianluca , Petretto Andrea , Emionite Laura , Monteverde Elena , Capitanio Selene , Inglese Elvira , Fabbi Marina , Bongioanni Francesca , Garaboldi Lucia , Bruzzi Paolo , Orengo Anna Maria , Raffaghello Lizzia , Sambuceti Gianmario 
Published: January 2016

AbstractEmerging evidence demonstrates that targeting energy metabolism is a promising strategy to fight cancer. Here we show that combining metformin and short-term starvation markedly impairs metabolism and growth of colon and breast cancer. The impairment in glycolytic flux caused by starvation is enhanced by metformin through its interference with hexokinase II activity, as documented by measurement of 18F-fluorodeoxyglycose uptake. Oxidative phosphorylation is additively compromised by combined treatment: metformin virtually abolishes Complex I function; starvation determines an uncoupled status of OXPHOS and amplifies the activity of respiratory Complexes II and IV thus combining a massive ATP depletion with a significant increase in reactive oxygen species. More importantly, the combined treatment profoundly impairs cancer glucose metabolism and virtually abolishes lesion growth in experimental models of breast and colon carcinoma. Our results strongly suggest that energy metabolism is a promising target to reduce cancer progression.
DNMT3L enables accumulation and inheritance of epimutations in transgenic Drosophila
Authors: Basu Amitava , Tomar Archana , Dasari Vasanthi , Mishra Rakesh Kumar , Khosla Sanjeev 
Published: January 2016

AbstractDNMT3L is an important epigenetic regulator in mammals, integrating DNA methylation and histone modification based epigenetic circuits. Here we show DNMT3L to be a part of the machinery that enables inheritance of epigenetic modifications from one generation to the next. Ectopic expression of DNMT3L in Drosophila, which lacks DNMT3L and its normal interacting partners DNMT3A and DNMT3B, lead to nuclear reprogramming that was gradual and progressive, resulting in melanotic tumors that were observed only when these flies were maintained for five generations. This global gene expression misregulation was accompanied by aberrations in the levels of H3K4me3 and H3K36me3, globally as well as at specific gene promoters. The levels of these epigenetic aberrations (epimutations) also increased progressively across successive generations. The accumulation and inheritance of epimutations across multiple generations recapitulates the important role of DNMT3L in intergenerational epigenetic inheritance in mammals.