bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Seeding Rate on Weed-Suppression Activity and Yield ofIndicaand TropicalJaponicaRice Cultivars
Authors: Gealy David R. , Duke Sara
Published: July 2017

Weeds are ubiquitous and economically damaging in southern U.S. rice systems. Barnyardgrass has consistently been one of the most prevalent and troublesome of these. Although most rice cultivars do not suppress weeds dramatically, certainIndicacultivars and commercial hybrids are known to suppress barnyardgrass aggressively in conventional, drill-seeded rice systems in the southern United States. A field study was conducted to determine the degree to which either reducing or increasing standard seeding rates would affect natural suppression of weeds by conventional inbred and weed-suppressive cultivars. Five cultivars were evaluated at three seeding rates (160 [low], 320 [medium; conventional recommendation for inbred cultivars], and 480 [high] seeds m−2) and two weed levels (weed-free and weedy). Cultivars included a conventional, non–weed suppressive long-grain, ‘Wells’; high-tillering weed-suppressive cultivars ‘PI312777,’ ‘Rondo,’ and ‘4612’ from Asia; and the commercial hybrid ‘XL723.’ Overall, PI 312777 produced the most tillers, whereas XL 723 exhibited the greatest midseason shoot biomass and the greatest weed suppression. Yields of PI 312777 and 4612, both of which areIndicacultivars considered to be good weed suppressors, changed minimally across all seeding rates when compared with the other cultivars and thus tolerated weeds at the low rate nearly as well as at the high rate. Such a tolerance to weeds might be useful in the maintenance of weed suppression at reduced rice-seeding rates and suggests that reduced seeding rates of PI 312777 and 4612 would be less risky for yield loss when compared with the other cultivars tested. Visual suppression ratings were positively correlated with rice yield within weed-infested plots, suggesting that yield performance under weed pressure might be a good indicator of weed-suppression ability of cultivars in these systems. In contrast with PI 312777 and 4612, yields of the conventional inbred cultivar and commercial hybrid appeared to benefit from the high seeding rate. Overall, moderate to high seeding rates are likely to be needed for consistent weed suppression for all of the cultivar types evaluated in this study.
High performance platinum single atom electrocatalyst for oxygen reduction reaction
Authors: Liu Jing , Jiao Menggai , Lu Lanlu , Barkholtz Heather M. , Li Yuping , Wang Ying , Jiang Luhua , Wu Zhijian , Liu Di-jia , Zhuang Lin , Ma Chao , Zeng Jie , Zhang Bingsen , Su Dangsheng , Song Ping , Xing Wei , Xu Weilin , Wang Ying , Jiang Zheng , Sun Gongquan
Published: July 2017

For the large-scale sustainable implementation of polymer electrolyte membrane fuel cells in vehicles, high-performance electrocatalysts with low platinum consumption are desirable for use as cathode material during the oxygen reduction reaction in fuel cells. Here we report a carbon black-supported cost-effective, efficient and durable platinum single-atom electrocatalyst with carbon monoxide/methanol tolerance for the cathodic oxygen reduction reaction. The acidic single-cell with such a catalyst as cathode delivers high performance, with power density up to 680 mW cm−2 at 80 °C with a low platinum loading of 0.09 mgPt cm−2, corresponding to a platinum utilization of 0.13 gPt kW−1 in the fuel cell. Good fuel cell durability is also observed. Theoretical calculations reveal that the main effective sites on such platinum single-atom electrocatalysts are single-pyridinic-nitrogen-atom-anchored single-platinum-atom centres, which are tolerant to carbon monoxide/methanol, but highly active for the oxygen reduction reaction.
Actomyosin drives cancer cell nuclear dysmorphia and threatens genome stability
Authors: Takaki Tohru , Montagner Marco , Serres Murielle P. , Le Berre Maël , Russell Matt , Collinson Lucy , Szuhai Karoly , Howell Michael , Boulton Simon J. , Sahai Erik , Petronczki Mark
Published: July 2017

Altered nuclear shape is a defining feature of cancer cells. The mechanisms underlying nuclear dysmorphia in cancer remain poorly understood. Here we identify PPP1R12A and PPP1CB, two subunits of the myosin phosphatase complex that antagonizes actomyosin contractility, as proteins safeguarding nuclear integrity. Loss of PPP1R12A or PPP1CB causes nuclear fragmentation, nuclear envelope rupture, nuclear compartment breakdown and genome instability. Pharmacological or genetic inhibition of actomyosin contractility restores nuclear architecture and genome integrity in cells lacking PPP1R12A or PPP1CB. We detect actin filaments at nuclear envelope rupture sites and define the Rho-ROCK pathway as the driver of nuclear damage. Lamin A protects nuclei from the impact of actomyosin activity. Blocking contractility increases nuclear circularity in cultured cancer cells and suppresses deformations of xenograft nuclei in vivo. We conclude that actomyosin contractility is a major determinant of nuclear shape and that unrestrained contractility causes nuclear dysmorphia, nuclear envelope rupture and genome instability.
Electron ptychographic microscopy for three-dimensional imaging
Authors: Gao Si , Wang Peng , Zhang Fucai , Martinez Gerardo T. , Nellist Peter D. , Pan Xiaoqing , Kirkland Angus I.
Published: July 2017

Knowing the three-dimensional structural information of materials at the nanometer scale is essential to understanding complex material properties. Electron tomography retrieves three-dimensional structural information using a tilt series of two-dimensional images. In this paper, we report an alternative combination of electron ptychography with the inverse multislice method. We demonstrate depth sectioning of a nanostructured material into slices with 0.34 nm lateral resolution and with a corresponding depth resolution of about 24–30 nm. This three-dimensional imaging method has potential applications for the three-dimensional structure determination of a range of objects, ranging from inorganic nanostructures to biological macromolecules.
High-T
c superconductivity in undoped ThFeAsN
Authors: Shiroka T. , Shang T. , Wang C. , Cao G.-H. , Eremin I. , Ott H.-R. , Mesot J.
Published: July 2017

Unlike the widely studied ReFeAsO series, the newly discovered iron-based superconductor ThFeAsN exhibits a remarkably high critical temperature of 30 K, without chemical doping or external pressure. Here we investigate in detail its magnetic and superconducting properties via muon-spin rotation/relaxation and nuclear magnetic resonance techniques and show that ThFeAsN exhibits strong magnetic fluctuations, suppressed below ~35 K, but no magnetic order. This contrasts strongly with the ReFeAsO series, where stoichiometric parent materials order antiferromagnetically and superconductivity appears only upon doping. The ThFeAsN case indicates that Fermi-surface modifications due to structural distortions and correlation effects are as important as doping in inducing superconductivity. The direct competition between antiferromagnetism and superconductivity, which in ThFeAsN (as in LiFeAs) occurs at already zero doping, may indicate a significant deviation of the s-wave superconducting gap in this compound from the standard s± scenario.
Ubiquitination of stalled ribosome triggers ribosome-associated quality control
Authors: Matsuo Yoshitaka , Ikeuchi Ken , Saeki Yasushi , Iwasaki Shintaro , Schmidt Christian , Udagawa Tsuyoshi , Sato Fumiya , Tsuchiya Hikaru , Becker Thomas , Tanaka Keiji , Ingolia Nicholas T. , Beckmann Roland , Inada Toshifumi
Published: July 2017

Translation arrest by polybasic sequences induces ribosome stalling, and the arrest product is degraded by the ribosome-mediated quality control (RQC) system. Here we report that ubiquitination of the 40S ribosomal protein uS10 by the E3 ubiquitin ligase Hel2 (or RQT1) is required for RQC. We identify a RQC-trigger (RQT) subcomplex composed of the RNA helicase-family protein Slh1/Rqt2, the ubiquitin-binding protein Cue3/Rqt3, and yKR023W/Rqt4 that is required for RQC. The defects in RQC of the RQT mutants correlate with sensitivity to anisomycin, which stalls ribosome at the rotated form. Cryo-electron microscopy analysis reveals that Hel2-bound ribosome are dominantly the rotated form with hybrid tRNAs. Ribosome profiling reveals that ribosomes stalled at the rotated state with specific pairs of codons at P-A sites serve as RQC substrates. Rqt1 specifically ubiquitinates these arrested ribosomes to target them to the RQT complex, allowing subsequent RQC reactions including dissociation of the stalled ribosome into subunits.
RORα controls hepatic lipid homeostasis via negative regulation of PPARγ transcriptional network
Authors: Kim Kyeongkyu , Boo Kyungjin , Yu Young Suk , Oh Se Kyu , Kim Hyunkyung , Jeon Yoon , Bhin Jinhyuk , Hwang Daehee , Kim Keun Il , Lee Jun-Su , Im Seung-Soon , Yoon Seul Gi , Kim Il Yong , Seong Je Kyung , Lee Ho , Fang Sungsoon , Baek Sung Hee
Published: July 2017

The retinoic acid receptor-related orphan receptor-α (RORα) is an important regulator of various biological processes, including cerebellum development, circadian rhythm and cancer. Here, we show that hepatic RORα controls lipid homeostasis by negatively regulating transcriptional activity of peroxisome proliferators-activated receptor-γ (PPARγ) that mediates hepatic lipid metabolism. Liver-specific Rorα-deficient mice develop hepatic steatosis, obesity and insulin resistance when challenged with a high-fat diet (HFD). Global transcriptome analysis reveals that liver-specific deletion of Rorα leads to the dysregulation of PPARγ signaling and increases hepatic glucose and lipid metabolism. RORα specifically binds and recruits histone deacetylase 3 (HDAC3) to PPARγ target promoters for the transcriptional repression of PPARγ. PPARγ antagonism restores metabolic homeostasis in HFD-fed liver-specific Rorα deficient mice. Our data indicate that RORα has a pivotal role in the regulation of hepatic lipid homeostasis. Therapeutic strategies designed to modulate RORα activity may be beneficial for the treatment of metabolic disorders.
Major agricultural changes required to mitigate phosphorus losses under climate change
Authors: Ockenden M. C. , Hollaway M. J. , Beven K. J. , Collins A. L. , Evans R. , Falloon P. D. , Forber K. J. , Hiscock K. M. , Kahana R. , Macleod C. J. A. , Tych W. , Villamizar M. L. , Wearing C. , Withers P. J. A. , Zhou J. G. , Barker P. A. , Burke S. , Freer J. E. , Johnes P. J. , Snell M. A. , Surridge B. W. J. , Haygarth P. M.
Published: July 2017

Phosphorus losses from land to water will be impacted by climate change and land management for food production, with detrimental impacts on aquatic ecosystems. Here we use a unique combination of methods to evaluate the impact of projected climate change on future phosphorus transfers, and to assess what scale of agricultural change would be needed to mitigate these transfers. We combine novel high-frequency phosphorus flux data from three representative catchments across the UK, a new high-spatial resolution climate model, uncertainty estimates from an ensemble of future climate simulations, two phosphorus transfer models of contrasting complexity and a simplified representation of the potential intensification of agriculture based on expert elicitation from land managers. We show that the effect of climate change on average winter phosphorus loads (predicted increase up to 30% by 2050s) will be limited only by large-scale agricultural changes (e.g., 20–80% reduction in phosphorus inputs).
First-order spatial coherence measurements in a thermalized two-dimensional photonic quantum gas
Authors: Damm Tobias , Dung David , Vewinger Frank , Weitz Martin , Schmitt Julian
Published: July 2017

Phase transitions between different states of matter can profoundly modify the order in physical systems, with the emergence of ferromagnetic or topological order constituting important examples. Correlations allow the quantification of the degree of order and the classification of different phases. Here we report measurements of first-order spatial correlations in a harmonically trapped two-dimensional photon gas below, at and above the critical particle number for Bose–Einstein condensation, using interferometric measurements of the emission of a dye-filled optical microcavity. For the uncondensed gas, the transverse coherence decays on a length scale determined by the thermal de Broglie wavelength of the photons, which shows the expected scaling with temperature. At the onset of Bose–Einstein condensation, true long-range order emerges, and we observe quantum statistical effects as the thermal wave packets overlap. The excellent agreement with equilibrium Bose gas theory prompts microcavity photons as promising candidates for studies of critical scaling and universality in optical quantum gases.
The Maintenance of Telomere Length in CD28+ T Cells During T Lymphocyte Stimulation
Authors: Huang Ejun , Tedone Enzo , O’Hara Ryan , Cornelius Crystal , Lai Tsung-Po , Ludlow Andrew , Wright Woodring E. , Shay Jerry W.
Published: July 2017

Telomerase activity is not readily detected in resting human T lymphocytes, however upon antigen presentation, telomerase is transiently upregulated. Presently, it is not known if telomerase activation is necessary for the proliferation of T cells or for the maintenance of telomere lengths. In this study, we found that telomerase activation is not required for the short- term proliferation of T cells and that telomeres progressively shorten in a heterogeneous population of T cells, even if telomerase is detected. By measuring telomerase activity at the single-cell level using quantitative ddPCR techniques (ddTRAP) and by monitoring changes in the shortest telomeres with more sensitive telomere length measurement assays, we show that only a subset of CD28+ T-cells have robust telomerase activity upon stimulation and are capable of maintaining their telomere lengths during induced proliferation. The study of this T-cell subset may lead to a better understanding on how telomerase is regulated and functions in immune cells.
Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family
Authors: Gasparini Alessandra , Tosatto Silvio C. E. , Murgia Alessandra , Leonardi Emanuela
Published: July 2017

The emergence of genes implicated across multiple comorbid neurologic disorders allows to identify shared underlying molecular pathways. Recently, investigation of patients with diverse neurologic disorders found TANC1 and TANC2 as possible candidate disease genes. While the TANC proteins have been reported as postsynaptic scaffolds influencing synaptic spines and excitatory synapse strength, their molecular functions remain unknown. Here, we conducted a comprehensive in silico analysis of the TANC protein family to characterize their molecular role and understand possible neurobiological consequences of their disruption. The known Ankyrin and tetratricopeptide repeat (TPR) domains have been modeled. The newly predicted N-terminal ATPase domain may function as a regulated molecular switch for downstream signaling. Several putative conserved protein binding motifs allowed to extend the TANC interaction network. Interestingly, we highlighted connections with different signaling pathways converging to modulate neuronal activity. Beyond a known role for TANC family members in the glutamate receptor pathway, they seem linked to planar cell polarity signaling, Hippo pathway, and cilium assembly. This suggests an important role in neuron projection, extension and differentiation.
Efficient and Reversible Electron Doping of Semiconductor-Enriched Single-Walled Carbon Nanotubes by Using Decamethylcobaltocene
Authors: Xu Jian-Long , Dai Rui-Xuan , Xin Yan , Sun Yi-Lin , Li Xian , Yu Yang-Xin , Xiang Lan , Xie Dan , Wang Sui-Dong , Ren Tian-Ling
Published: July 2017

Single-walled carbon nanotubes (SWCNTs) offer great potential for field-effect transistors and integrated circuit applications due to their extraordinary electrical properties. To date, as-made SWCNT transistors are usually p-type in air, and it still remains challenging for realizing n-type devices. Herein, we present efficient and reversible electron doping of semiconductor-enriched single-walled carbon nanotubes (s-SWCNTs) by firstly utilizing decamethylcobaltocene (DMC) deposited by a simple spin-coating process at room temperature as an electron donor. A n-type transistor behavior with high on current, large I
on
/I
off
ratio and excellent uniformity is obtained by surface charge transfer from the electron donor DMC to acceptor s-SWCNTs, which is further corroborated by the Raman spectra and the ab initio simulation results. The DMC dopant molecules could be reversibly removed by immersion in N, N-Dimethylformamide solvent, indicating its reversibility and providing another way to control the carrier concentration effectively as well as selective removal of surface dopants on demand. Furthermore, the n-type behaviors including threshold voltage, on current, field-effect mobility, contact resistances, etc. are well controllable by adjusting the surface doping concentration. This work paves the way to explore and obtain high-performance n-type nanotubes for future complementary CMOS circuit and system applications.
Thresholds of biodiversity and ecosystem function in a forest ecosystem undergoing dieback
Authors: Evans P. M. , Newton A. C. , Cantarello E. , Martin P. , Sanderson N. , Jones D. L. , Barsoum N. , Cottrell J. E. , A’Hara S. W. , Fuller L.
Published: July 2017

Ecological thresholds, which represent points of rapid change in ecological properties, are of major scientific and societal concern. However, very little research has focused on empirically testing the occurrence of thresholds in temperate terrestrial ecosystems. To address this knowledge gap, we tested whether a number of biodiversity, ecosystem functions and ecosystem condition metrics exhibited thresholds in response to a gradient of forest dieback, measured as changes in basal area of living trees relative to areas that lacked recent dieback. The gradient of dieback was sampled using 12 replicate study areas in a temperate forest ecosystem. Our results provide novel evidence of several thresholds in biodiversity (namely species richness of ectomycorrhizal fungi, epiphytic lichen and ground flora); for ecological condition (e.g. sward height, palatable seedling abundance) and a single threshold for ecosystem function (i.e. soil respiration rate). Mechanisms for these thresholds are explored. As climate-induced forest dieback is increasing worldwide, both in scale and speed, these results imply that threshold responses may become increasingly widespread.
Evaluation of two lead malaria transmission blocking vaccine candidate antibodies in natural parasite-vector combinations
Authors: Bompard Anais , Da Dari F. , Yerbanga Rakiswendé S. , Biswas Sumi , Kapulu Melissa , Bousema Teun , Lefèvre Thierry , Cohuet Anna , Churcher Thomas S.
Published: July 2017

Transmission blocking vaccines (TBV) which aim to control malaria by inhibiting human-to-mosquito transmission show considerable promise though their utility against naturally circulating parasites remains unknown. The efficacy of two lead candidates targeting Pfs25 and Pfs230 antigens to prevent onwards transmission of naturally occurring parasites to a local mosquito strain is assessed using direct membrane feeding assays and murine antibodies in Burkina Faso. The transmission blocking activity of both candidates depends on the level of parasite exposure (as assessed by the mean number of oocysts in control mosquitoes) and antibody titers. A mathematical framework is devised to allow the efficacy of different candidates to be directly compared and determine the minimal antibody titers required to halt transmission in different settings. The increased efficacy with diminishing parasite exposure indicates that the efficacy of vaccines targeting either Pfs25 or Pfs230 may increase as malaria transmission declines. This has important implications for late-stage candidate selection and assessing how they can support the drive for malaria elimination.
Constraining shifts in North Atlantic plate motions during the Palaeocene by U-Pb dating of Svalbard tephra layers
Authors: Jones Morgan T. , Augland Lars E. , Shephard Grace E. , Burgess Seth D. , Eliassen Gauti T. , Jochmann Malte M. , Friis Bjarki , Jerram Dougal A. , Planke Sverre , Svensen Henrik H.
Published: July 2017

Radioisotopic dating of volcanic minerals is a powerful method for establishing absolute time constraints in sedimentary basins, which improves our understanding of the chronostratigraphy and evolution of basin processes. The relative plate motions of Greenland, North America, and Eurasia changed several times during the Palaeogene. However, the timing of a key part of this sequence, namely the initiation of compression between Greenland and Svalbard, is currently poorly constrained. The formation of the Central Basin in Spitsbergen is inherently linked to changes in regional plate motions, so an improved chronostratigraphy of the sedimentary sequence is warranted. Here we present U-Pb zircon dates from tephra layers close to the basal unconformity, which yield a weighted-mean 206Pb/238U age of 61.596 ± 0.028 Ma (2σ). We calculate that sustained sedimentation began at ~61.8 Ma in the eastern Central Basin based on a sediment accumulation rate of 71.6 ± 7.6 m/Myr. The timing of basin formation is broadly coeval with depositional changes at the Danian-Selandian boundary around the other margins of Greenland, including the North Sea, implying a common tectonic driving force. Furthermore, these stratigraphic tie points place age constraints on regional plate reorganization events, such as the onset of seafloor spreading in the Labrador Sea.
Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity
Authors: Venkatasubramanian Prashanna Balaji , Toydemir Gamze , de Wit Nicole , Saccenti Edoardo , Martins dos Santos Vitor A. P. , van Baarlen Peter , Wells Jerry M. , Suarez-Diez Maria , Mes Jurriaan J.
Published: July 2017

Intestinal epithelial cells, like Caco-2, are commonly used to study the interaction between food, other luminal factors and the host, often supported by microarray analysis to study the changes in gene expression as a result of the exposure. However, no compiled dataset for Caco-2 has ever been initiated and Caco-2-dedicated gene expression networks are barely available. Here, 341 Caco-2-specific microarray samples were collected from public databases and from in-house experiments pertaining to Caco-2 cells exposed to pathogens, probiotics and several food compounds. Using these datasets, a gene functional association network specific for Caco-2 was generated containing 8937 nodes 129711 edges. Two in silico methods, a modified version of biclustering and the new Differential Expression Correlation Analysis, were developed to identify Caco-2-specific gene targets within a pathway of interest. These methods were subsequently applied to the AhR and Nrf2 signalling pathways and altered expression of the predicted target genes was validated by qPCR in Caco-2 cells exposed to coffee extracts, known to activate both AhR and Nrf2 pathways. The datasets and in silico method(s) to identify and predict responsive target genes can be used to more efficiently design experiments to study Caco-2/intestinal epithelial-relevant biological processes.
Genetic variation and population structure of Botswana populations as identified with AmpFLSTR Identifiler short tandem repeat (STR) loci
Authors: Tau Tiroyamodimo , Wally Anthony , Fanie Thokozile Patricia , Ngono Goitseone Lorato , Mpoloka Sununguko Wata , Davison Sean , D’Amato María Eugenia
Published: July 2017

Population structure was investigated in 990 Botswana individuals according to ethno-linguistics, Bantu and Khoisan, and geography (the nine administrative districts) using the Identifiler autosomal microsatellite markers. Genetic diversity and forensic parameters were calculated for the overall population, and according to ethno-linguistics and geography. The overall combined power of exclusion (CPE) was 0.9999965412 and the combined match probability 6,28 × 10−19. CPE was highest for the Khoisan Tuu ethnolinguistic group and the Northeast District at 0.9999582029 and 0.9999922652 respectively. CMP ranged from 6.28 × 10−19 (Khoisan Tuu) to 1,02 × 10−18 (Northwest district). Using pairwise genetic distances (FST), analysis of molecular variance (AMOVA), factorial correspondence analysis (FCA), and the unsupervised Bayesian clustering method found in STRUCTURE and TESS, ethno-linguistics were found to have a greater influence on population structure than geography. FCA showed clustering between Bantu and Khoisan, and within the Bantu. This Bantu sub-structuring was not seen with STRUCTURE and TESS, which detected clustering only between Bantu and Khoisan. The patterns of population structure revealed highlight the need for regional reference databases that include ethno-linguistic and geographic location information. These markers have important potential for bio-anthropological studies as well as for forensic applications.
The polarization and the fundamental sensitivity of 39K (133Cs)-85Rb-4He hybrid optical pumping spin exchange relaxation free atomic magnetometers
Authors: Liu Jian-Hua , Jing Dong-Yang , Wang Liang-Liang , Li Yang , Quan Wei , Fang Jian-Cheng , Liu Wu-Ming
Published: July 2017

The hybrid optical pumping spin exchange relaxation free (SERF) atomic magnetometers can realize ultrahigh sensitivity measurement of magnetic field and inertia. We have studied the 85Rb polarization of two types of hybrid optical pumping SERF magnetometers based on 39K-85Rb-4He and 133Cs-85Rb-4He respectively. Then we found that 85Rb polarization varies with the number density of buffer gas 4He and quench gas N2, pumping rate of pump beam and cell temperature respectively, which will provide an experimental guide for the design of the magnetometer. We obtain a general formula on the fundamental sensitivity of the hybrid optical pumping SERF magnetometer due to shot-noise. The formula describes that the fundamental sensitivity of the magnetometer varies with the number density of buffer gas and quench gas, the pumping rate of pump beam, external magnetic field, cell effective radius, measurement volume, cell temperature and measurement time. We obtain a highest fundamental sensitivity of 1.5073 aT/Hz1/2 (1 aT = 10−18T) with 39K-85Rb-4He magnetometer between above two types of magnetometers when 85Rb polarization is 0.1116. We estimate the fundamental sensitivity limit of the hybrid optical pumping SERF magnetometer to be superior to 1.8359 × 10−2aT/Hz1/2, which is higher than the shot-noise-limited sensitivity of 1 aT/Hz1/2 of K SERF atomic magnetometer.
Urinary concentrations of phthalate metabolites in early pregnancy associated with clinical pregnancy loss in Chinese women
Authors: Gao Hui , Zhang Yun-wei , Huang Kun , Yan Shuang-qin , Mao Lei-jing , Ge Xing , Xu Ye-qing , Xu Yuan-yuan , Sheng Jie , Jin Zhong-xiu , Zhu Peng , Tao Xu-guang , Hao Jia-hu , Tao Fang-biao
Published: July 2017

Limited evidence revealed conflicting results on relationship between phthalate exposure and clinical pregnancy loss (gestational weeks >6). A prospective cohort study in Chinese pregnant women (n = 3220) was conducted to investigate the association between urinary phthalate metabolites and clinical pregnancy loss (gestational weeks 6 to 27; n = 109). Morning urine samples during gestational weeks 5 to 14 (mean 10.42) were collected to measure monomethyl phthalate (MMP), monoethyl phthalate (MEP), monobutyl phthalate (MBP), monobenzyl phthalate (MBzP), mono (2-ethylhexyl) phthalate (MEHP), mono (2-ethyl-5-oxohexyl) phthalate (MEOHP) and mono (2-ethyl-5-hydroxyhexyl) phthalate (MEHHP). The concentrations of low- and high-molecular weight phthalate metabolites (ΣLMWP <250 Da and ΣHMWP >250 Da) were calculated. Adjusted logistic regression models showed increased risks of clinical pregnancy loss in women with higher creatinine- normalized concentrations of MEP, MBP, MEOHP, MEHHP, ΣLMWP and ΣHMWP. Stratified analysis by gestational weeks (10 weeks) of miscarriage indicated positive associations of MEP, MEOHP, MEHHP and ΣHMWP with embryonic loss (during gestational weeks 6 to 10). The only association of foetal loss (during gestational weeks 11 to 27) was observed with MEHHP. Our findings suggested that Chinese women who were exposed to phthalates during early pregnancy had an increased risk of clinical pregnancy loss, especially embryonic loss.
Mycobacterial DNA-binding protein 1 is critical for long term survival of Mycobacterium smegmatis and simultaneously coordinates cellular functions
Authors: Enany Shymaa , Yoshida Yutaka , Tateishi Yoshitaka , Ozeki Yuriko , Nishiyama Akihito , Savitskaya Anna , Yamaguchi Takehiro , Ohara Yukiko , Yamamoto Tadashi , Ato Manabu , Matsumoto Sohkichi
Published: July 2017

Bacteria can proliferate perpetually without ageing, but they also face conditions where they must persist. Mycobacteria can survive for a long period. This state appears during mycobacterial diseases such as tuberculosis and leprosy, which are chronic and develop after long-term persistent infections. However, the fundamental mechanisms of the long-term living of mycobacteria are unknown. EveryMycobacteriumspecies expresses Mycobacterial DNA-binding protein 1 (MDP1), a histone-like nucleoid associated protein.Mycobacterium smegmatisis a saprophytic fast grower and used as a model of mycobacterial persistence, since it shares the characteristics of the long-term survival observed in pathogenic mycobacteria. Here we show that MDP1-deficientM. smegmatisdies more rapidly than the parental strain after entering stationary phase. Proteomic analyses revealed 21 upregulated proteins with more than 3-fold in MDP1-deficient strain, including DnaA, a replication initiator, NDH, a NADH dehydrogenase that catalyzes downhill electron transfer, Fas1, a critical fatty acid synthase, and antioxidants such as AhpC and KatG. Biochemical analyses showed elevated levels of DNA and ATP syntheses, a decreased NADH/NAD+ratio, and a loss of resistance to oxidative stress in the MDP1-knockout strain. This study suggests the importance of MDP1-dependent simultaneous control of the cellular functions in the long-term survival of mycobacteria.
Interaction patterns and individual dynamics shape the way we move in synchrony
Authors: Alderisio Francesco , Fiore Gianfranco , Salesse Robin N. , Bardy Benoît G. , Bernardo Mario di
Published: July 2017

An important open problem in Human Behaviour is to understand how coordination emerges in human ensembles. This problem has been seldom studied quantitatively in the existing literature, in contrast to situations involving dual interaction. Here we study motor coordination (or synchronisation) in a group of individuals where participants are asked to visually coordinate an oscillatory hand motion. We separately tested two groups of seven participants. We observed that the coordination level of the ensemble depends on group homogeneity, as well as on the pattern of visual couplings (who looked at whom). Despite the complexity of social interactions, we show that networks of coupled heterogeneous oscillators with different structures capture well the group dynamics. Our findings are relevant to any activity requiring the coordination of several people, as in music, sport or at work, and can be extended to account for other perceptual forms of interaction such as sound or feel.
Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)
Authors: Souza Carla A. , Murphy Nicholas , Villacorta-Rath Cecilia , Woodings Laura N. , Ilyushkina Irina , Hernandez Cristian E. , Green Bridget S. , Bell James J. , Strugnell Jan M.
Published: July 2017

Double digest restriction site-associated DNA sequencing (ddRADseq) and target capture sequencing methods are used to explore population and phylogenetic questions in non-model organisms. ddRADseq offers a simple and reliable protocol for population genomic studies, however it can result in a large amount of missing data due to allelic dropout. Target capture sequencing offers an opportunity to increase sequencing coverage with little missing data and consistent orthologous loci across samples, although this approach has generally been applied to conserved markers for deeper evolutionary questions. Here, we combine both methods to generate high quality sequencing data for population genomic studies of all marine lobster species from the genus Jasus. We designed probes based on ddRADseq libraries of two lobster species (Jasus edwardsii and Sagmariasus verreauxi) and evaluated the captured sequencing data in five other Jasus species. We validated 4,465 polymorphic loci amongst these species using a cost effective sequencing protocol, of which 1,730 were recovered from all species, and 4,026 were present in at least three species. The method was also successfully applied to DNA samples obtained from museum specimens. This data will be further used to assess spatial-temporal genetic variation in Jasus species found in the Southern Hemisphere.
PyroTyping, a novel pyrosequencing-based assay for Mycobacterium tuberculosis genotyping
Authors: Molina-Moya B. , Lacoma A. , García-Sierra N. , Blanco S. , Haba L. , Samper S. , Ruiz-Manzano J. , Prat C. , Arnold C. , Domínguez J.
Published: July 2017

We developed a novel method, PyroTyping, for discrimination of Mycobacterium tuberculosis isolates combining pyrosequencing and IS6110 polymorphism. A total of 100 isolates were analysed with IS6110-restriction fragment length polymorphism (RFLP), spoligotyping, mycobacterial interspersed repetitive units – variable number tandem repeats (MIRU-VNTR), and PyroTyping. PyroTyping results regarding clustering or discrimination of the isolates were highly concordant with the other typing methods performed. PyroTyping is more rapid than RFLP and presents the same discriminatory power, thus, it may be useful for taking timely decisions for tuberculosis control.
A unique Cretaceous–Paleogene lineage of piranha-jawed pycnodont fishes
Authors: Vullo Romain , Cavin Lionel , Khalloufi Bouziane , Amaghzaz Mbarek , Bardet Nathalie , Jalil Nour-Eddine , Jourani Essaid , Khaldoune Fatima , Gheerbrant Emmanuel
Published: July 2017

The extinct group of the Pycnodontiformes is one of the most characteristic components of the Mesozoic and early Cenozoic fish faunas. These ray-finned fishes, which underwent an explosive morphological diversification during the Late Cretaceous, are generally regarded as typical shell-crushers. Here we report unusual cutting-type dentitions from the Paleogene of Morocco which are assigned to a new genus of highly specialized pycnodont fish. This peculiar taxon represents the last member of a new, previously undetected 40-million-year lineage (Serrasalmimidae fam. nov., including two other new genera and Polygyrodus White, 1927) ranging back to the early Late Cretaceous and leading to exclusively carnivorous predatory forms, unique and unexpected among pycnodonts. Our discovery indicates that latest Cretaceous–earliest Paleogene pycnodonts occupied more diverse trophic niches than previously thought, taking advantage of the apparition of new prey types in the changing marine ecosystems of this time interval. The evolutionary sequence of trophic specialization characterizing this new group of pycnodontiforms is strikingly similar to that observed within serrasalmid characiforms, from seed- and fruit-eating pacus to flesh-eating piranhas.
Cyclin-dependent Kinase 5: Novel role of gene variants identified in ADHD
Authors: Maitra Subhamita , Chatterjee Mahasweta , Sinha Swagata , Mukhopadhyay Kanchan
Published: July 2017

Cortical neuronal migration and formation of filamentous actin cytoskeleton, needed for development, normal cell growth and differentiation, are regulated by the cyclin-dependent kinase 5 (Cdk5). Attention deficit hyperactivity disorder (ADHD) is associated with delayed maturation of the brain and hence we hypothesized that cdk5 may have a role in ADHD. Eight functional CDK5 gene variants were analyzed in 848 Indo-Caucasoid individuals including 217 families with ADHD probands and 250 healthy volunteers. Only three variants, rs2069454, rs2069456 and rs2069459, predicted to affect transcription, were found to be bimorphic. Significant difference in rs2069456 “AC” genotype frequency was noticed in the probands, more specifically in the males. Family based analysis revealed over transmission of rs2069454 “C” and rs2069456 “A” to the probands. Quantitative trait analysis exhibited association of haplotypes with inattention, domain specific impulsivity, and behavioral problem, though no significant contribution was noticed on the age of onset of ADHD. Gene variants also showed significant association with cognitive function and co-morbidity. Probands having rs2069459 “TT” showed betterment during follow up. It may be inferred from this pilot study that CDK5 may affect ADHD etiology, possibly by attenuating synaptic neurotransmission and could be a useful target for therapeutic intervention.
Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation
Authors: Nelson Andrew C. , Mould Arne W. , Bikoff Elizabeth K. , Robertson Elizabeth J.
Published: July 2017

Trophoblast stem cells (TSCs) give rise to specialized cell types within the placenta. However, the regulatory mechanisms that guide trophoblast cell fate decisions during placenta development remain ill defined. Here we exploited ATAC-seq and transcriptional profiling strategies to describe dynamic changes in gene expression and chromatin accessibility during TSC differentiation. We detect significantly increased chromatin accessibility at key genes upregulated as TSCs exit from the stem cell state. However, downregulated gene expression is not simply due to the loss of chromatin accessibility in proximal regions. Additionally, transcriptional targets recognized by the zinc finger transcriptional repressor Prdm1/Blimp1, an essential regulator of placenta development, were identified in ChIP-seq experiments. Comparisons with previously reported ChIP-seq datasets for primordial germ cell-like cells and E18.5 small intestine, combined with functional annotation analysis revealed that Blimp1 has broadly shared as well as cell type-specific functional activities unique to the trophoblast lineage. Importantly, Blimp1 not only silences TSC gene expression but also prevents aberrant activation of divergent developmental programmes. Overall the present study provides new insights into the chromatin landscape and Blimp1-dependent regulatory networks governing trophoblast gene expression.
Enhancer of Zeste homolog 2 (EZH2) induces epithelial-mesenchymal transition in endometriosis
Authors: Zhang Qi , Dong Peixin , Liu Xishi , Sakuragi Noriaki , Guo Sun-Wei
Published: July 2017

EZH2, a subunit of the polycomb repressive complex 2 (PRC2) catalyzing trimethylation of histone H3 lysine 27 (H3K27), induces epithelial-mesenchymal transition (EMT) in cancers. However, whether EZH2 regulates EMT in endometriosis is unclear. Here, we show that EZH2 expression, along with its associated PRC2 proteins, is significantly elevated in ectopic and eutopic endometrium from women with endometriosis as compared with control endometrium. EZH2 knockdown or inhibition restored the epithelial phenotypes of endometriotic epithelial cells, concomitant with the upregulation of E-cadherin and downregulation of vimentin and transcription factors (Snail and Slug) as well as reduced cellular migratory and invasive propensity. Conversely, overexpression of EZH2 induced the expression of Snail, Slug and vimentin and suppresses E-cadherin expression. In vivo administration of 3-Deazaneplanocin A (DZNep), an EZH2 inhibitor, significantly inhibited the growth of endometriotic lesions and improved generalized hyperalgesia, along with attenuated EMT and reduced fibrosis in endometriosis. Notably, platelets induced EZH2 upregulation and increased H3K27 and H3K9 trimethylation levels in endometriotic epithelial cells. These data identify EZH2 as a novel driver of EMT in endometriosis, implicates the link between wound healing and epigenetic changes in the context of endometriosis, and underscore the role of platelets in the development of endometriosis.
Memory-type ST2+CD4+ T cells participate in the steroid-resistant pathology of eosinophilic pneumonia
Authors: Mato Naoko , Hirahara Kiyoshi , Ichikawa Tomomi , Kumagai Jin , Nakayama Masayuki , Yamasawa Hideaki , Bando Masashi , Hagiwara Koichi , Sugiyama Yukihiko , Nakayama Toshinori
Published: July 2017

The lung develops an unique epithelial barrier system to protect host from continuous invasion of various harmful particles. Interleukin (IL-)33 released from epithelial cells in the lung drives the type 2 immune response by activating ST2− expressed immune cells in various allergic diseases. However, the involvement of memory-type ST2+CD4+ T cells in such lung inflammation remains unclear. Here we demonstrated that intratracheal administration of IL-33 resulted in the substantial increase of numbers of tissue-resident memory-type ST2+CD4+ T cells in the lung. Following enhanced production of IL-5 and IL-13, eosinophilic lung inflammation sequentially developed. IL-33-mediated eosinophilic lung inflammation was not fully developed in T cell-deficient Foxn1
nu
mice and NSG mice. Dexamethasone treatment showed limited effects on both the cell number and function of memory-type ST2+CD4+ T cells. Thus our study provides novel insight into the pathogenesis of eosinophilic lung disease, showing that memory-type ST2+CD4+ T cells are involved in IL-33-induced eosinophilic inflammation and elicited steroid-resistance.
Scheduled feeding restores memory and modulates c-Fos expression in the suprachiasmatic nucleus and septohippocampal complex
Authors: Ruby Norman F. , Fisher Nathan , Patton Danica F. , Paul Matthew J. , Fernandez Fabian , Heller H. Craig
Published: July 2017

Disruptions in circadian timing impair spatial memory in humans and rodents. Circadian-arrhythmic Siberian hamsters (Phodopus sungorus) exhibit substantial deficits in spatial working memory as assessed by a spontaneous alternation (SA) task. The present study found that daily scheduled feeding rescued spatial memory deficits in these arrhythmic animals. Improvements in memory persisted for at least 3 weeks after the arrhythmic hamsters were switched back to ad libitum feeding. During ad libitum feeding, locomotor activity resumed its arrhythmic state, but performance on the SA task varied across the day with a peak in daily performance that corresponded to the previous daily window of food anticipation. At the end of scheduled feeding, c-Fos brain mapping revealed differential gene expression in entrained versus arrhythmic hamsters in the suprachiasmatic nucleus (SCN) that paralleled changes in the medial septum and hippocampus, but not in other neural structures. These data show that scheduled feeding can improve cognitive performance when SCN timing has been compromised, possibly by coordinating activity in the SCN and septohippocampal pathway.
Direct estimation of the global distribution of vertical velocity within cirrus clouds
Authors: Barahona Donifan , Molod Andrea , Kalesse Heike
Published: July 2017

Cirrus clouds determine the radiative balance of the upper troposphere and the transport of water vapor across the tropopause. The representation of vertical wind velocity, W, in atmospheric models constitutes the largest source of uncertainty in the calculation of the cirrus formation rate. Using global atmospheric simulations with a spatial resolution of 7 km we obtain for the first time a direct estimate of the distribution of W at the scale relevant for cirrus formation, validated against long-term observations at two different ground sites. The standard deviation in W, σ
w
, varies widely over the globe with the highest values resulting from orographic uplift and convection, and the lowest occurring in the Arctic. Globally about 90% of the simulated σ
w
values are below 0.1 m s−1 and about one in 104 cloud formation events occur in environments with σ
w
 > 0.8 m s−1. Combining our estimate with reanalysis products and an advanced cloud formation scheme results in lower homogeneous ice nucleation frequency than previously reported, and a decreasing average ice crystal concentration with decreasing temperature. These features are in agreement with observations and suggest that the correct parameterization of σ
w
is critical to simulate realistic cirrus properties.
Image-Based Chemical Structure Determination
Authors: Ofner Johannes , Brenner Florian , Wieland Karin , Eitenberger Elisabeth , Kirschner Johannes , Eisenmenger-Sittner Christoph , Török Szilvia , Döme Balazs , Konegger Thomas , Kasper-Giebl Anne , Hutter Herbert , Friedbacher Gernot , Lendl Bernhard , Lohninger Hans
Published: July 2017

Chemical imaging is a powerful tool for understanding the chemical composition and nature of heterogeneous samples. Recent developments in elemental, vibrational, and mass-spectrometric chemical imaging with high spatial resolution (50–200 nm) and reasonable timescale (a few hours) are capable of providing complementary chemical information about various samples. However, a single technique is insufficient to provide a comprehensive understanding of chemically complex materials. For bulk samples, the combination of different analytical methods and the application of statistical methods for extracting correlated information across different techniques is a well-established and powerful concept. However, combined multivariate analytics of chemical images obtained via different imaging techniques is still in its infancy, hampered by a lack of analytical methodologies for data fusion and analysis. This study demonstrates the application of multivariate statistics to chemical images taken from the same sample via various methods to assist in chemical structure determination.
In vivo Raman spectral analysis of impaired cervical remodeling in a mouse model of delayed parturition
Authors: O’Brien Christine M. , Herington Jennifer L. , Brown Naoko , Pence Isaac J. , Paria Bibhash C. , Slaughter James C. , Reese Jeff , Mahadevan-Jansen Anita
Published: July 2017

Monitoring cervical structure and composition during pregnancy has high potential for prediction of preterm birth (PTB), a problem affecting 15 million newborns annually. We usein vivoRaman spectroscopy, a label-free, light-based method that provides a molecular fingerprint to non-invasively investigate normal and impaired cervical remodeling. Prostaglandins stimulate uterine contractions and are clinically used for cervical ripening during pregnancy. Deletion of cyclooxygenase-1 (Cox-1), an enzyme involved in production of these prostaglandins, results in delayed parturition in mice. Contrary to expectation, Cox-1 null mice displayed normal uterine contractility; therefore, this study sought to determine whether cervical changes could explain the parturition differences in Cox-1 null mice and gestation-matched wild type (WT) controls. Raman spectral changes related to extracellular matrix proteins, lipids, and nucleic acids were tracked over pregnancy and found to be significantly delayed in Cox-1 null mice at term. A cervical basis for the parturition delay was confirmed by otherex vivotests including decreased tissue distensibility, hydration, and elevated progesterone levels in the Cox-1 null mice at term. In conclusion,in vivoRaman spectroscopy non-invasively detected abnormal remodeling in the Cox-1 null mouse, and clearly demonstrated that the cervix plays a key role in their delayed parturition.