bluuebunny/crossref_metadata_2025 huggingface dataset:
Cyanobacterial photosynthesis under sulfidic conditions: insights from the isolate Leptolyngbya sp. strain hensonii
Authors: Hamilton Trinity L , Klatt Judith M , de Beer Dirk , Macalady Jennifer L
Published: January 2018

We report the isolation of a pinnacle-forming cyanobacterium isolated from a microbial mat covering the sediment surface at Little Salt Spring—a flooded sinkhole in Florida with a perennially microoxic and sulfidic water column. The draft genome of the isolate encodes all of the enzymatic machinery necessary for both oxygenic and anoxygenic photosynthesis, as well as genes for methylating hopanoids at the C-2 position. The physiological response of the isolate to H2S is complex: (i) no induction time is necessary for anoxygenic photosynthesis; (ii) rates of anoxygenic photosynthesis are regulated by both H2S and irradiance; (iii) O2 production is inhibited by H2S concentrations as low as 1 µm and the recovery rate of oxygenic photosynthesis is dependent on irradiance; (iv) under the optimal light conditions for oxygenic photosynthesis, rates of anoxygenic photosynthesis are nearly double those of oxygenic photosynthesis. We hypothesize that the specific adaptation mechanisms of the isolate to H2S emerged from a close spatial interaction with sulfate-reducing bacteria. The new isolate, Leptolyngbya sp. strain hensonii, is not closely related to other well-characterized Cyanobacteria that can perform anoxygenic photosynthesis, which further highlights the need to characterize the diversity and biogeography of metabolically versatile Cyanobacteria. The isolate will be an ideal model organism for exploring the adaptation of Cyanobacteria to sulfidic conditions.
Enhancement of the ‘tractor-beam’ pulling force on an optically bound structure
Authors: Damková Jana , Chvátal Lukáš , Ježek Jan , Oulehla Jindřich , Brzobohatý Oto , Zemánek Pavel
Published: January 2018

Recently, increasing attention has been devoted to mastering a new technique of optical delivery of micro-objects tractor-beam’1, 2, 3, 4, 5, 6, 7, 8, 9. Such beams have uniform intensity profiles along their propagation direction and can exert a negative force that, in contrast to the familiar pushing force associated with radiation pressure, pulls the scatterer toward the light source. It was experimentally observed that under certain circumstances, the pulling force can be significantly enhanced6 if a non-spherical scatterer, for example, a linear chain of optically bound objects10, 11, 12, is optically transported. Here we demonstrate that motion of two optically bound objects in a tractor beam strongly depends on theirs mutual distance and spatial orientation. Such configuration-dependent optical forces add extra flexibility to our ability to control matter with light. Understanding these interactions opens the door to new applications involving the formation, sorting or delivery of colloidal self-organized structures.
The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean
Authors: Vincent Flora J , Colin Sébastien , Romac Sarah , Scalco Eleonora , Bittner Lucie , Garcia Yonara , Lopes Rubens M , Dolan John R , Zingone Adriana , de Vargas Colomban , Bowler Chris
Published: January 2018

Diatoms are a diverse and ecologically important group of phytoplankton. Although most species are considered free living, several are known to interact with other organisms within the plankton. Detailed imaging and molecular characterization of any such partnership is, however, limited, and an appraisal of the large-scale distribution and ecology of such consortia was never attempted. Here, observation of Tara Oceans samples from the Benguela Current led to the detection of an epibiotic association between a pennate diatom and a tintinnid ciliate. We identified the diatom as Fragilariopsis doliolus that possesses a unique feature to form barrel-shaped chains, associated with seven different genera of tintinnids including five previously undescribed associations. The organisms were commonly found together in the Atlantic and Pacific Ocean basins, and live observations of the interaction have been recorded for the first time. By combining confocal and scanning electron microscopy of individual consortia with the sequencing of high-resolution molecular markers, we analyzed their distribution in the global ocean, revealing morpho-genetically distinct tintinnid haplotypes and biogeographically structured diatom haplotypes. The diatom was among the most abundant in the global ocean. We show that the consortia were particularly prevalent in nutrient-replete conditions, rich in potential predators. These observations support the hypothesis of a mutualistic symbiosis, wherein diatoms acquire increased motility and tintinnids benefit from silicification through increased protection, and highlight that such associations may be more prevalent than currently appreciated.
Three-dimensional bicontinuous nanoporous materials by vapor phase dealloying
Authors: Lu Zhen , Li Cheng , Han Jiuhui , Zhang Fan , Liu Pan , Wang Hao , Wang Zhili , Cheng Chun , Chen Linghan , Hirata Akihiko , Fujita Takeshi , Erlebacher Jonah , Chen Mingwei
Published: January 2018

Three-dimensional bicontinuous open (3DBO) nanoporosity has been recognized as an important nanoarchitecture for catalysis, sensing, and energy storage. Dealloying, i.e., selectively removing a component from an alloy, is an efficient way to fabricate nanoporous materials. However, current electrochemical and liquid-metal dealloying methods can only be applied to a limited number of alloys and usually require an etching process with chemical waste. Here, we report a green and universal approach, vapor-phase dealloying, to fabricate nanoporous materials by utilizing the vapor pressure difference between constituent elements in an alloy to selectively remove a component with a high partial vapor pressure for 3DBO nanoporosity. We demonstrate that extensive elements, regardless of chemical activity, can be fabricated as nanoporous materials with tunable pore sizes. Importantly, the evaporated components can be fully recovered. This environmentally friendly dealloying method paves a way to fabricate 3DBO nanoporous materials for a wide range of structural and functional applications.
Structural basis of SALM5-induced PTPδ dimerization for synaptic differentiation
Authors: Lin Zhaohan , Liu Jianmei , Ding Huandi , Xu Fei , Liu Heli
Published: January 2018

SALM5, a synaptic adhesion molecule implicated in autism, induces presynaptic differentiation through binding to the LAR family receptor protein tyrosine phosphatases (LAR-RPTPs) that have been highlighted as presynaptic hubs for synapse formation. The mechanisms underlying SALM5/LAR-RPTP interaction remain unsolved. Here we report crystal structures of human SALM5 LRR-Ig alone and in complex with human PTPδ Ig1–3 (MeA−). Distinct from other LAR-RPTP ligands, SALM5 mainly exists as a dimer with LRR domains from two protomers packed in an antiparallel fashion. In the 2:2 heterotetrameric SALM5/PTPδ complex, a SALM5 dimer bridges two separate PTPδ molecules. Structure-guided mutations and heterologous synapse formation assays demonstrate that dimerization of SALM5 is prerequisite for its functionality in inducing synaptic differentiation. This study presents a structural template for the SALM family and reveals a mechanism for how a synaptic adhesion molecule directly induces cis-dimerization of LAR-RPTPs into higher-order signaling assembly.
Self-generated surface magnetic fields inhibit laser-driven sheath acceleration of high-energy protons
Authors: Nakatsutsumi M. , Sentoku Y. , Korzhimanov A. , Chen S. N. , Buffechoux S. , Kon A. , Atherton B. , Audebert P. , Geissel M. , Hurd L. , Kimmel M. , Rambo P. , Schollmeier M. , Schwarz J. , Starodubtsev M. , Gremillet L. , Kodama R. , Fuchs J.
Published: January 2018

High-intensity lasers interacting with solid foils produce copious numbers of relativistic electrons, which in turn create strong sheath electric fields around the target. The proton beams accelerated in such fields have remarkable properties, enabling ultrafast radiography of plasma phenomena or isochoric heating of dense materials. In view of longer-term multidisciplinary purposes (e.g., spallation neutron sources or cancer therapy), the current challenge is to achieve proton energies well in excess of 100 MeV, which is commonly thought to be possible by raising the on-target laser intensity. Here we present experimental and numerical results demonstrating that magnetostatic fields self-generated on the target surface may pose a fundamental limit to sheath-driven ion acceleration for high enough laser intensities. Those fields can be strong enough (~105 T at laser intensities ~1021 W cm–2) to magnetize the sheath electrons and deflect protons off the accelerating region, hence degrading the maximum energy the latter can acquire.
A general and flexible method for signal extraction from single-cell RNA-seq data
Authors: Risso Davide , Perraudeau Fanny , Gribkova Svetlana , Dudoit Sandrine , Vert Jean-Philippe
Published: January 2018

Single-cell RNA-sequencing (scRNA-seq) is a powerful high-throughput technique that enables researchers to measure genome-wide transcription levels at the resolution of single cells. Because of the low amount of RNA present in a single cell, some genes may fail to be detected even though they are expressed; these genes are usually referred to as dropouts. Here, we present a general and flexible zero-inflated negative binomial model (ZINB-WaVE), which leads to low-dimensional representations of the data that account for zero inflation (dropouts), over-dispersion, and the count nature of the data. We demonstrate, with simulated and real data, that the model and its associated estimation procedure are able to give a more stable and accurate low-dimensional representation of the data than principal component analysis (PCA) and zero-inflated factor analysis (ZIFA), without the need for a preliminary normalization step.
High resolution time series reveals cohesive but short-lived communities in coastal plankton
Authors: Martin-Platero Antonio M. , Cleary Brian , Kauffman Kathryn , Preheim Sarah P. , McGillicuddy Dennis J. , Alm Eric J. , Polz Martin F.
Published: January 2018

Because microbial plankton in the ocean comprise diverse bacteria, algae, and protists that are subject to environmental forcing on multiple spatial and temporal scales, a fundamental open question is to what extent these organisms form ecologically cohesive communities. Here we show that although all taxa undergo large, near daily fluctuations in abundance, microbial plankton are organized into clearly defined communities whose turnover is rapid and sharp. We analyze a time series of 93 consecutive days of coastal plankton using a technique that allows inference of communities as modular units of interacting taxa by determining positive and negative correlations at different temporal frequencies. This approach shows both coordinated population expansions that demarcate community boundaries and high frequency of positive and negative associations among populations within communities. Our analysis thus highlights that the environmental variability of the coastal ocean is mirrored in sharp transitions of defined but ephemeral communities of organisms.
GWAS in childhood acute lymphoblastic leukemia reveals novel genetic associations at chromosomes 17q12 and 8q24.21
Authors: Wiemels Joseph L. , Walsh Kyle M. , de Smith Adam J. , Metayer Catherine , Gonseth Semira , Hansen Helen M. , Francis Stephen S. , Ojha Juhi , Smirnov Ivan , Barcellos Lisa , Xiao Xiaorong , Morimoto Libby , McKean-Cowdin Roberta , Wang Rong , Yu Herbert , Hoh Josephine , DeWan Andrew T. , Ma Xiaomei
Published: January 2018

Childhood acute lymphoblastic leukemia (ALL) (age 0–14 years) is 20% more common in Latino Americans than non-Latino whites. We conduct a genome-wide association study in a large sample of 3263 Californian children with ALL (including 1949 of Latino heritage) and 3506 controls matched on month and year of birth, sex, and ethnicity, and an additional 12,471 controls from the Kaiser Resource for Genetic Epidemiology Research on Aging Cohort. Replication of the strongest genetic associations is performed in two independent datasets from the Children’s Oncology Group and the California Childhood Leukemia Study. Here we identify new risk loci on 17q12 near IKZF3/ZPBP2/GSDMB/ORMDL3, a locus encompassing a transcription factor important for lymphocyte development (IKZF3), and at an 8q24 region known for structural contacts with the MYC oncogene. These new risk loci may impact gene expression via local (four 17q12 genes) or long-range (8q24) interactions, affecting function of well-characterized hematopoietic and growth-regulation pathways.
Fibroblast growth factor 21 increases insulin sensitivity through specific expansion of subcutaneous fat
Authors: Li Huating , Wu Guangyu , Fang Qichen , Zhang Mingliang , Hui Xiaoyan , Sheng Bin , Wu Liang , Bao Yuqian , Li Peng , Xu Aimin , Jia Weiping
Published: January 2018

Although the pharmacological effects of fibroblast growth factor 21 (FGF21) are well-documented, uncertainty about its role in regulating excessive energy intake remains. Here, we show that FGF21 improves systemic insulin sensitivity by promoting the healthy expansion of subcutaneous adipose tissue (SAT). Serum FGF21 levels positively correlate with the SAT area in insulin-sensitive obese individuals. FGF21 knockout mice (FGF21KO) show less SAT mass and are more insulin-resistant when fed a high-fat diet. Replenishment of recombinant FGF21 to a level equivalent to that in obesity restores SAT mass and reverses insulin resistance in FGF21KO, but not in adipose-specific βklotho knockout mice. Moreover, transplantation of SAT from wild-type to FGF21KO mice improves insulin sensitivity in the recipients. Mechanistically, circulating FGF21 upregulates adiponectin in SAT, accompanied by an increase of M2 macrophage polarization. We propose that elevated levels of endogenous FGF21 in obesity serve as a defense mechanism to protect against systemic insulin resistance.
Ice volume and climate changes from a 6000 year sea-level record in French Polynesia
Authors: Hallmann N. , Camoin G. , Eisenhauer A. , Botella A. , Milne G. A. , Vella C. , Samankassou E. , Pothin V. , Dussouillez P. , Fleury J. , Fietzke J.
Published: January 2018

Mid- to late-Holocene sea-level records from low-latitude regions serve as an important baseline of natural variability in sea level and global ice volume prior to the Anthropocene. Here, we reconstruct a high-resolution sea-level curve encompassing the last 6000 years based on a comprehensive study of coral microatolls, which are sensitive low-tide recorders. Our curve is based on microatolls from several islands in a single region and comprises a total of 82 sea-level index points. Assuming thermosteric contributions are negligible on millennial time scales, our results constrain global ice melting to be 1.5–2.5 m (sea-level equivalent) since ~5500 years before present. The reconstructed curve includes isolated rapid events of several decimetres within a few centuries, one of which is most likely related to loss from the Antarctic ice sheet mass around 5000 years before present. In contrast, the occurrence of large and flat microatolls indicates periods of significant sea-level stability lasting up to ~300 years.
Active State Organization of Spontaneous Behavioral Patterns
Authors: Hillar C. , Onnis G. , Rhea D. , Tecott L.
Published: January 2018

We report the development and validation of a principled analytical approach to reveal the manner in which diverse mouse home cage behaviors are organized. We define and automate detection of two mutually-exclusive low-dimensional spatiotemporal units of behavior: “Active” and “Inactive” States. Analyses of these features using a large multimodal 16-strain behavioral dataset provide a series of novel insights into how feeding, drinking, and movement behaviors are coordinately expressed in Mus Musculus. Moreover, we find that patterns of Active State expression are exquisitely sensitive to strain, and classical supervised machine learning incorporating these features provides 99% cross-validated accuracy in genotyping animals using behavioral data alone. Altogether, these findings advance understanding of the organization of spontaneous behavior and provide a high-throughput phenotyping strategy with wide applicability to behavioral neuroscience and animal models of disease.
Rapid updating of spatial working memory across saccades
Authors: Boon Paul J. , Zeni Silvia , Theeuwes Jan , Belopolsky Artem V.
Published: January 2018

Each time we make an eye movement, positions of objects on the retina change. In order to keep track of relevant objects their positions have to be updated. The situation becomes even more complex if the object is no longer present in the world and has to be held in memory. In the present study, we used saccadic curvature to investigate the time-course of updating a memorized location across saccades. Previous studies have shown that a memorized location competes with a saccade target for selection on the oculomotor map, which leads to saccades curving away from it. In our study participants performed a sequence of two saccades while keeping a location in memory. The trajectory of the second saccade was used to measure when the memorized location was updated after the first saccade. The results showed that the memorized location was rapidly updated with the eyes curving away from its spatial coordinates within 130 ms after the first eye movement. The time-course of updating was comparable to the updating of an exogenously attended location, and depended on how well the location was memorized.
Analogues of Disulfides from Allium stipitatum Demonstrate Potent Anti-tubercular Activities through Drug Efflux Pump and Biofilm Inhibition
Authors: Danquah Cynthia A. , Kakagianni Eleftheria , Khondkar Proma , Maitra Arundhati , Rahman Mukhlesur , Evangelopoulos Dimitrios , McHugh Timothy D. , Stapleton Paul , Malkinson John , Bhakta Sanjib , Gibbons Simon
Published: January 2018

Disulfides from Allium stipitatum, commonly known as Persian shallot, were previously reported to possess antibacterial properties. Analogues of these compounds, produced by S-methylthiolation of appropriate thiols using S-methyl methanethiosulfonate, exhibited antimicrobial activity, with one compound inhibiting the growth of Mycobacterium tuberculosis at 17 µM (4 mg L−1) and other compounds inhibiting Escherichia coli and multi-drug-resistant (MDR) Staphylococcus aureus at concentrations ranging between 32–138 µM (8–32 mg L−1). These compounds also displayed moderate inhibitory effects on Klebsiella and Proteus species. Whole-cell phenotypic bioassays such as the spot-culture growth inhibition assay (SPOTi), drug efflux inhibition, biofilm inhibition and cytotoxicity assays were used to evaluate these compounds. Of particular note was their ability to inhibit mycobacterial drug efflux and biofilm formation, while maintaining a high selectivity towards M. tuberculosis H37Rv. These results suggest that methyl disulfides are novel scaffolds which could lead to the development of new drugs against tuberculosis (TB).
Non-marine palaeoenvironment associated to the earliest tetrapod tracks
Authors: Qvarnström Martin , Szrek Piotr , Ahlberg Per E. , Niedźwiedzki Grzegorz
Published: January 2018

Opinions differ on whether the evolution of tetrapods (limbed vertebrates) from lobe-finned fishes was directly linked to terrestrialization. The earliest known tetrapod fossils, from the Middle Devonian (approximately 390 million years old) of Zachełmie Quarry in Poland, are trackways made by limbs with digits; they document a direct environmental association and thus have the potential to help answer this question. However, the tetrapod identity of the tracks has recently been challenged, despite their well-preserved morphology, on account of their great age and supposedly shallow marine (intertidal or lagoonal) depositional environment. Here we present a new palaeoenvironmental interpretation of the track-bearing interval from Zachełmie, showing that it represents a succession of ephemeral lakes with a restricted and non-marine biota, rather than a marginal marine environment as originally thought. This context suggests that the trackmaker was capable of terrestrial locomotion, consistent with the appendage morphology recorded by the footprints, and thus provides additional support for a tetrapod identification.
Soluble LRP1 is an independent biomarker of epicardial fat volume in patients with type 1 diabetes mellitus
Authors: de Gonzalo-Calvo David , Colom Cristina , Vilades David , Rivas-Urbina Andrea , Moustafa Abdel-Hakim , Pérez-Cuellar Montserrat , Sánchez-Quesada Jose Luis , Pérez Antonio , LLorente-Cortes Vicenta
Published: January 2018

Epicardial adipose tissue (EAT) is a metabolically active tissue intimately associated with metabolic syndrome and cardiovascular disease. Quantification of EAT volume is an interesting clinical tool for the evaluation of cardiometabolic disease. Nevertheless, current methodology presents serious disadvantages. The soluble form of the receptor LRP1 (sLRP1) is a non-invasive biomarker of EAT in general population. Here, we analysed the potential of circulating sLRP1 as biomarker of EAT volume in patients with type 1 diabetes mellitus (T1DM). The study included a well-characterized cohort of T1DM patients without clinical cardiovascular disease (N = 73). EAT volume was assessed by a multidetector computed tomography (MDCT). sLRP1 and panel of inflammatory and endocrine mediators were measured using commercially available ELISA. EAT volume showed a direct association with circulating sLRP1 (β = 0.398, P = 0.001) in univariate linear regression analysis. This association was higher than that observed for other potential inflammatory and endocrine biomarkers. Using multivariate linear regression analyses, we demonstrated that the association between EAT volume and circulating sLRP1 was independent of potential confounding factors, including age, sex, body mass index, CRP, HbA1c and LDL-C (P < 0.050 for all multivariate linear regression models). In conclusion, sLRP1 is an independent biomarker of EAT in T1DM patients.
Genetic evidence for panmixia in a colony-breeding crater lake cichlid fish
Authors: Lehtonen T. K. , Elmer K. R. , Lappalainen M. , Meyer A.
Published: January 2018

Fine-scaled genetic structuring, as seen for example in many lacustrine fish, typically relates to the patterns of migration, habitat use, mating system or other ecological factors. Because the same processes can also affect the propensity of population differentiation and divergence, assessments of species from rapidly speciating clades, or with particularly interesting ecological traits, can be especially insightful. For this study, we assessed the spatial genetic relationships, including the genetic evidence for sex-biased dispersal, in a colony-breeding cichlid fish, Amphilophus astorquii, endemic to Crater Lake Apoyo in Nicaragua, using 11 polymorphic microsatellite loci (n = 123 individuals from three colonies). We found no population structure in A. astorquii either within colonies (no spatial genetic autocorrelation, r ~0), or at the lake-wide level (pairwise population differentiation FST = 0–0.013 and no clustering), and there was no sex-bias (male and female AIc values bounded 0) to this lack of genetic structure. These patterns may be driven by the colony-breeding reproductive behaviour of A. astorquii. The results suggest that strong philopatry or spatial assortative mating are unlikely to explain the rapid speciation processes associated with the history of this species in Lake Apoyo.
Non-structural carbohydrates regulated by season and species in the subtropical monsoon broad-leaved evergreen forest of Yunnan Province, China
Authors: Liu Wande , Su Jianrong , Li Shuaifeng , Lang Xuedong , Huang Xiaobo
Published: January 2018

Non-structural carbohydrates (NSC) play important roles in adapting to environments in plants. Despite extensive research on the seasonal dynamics and species differences of NSC, the relative contributions of season and species to NSC is not well understood. We measured the concentration of starch, soluble sugar, NSC, and the soluble sugar:starch ratio in leaves, twigs, trunks and roots of twenty dominant species for dry and wet season in monsoon broad-leaved evergreen forest, respectively. The majority of concentration of NSC and starch in the roots, and the leaves contained the highest concentration of soluble sugar. A seasonal variation in starch and NSC concentrations higher in the dry season. Conversely, the wet season samples had higher concentration of soluble sugar and the sugar:starch ratio. Significant differences exist for starch, soluble sugar and NSC concentrations and the sugar:starch ratio across species. Most species had higher starch and NSC concentrations in the dry season and higher soluble sugar concentration and the sugar:starch ratio in wet season. Repeated variance analysis showed that starch and NSC concentrations were strongly affected by season although the effect of seasons, species, and the interaction of the two on the starch, soluble sugar, and NSC concentrations were significant.
Multi-stage volcanic island flank collapses with coeval explosive caldera-forming eruptions
Authors: Hunt James E. , Cassidy Michael , Talling Peter J.
Published: January 2018

Volcanic flank collapses and explosive eruptions are among the largest and most destructive processes on Earth. Events at Mount St. Helens in May 1980 demonstrated how a relatively small (<5 km3) flank collapse on a terrestrial volcano could immediately precede a devastating eruption. The lateral collapse of volcanic island flanks, such as in the Canary Islands, can be far larger (>300 km3), but can also occur in complex multiple stages. Here, we show that multistage retrogressive landslides on Tenerife triggered explosive caldera-forming eruptions, including the Diego Hernandez, Guajara and Ucanca caldera eruptions. Geochemical analyses were performed on volcanic glasses recovered from marine sedimentary deposits, called turbidites, associated with each individual stage of each multistage landslide. These analyses indicate only the lattermost stages of subaerial flank failure contain materials originating from respective coeval explosive eruption, suggesting that initial more voluminous submarine stages of multi-stage flank collapse induce these aforementioned explosive eruption. Furthermore, there are extended time lags identified between the individual stages of multi-stage collapse, and thus an extended time lag between the initial submarine stages of failure and the onset of subsequent explosive eruption. This time lag succeeding landslide-generated static decompression has implications for the response of magmatic systems to un-roofing and poses a significant implication for ocean island volcanism and civil emergency planning.
Chikungunya virus nsP1 interacts directly with nsP2 and modulates its ATPase activity
Authors: Kumar Sameer , Kumar Abhishek , Mamidi Prabhudutta , Tiwari Atul , Kumar Sriram , Mayavannan Animamalar , Mudulli Sagarika , Singh Ajit Kumar , Subudhi Bharat Bhusan , Chattopadhyay Soma
Published: January 2018

Chikungunya virus (CHIKV) is a mosquito-borne virus, which has created an alarming threat in the world due to unavailability of vaccine and antiviral compounds. The CHIKV nsP2 contains ATPase, RTPase, helicase and protease activities, whereas, nsP1 is a viral capping enzyme. In alphaviruses, the four non-structural proteins form the replication complex in the cytoplasm and this study characterizes the interaction between CHIKV nsP1 and nsP2. It was observed that, both the proteins co-localize in the cytoplasm and interact in the CHIKV infected cells by confocal microscopy and immunoprecipitation assay. Further, it was demonstrated through mutational analysis that, the amino acids 1-95 of nsP2 and 170-288 of nsP1 are responsible for their direct interaction. Additionally, it was noticed that, the ATPase activity of nsP2 is enhanced in the presence of nsP1, indicating the functional significance of this interaction. In silico analysis showed close (≤1.7 Å) polar interaction (hydrogen bond) between Glu4, Arg7, 96, 225 of nsP2 with Lys256, 206, Val367 and Phe312 of nsP1 respectively. Hence, this investigation provides molecular characterization of CHIKV nsP1-nsP2 interaction which might be a useful target for rational designing of antiviral drugs.
A surrogate reporter system for multiplexable evaluation of CRISPR/Cas9 in targeted mutagenesis
Authors: Zhang Hongmin , Zhou Yuexin , Wang Yinan , Zhao Yige , Qiu Yeting , Zhang Xinyi , Yue Di , Zhou Zhuo , Wei Wensheng
Published: January 2018

Engineered nucleases in genome editing manifest diverse efficiencies at different targeted loci. There is therefore a constant need to evaluate the mutation rates at given loci. T7 endonuclease 1 (T7E1) and Surveyor mismatch cleavage assays are the most widely used methods, but they are labour and time consuming, especially when one must address multiple samples in parallel. Here, we report a surrogate system, called UDAR (Universal Donor As Reporter), to evaluate the efficiency of CRISPR/Cas9 in targeted mutagenesis. Based on the non-homologous end-joining (NHEJ)-mediated knock-in strategy, the UDAR-based assay allows us to rapidly evaluate the targeting efficiencies of sgRNAs. With one-step transfection and fluorescence-activated cell sorting (FACS) analysis, the UDAR assay can be completed on a large scale within three days. For detecting mutations generated by the CRISPR/Cas9 system, a significant positive correlation was observed between the results from the UDAR and T7E1 assays. Consistently, the UDAR assay could quantitatively assess bleomycin- or ICRF193-induced double-strand breaks (DSBs), which suggests that this novel strategy is broadly applicable to assessing the DSB-inducing capability of various agents. With the increasing impact of genome editing in biomedical studies, the UDAR method can significantly benefit the evaluation of targeted mutagenesis, especially for high-throughput purposes.
Preparation of polyaniline/PbS core-shell nano/microcomposite and its application for photocatalytic H2 electrogeneration from H2O
Authors: Rabia Mohamed , Mohamed H. S. H. , Shaban Mohamed , Taha S.
Published: January 2018

Lead sulfide (PbS) and polyaniline (PANI) nano/microparticles were prepared. Then, PANI/PbS core-shell nano/microcomposites (I, II, and III) were prepared by oxidative polymerization of different aniline concentrations (0.01, 0.03, and 0.05 M), respectively, in the presence of 0.05 M PbS. FT-IR, XRD, SEM, HR-TEM, and UV-Vis analyses were carried out to characterize the samples. From the FT-IR data, there are redshifts in PbS and PANI nano/microparticles bands in comparison with PANI/PbS nano/microcomposites. The average crystallite sizes of PANI/PbS core-shell nano/microcomposites (I, II, and III) from XRD analyses were 46.5, 55, and 42.16 nm, respectively. From the optical analyses, nano/microcomposite (II) has the optimum optical properties with two band gaps values of 1.41 and 2.79 eV. Then, the nano/microcomposite (II) membrane electrode supported on ITO glass was prepared and applied on the photoelectrochemical (PEC) H2generation from H2O. The characteristics current-voltage and current-time behaviors were measured at different wavelengths from 390 to 636 nm. Also, the incident photon-to-current conversion efficiency (IPCE) under monochromatic illumination condition was calculated. The optimum values for IPCE were 36.5 and 35.2% at 390 and 405 nm, respectively. Finally, a simple mechanism for PEC H2generation from H2O using the nano/microcomposite (II) membrane electrode was mentioned.
Decadal climate predictability in the southern Indian Ocean captured by SINTEX-F using a simple SST-nudging scheme
Authors: Morioka Yushi , Doi Takeshi , Behera Swadhin K.
Published: January 2018

Decadal climate variability in the southern Indian Ocean has great influences on southern African climate through modulation of atmospheric circulation. Although many efforts have been made to understanding physical mechanisms, predictability of the decadal climate variability, in particular, the internally generated variability independent from external atmospheric forcing, remains poorly understood. This study investigates predictability of the decadal climate variability in the southern Indian Ocean using a coupled general circulation model, called SINTEX-F. The ensemble members of the decadal reforecast experiments were initialized with a simple sea surface temperature (SST) nudging scheme. The observed positive and negative peaks during late 1990s and late 2000s are well reproduced in the reforecast experiments initiated from 1994 and 1999, respectively. The experiments initiated from 1994 successfully capture warm SST and high sea level pressure anomalies propagating from the South Atlantic to the southern Indian Ocean. Also, the other experiments initiated from 1999 skillfully predict phase change from a positive to negative peak. These results suggest that the SST-nudging initialization has the essence to capture the predictability of the internally generated decadal climate variability in the southern Indian Ocean.
Anti-cancer activities of allyl isothiocyanate and its conjugated silicon quantum dots
Authors: Liu Peng , Behray Mehrnaz , Wang Qi , Wang Wei , Zhou Zhigang , Chao Yimin , Bao Yongping
Published: January 2018

Allyl isothiocyanate (AITC), a dietary phytochemical in some cruciferous vegetables, exhibits promising anticancer activities in many cancer models. However, previous data showed AITC to have a biphasic effect on cell viability, DNA damage and migration in human hepatoma HepG2 cells. Moreover, in a 3D co-culture of HUVEC with pericytes, it inhibited tube formation at high doses but promoted this at low doses, which confirmed its biphasic effect on angiogenesis. siRNA knockdown of Nrf2 and glutathione inhibition abolished the stimulation effect of AITC on cell migration and DNA damage. The biological activity of a novel AITC-conjugated silicon quantum dots (AITC-SiQDs) has been investigated for the first time. AITC-SiQDs showed similar anti-cancer properties to AITC at high doses while avoiding the low doses stimulation effect. In addition, AITC-SiQDs showed a lower and long-lasting activation of Nrf2 translocation into nucleus which correlated with their levels of cellular uptake, as detected by the intrinsic fluorescence of SiQDs. ROS production could be one of the mechanisms behind the anti-cancer effect of AITC-SiQDs. These data provide novel insights into the biphasic effect of AITC and highlight the application of nanotechnology to optimize the therapeutic potential of dietary isothiocyanates in cancer treatment.
Neural predictors of cognitive improvement by multi-strategic memory training based on metamemory in older adults with subjective memory complaints
Authors: Park Soowon , Ryu Seung-Ho , Yoo Yongjoon , Yang Jin-Ju , Kwon Hunki , Youn Jung-Hae , Lee Jong-Min , Cho Seong-Jin , Lee Jun-Young
Published: January 2018

Previous studies have indicated that memory training may help older people improve cognition. However, evidence regarding who will benefit from such memory trainings has not been fully discovered yet. Understanding the clinical and neural inter-individual differences for predicting cognitive improvement is important for maximizing the training efficacy of memory-training programs. The purpose of this study was to find the individual characteristics and brain morphological characteristics that predict cognitive improvement after a multi-strategic memory training based on metamemory concept. Among a total of 49 older adults, 39 participated in the memory-training program and 10 did not. All of them underwent brain MRIs at the entry of the training and received the neuropsychological tests twice, before and after the training. Stepwise regression analysis showed that lower years of education predicted cognitive improvement in the training group. In MRI, thinner cortices of precuneus, cuneus and posterior cingulate gyrus and higher white matter anisotropy of the splenium of corpus callosum predicted cognitive improvement in the training group. Old age, lower education level and individual differences in cortical thickness and white matter microstructure of the episodic memory network may predict outcomes following multi-strategic training.
Trends in Fetal Growth Between 2000 to 2014 in Singleton Live Births from Israel
Authors: Agay-Shay Keren , Rudolf Mary , Rubin Lisa , Haklai Ziona , Grotto Itamar
Published: January 2018

Trends in birthweight and abnormal fetal growth, namely term low birthweight (LBW), macrosomia, small-for-gestational age (SGA) and large-for-gestational age (LGA), are important indicators of changes in the health of populations. We performed this epidemiological study to evaluate these trends among 2,039,415 singleton live births from Israel over a period of 15 years. Birth certificate data was obtained from the Ministry of Health. Multivariable linear and logistic regression models were used to evaluate crude and adjusted estimates compared to the baseline of 2000 and polynomial trends. During the study period we observed a significant decrease in the rates of infants born SGA and LGA (10.7% to 9.2%, 10.2% to 9.6% respectively). After adjustment, based on the imputed data set, term mean birthweight increased by 6.0 grams (95% CI: 2.9, 9.1), and term LBW odds decreased by 19% in 2014 compared to 2000 (adj ORs: 0.81; 95% CI: 0.77, 0.85). Significant decreases were also observed for adjusted SGA, LGA and macrosomia rates. The decrease in abnormal fetal growth rates were not entirely explained by changes in sociodemographic characteristics or gestational age and may imply real improvement in child intrauterine growth in Israel during the last 15 years, especially in the Jewish population.
Contrasting patterns of prehistoric human diet and subsistence in northernmost Europe
Authors: Pääkkönen Mirva , Bläuer Auli , Olsen Bjørnar , Evershed Richard P. , Asplund Henrik
Published: January 2018

Current archaeological evidence indicates the transition from hunting-fishing-gathering to agriculture in Northern Europe was a gradual process. This transition was especially complex in the prehistoric North Fennoscandian landscape where the high latitude posed a challenge to both domestic animal breeding and cereal cultivation. The conditions varied, the coastal dwellers had access to rich marine resources and enjoyed a milder climate due to the Gulf Stream, while those living in the inland Boreal forest zone faced longer and colder winters and less diversity in animal and plant resources. Thus, the coastal area provided more favourable conditions for early agriculture compared to those found inland. Interestingly, a cultural differentiation between these areas is archaeologically visible from the late 2nd millennium BC onwards. This is most clearly seen in regionally distinct pottery styles, offering unique opportunities to probe diet and subsistence through the organic residues preserved in ceramic vessels. Herein, we integrate the lipid biomarker, compound-specific stable carbon isotopes (δ13C), and zooarchaeological evidence to reveal culturally distinct human diets and subsistence patterns. In northern Norway, some of the coastal people adopted dairying as part of their subsistence strategy, while the inhabitants of the interior, in common with northern Finland, continued their hunter-gatherer-fisher lifestyles.
In situ formation of artificial moth-eye structure by spontaneous nano-phase separation
Authors: Li Tong , He Junhui , Zhang Yue , Yao Lin , Ren Tingting , Jin Binbin
Published: January 2018

Unprecedented in situ formation of artificial moth-eye structure is demonstrated by spontaneous nano-phase separation of a silica-based system on substrate. The moth-eye thin film with a homogenously distributed nipples array shows broadband antireflection functionalities. The mechanism of nano-phase separation is unveiled as spinodal decomposition by chemical freezing method and thermodynamic analysis. The current method may provide a new avenue to ready fabrication of patterned nanostructures toward a variety of applications.
Climate Degradation and Extreme Icing Events Constrain Life in Cold-Adapted Mammals
Authors: Berger J. , Hartway C. , Gruzdev A. , Johnson M.
Published: January 2018

Despite the growth in knowledge about the effects of a warming Arctic on its cold-adapted species, the mechanisms by which these changes affect animal populations remain poorly understood. Increasing temperatures, declining sea ice and altered wind and precipitation patterns all may affect the fitness and abundance of species through multiple direct and indirect pathways. Here we demonstrate previously unknown effects of rain-on-snow (ROS) events, winter precipitation, and ice tidal surges on the Arctic’s largest land mammal. Using novel field data across seven years and three Alaskan and Russian sites, we show arrested skeletal growth in juvenile muskoxen resulting from unusually dry winter conditions and gestational ROS events, with the inhibitory effects on growth from ROS events lasting up to three years post-partum. Further, we describe the simultaneous entombment of 52 muskoxen in ice during a Chukchi Sea winter tsunami (ivuniq in Iñupiat), and link rapid freezing to entrapment of Arctic whales and otters. Our results illustrate how once unusual, but increasingly frequent Arctic weather events affect some cold-adapted mammals, and suggest that an understanding of species responses to a changing Arctic can be enhanced by coalescing groundwork, rare events, and insights from local people.
Comprehensive list of SUMO targets in Caenorhabditis elegans and its implication for evolutionary conservation of SUMO signaling
Authors: Drabikowski Krzysztof , Ferralli Jacqueline , Kistowski Michal , Oledzki Jacek , Dadlez Michal , Chiquet-Ehrismann Ruth
Published: January 2018

Post-translational modification by small ubiquitin-related modifier (SUMO) is a key regulator of cell physiology, modulating protein-protein and protein-DNA interactions. Recently, SUMO modifications were postulated to be involved in response to various stress stimuli. We aimed to identify the near complete set of proteins modified by SUMO and the dynamics of the modification in stress conditions in the higher eukaryote, Caenorhabditis elegans. We identified 874 proteins modified by SUMO in the worm. We have analyzed the SUMO modification in stress conditions including heat shock, DNA damage, arsenite induced cellular stress, ER and osmotic stress. In all these conditions the global levels of SUMOylation was significantly increased. These results show the evolutionary conservation of SUMO modifications in reaction to stress. Our analysis showed that SUMO targets are highly conserved throughout species. By comparing the SUMO targets among species, we approximated the total number of proteins modified in a given proteome to be at least 15–20%. We developed a web server designed for convenient prediction of potential SUMO modification based on experimental evidences in other species.
Magneto Acoustic Spin Hall Oscillators
Authors: Torunbalci Mustafa Mert , Gosavi Tanay Arun , Camsari Kerem Yunus , Bhave Sunil Ashok
Published: January 2018

This paper introduces a novel oscillator that combines the tunability of spin Hall-driven nano oscillators with the high quality factor (Q) of high overtone bulk acoustic wave resonators (HBAR), integrating both reference and tunable oscillators on the same chip with CMOS. In such magneto acoustic spin Hall (MASH) oscillators, voltage oscillations across the magnetic tunnel junction (MTJ) that arise from a spin-orbit torque (SOT) are shaped by the transmission response of the HBAR that acts as a multiple peak-bandpass filter and a delay element due to its large time constant, providing delayed feedback. The filtered voltage oscillations can be fed back to the MTJ via (a) strain, (b) current, or (c) magnetic field. We develop a SPICE-based circuit model by combining experimentally benchmarked models including the stochastic Landau-Lifshitz-Gilbert (sLLG) equation for magnetization dynamics and the Butterworth Van Dyke (BVD) circuit for the HBAR. Using the self-consistent model, we project up to ~50X enhancement in the oscillator linewidth with Q reaching up to 52825 at 3 GHz, while preserving the tunability by locking the STNO to the nearest high Q peak of the HBAR. We expect that our results will inspire MEMS-based solutions to spintronic devices by combining attractive features of both fields for a variety of applications.
Evidence of the Zanclean megaflood in the eastern Mediterranean Basin
Authors: Micallef Aaron , Camerlenghi Angelo , Garcia-Castellanos Daniel , Cunarro Otero Daniel , Gutscher Marc-André , Barreca Giovanni , Spatola Daniele , Facchin Lorenzo , Geletti Riccardo , Krastel Sebastian , Gross Felix , Urlaub Morelia
Published: January 2018

The Messinian salinity crisis (MSC) - the most abrupt, global-scale environmental change since the end of the Cretaceous – is widely associated with partial desiccation of the Mediterranean Sea. A major open question is the way normal marine conditions were abruptly restored at the end of the MSC. Here we use geological and geophysical data to identify an extensive, buried and chaotic sedimentary body deposited in the western Ionian Basin after the massive Messinian salts and before the Plio-Quaternary open-marine sedimentary sequence. We show that this body is consistent with the passage of a megaflood from the western to the eastern Mediterranean Sea via a south-eastern Sicilian gateway. Our findings provide evidence for a large amplitude drawdown in the Ionian Basin during the MSC, support the scenario of a Mediterranean-wide catastrophic flood at the end of the MSC, and suggest that the identified sedimentary body is the largest known megaflood deposit on Earth.
Characterization of a Novel Tectivirus Phage Toil and Its Potential as an Agent for Biolipid Extraction
Authors: Gill Jason J. , Wang Baixin , Sestak Emily , Young Ryland , Chu Kung-Hui
Published: January 2018

The oleaginous bacterium Rhodococcus opacus PD630 is metabolically diverse and can be cultivated on various renewable resources to serve as a sustainable triacylglycerol (TAG) feedstock for biodiesel production. Current methods for TAG extraction are costly, but infection of cultures by lytic bacteriophages (phages) may be a viable approach for achieving release of intracellular lipid from oleaginous bacteria such as R. opacus. This study reports the novel tectiviral phage Toil capable of releasing intracellular contents including a fluorescent protein marker and TAGs into the supernatant after phage infection of R. opacus PD631, a domesticated derivative of strain PD630. Phage Toil is placed in the Tectiviridae by its morphology, the presence of a lipid membrane, its genome architecture and the presence of terminal covalently-linked proteins. Toil is the first tectivirus capable of infecting a member of the Actinobacteria. Microscopy shows that infected cells do not undergo sudden lysis but instead maintain their original shape for several hours, with the cellular morphology gradually deteriorating. Approximately 30% of intracellular TAGs could be recovered from the culture supernatants of Toil-infected PD631 cells. Phage Toil has potential to be used as an agent in extraction of TAGs from oleaginous bacterium R. opacus. Importance: This study reported the first tectivirus (Phage Toil) capable of infecting a member of the Actinobacteria. In this study, we showed that Phage Toil can infect oleaginous bacterium Rhodococcus opacus to release intracellular contents such as a fluorescent protein marker and TAG lipid granules, which can serve as a starting material for biodiesel production. This study demonstrates a new method to extract TAGs by using this phage. Additionally, Phage Toil can be a new model phage to advance knowledge regarding phage infection mechanisms in Rhodococcus and other mycolic acid-containing bacteria such as Mycobacterium.