bluuebunny/crossref_metadata_2025 huggingface dataset:
Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network
Authors: Bouma-Gregson Keith , Olm Matthew R , Probst Alexander J , Anantharaman Karthik , Power Mary E , Banfield Jillian F
Published: February 2019

Blooms of planktonic cyanobacteria have long been of concern in lakes, but more recently, harmful impacts of riverine benthic cyanobacterial mats been recognized. As yet, we know little about how various benthic cyanobacteria are distributed in river networks, or how environmental conditions or other associated microbes in their consortia affect their biosynthetic capacities. We performed metagenomic sequencing for 22 Oscillatoriales-dominated (Cyanobacteria) microbial mats collected across the Eel River network in Northern California and investigated factors associated with anatoxin-a producing cyanobacteria. All microbial communities were dominated by one or two cyanobacterial species, so the key mat metabolisms involve oxygenic photosynthesis and carbon oxidation. Only a few metabolisms fueled the growth of the mat communities, with little evidence for anaerobic metabolic pathways. We genomically defined four cyanobacterial species, all which shared <96% average nucleotide identity with reference Oscillatoriales genomes and are potentially novel species in the genus Microcoleus. One of the Microcoleus species contained the anatoxin-a biosynthesis genes, and we describe the first anatoxin-a gene cluster from the Microcoleus clade within Oscillatoriales. Occurrence of these four Microcoleus species in the watershed was correlated with total dissolved nitrogen and phosphorus concentrations, and the species that contains the anatoxin-a gene cluster was found in sites with higher nitrogen concentrations. Microbial assemblages in mat samples with the anatoxin-a gene cluster consistently had a lower abundance of Burkholderiales (Betaproteobacteria) species than did mats without the anatoxin-producing genes. The associations of water nutrient concentrations and certain co-occurring microbes with anatoxin-a producing Microcoleus motivate further exploration for their roles as potential controls on the distributions of toxigenic benthic cyanobacteria in river networks.
Molecular evidence for novel mercury methylating microorganisms in sulfate-impacted lakes
Authors: Jones Daniel S , Walker Gabriel M , Johnson Nathan W , Mitchell Carl P J , Coleman Wasik Jill K , Bailey Jake V
Published: February 2019

Methylmercury (MeHg) is a bioaccumulative neurotoxin that is produced by certain anaerobic microorganisms, but the abundance and importance of different methylating populations in the environment is not well understood. We combined mercury geochemistry, hgcA gene cloning, rRNA methods, and metagenomics to compare microbial communities associated with MeHg production in two sulfate-impacted lakes on Minnesota’s Mesabi Iron Range. The two lakes represent regional endmembers among sulfate-impacted sites in terms of their dissolved sulfide concentrations and MeHg production potential. rRNA amplicon sequencing indicates that sediments and anoxic bottom waters from both lakes contained diverse communities with multiple clades of sulfate reducing Deltaproteobacteria and Clostridia. In hgcA gene clone libraries, however, hgcA sequences were from taxa associated with methanogenesis and iron reduction in addition to sulfate reduction, and the most abundant clones were from unknown groups. We therefore applied metagenomics to identify the unknown populations in the lakes with the capability to methylate mercury, and reconstructed 27 genomic bins with hgcA. Some of the most abundant potential methylating populations were from phyla that are not typically associated with MeHg production, including a relative of the Aminicenantes (formerly candidate phylum OP8) and members of the Kiritimatiellaeota (PVC superphylum) and Spirochaetes that, together, were more than 50% of the potential methylators in some samples. These populations do not have genes for sulfate reduction, and likely degrade organic compounds by fermentation or other anaerobic processes. Our results indicate that previously unrecognized populations with hgcAB are abundant and may be important for MeHg production in some freshwater ecosystems.
Planar cell polarity protein Dishevelled 3 (Dvl3) regulates ectoplasmic specialization (ES) dynamics in the testis through changes in cytoskeletal organization
Authors: Li Linxi , Mao Baiping , Yan Ming , Wu Siwen , Ge Renshan , Lian Qingquan , Cheng C. Yan
Published: February 2019

In the mammalian testes, such as in rats, the directional alignment of polarized elongating/elongated spermatids, in particular step 17–19 spermatids, across the plane of seminiferous epithelium resembles planar cell polarity (PCP) found in hair cells of the cochlea. It is obvious that spermatid PCP is necessary to support the simultaneous development of maximal number of elongating/elongated spermatids to sustain the daily production of > 50 million sperm per adult rat. Studies have shown that the testis indeed expresses multiple PCP proteins necessary to support spermatid PCP. Herein, using physiological and biochemical assays, and morphological analysis, and with the technique of RNA interference (RNAi) to knockdown PCP protein Dishevelled (Dvl) 1 (Dvl1), Dvl2, Dvl3, or Dvl1/2/3, Dvl proteins, in particular Dvl3, it was shown that Dvl3 played a crucial role of support Sertoli cell tight junction (TJ)-permeability barrier function through changes in the organization of actin- and microtubule (MT)-based cytoskeletons. More important, an in vivo knockdown of Dvl1/2/3 in the testis, defects of spermatid polarity were remarkably noted across the seminiferous epithelium, concomitant with defects of spermatid adhesion and spermatid transport, leading to considerably defects in spermatogenesis. More important, Dvl1/2/3 triple knockdown in the testis also impeded the organization of actin- and MT-based cytoskeletons owing to disruptive spatial expression of actin- and MT-regulatory proteins. In summary, PCP Dishevelled proteins, in particular, Dvl3 is a regulator of Sertoli cell blood–testis barrier (BTB)  and also spermatid PCP function through its effects on the actin- and MT-based cytoskeletons in Sertoli cells.
Modified carbon nitride nanozyme as bifunctional glucose oxidase-peroxidase for metal-free bioinspired cascade photocatalysis
Authors: Zhang Peng , Sun Dengrong , Cho Ara , Weon Seunghyun , Lee Seonggyu , Lee Jinwoo , Han Jeong Woo , Kim Dong-Pyo , Choi Wonyong
Published: February 2019

Nanomaterials-based biomimetic catalysts with multiple functions are necessary to address challenges in artificial enzymes mimicking physiological processes. Here we report a metal-free nanozyme of modified graphitic carbon nitride and demonstrate its bifunctional enzyme-mimicking roles. With oxidase mimicking, hydrogen peroxide is generated from the coupled photocatalysis of glucose oxidation and dioxygen reduction under visible-light irradiation with a near 100% apparent quantum efficiency. Then, the in situ generated hydrogen peroxide serves for the subsequent peroxidase-mimicking reaction that oxidises a chromogenic substrate on the same catalysts in dark to complete the bifunctional oxidase-peroxidase for biomimetic detection of glucose. The bifunctional cascade catalysis is successfully demonstrated in microfluidics for the real-time colorimetric detection of glucose with a low detection limit of 0.8 μM within 30 s. The artificial nanozymes with physiological functions provide the feasible strategies for mimicking the natural enzymes and realizing the biomedical diagnostics with a smart and miniature device.
Ti and its alloys as examples of cryogenic focused ion beam milling of environmentally-sensitive materials
Authors: Chang Yanhong , Lu Wenjun , Guénolé Julien , Stephenson Leigh T. , Szczpaniak Agnieszka , Kontis Paraskevas , Ackerman Abigail K. , Dear Felicity F. , Mouton Isabelle , Zhong Xiankang , Zhang Siyuan , Dye David , Liebscher Christian H. , Ponge Dirk , Korte-Kerzel Sandra , Raabe Dierk , Gault Baptiste
Published: February 2019

Hydrogen pick-up leading to hydride formation is often observed in commercially pure Ti (CP-Ti) and Ti-based alloys prepared for microscopic observation by conventional methods, such as electro-polishing and room temperature focused ion beam (FIB) milling. Here, we demonstrate that cryogenic FIB milling can effectively prevent undesired hydrogen pick-up. Specimens of CP-Ti and a Ti dual-phase alloy (Ti-6Al-2Sn-4Zr-6Mo, Ti6246, in wt.%) were prepared using a xenon-plasma FIB microscope equipped with a cryogenic stage reaching −135 °C. Transmission electron microscopy (TEM), selected area electron diffraction, and scanning TEM indicated no hydride formation in cryo-milled CP-Ti lamellae. Atom probe tomography further demonstrated that cryo-FIB significantly reduces hydrogen levels within the Ti6246 matrix compared with conventional methods. Supported by molecular dynamics simulations, we show that significantly lowering the thermal activation for H diffusion inhibits undesired environmental hydrogen pick-up during preparation and prevents pre-charged hydrogen from diffusing out of the sample, allowing for hydrogen embrittlement mechanisms of Ti-based alloys to be investigated at the nanoscale.
A network-centric approach to drugging TNF-induced NF-κB signaling
Authors: Pabon Nicolas A. , Zhang Qiuhong , Cruz J. Agustin , Schipper David L. , Camacho Carlos J. , Lee Robin E. C.
Published: February 2019

Target-centric drug development strategies prioritize single-target potency in vitro and do not account for connectivity and multi-target effects within a signal transduction network. Here, we present a systems biology approach that combines transcriptomic and structural analyses with live-cell imaging to predict small molecule inhibitors of TNF-induced NF-κB signaling and elucidate the network response. We identify two first-in-class small molecules that inhibit the NF-κB signaling pathway by preventing the maturation of a rate-limiting multiprotein complex necessary for IKK activation. Our findings suggest that a network-centric drug discovery approach is a promising strategy to evaluate the impact of pharmacologic intervention in signaling.
Quantitative sensing and signalling of single-stranded DNA during the DNA damage response
Authors: Bantele Susanne C. S. , Lisby Michael , Pfander Boris
Published: February 2019

The DNA damage checkpoint senses the presence of DNA lesions and controls the cellular response thereto. A crucial DNA damage signal is single-stranded DNA (ssDNA), which is frequently found at sites of DNA damage and recruits the sensor checkpoint kinase Mec1-Ddc2. However, how this signal – and therefore the cell's DNA damage load – is quantified, is poorly understood. Here, we use genetic manipulation of DNA end resection to induce quantitatively different ssDNA signals at a site-specific double strand break in budding yeast and identify two distinct signalling circuits within the checkpoint. The local checkpoint signalling circuit leading to γH2A phosphorylation is unresponsive to increased amounts of ssDNA, while the global checkpoint signalling circuit, which triggers Rad53 activation, integrates the ssDNA signal quantitatively. The global checkpoint signal critically depends on the 9-1-1 and its downstream acting signalling axis, suggesting that ssDNA quantification depends on at least two sensor complexes.
Stokes flow analogous to viscous electron current in graphene
Authors: Mayzel Jonathan , Steinberg Victor , Varshney Atul
Published: February 2019

Electron transport in two-dimensional conducting materials such as graphene, with dominant electron–electron interaction, exhibits unusual vortex flow that leads to a nonlocal current-field relation (negative resistance), distinct from the classical Ohm’s law. The transport behavior of these materials is best described by low Reynolds number hydrodynamics, where the constitutive pressure–speed relation is Stoke’s law. Here we report evidence of such vortices observed in a viscous flow of Newtonian fluid in a microfluidic device consisting of a rectangular cavity—analogous to the electronic system. We extend our experimental observations to elliptic cavities of different eccentricities, and validate them by numerically solving bi-harmonic equation obtained for the viscous flow with no-slip boundary conditions. We verify the existence of a  predicted threshold at which vortices appear. Strikingly, we find that a two-dimensional theoretical model captures the essential features of three-dimensional Stokes flow in experiments.
Dimerization energetics of curli fiber subunits CsgA and CsgB
Authors: Dunbar Martha , DeBenedictis Elizabeth , Keten Sinan
Published: February 2019

Curli fibers are functional amyloids that exhibit strong adhesion and robust self-assembly as biofilm structural components; however, the binding energetics and mechanical properties of wild-type curli are not well understood. To address this, we present dimer structures made up of the major and minor curli subunits (CsgA and CsgB), perform free energy calculations to obtain absolute binding energies, and estimate the Young’s modulus and persistence length of curli fibers. Equilibrium molecular dynamics simulations are used to evaluate nonbonded interactions. Binding energies are most favorable for CsgB–CsgA, while CsgA–CsgA dimers have a higher binding energy than CsgB–CsgB despite possessing less favorable nonbonded interaction energies. Decomposing each potential of mean force of separation indicated that solvent effects positively impact CsgA–CsgA binding but not CsgB–CsgB and CsgB–CsgA. Charged residues and conserved polar residues were also notable contributors to attractive nonbonded interactions, underlining their importance in dimer assembly. Our findings elucidate sequence effects on binding energy contributions and establish theoretical limits for the elasticity, persistence length, and strength of curli fibers.
Mechanism of surface uranium hydride formation during corrosion of uranium
Authors: Ji Hefei , Wu Haoxi , Pan Qifa , Cai Dingzhou , Meng Xiandong , Chen Xianglin , Shi Peng , Wang Xiaolin
Published: February 2019

Uranium is widely used in the nuclear industry and it is well known that uranium hydride, UH3, forms when uranium is exposed to air. The associated volume change during this transition can cause the surface region to crack, compromising structural integrity. Here, hydriding regions beneath hydride surface craters are studied by secondary ion mass spectroscopy (SIMS) and X-ray photoelectron spectroscopy (XPS). Our results indicate that strain transition regions exist, which are induced by hydrogen with a certain thickness between hydride craters and the uranium bulk. The SIMS and XPS results suggest that hydrogen exists covalently with uranium and oxygen in these transition regions. A micro-scale induction period model based on the transition region and previous hydriding models is developed. Within the so-called micro-scale induction period, hydrogen diffuses and accumulates at particular sites before reaching the critical concentration required to form stoichiometric UH3 in the transition regions.
Lateral parabrachial neurons innervate orexin neurons projecting to brainstem arousal areas in the rat
Authors: Arima Yosuke , Yokota Shigefumi , Fujitani Masashi
Published: February 2019

Orexin (ORX) neurons in the hypothalamus send their axons to arousal-promoting areas. We have previously shown that glutamatergic neurons in the lateral parabrachial nucleus (LPB) innervate ORX neurons. In this study, we examined potential pathways from the LPB to ORX neurons projecting to arousal-promoting areas in the brainstem by a combination of tract-tracing techniques in male Wistar rats. We injected the anterograde tracer biotinylated dextranamine (BDA) into the LPB and the retrograde tracer cholera toxin B subunit (CTb) into the ventral tegmental area, dorsal raphe nucleus, pedunculopontine tegmental nucleus, laterodorsal tegmental area, or locus coeruleus (LC). We then analyzed the BDA-labeled fibers and ORX-immunoreactive neurons in the hypothalamus. We found that double-labeled ORX and CTb neurons were the most abundant after CTb was injected into the LC. We also observed prominently overlapping distribution of BDA-labeled fibers, arising from neurons located in the lateral-most part of the dorsomedial nucleus and adjacent dorsal perifornical area. In these areas, we confirmed by confocal microscopy that BDA-labeled synaptophysin-immunoreactive axon terminals were in contiguity with cell bodies and dendrites of CTb-labeled ORX-immunoreactive neurons. These results suggest that the LPB innervates arousal-promoting areas via ORX neurons and is likely to promote arousal responses to stimuli.
Retrospective analysis of the association between intraoperative magnesium sulfate infusion and postoperative acute kidney injury after major laparoscopic abdominal surgery
Authors: Oh Tak Kyu , Oh Ah-Young , Ryu Jung-Hee , Koo Bon-Wook , Lee Yea Ji , Do Sang-Hwan
Published: February 2019

Magnesium sulfate can be used as a co-adjuvant drug during the perioperative period and has multiple benefits. Recent evidence suggested that perioperative magnesium sulfate infusion may lower the risk of postoperative acute kidney injury (AKI). We investigated the association between intraoperative magnesium sulfate infusion and incidence of AKI after major laparoscopic abdominal surgery. We retrospectively analyzed the medical records of adult patients 20 years or older who underwent elective major laparoscopic abdominal surgery (>2 hours) between 2010 and 2016. We investigated the association between intraoperative magnesium sulfate infusion and the incidence of postoperative AKI until postoperative day (POD) 3 using a multivariable logistic regression analysis. We included 3,828 patients in this analysis; 357 patients (9.3%) received an intraoperative magnesium sulfate infusion and 186 patients (4.9%) developed postoperative AKI by POD 3. A multivariable logistic regression analysis showed that magnesium infusion was associated with a significant decrease (63%) in postoperative AKI (odds ratio, 0.37; 95% confidence interval, 0.14–0.94; P = 0.037). Our study suggested that intraoperative magnesium sulfate infusion is associated with a reduced risk of postoperative AKI until POD 3 for patients who underwent laparoscopic major abdominal surgery. Well-designed, prospective studies should be conducted to further substantiate these findings.
Differential expression of a prophage-encoded glycocin and its immunity protein suggests a mutualistic strategy of a phage and its host
Authors: Denham Emma L. , Piersma Sjouke , Rinket Marleen , Reilman Ewoud , de Goffau Marcus C. , van Dijl Jan Maarten
Published: February 2019

Sublancin 168 is a highly potent and stable antimicrobial peptide secreted by the Gram-positive bacterium Bacillus subtilis. Production of sublancin gives B. subtilis a major competitive growth advantage over a range of other bacteria thriving in the same ecological niches, the soil and plant rhizosphere. B. subtilis protects itself against sublancin by producing the cognate immunity protein SunI. Previous studies have shown that both the sunA gene for sublancin and the sunI immunity gene are encoded by the prophage SPβ. The sunA gene is under control of several transcriptional regulators. Here we describe the mechanisms by which sunA is heterogeneously expressed within a population, while the sunI gene encoding the immunity protein is homogeneously expressed. The key determinants in heterogeneous sunA expression are the transcriptional regulators Spo0A, AbrB and Rok. Interestingly, these regulators have only a minor influence on sunI expression and they have no effect on the homogeneous expression of sunI within a population of growing cells. Altogether, our findings imply that the homogeneous expression of sunI allows even cells that are not producing sublancin to protect themselves at all times from the active sublancin produced at high levels by their isogenic neighbors. This suggests a mutualistic evolutionary strategy entertained by the SPβ prophage and its Bacillus host, ensuring both stable prophage maintenance and a maximal competitive advantage for the host at minimal costs.
ZipN is an essential FtsZ membrane tether and contributes to the septal localization of SepJ in the filamentous cyanobacterium Anabaena
Authors: Camargo Sergio , Picossi Silvia , Corrales-Guerrero Laura , Valladares Ana , Arévalo Sergio , Herrero Antonia
Published: February 2019

The organismic unit of heterocyst-forming cyanobacteria is a filament of communicating cells connected by septal junctions, proteinaceous structures bridging the cytoplasms of contiguous cells. This distinct bacterial organization is preserved during cell division. In Anabaena, deletion of the zipN gene could not be segregated. We generated strain CSL109 that expresses zipN from a synthetic regulatable promoter. Under conditions of ZipN depletion, cells progressively enlarged, reflecting restricted cell division, and showed drastic morphological alterations including cell detachment from the filaments, to finish lysing. In contrast to the wild-type localization in midcell Z-rings, FtsZ was found in delocalized aggregates in strain CSL109. Consistently, the proportion of membrane-associated to soluble FtsZ in fractionated cell extracts was lower in CSL109. Bacterial two-hybrid analysis showed that ZipN interacts with FtsZ and other cell-division proteins including cytoplasmic Ftn6 and SepF, and polytopic FtsW, FtsX, FtsQ and FtsI. Additionally, ZipN interacted with the septal protein SepJ, and in CSL109 depletion of ZipN was concomitant with a progressive loss of septal specificity of SepJ. Thus, in Anabaena ZipN represents an essential FtsZ membrane tether and an organizer of the divisome, and it contributes to the conformation of septal structures for filament integrity and intercellular communication.
Inhibition of Tropomyosin Receptor Kinase A Signaling Negatively Regulates Megakaryopoiesis and induces Thrombopoiesis
Authors: Kizilyer Ayse , Singh Meera V. , Singh Vir B. , Suwunnakorn Sumanun , Palis James , Maggirwar Sanjay B.
Published: February 2019

Neurotrophin signaling modulates the differentiation and function of mature blood cells. The expression of neurotrophin receptors and ligands by hematopoietic and stromal cells of the bone marrow indicates that neurotrophins have the potential to regulate hematopoietic cell fate decisions. This study investigates the role of neurotrophins and Tropomyosin receptor kinases (Trk) in the development of megakaryocytes (MKs) and their progeny cells, platelets. Results indicate that primary human MKs and MK cells lines, DAMI, Meg-01 and MO7e express TrkA, the primary receptor for Nerve Growth Factor (NGF) signaling. Activation of TrkA by NGF enhances the expansion of human MK progenitors (MKPs) and, to some extent, MKs. Whereas, inhibition of TrkA receptor by K252a leads to a 50% reduction in the number of both MKPs and MKs and is associated with a 3-fold increase in the production of platelets. In order to further confirm the role of TrkA signaling in platelet production, TrkA deficient DAMI cells were generated using CRISPR-Cas9 technology. Comparative analysis of wild-type and TrkA-deficient Dami cells revealed that loss of TrkA signaling induced apoptosis of MKs and increased platelet production. Overall, these findings support a novel role for TrkA signaling in platelet production and highlight its potential as therapeutic target for Thrombocytopenia.
Mesalamine and azathioprine modulate junctional complexes and restore epithelial barrier function in intestinal inflammation
Authors: Khare Vineeta , Krnjic Anita , Frick Adrian , Gmainer Christina , Asboth Mario , Jimenez Kristine , Lang Michaela , Baumgartner Maximilian , Evstatiev Rayko , Gasche Christoph
Published: February 2019

Disruption of mucosal structure and barrier function contribute to the pathogenesis of inflammatory bowel disease (IBD). Efficacy of therapy in IBD is based on endoscopic mucosal healing, which occurs by a dynamic interplay of epithelial cell regeneration, migration and differentiation. Both mesalamine (5-ASA) and azathioprine (AZTP) promote this process through mechanisms not clearly understood. We examined molecular pathways implicated in epithelial barrier function that were altered by 5-ASA and AZTP. Paracellular permeability induced by inflammatory mediators was mitigated by both compounds through restoration of cellular anchoring complexes. 5-ASA and AZTP induced rearrangement and membranous localization of junctional proteins and modulated genes involved in tight junctions. Intestinal organoids from wildtype-mice treated with TNF-α and IL-10- deficient-mice displayed impaired epithelial barrier with loss of membranous E-cadherin and reduced Desmoglein-2 expression. These effects were counteracted by 5-ASA and AZTP. Unlike AZTP that exhibited antiproliferative effects, 5-ASA promoted wound healing in colon epithelial cells. Both affected cellular senescence, cell cycle distribution and restricted cells in G1 or S phase without inducing apoptosis. This study provides mechanistic evidence that molecular actions of 5-ASA and AZTP on intestinal epithelia are fundamental in the resolution of barrier dysfunction.
Transcriptome analysis reveals the impact of arbuscular mycorrhizal symbiosis on Sesbania cannabina expose to high salinity
Authors: Ren Cheng-Gang , Kong Cun-Cui , Yan Kun , Xie Zhi-Hong
Published: February 2019

Arbuscular mycorrhiza can improve the salt-tolerance of host plant. A systematic study of mycorrhizal plant responses to salt stress may provide insights into the acquired salt tolerance. Here, the transcriptional profiles of mycorrhizal Sesbania cannabina shoot and root under saline stress were obtained by RNA-Seq. Using weighted gene coexpression network analysis and pairwise comparisons, we identified coexpressed modules, networks and hub genes in mycorrhizal S. cannabina in response to salt stress. In total, 10,371 DEGs were parsed into five coexpression gene modules. One module was positively correlated with both salt treatment and arbuscular mycorrhizal (AM) inoculation, and associated with photosynthesis and ROS scavenging in both enzymatic and nonenzymatic pathways. The hub genes in the module were mostly transcription factors including WRKY, MYB, ETHYLENE RESPONSE FACTOR, and TCP members involved in the circadian clock and might represent central regulatory components of acquired salinity tolerance in AM S. cannabina. The expression patterns of 12 genes involved in photosynthesis, oxidation-reduction processes, and several transcription factors revealed by qRT-PCR confirmed the RNA-Seq data. This large-scale assessment of Sesbania genomic resources will help in exploring the molecular mechanisms underlying plant–AM fungi interaction in salt stress responses.
Directed Differentiation of Human Pluripotent Stem Cells to Podocytes under Defined Conditions
Authors: Qian Tongcheng , Hernday Shaenah E. , Bao Xiaoping , Olson William R. , Panzer Sarah E. , Shusta Eric V. , Palecek Sean P.
Published: February 2019

A major cause of chronic kidney disease (CKD) is glomerular disease, which can be attributed to a spectrum of podocyte disorders. Podocytes are non-proliferative, terminally differentiated cells. Thus, the limited supply of primary podocytes impedes CKD research. Differentiation of human pluripotent stem cells (hPSCs) into podocytes has the potential to produce podocytes for disease modeling, drug screening, and cell therapies. In the podocyte differentiation process described here, hPSCs are first induced to primitive streak-like cells by activating canonical Wnt signaling. Next, these cells progress to mesoderm precursors, proliferative nephron progenitors, and eventually become mature podocytes by culturing in a serum-free medium. Podocytes generated via this protocol adopt podocyte morphology, express canonical podocyte markers, and exhibit podocyte phenotypes, including albumin uptake and TGF-β1 triggered cell death. This study provides a simple, defined strategy to generate podocytes for in vitro modeling of podocyte development and disease or for cell therapies.
Metformin and glucose starvation decrease the migratory ability of hepatocellular carcinoma cells: targeting AMPK activation to control migration
Authors: Ferretti Anabela C. , Hidalgo Florencia , Tonucci Facundo M. , Almada Evangelina , Pariani Alejandro , Larocca María C. , Favre Cristián
Published: February 2019

Hepatocellular carcinoma (HCC) is a highly metastatic cancer with very poor prognosis. AMP activated kinase (AMPK) constitutes a candidate to inhibit HCC progression. First, AMPK is downregulated in HCC. Second, glucose starvation induces apoptosis in HCC cells via AMPK. Correspondingly, metformin activates AMPK and inhibits HCC cell proliferation. Nevertheless, the effect of AMPK activation on HCC cell invasiveness remains elusive. Here, migration/invasion was studied in HCC cells exposed to metformin and glucose starvation. Cell viability, proliferation and differentiation, as well as AMPK and PKA activation were analyzed. In addition, invasiveness in mutants of the AMPKα activation loop was assessed. Metformin decreased cell migration, invasion and epithelial-mesenchymal transition, and interference with AMPKα expression avoided metformin actions. Those antitumor effects were potentiated by glucose deprivation. Metformin activated AMPK at the same time that inhibited PKA, and both effects were enhanced by glucose starvation. Given that AMPKα(S173) phosphorylation by PKA decreases AMPK activation, we hypothesized that the reduction of PKA inhibitory effect by metformin could explain the increased antitumor effects observed. Supporting this, in AMPK activating conditions, cell migration/invasion was further impaired in AMPKα(S173C) mutant cells. Metformin emerges as a strong inhibitor of migration/invasion in HCC cells, and glucose restriction potentiates this effect.
Organochlorinated pesticides expedite the enzymatic degradation of DNA
Authors: Qin Chao , Yang Bing , Zhang Wei , Ling Wanting , Liu Cun , Liu Juan , Li Xu , Gao Yanzheng
Published: February 2019

Extracellular DNA in the environment may play important roles in genetic diversity and biological evolution. However, the influence of environmental persistent organic contaminants such as organochlorinated pesticides (e.g., hexachlorocyclohexanes [HCHs]) on the enzymatic degradation of extracellular DNA has not been elucidated. In this study, we observed expedited enzymatic degradation of extracellular DNA in the presence of α-HCH, β-HCH and γ-HCH. The HCH-expedited DNA degradation was not due to increased deoxyribonuclease I (DNase I) activity. Our spectroscopic and computational results indicate that HCHs bound to DNA bases (most likely guanine) via Van der Waals forces and halogen bonds. This binding increased the helicity and accumulation of DNA base pairs, leading to a more compact DNA structure that exposed more sites susceptible to DNase I and thus expedited DNA degradation. This study provided insight into the genotoxicity and ecotoxicity of pesticides and improved our understanding of DNA persistence in contaminated environments.
The temporal geographically-explicit network of public transport in Changchun City, Northeast China
Authors: Huang Qiuyang , Yang Yongjian , Yuan Zhilu , Jia Hongfei , Huang Liping , Du Zhanwei
Published: February 2019

The vehicle trajectory data is a feasible way for us to understand and reveal urban traffic conditions and human mobility. Therefore, it is extremely valuable to have a fine-grained picture of large-scale vehicle trajectory data, particularly in two different modes, taxis and buses, over the same period at an urban scale. This paper integrates the trajectory data of approximately 7,000 taxis and 1,500 buses in Changchun City, China and accesses the temporal geographically-explicit network of public transport via sequential snapshots of vehicle trajectory data every 30 seconds of the first week in March 2018. In order to reveal urban traffic conditions and human mobility, we construct two-layer urban traffic network (UTN) between these two different transport modes, take crossings as nodes and roads as edges weighted by the volume or average speed of vehicles in each hour. We released this temporal geographically-explicit network of public transport and the dynamics, weighted and directed UTN in simple formats for easy access.
An emissions-socioeconomic inventory of Chinese cities
Authors: Shan Yuli , Liu Jianghua , Liu Zhu , Shao Shuai , Guan Dabo
Published: February 2019

As the centre of human activity and being under the threat of climate change, cities are considered to be major components in the implementation of climate change mitigation and CO2 emission reduction strategies. Inventories of cities’ emissions serve as the foundation for the analysis of emissions characteristics and policymaking. China is the world’s top energy consumer and CO2 emitter, and it is facing great potential harm from climate change. Consequently, China is taking increasing responsibility in the fight against global climate change. Many energy/emissions control policies have been implemented in China, most of which are designed at the national level. However, cities are at different stages of industrialization and have distinct development pathways; they need specific control policies designed based on their current emissions characteristics. This study is the first to construct emissions inventories for 182 Chinese cities. The inventories are constructed using 17 fossil fuels and 47 socioeconomic sectors. These city-level emissions inventories have a scope and format consistent with China’s national/provincial inventories. Some socioeconomic data of the cities, such as GDP, population, industrial structures, are included in the datasets as well. The dataset provides transparent, accurate, complete, comparable, and verifiable data support for further city-level emissions studies and low-carbon/sustainable development policy design. The dataset also offers insights for other countries by providing an emissions accounting method with limited data.
Brain-wide distribution of reporter expression in five transgenic tetracycline-transactivator mouse lines
Authors: Lillehaug Sveinung , Yetman Michael J. , Puchades Maja A. , Checinska Martyna M. , Kleven Heidi , Jankowsky Joanna L. , Bjaalie Jan G. , Leergaard Trygve B.
Published: February 2019

The spatial pattern of transgene expression in tetracycline-controlled mouse models is governed primarily by the driver line used to introduce the tetracycline-controlled transactivator (tTA). Detailed maps showing where each tTA driver activates expression are therefore essential for designing and using tet-regulated models, particularly in brain research where cell type and regional specificity determine the circuits affected by conditional gene expression. We have compiled a comprehensive online repository of serial microscopic images showing brain-wide reporter expression for five commonly used tTA driver lines. We have spatially registered all images to a common three-dimensional mouse brain anatomical reference atlas for direct comparison of spatial distribution across lines. The high-resolution images and associated metadata are shared via the web page of the EU Human Brain Project. Images can be inspected using an interactive viewing tool that includes an optional overlay feature providing anatomical delineations and reference atlas coordinates. Interactive viewing is supplemented by semi-quantitative analyses of expression levels within anatomical subregions for each tTA driver line.
Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus
Authors: Liao Yong Yan , Xu Peng Wei , Kwan Kit Yue , Ma Zhi Yun , Fang Huai Yi , Xu Jun Yang , Wang Peng Liang , Yang Shao Yu , Xie Shang Bo , Xu Shu Qing , Qian Dan , Li Wei Feng , Bai Li Rong , Zhou Da Jie , Zhang Yan Qiu , Lei Juan , Liu Ke , Li Fan , Li Jian , Zhu Peng , Wang Yu Jun , Wu Hai Ping , Xu You Hou , Huang Hu , Zhang Chi , Liu Jin Xia , Han Jun Feng
Published: February 2019

Chinese horseshoe crabs (Tachypleus tridentatus), ancient marine arthropods dating back to the mid-Palaeozoic Era, have provided valuable resources for the detection of bacterial or fungal contamination. However, excessive exploitation for the amoebocyte lysate of Tachypleus has dramatically decreased the population of the Chinese horseshoe crabs. Thus, we present sequencing, assembly and annotation of T. tridentatus, with the hope of understanding the genomic feature of the living fossil and assisting scientists with the protection of this endangered species. The final genome contained a total size of 1.943 Gb, covering 90.23% of the estimated genome size. The transcriptome of three larval stages was constructed to investigate the candidate gene involved in the larval development and validate annotation. The completeness of the genome and gene models was estimated by BUSCO, reaching 96.2% and 95.4%, respectively. The synonymous substitution distribution of paralogues revealed that T. tridentatus had undergone two rounds of whole-genome duplication. All genomic and transcriptome data have been deposited in public databases, ready to be used by researchers working on horseshoe crabs.
Global transcriptome analysis of pig induced pluripotent stem cells derived from six and four reprogramming factors
Authors: Fukuda Tomokazu , Doi Koji , Donai Kenichiro , Takahashi Kouhei , Kobayashi Hisato , Hirano Takashi , Nishimori Katsuhiko , Yasue Hiroshi
Published: February 2019

Pigs are important, both for agriculture and as animal models for human diseases. However, due to the lack of embryonic stem cells, the possibility of genetic modification is quite limited. To overcome this limitation, induced pluripotent stem (iPS) cells have been derived from pigs. Despite the public availability of a large number of expression datasets from mice, rats, and primates-derived iPS cells, the expression profile of pig-derived iPS cells is quite limited. Furthermore, there is no dataset focused on the profiling of pig-derived iPS cell with six reprogramming factors (Oct3/4, Sox2, Klf4, c-Myc, Lin28, and Nanog). Here, we used Illumina RNA sequencing platform to characterize the mRNA expression of four-factor derived and six-factor derived pig iPS cells. We observed that the expression levels of whole genes in our established six factors derived iPS cells and parent fibroblast, and compared with that of iPS cells with four factors in public database. These data are valuable in understanding species difference in the reprogramming process of stem cells, and could help identify the key regulating genes involved in the process.
Small molecule reaction networks that model the ROS dynamics of the rhizosphere
Authors: Taran Olga , Patel Vraj , Lynn David G.
Published: February 2019

Molecules released by plants and bacteria form complex abiotic reaction diffusion networks that might regulate the ROS dynamics along the roots of the plants.
Unified enantioselective total syntheses of (−)-scholarisine G, (+)-melodinine E, (−)-leuconoxine and (−)-mersicarpine
Authors: Liu Yao , Wang Honggen
Published: February 2019

A unified strategy enabled the enantioselective syntheses of (−)-scholarisine G, (+)-melodinine E, (−)-leuconoxine and (−)-mersicarpine from a common 2-alkylated indole bearing an all-carbon quaternary stereogenic center.
Revisiting the reactive chemistry of FOX-7: cyclization of FOX-7 affords the fused-ring polynitro compounds
Authors: Yan Chao , Qi Xiujuan , Wang Kangcai , Jin Yunhe , Cheng Guangbin , Liu Tianlin , Yang Hongwei , Zhang Qinghua
Published: February 2019

A new FOX-7 derivatization strategy was developed to synthesize fused-ring and cyclic polynitro compounds, which enriches the unpredictable reactive chemistry of FOX-7.
Unraveling ultrafast dynamics of the photoswitchable bridged dithienylethenes under structural constraints
Authors: Hamdi Ismail , Buntinx Guy , Poizat Olivier , Delbaere Stéphanie , Perrier Aurélie , Yamashita Rikiya , Muraoka Ken-ichi , Takeshita Michinori , Aloïse Stéphane
Published: February 2019

Photochemistry of the bridged dithienylethene series with evidence of anti-parallel/parallel interconversion along the triplet pathway.
Comparison of ultrafast intense-field photodynamics in aniline and nitrobenzene: stability under amino and nitro substitution
Authors: Scarborough Timothy D. , McAcy Collin J. , Beck Joshua , Uiterwaal Cornelis J. G. J.
Published: February 2019

Intense-field stability of photoionization and fragmentation are compared for aniline (C6H5–NH2) and nitrobenzene (C6H5–NO2), with amine vs. nitro substitutions explored.
Chalcogen stabilized trimetallic clusters: synthesis, structures, and bonding of [(Cp*M)3(E)6+m(BH)n] (M = Nb or Ta; E = S or Se;m= 0 or 1 or 2;n= 0 or 1)
Authors: Kar Sourav , Bairagi Subhash , Saha Koushik , Raghavendra Beesam , Ghosh Sundargopal
Published: February 2019

An unusual trimetallic octaselenide complex, [(Cp*Ta)3(μ-Se)4{μ-Se2(Se2)}], has been synthesized and structurally characterized.
Selective reduction of formamides to O-silylated hemiaminals or methylamines with HSiMe2Ph catalyzed by iridium complexes
Authors: Guzmán Jefferson , Bernal Ana M. , García-Orduña Pilar , Lahoz Fernando J. , Oro Luis A. , Fernández-Alvarez Francisco J.
Published: February 2019

Ir–NSitBu based catalysts allow the control of the selective reduction of formamides with HSiMe2Ph to afford O-silylated hemiaminals or methylamines.
Complex relationship between TAS2 receptor variations, bitterness perception, and alcohol consumption observed in a population of wine consumers
Authors: Fu Denggang , Riordan Sara , Kieran Shannon , Andrews Ron A. , Ring Huijun Z. , Ring Brian Z.
Published: February 2019

Our ability to taste bitterness affects our food choices and alcohol consumption.
Fabrication of a three-dimensional visible-light-driven Ag–AgBr/TiO2/graphene aerogel composite for enhanced photocatalytic destruction of organic dyes and bacteria
Authors: Zhang Mingjing , Chen Yuexing , Chen Bangjie , Zhang Yunsong , Lin Li , Han Xiaowen , Zou Ping , Wang Guangtu , Zeng Jun , Zhao Maojun
Published: February 2019

The configuration of Ag–AgBr/TiO2/GA integrated critical components of solar absorption and charge separation for environmental remediation and antibacterial treatment.
Photophysical properties and photodynamic therapy activity of ameso-tetra(4-carboxyphenyl)porphyrin tetramethyl ester–graphene quantum dot conjugate
Authors: Managa Muthumuni , Ngoy Bokolombe Pitchou , Nyokong Tebello
Published: February 2019

Ameso-tetra(4-carboxyphenyl)porphyrin tetramethyl ester and the Zn and GaCl derivatives were π–π stacked with graphene quantum dots to form conjugates and their photophysical and photodynamic therapy properties were investigated.
A novel protocol for the synthesis of pyrano[2,3-h]coumarins in the presence of Fe3O4@SiO2@(CH2)3OCO2Na as a magnetically heterogeneous catalyst
Authors: Tanuraghaj Hamideh Mohamadi , Farahi Mahnaz
Published: February 2019

In this study, sodium carbonate functionalized silica coated-iron oxide nanoparticles (Fe3O4@SiO2@(CH2)3OCO2Na) were synthesized, characterized and applied as a heterogeneous basic nanocatalyst for the synthesis of pyrano[2,3-h]coumarins.
Magnetic imaging using geometrically constrained nano-domain walls
Authors: Corte-León Héctor , Rodríguez Luis Alfredo , Pancaldi Matteo , Gatel Christophe , Cox David , Snoeck Etienne , Antonov Vladimir , Vavassori Paolo , Kazakova Olga
Published: February 2019

Decoupled spatial and magnetic sensitivity in custom-made magnetic force microscope probes for advance nanomagnetic devices.
Gap-mode excitation, manipulation, and refractive-index sensing application by gold nanocube arrays
Authors: Li Liang , Wu Shaolong , Li Liujing , Zhou Zhongyuan , Ding Hao , Xiao Chenhong , Li Xiaofeng
Published: February 2019

The gap mode is manipulated by Au nanocube arrays fabricated by the electrostatic-adhesion method with the application for refractive-index sensing.
Enhanced oxide-ion conductivity of solid-state electrolyte mesocrystals
Authors: Tsukiyama Keishi , Takasaki Mihiro , Kitamura Naoto , Idemoto Yasushi , Oaki Yuya , Osada Minoru , Imai Hiroaki
Published: February 2019

Enhanced oxide-ion conductivities were observed on mesocrystalline structures that were produced by evaporation-induced self-assembly of rare earth-doped CeO2 nanocubes 4–5 nm in size.
Intentional anion incorporation to rationally modulate the size, shape and optical properties of lanthanide oxide nanocrystals
Authors: Fang Zhenlan , Zhao Fangyu , Zhang Yuwei , Ding Weilinsen , Zhang Lantian , Liu Meili , Xu Wenlong , Thapa Kedar Bahadur , Huang Wei , Ju Qiang
Published: February 2019

Intentional anion incorporation has been proposed as an efficient route to rationally tune the size, morphology and optical properties of lanthanide oxide nanocrystals.
Nanostructures inducing distinctive photocatalytic and photoelectrochemical performance via the introduction of rGO into CdxZn1−xS
Authors: Kai Shuangshuang , Xi Baojuan , Wei Denghu , Xiong Shenglin
Published: February 2019

WZ/ZB-Cd0.6Zn0.4S and WZ-Cd0.6Zn0.4S-RGO are prepared via the one-pot hydrothermal method. The introduction of graphene changes crystal structure and internal electric field, resulting in the different photocatalytic and photoelectrochemical performance.
High-throughput screen for sorting cells capable of producing the biofuel feedstock botryococcene
Authors: Chacko Allen R. , Amster Daniel E. , Johnson Tyler E. , Newman Sara R. , Gladchuk Angelina V. , Sohn Christine J. , Prunkard Donna E. , Yakelis Neal A. , Freeman Jon O.
Published: February 2019

Botryococcene is a branched triterpene produced by the algae Botryococcus braunii.
Rapid one-pot synthesis of tapered star copolymers via ultra-fast coupling of polystyryllithium chain ends
Authors: von Tiedemann Philipp , Maciol Kamil , Preis Jasmin , Sajkiewicz Paweł , Frey Holger
Published: February 2019

Efficient coupling of sterically demanding polystyryllithium (PS-Li) chain ends is achieved using tetra[3-(chloro-dimethylsilyl)propyl]silane (TCDMSPS) as a linking agent. This general approach is employed for the rapid synthesis of tapered star copolymers.
Chiral phosphoric acid-catalyzed asymmetric C(sp3)–H functionalization of biomass-derived 2,5-dimethylfuran via two sequential Cope-type rearrangements
Authors: Xu Lubin , Chen Haohua , Liu Jian , Zhou Lan , Liu Qing , Lan Yu , Xiao Jian
Published: February 2019

The first organocatalytic asymmetric C(sp3)–H functionalization of biomass-derived 2,5-dimethylfuran with alcohols to afford enantioenriched furan-derived 3,3′-disubstituted oxindoles in high enantioselectivity.
Identification and quantification of seven sesquiterpene lactones in Inula britannica by HPLC-DAD-MS
Authors: Wang Tianyi , Guo Sen , Zhang Shanshan , Yue Wenping , Ho Chi-Tang , Bai Naisheng
Published: February 2019

Inula britannica is a traditional Chinese medicinal herb.
Direct ink writing with high-strength and swelling-resistant biocompatible physically crosslinked hydrogels
Authors: Jiang Pan , Yan Changyou , Guo Yuxiong , Zhang Xiaoqin , Cai Meirong , Jia Xin , Wang Xiaolong , Zhou Feng
Published: February 2019

The 3D printing of physically crosslinked hydrogel architectures with high strength and swelling resistance is achieved with biocompatible PVA and natural κ-carrageenan hybrid inks.
Tin-assisted growth of all-inorganic perovskite nanoplatelets with controllable morphologies and complementary emissions
Authors: Ding Yanxi , Li Tan , Li Xiaoyun , Tsiwah Emmanuel Acheampong , Liu Chengzhen , Gao Peng , Zeng Tao , Chen Yunxia , Zhao Xiujian , Xie Yi
Published: February 2019

The Sn4+-assisted growth of CsPbBr3 nanoplatelets with the quantum confinement effect enables controllable morphologies and formation of dual photoluminescence emission.
Water flow in carbon nanotubes: the role of tube chirality
Authors: Sam Alan , K. Vishnu Prasad , Sathian Sarith P.
Published: February 2019

Flow rate of water in CNTs of different types.