bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractSublancin 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

AbstractThe 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

AbstractNeurotrophin 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

AbstractDisruption 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

AbstractArbuscular 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

AbstractA 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

AbstractHepatocellular 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

AbstractExtracellular 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

AbstractThe 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

AbstractAs 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

AbstractThe 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

AbstractChinese 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

AbstractPigs 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.
Melatonin suppresses lung cancer metastasis by inhibition of epithelial–mesenchymal transition through targeting to Twist
Authors: Chao Chia-Chia , Chen Po-Chun , Chiou Pei-Chen , Hsu Chin-Jung , Liu Po-I , Yang Yi-Chen , Reiter Russel J. , Yang Shun-Fa , Tang Chih-Hsin 
Published: February 2019

Abstract
The epithelial–mesenchymal transition (EMT) phenotype, whereby mature epithelial cells undergo phenotype transition and differentiate into motile, invasive cells, has been indicated in tumor metastasis. The melatonin hormone secreted by the pineal gland has an antioxidant effect and protects cells against carcinogenic substances that reduce tumor progression. However, the effects of melatonin in EMT and lung cancer metastasis are largely unknown. We found that melatonin down-regulated EMT by inhibiting Twist/Twist1 (twist family bHLH transcription factor 1) expression. This effect was mediated by MT1 receptor, PLC, p38/ERK and β-catenin signaling cascades. Twist expression was positively correlated with tumor stage and negatively correlated with MT1 expression in lung cancer specimens. Furthermore, melatonin inhibited EMT marker expression and lung cancer metastasis to liver in vivo. Finally, melatonin shows promise in the treatment of lung cancer metastasis and deserves further study.
Eligibility and Speech Sound Disorders: Assessment of Social Impact
Authors: Krueger Breanna I. 
Published: February 2019

Purpose
The purpose of this article is to discuss the social impact of speech sound disorders for children, specifically in the public school system, and to examine different methods of social impact assessment for speech-language therapy services using 3 hypothetical cases.

Method
This article presents 3 common cases seen by school-based speech-language pathologists and discusses the types of assessments that may be conducted for each child's needs. One child has errors on many sounds, 1 child has errors on only /r/, and 1 child produces strident sounds with a lateral lisp.

Results
As these are hypothetical cases, possibilities are discussed for each case. Similarities and differences exist among the 3 cases in terms of assessing the social impact of their speech sound disorder; however, each child could qualify for services based on social impact assessments.

Conclusion
Social impact assessments are an important portion of a speech sound evaluation; however, they are often overlooked. Emphasis is placed on articulation assessments and/or commonly accepted developmental norms. The determination of social impact supplies a more complete picture for making eligibility decisions for children with speech sound disorders and may lead to more meaningful treatment methods for the student.