bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular imaging with engineered physiology
Authors: Desai Mitul , Slusarczyk Adrian L. , Chapin Ashley , Barch Mariya , Jasanoff Alan 
Published: December 2016

AbstractIn vivo imaging techniques are powerful tools for evaluating biological systems. Relating image signals to precise molecular phenomena can be challenging, however, due to limitations of the existing optical, magnetic and radioactive imaging probe mechanisms. Here we demonstrate a concept for molecular imaging which bypasses the need for conventional imaging agents by perturbing the endogenous multimodal contrast provided by the vasculature. Variants of the calcitonin gene-related peptide artificially activate vasodilation pathways in rat brain and induce contrast changes that are readily measured by optical and magnetic resonance imaging. CGRP-based agents induce effects at nanomolar concentrations in deep tissue and can be engineered into switchable analyte-dependent forms and genetically encoded reporters suitable for molecular imaging or cell tracking. Such artificially engineered physiological changes, therefore, provide a highly versatile means for sensitive analysis of molecular events in living organisms.
Kaleidoscopic imaging patterns of complex structures fabricated by laser-induced deformation
Authors: Zhang Haoran , Yang Fengyou , Dong Jianjie , Du Lena , Wang Chuang , Zhang Jianming , Guo Chuan Fei , Liu Qian 
Published: December 2016

AbstractComplex surface structures have stimulated a great deal of interests due to many potential applications in surface devices. However, in the fabrication of complex surface micro-/nanostructures, there are always great challenges in precise design, or good controllability, or low cost, or high throughput. Here, we present a route for the accurate design and highly controllable fabrication of surface quasi-three-dimensional (quasi-3D) structures based on a thermal deformation of simple two-dimensional laser-induced patterns. A complex quasi-3D structure, coaxially nested convex–concave microlens array, as an example, demonstrates our capability of design and fabrication of surface elements with this method. Moreover, by using only one relief mask with the convex–concave microlens structure, we have gotten hundreds of target patterns at different imaging planes, offering a cost-effective solution for mass production in lithography and imprinting, and portending a paradigm in quasi-3D manufacturing.
Autonomy in materials research: a case study in carbon nanotube growth
Authors: Nikolaev Pavel , Hooper Daylond , Webber Frederick , Rao Rahul , Decker Kevin , Krein Michael , Poleski Jason , Barto Rick , Maruyama Benji 
Published: December 2016

AbstractAdvances in materials are an important contributor to our technological progress, and yet the process of materials discovery and development itself is slow. Our current research process is human-centred, where human researchers design, conduct, analyse and interpret experiments, and then decide what to do next. We have built an Autonomous Research System (ARES)—an autonomous research robot capable of first-of-its-kind closed-loop iterative materials experimentation. ARES exploits advances in autonomous robotics, artificial intelligence, data sciences, and high-throughput and in situ techniques, and is able to design, execute and analyse its own experiments orders of magnitude faster than current research methods. We applied ARES to study the synthesis of single-walled carbon nanotubes, and show that it successfully learned to grow them at targeted growth rates. ARES has broad implications for the future roles of humans and autonomous research robots, and for human-machine partnering. We believe autonomous research robots like ARES constitute a disruptive advance in our ability to understand and develop complex materials at an unprecedented rate.
The competing mini-dumbbell mechanism: new insights into CCTG repeat expansion
Authors: Guo Pei , Lam Sik Lok 
Published: December 2016

AbstractCCTG repeat expansions in intron 1 of the cellular nucleic acid-binding protein gene are associated with myotonic dystrophy type 2. Recently, we have reported a novel mini-dumbbell (MDB) structure formed by two CCTG or TTTA repeats, which potentially has a critical role in repeat expansions. Here we present a mechanism, called the competing MDB mechanism, to explain how the formation of MDB can lead to efficient mismatch repair (MMR) escape and thus CCTG repeat expansions during DNA replication. In a long tract of CCTG repeats, two competing MDBs can be formed in any segment of three repeats. Fast exchange between these MDBs will make the commonly occupied repeat behave like a mini-loop. Further participations of the 5′- or 3′-flanking repeat in forming competing MDBs will make the mini-loop shift in the 5′- or 3′-direction, thereby providing a pathway for the mini-loop to escape from MMR. To avoid the complications due to the formation of hairpin conformers in longer CCTG repeats, we made use of TTTA repeats as model sequences to demonstrate the formation of competing MDBs and shifting of mini-loop in a long tract of repeating sequence.
Multiparameter mechanical and morphometric screening of cells
Authors: Masaeli Mahdokht , Gupta Dewal , O’Byrne Sean , Tse Henry T. K. , Gossett Daniel R. , Tseng Peter , Utada Andrew S. , Jung Hea-Jin , Young Stephen , Clark Amander T. , Di Carlo Dino 
Published: December 2016

AbstractWe introduce a label-free method to rapidly phenotype and classify cells purely based on physical properties. We extract 15 biophysical parameters from cells as they deform in a microfluidic stretching flow field via high-speed microscopy and apply machine-learning approaches to discriminate different cell types and states. When employing the full 15 dimensional dataset, the technique robustly classifies individual cells based on their pluripotency, with accuracy above 95%. Rheological and morphological properties of cells while deforming were critical for this classification. We also show the application of this method in accurate classifying cells based on their viability, drug screening and detecting populations of malignant cells in mixed samples. We show that some of the extracted parameters are not linearly independent, and in fact we reach maximum classification accuracy by using only a subset of parameters. However, the informative subsets could vary depending on cell types in the sample. This work shows the utility of an assay purely based on intrinsic biophysical properties of cells to identify changes in cell state. In addition to a label-free alternative to flow cytometry in certain applications, this work, also can provide novel intracellular metrics that would not be feasible with labeled approaches (i.e. flow cytometry).
Conditional knockout of N-WASP in mouse fibroblast caused keratinocyte hyper proliferation and enhanced wound closure
Authors: Jain Neeraj , Kalailingam Pazhanichamy , Tan Kai Wei , Tan Hui Bing , Sng Ming Keat , Chan Jeremy Soon Kiat , Tan Nguan Soon , Thanabalu Thirumaran 
Published: December 2016

AbstractNeural-Wiskott Aldrich Syndrome Protein (N-WASP) is expressed ubiquitously, regulates actin polymerization and is essential during mouse development. We have previously shown that N-WASP is critical for cell-ECM adhesion in fibroblasts. To characterize the role of N-WASP in fibroblast for skin development, we generated a conditional knockout mouse model in which fibroblast N-WASP was ablated using the Cre recombinase driven by Fibroblast Specific Protein promoter (Fsp-Cre). N-WASPFKO (N-WASPfl/fl; Fsp-cre) were born following Mendelian genetics, survived without any visible abnormalities for more than 1 year and were sexually reproductive, suggesting that expression of N-WASP in fibroblast is not critical for survival under laboratory conditions. Histological sections of N-WASPFKO mice skin (13 weeks old) showed thicker epidermis with higher percentage of cells staining for proliferation marker (PCNA), suggesting that N-WASP deficient fibroblasts promote keratinocyte proliferation. N-WASPFKO mice skin had elevated collagen content, elevated expression of FGF7 (keratinocyte growth factor) and TGFβ signaling proteins. Wound healing was faster in N-WASPFKO mice compared to control mice and N-WASP deficient fibroblasts were found to have enhanced collagen gel contraction properties. These results suggest that N-WASP deficiency in fibroblasts improves wound healing by growth factor-mediated enhancement of keratinocyte proliferation and increased wound contraction in mice.
UV Degradation and Recovery of Perovskite Solar Cells
Authors: Lee Sang-Won , Kim Seongtak , Bae Soohyun , Cho Kyungjin , Chung Taewon , Mundt Laura E. , Lee Seunghun , Park Sungeun , Park Hyomin , Schubert Martin C. , Glunz Stefan W. , Ko Yohan , Jun Yongseok , Kang Yoonmook , Lee Hae-Seok , Kim Donghwan 
Published: December 2016

AbstractAlthough the power conversion efficiency of perovskite solar cells has increased from 3.81% to 22.1% in just 7 years, they still suffer from stability issues, as they degrade upon exposure to moisture, UV light, heat, and bias voltage. We herein examined the degradation of perovskite solar cells in the presence of UV light alone. The cells were exposed to 365 nm UV light for over 1,000 h under inert gas at <0.5 ppm humidity without encapsulation. 1-sun illumination after UV degradation resulted in recovery of the fill factor and power conversion efficiency. Furthermore, during exposure to consecutive UV light, the diminished short circuit current density (Jsc) and EQE continuously restored. 1-sun light soaking induced recovery is considered to be caused by resolving of stacked charges and defect state neutralization. The Jsc and EQE bounce-back phenomenon is attributed to the beneficial effects of PbI2 which is generated by the decomposition of perovskite material.
Energy metabolism regulated by HDAC inhibitor attenuates cardiac injury in hemorrhagic rat model
Authors: Kuai Qiyuan , Wang Chunyan , Wang Yanbing , Li Weijing , Zhang Gongqing , Qiao Zhixin , He Min , Wang Xuanlin , Wang Yu , Jiang Xingwei , Su Lihua , He Yuezhong , Ren Suping , Yu Qun 
Published: December 2016

AbstractA disturbance of energy metabolism reduces cardiac function in acute severe hemorrhagic patients. Alternatively, adequate energy supply reduces heart failure and increases survival. However, the approach to regulating energy metabolism conductive to vital organs is limited, and the underlying molecular mechanism remains unknown. This study assesses the ability of histone deacetylase inhibitors (HDACIs) to preserve cardiac energy metabolism during lethal hemorrhagic injury. In the lethally hemorrhagic rat and hypoxic myocardial cells, energy metabolism and heart function were well maintained following HDACI treatment, as evident by continuous ATP production with normal cardiac contraction. Valproic acid (VPA) regulated the energy metabolism of hemorrhagic heart by reducing lactate synthesis and protecting the mitochondrial ultrastructure and respiration, which were attributable to the inhibition of lactate dehydrogenase A activity and the increased myeloid cell leukemia-1 (mcl-1) gene expression, ultimately facilitating ATP production and consumption. MCL-1, the key target of VPA, mediated this cardioprotective effect under acute severe hemorrhage conditions. Our results suggest that HDACIs promote cardioprotection by improving energy metabolism during hemorrhagic injury and could therefore be an effective strategy to counteract this process in the clinical setting.
The mechanism of transactivation regulation due to polymorphic short tandem repeats (STRs) using IGF1 promoter as a model
Authors: Chen Holly Y. , Ma Suk Ling , Huang Wei , Ji Lindan , Leung Vincent H. K. , Jiang Honglin , Yao Xiaoqiang , Tang Nelson L. S. 
Published: December 2016

AbstractFunctional short tandem repeats (STR) are polymorphic in the population, and the number of repeats regulates the expression of nearby genes (known as expression STR, eSTR). STR in IGF1 promoter has been extensively studied for its association with IGF1 concentration in blood and various clinical traits and represents an important eSTR. We previously used an in-vitro luciferase reporter model to examine the interaction between STRs and SNPs in IGF1 promoter. Here, we further explored the mechanism how the number of repeats of the STR regulates gene transcription. An inverse correlation between the number of repeats and the extent of transactivation was found in a haplotype consisting of three promoter SNPs (C-STR-T-T). We showed that these adjacent SNPs located outside the STR were required for the STR to function as eSTR. The C allele of rs35767 provides a binding site for CCAAT/enhancer-binding-protein δ (C/EBPD), which is essential for the gradational transactivation property of eSTR and FOXA3 may also be involved. Therefore, we propose a mechanism in which the gradational transactivation by the eSTR is caused by the interaction of one or more transcriptional complexes located outside the STR, rather than by direct binding to a repeat motif of the STR.
MicroRNAs modulate adaption to multiple abiotic stresses in Chlamydomonas reinhardtii
Authors: Gao Xiang , Zhang Fengge , Hu Jinlu , Cai Wenkai , Shan Ge , Dai Dongsheng , Huang Kaiyao , Wang Gaohong 
Published: December 2016

AbstractMicroRNAs play an important role in abiotic stress responses in higher plants and animals, but their role in stress adaptation in algae remains unknown. In this study, the expression of identified and putative miRNAs in Chlamydomonas reinhardtii was assessed using quantitative polymerase chain reaction; some of the miRNAs (Cre-miR906-3p) were up-regulated, whereas others (Cre-miR910) were down-regulated when the species was subjected to multiple abiotic stresses. With degradome sequencing data, we also identified ATP4 (the d-subunit of ATP synthase) and NCR2 (NADPH: cytochrome P450 reductase) as one of the several targets of Cre-miR906-3p and Cre-miR910, respectively. Q-PCR data indicated that ATP4, which was expressed inversely in relation to Cre-miR906-3p under stress conditions. Overexpressing of Cre-miR906-3p enhanced resistance to multiple stresses; conversely, overexpressing of ATP4 produced the opposite effect. These data of Q-PCR, degradome sequencing and adaptation of overexpressing lines indicated that Cre-miR906-3p and its target ATP4 were a part of the same pathway for stress adaptation. We found that Cre-miR910 and its target NCR2 were also a part of this pathway. Overexpressing of Cre-miR910 decreased, whereas that of NCR2 increased the adaption to multiple stresses. Our findings suggest that the two classes of miRNAs synergistically mediate stress adaptation in algae.
Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members
Authors: Ariani Pietro , Regaiolo Alice , Lovato Arianna , Giorgetti Alejandro , Porceddu Andrea , Camiolo Salvatore , Wong Darren , Castellarin Simone , Vandelle Elodie , Polverari Annalisa 
Published: December 2016

AbstractThe Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes. Most of the grapevine ATL genes lacked introns and were scattered among the 19 chromosomes, with a high level of duplication retention. Expression profiling revealed that some ATL genes are expressed specifically during early or late development and may participate in the juvenile to mature plant transition, whereas others may play a role in pathogen and/or abiotic stress responses, making them key candidates for further functional analysis. Our data offer the first genome-wide overview and annotation of the grapevine ATL family, and provide a basis for investigating the roles of specific family members in grapevine physiology and stress responses, as well as potential biotechnological applications.
Melanosome transfer to keratinocyte in the chicken embryonic skin is mediated by vesicle release associated with Rho-regulated membrane blebbing
Authors: Tadokoro Ryosuke , Murai Hidetaka , Sakai Ken-ichiro , Okui Takahiro , Yokota Yasuhiro , Takahashi Yoshiko 
Published: December 2016

AbstractDuring skin pigmentation in amniotes, melanin synthesized in the melanocyte is transferred to keratinocytes by a particle called the melanosome. Previous studies, mostly using dissociated cultured cells, have proposed several different models that explain how the melanosome transfer is achieved. Here, using a technique that labels the plasma membrane of melanocytes within a three-dimensional system that mimics natural tissues, we have visualized the plasma membrane of melanocytes with EGFP in chicken embryonic skin. Confocal time-lapse microscopy reveals that the melanosome transfer is mediated, at least in part, by vesicles produced by plasma membrane. Unexpectedly, the vesicle release is accompanied by the membrane blebbing of melanocytes. Blebs that have encapsulated a melanosome are pinched off to become vesicles, and these melanosome-containing vesicles are finally engulfed by neighboring keratinocytes. For both the membrane blebbing and vesicle release, Rho small GTPase is essential. We further show that the membrane vesicle-mediated melanosome transfer plays a significant role in the skin pigmentation. Given that the skin pigmentation in inter-feather spaces in chickens is similar to that in inter-hair spaces of humans, our findings should have important consequences in cosmetic medicine.
Calcium ions function as a booster of chromosome condensation
Authors: Phengchat Rinyaporn , Takata Hideaki , Morii Kenichi , Inada Noriko , Murakoshi Hideji , Uchiyama Susumu , Fukui Kiichi 
Published: December 2016

AbstractChromosome condensation is essential for the faithful transmission of genetic information to daughter cells during cell division. The depletion of chromosome scaffold proteins does not prevent chromosome condensation despite structural defects. This suggests that other factors contribute to condensation. Here we investigated the contribution of divalent cations, particularly Ca2+, to chromosome condensation in vitro and in vivo. Ca2+ depletion caused defects in proper mitotic progression, particularly in chromosome condensation after the breakdown of the nuclear envelope. Fluorescence lifetime imaging microscopy-Förster resonance energy transfer and electron microscopy demonstrated that chromosome condensation is influenced by Ca2+. Chromosomes had compact globular structures when exposed to Ca2+ and expanded fibrous structures without Ca2+. Therefore, we have clearly demonstrated a role for Ca2+ in the compaction of chromatin fibres.
Arabidopsis thaliana as a suitable model host for research on interactions between plant and foliar nematodes, parasites of plant shoot
Authors: Wang Dong-Wei , Peng Xiao-Fang , Xie Hui , Xu Chun-Ling , Cheng De-Qiang , Li Jun-Yi , Wu Wen-Jia , Wang Ke 
Published: December 2016

AbstractThe rice white tip nematode (RWTN), Aphelenchoides besseyi and the chrysanthemum foliar nematode (CFN), Aphelenchoides ritzemabosi are migratory plant parasitic nematodes that infect the aboveground parts of plants. In this research, Arabidopsis thaliana was infected by RWTN and CFN under indoor aseptic cultivation, and the nematodes caused recognizable symptoms in the leaves. Furthermore, RWTN and CFN completed their life cycles and proliferated. Therefore, A. thaliana was identified as a new host of RWTN and CFN. The optimum inoculum concentration for RWTN and CFN was 100 nematodes/plantlet, and the optimum inoculum times were 21 and 24 days, respectively. For different RWTN populations, the pathogenicity and reproduction rates were different in the A. thaliana Col-0 ecotype and were positively correlated. The optimum A. thaliana ecotypes were Col-0 and WS, which were the most susceptible to RWTN and CFN, respectively. Additionally, RWTN was ectoparasitic and CFN was ecto- and endoparasitic in A. thaliana. The RWTN and CFN migrated from inoculated leaves to the entire plantlet, and the number of nematodes in different parts of A. thaliana was not correlated with distance from the inoculum point. This is a detailed study of the behavior and infection process of foliar nematodes on A. thaliana.
The Disinfection Characteristics of Ebola Virus Outbreak Variants
Authors: Cook Bradley W. M. , Cutts Todd A. , Nikiforuk Aidan M. , Leung Anders , Kobasa Darwyn , Theriault Steven S. 
Published: December 2016

AbstractThe recent Ebola virus outbreak in West Africa has forced experts to re-evaluate their understanding of how to best disinfect areas contaminated with infectious bodily fluids. Recent research has found that Ebola virus remains viable in blood for 7–10 days making appropriate disinfection crucial to infection control. We sought to determine if the three most important outbreak variants ofZaire ebolavirus(Mayinga, Kikwit and Makona) exhibit separate phenotypes when challenged with a range of sodium hypochlorite (NaOCl) concentrations or 70% ethanol (EtOH) at average West African temperature. The time dependent killing of Ebola virus was evaluated by measuring infectious virus and viral RNA (vRNA), to determine if RNA detection is a viable method for decontamination measurement in areas without high containment laboratory access. Makona was less susceptible to weaker concentrations of NaOCl (0.05 and 0.1%) than Mayinga and Kikwit. At the recommended concentration of NaOCl (≥0.5%) all of the variants were inert after 5 minutes of contact time. Similarly, all variants were inactivated by 70% EtOH after 2.5 minutes, only Makona was detected at 1 minute. In multiple instances, high amounts of vRNA was detected in the absence of infectious virus, suggesting that it does not serve as an accurate measure of remaining infectivity after cleansing.
Improved in-cell structure determination of proteins at near-physiological concentration
Authors: Ikeya Teppei , Hanashima Tomomi , Hosoya Saori , Shimazaki Manato , Ikeda Shiro , Mishima Masaki , Güntert Peter , Ito Yutaka 
Published: December 2016

AbstractInvestigating three-dimensional (3D) structures of proteins in living cells by in-cell nuclear magnetic resonance (NMR) spectroscopy opens an avenue towards understanding the structural basis of their functions and physical properties under physiological conditions inside cells. In-cell NMR provides data at atomic resolution non-invasively, and has been used to detect protein-protein interactions, thermodynamics of protein stability, the behavior of intrinsically disordered proteins, etc. in cells. However, so far only a single de novo 3D protein structure could be determined based on data derived only from in-cell NMR. Here we introduce methods that enable in-cell NMR protein structure determination for a larger number of proteins at concentrations that approach physiological ones. The new methods comprise (1) advances in the processing of non-uniformly sampled NMR data, which reduces the measurement time for the intrinsically short-lived in-cell NMR samples, (2) automatic chemical shift assignment for obtaining an optimal resonance assignment, and (3) structure refinement with Bayesian inference, which makes it possible to calculate accurate 3D protein structures from sparse data sets of conformational restraints. As an example application we determined the structure of the B1 domain of protein G at about 250 μM concentration in living E. coli cells.