bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted detection of Dehalococcoides mccartyi microbial protein biomarkers as indicators of reductive dechlorination activity in contaminated groundwater
Authors: Solis Manuel I. Villalobos , Abraham Paul E. , Chourey Karuna , Swift Cynthia M. , Löffler Frank E. , Hettich Robert L. 
Published: July 2019

AbstractDehalococcoides mccartyi (Dhc) bacterial strains expressing active reductive dehalogenase (RDase) enzymes play key roles in the transformation and detoxification of chlorinated pollutants, including chlorinated ethenes. Site monitoring regimes traditionally rely on qPCR to assess the presence of Dhc biomarker genes; however, this technique alone cannot directly inform about dechlorination activity. To supplement gene-centric approaches and provide a more reliable proxy for dechlorination activity, we sought to demonstrate a targeted proteomics approach that can characterize Dhc mediated dechlorination in groundwater contaminated with chlorinated ethenes. Targeted peptide selection was conducted in axenic cultures of Dhc strains 195, FL2, and BAV1. These experiments yielded 37 peptides from housekeeping and structural proteins (i.e., GroEL, EF-TU, rpL7/L2 and the S-layer), as well as proteins involved in the reductive dechlorination activity (i.e., FdhA, TceA, and BvcA). The application of targeted proteomics to a defined bacterial consortium and contaminated groundwater samples resulted in the detection of FdhA peptides, which revealed active dechlorination with Dhc strain-level resolution, and the detection of RDases peptides indicating specific reductive dechlorination steps. The results presented here show that targeted proteomics can be applied to groundwater samples and provide protein level information about Dhc dechlorination activity.
Ex Vivo and In Vivo Biocompatibility Assessment (Blood and Tissue) of Three-Dimensional Bacterial Nanocellulose Biomaterials for Soft Tissue Implants
Authors: Osorio M. , Cañas A. , Puerta J. , Díaz L. , Naranjo T. , Ortiz I. , Castro C. 
Published: July 2019

AbstractBacterial nanocellulose (BNC) is a promising biomedical material. However, the haemocompatibility (haemolysis and thrombogenicity) and acute and sub-chronic immune responses to three-dimensional (3D) BNC biomaterials have not been evaluated. Accordingly, this manuscript focused on the effect of 3D microporosity on BNC haemocompatibility and a comparison with 2D BNC architecture, followed by the evaluation of the immune response to 3D BNC. Blood ex vivo studies indicated that compared with other 2D and 3D BNC architectures, never-dried 2D BNC presented antihemolytic and antithrombogenic effects. Nevertheless, in vivo studies indicated that 3D BNC did not interfere with wound haemostasis and elicited a mild acute inflammatory response, not a foreign body or chronic inflammatory response. Moreover, compared with the polyethylene controls, the implant design with micropores ca. 60 µm in diameter showed a high level of collagen, neovascularization and low fibrosis. Cell/tissue infiltration increased to 91% after 12 weeks and was characterized by fibroblastic, capillary and extracellular matrix infiltration. Accordingly, 3D BNC biomaterials can be considered a potential implantable biomaterial for soft tissue augmentation or replacement.
AIM2 inflammasome-derived IL-1β induces postoperative ileus in mice
Authors: Hupa Kristof Johannes , Stein Kathy , Schneider Reiner , Lysson Mariola , Schneiker Bianca , Hornung Veit , Latz Eicke , Iwakura Yoichiro , Kalff Jörg C. , Wehner Sven 
Published: July 2019

AbstractPostoperative ileus (POI) is an intestinal dysmotility frequently occurring after abdominal surgery. An orchestrated neuroimmune response within the muscularis externa (ME) involves activation of resident macrophages, enteric glia and infiltration of blood-derived leukocytes. Interleukin-1 receptor type-I (IL1R1) signalling on enteric glia has been shown to be involved in POI development. Herein we investigated the distinct role of the IL1R1 ligands interleukin (IL) -1α and IL-1β and focused on the mechanism of IL-1β production. IL-1α and IL-1β deficient mice were protected from POI. Bone-marrow transplantation studies indicated that IL-1α originated from radio-resistant cells while IL-1β was released from the radio-sensitive infiltrating leukocytes. Mouse strains deficient in inflammasome formation identified the absent in melanoma 2 (AIM2) inflammasome to be crucial for IL-1β production in POI. Mechanistically, antibiotic-treated mice revealed a prominent role of the microbiome in IL-1β production. Our study provides new insights into distinct roles of IL-1α and IL-1β signalling during POI. While IL-1α release is most likely an immediate passive response to the surgical trauma, IL-1β production depends on AIM2 inflammasome formation and the microbiome. Selective interaction in this pathway might be a promising target to prevent POI in surgical patients.
High Serum Cyclophilin C levels as a risk factor marker for Coronary Artery Disease
Authors: Alfonso Amparo , Bayón Jeremías , Gegunde Sandra , Alonso Eva , Alvariño Rebeca , Santás-Álvarez Melisa , Testa-Fernández Ana , Rios-Vázquez Ramón , González-Juanatey Carlos , Botana Luis M. 
Published: July 2019

AbstractCyclophilins (Cyps) are ubiquitous proteins that belong to the immunophilins family consistently associated with inflammatory and cardiovascular diseases. While levels of CypA have been extensively studied, less data are available for other Cyps. The purpose of this case-control study was to determine the relationship of Cyps (A, B, C and D) with coronary artery disease (CAD) and eight inflammation markers. Serum levels of Cyps, interleukins and metalloproteinases were measured in serum collected from 84 subjects. Participants were divided into two sub-groups based on CAD diagnosis: 40 CAD patients and 44 control volunteers. Serum levels of CypA, CypB and CypC, IL-1β and IL-6 were significantly higher in CAD patients. Bivariate correlation analysis revealed a significant positive correlation between Cyps and several blood and biochemical parameters. When the ability of Cyps levels for CAD diagnosis was evaluated, higher sensitivity and selectivity values were obtained with CypC (c-statistic 0.891, p < 0.001) indicating that it is a good marker of CAD disease, while less conclusive results were obtained with CypA (c-statistic 0.748, p < 0.001) and CypB (c-statistic 0.655, p < 0.014). In addition, significant correlations of traditional CAD risk factors and CypC were observed. In summary, high levels of CypC are a risk factor for CAD and therefore it can be proposed as a new biomarker for this disease.
Optical coherence tomography complements confocal microscopy for investigation of multicellular tumour spheroids
Authors: Hari Neelam , Patel Priyanka , Ross Jacqueline , Hicks Kevin , Vanholsbeeck Frédérique 
Published: July 2019

AbstractKnowledge of optical properties, such as the refractive index (RI), of biological tissues is important in optical imaging, as they influence the distribution and propagation of light in tissue. To accurately study the response of cancerous cells to drugs, optimised imaging protocols are required. This study uses a simple custom-built spectral domain optical coherence tomography (OCT) system to conduct RI measurements of multicellular spheroids, three-dimensional (3D) in-vitro culture systems, of the cell line HCT116. The spheroid RIs are compared to study the effect of growth over time. To improve confocal microscopy imaging protocols, two immersion media (glycerol and ScaleView-A2) matching the spheroid RIs were trialled, with the aim to reduce the RI mismatch between the spheroid and the immersion medium and thus improve imaging depth with confocal microscopy. ScaleView-A2 (n = 1.380) aided in achieving greater depths of imaging of the multicellular spheroids under confocal microscopy. This improvement in imaging depth confirmed the utility of our RI measurements, proving the promising outlook of OCT as a complementary tool to microscopy in cancer research.
Identification of novel breakpoints for locus- and region-specific translocations in 293 cells by molecular cytogenetics before and after irradiation
Authors: Binz Regina L. , Tian Erming , Sadhukhan Ratan , Zhou Daohong , Hauer-Jensen Martin , Pathak Rupak 
Published: July 2019

AbstractThe human kidney embryonic 293 cell line (293 cells) is extensively used in biomedical and pharmaceutical research. These cells exhibit a number of numerical and structural chromosomal anomalies. However, the breakpoints responsible for these structural chromosomal rearrangements have not been comprehensively characterized. In addition, it is not known whether chromosomes with structural rearrangement are more sensitive to external toxic agents, such as ionizing radiation. We used G-banding, spectral karyotyping (SKY), and locus- and region-specific fluorescence in situ hybridization (FISH) probes designed in our lab or obtained from commercial vendor to address this gap. Our G-banding analysis revealed that the chromosome number varies from 66 to 71, with multiple rearrangements and partial additions and deletions. SKY analysis confirmed 3 consistent rearrangements, two simple and one complex in nature. Multicolor FISH analysis identified an array of breakpoints responsible for locus- and region-specific translocations. Finally, SKY analysis revealed that radio-sensitivity of structurally rearranged chromosomes is dependent on radiation dose. These findings will advance our knowledge in 293 cell biology and will enrich the understanding of radiation biology studies.
Enhanced cardiac repair by telomerase reverse transcriptase over-expression in human cardiac mesenchymal stromal cells
Authors: Le Thi Yen Loan , Pickett Hilda A. , Yang Andrian , Ho Joshua W. K. , Thavapalachandran Sujitha , Igoor Sindhu , Yang Sile F. , Farraha Melad , Voges Holly K. , Hudson James E. , dos Remedios Cristobal G. , Bryan Tracy M. , Kizana Eddy , Chong James J. H. 
Published: July 2019

AbstractWe have previously reported a subpopulation of mesenchymal stromal cells (MSCs) within the platelet-derived growth factor receptor-alpha (PDGFRα)/CD90 co-expressing cardiac interstitial and adventitial cell fraction. Here we further characterise PDGFRα/CD90-expressing cardiac MSCs (PDGFRα + cMSCs) and use human telomerase reverse transcriptase (hTERT) over-expression to increase cMSCs ability to repair the heart after induced myocardial infarction. hTERT over-expression in PDGFRα + cardiac MSCs (hTERT + PDGFRα + cMSCs) modulates cell differentiation, proliferation, survival and angiogenesis related genes. In vivo, transplantation of hTERT + PDGFRα + cMSCs in athymic rats significantly increased left ventricular function, reduced scar size, increased angiogenesis and proliferation of both cardiomyocyte and non-myocyte cell fractions four weeks after myocardial infarction. In contrast, transplantation of mutant hTERT + PDGFRα + cMSCs (which generate catalytically-inactive telomerase) failed to replicate this cardiac functional improvement, indicating a telomerase-dependent mechanism. There was no hTERT + PDGFRα + cMSCs engraftment 14 days after transplantation indicating functional improvement occurred by paracrine mechanisms. Mass spectrometry on hTERT + PDGFRα + cMSCs conditioned media showed increased proteins associated with matrix modulation, angiogenesis, cell proliferation/survival/adhesion and innate immunity function. Our study shows that hTERT can activate pro-regenerative signalling within PDGFRα + cMSCs and enhance cardiac repair after myocardial infarction. An increased understanding of hTERT’s role in mesenchymal stromal cells from various organs will favourably impact clinical regenerative and anti-cancer therapies.
USP10 is a critical factor for Tau-positive stress granule formation in neuronal cells
Authors: Piatnitskaia Svetlana , Takahashi Masahiko , Kitaura Hiroki , Katsuragi Yoshinori , Kakihana Taichi , Zhang Lu , Kakita Akiyoshi , Iwakura Yuriko , Nawa Hiroyuki , Miura Takeshi , Ikeuchi Takeshi , Hara Toshifumi , Fujii Masahiro 
Published: July 2019

AbstractTau aggregates in neurons of brain lesions is a hallmark pathology of tauopathies, including Alzheimer’s disease (AD). Recent studies suggest that the RNA-binding protein TIA1 initiates Tau aggregation by inducing the formation of stress granules (SGs) containing Tau. SGs are stress-inducible cytoplasmic protein aggregates containing many RNA-binding proteins that has been implicated as an initial site of multiple pathogenic protein aggregates in several neurodegenerative diseases. In this study, we found that ubiquitin-specific protease 10 (USP10) is a critical factor for the formation of Tau/TIA1/USP10-positive SGs. Proteasome inhibition or TIA1-overexpression in HT22 neuronal cells induced the formation of TIA1/Tau-positive SGs, and the formations were severely attenuated by depletion of USP10. In addition, the overexpression of USP10 without stress stimuli in HT22 cells induced TIA1/Tau/USP10-positive SGs in a deubiquitinase-independent manner. In AD brain lesions, USP10 was colocalized with Tau aggregates in the cell body of neurons. The present findings suggest that USP10 plays a key role in the initiation of pathogenic Tau aggregation in AD through SG formation.
Discovering consensus genomic regions in wheat for root-related traits by QTL meta-analysis
Authors: Soriano Jose Miguel , Alvaro Fanny 
Published: July 2019

AbstractRoot system architecture is crucial for wheat adaptation to drought stress, but phenotyping for root traits in breeding programmes is difficult and time-consuming owing to the belowground characteristics of the system. Identifying quantitative trait loci (QTLs) and linked molecular markers and using marker-assisted selection is an efficient way to increase selection efficiency and boost genetic gains in breeding programmes. Hundreds of QTLs have been identified for different root traits in the last few years. In the current study, consensus QTL regions were identified through QTL meta-analysis. First, a consensus map comprising 7352 markers was constructed. For the meta-analysis, 754 QTLs were retrieved from the literature and 634 of them were projected onto the consensus map. Meta-analysis grouped 557 QTLs in 94 consensus QTL regions, or meta-QTLs (MQTLs), and 18 QTLs remained as singletons. The recently published genome sequence of wheat was used to search for gene models within the MQTL peaks. As a result, gene models for 68 of the 94 Root_MQTLs were found, 35 of them related to root architecture and/or drought stress response. This work will facilitate QTL cloning and pyramiding to develop new cultivars with specific root architecture for coping with environmental constraints.
High-resolution multimodal photoacoustic microscopy and optical coherence tomography image-guided laser induced branch retinal vein occlusion in living rabbits
Authors: Nguyen Van Phuc , Li Yanxiu , Zhang Wei , Wang Xueding , Paulus Yannis M. 
Published: July 2019

AbstractJoint high-resolution multimodal photoacoustic microscopy (PAM) and optical coherence tomography (OCT) was developed to improve the efficiency for visualizing newly developed retinal neovascularization (RNV) and to monitor the dynamic changes of retinal vein occlusion (RVO) in living rabbits. The RNV and RVO models were created in New Zealand rabbits by Rose Bengal laser-induced RVO. Dual modalities imaging equipment, including color fundus photography, fluorescein angiography (FA), OCT, and PAM, was used to image and assess the changes of retinal vasculature. In vivo experimental results exhibited that not only the treatment boundaries and the position of the occluded vasculature but also the structure of individual RNV were markedly observed using PAM platform with great resolution and high image contrast. The laser light energy of 80 nJ was used to induce photoacoustic signal, which is approximately half the energy of the American National Standards Institute safety limit. A cross-sectional structure of RNV was identified with the OCT modality. Furthermore, vibrant transformations in the RNV and the retinal morphology were examined at different times after laser occlusion: days 4, 28, 35, 49, and 90. PAM revealed high contrast and high resolution vascular imaging of the retina and choroid with amplified penetration depth. Through the present custom-built imaging system, both RNV and RVO can be reconstructed and observed in two and three dimensions. A unique dual modality A unique dual modality PAM and OCT can help precisely visualize and distinguish individual microvessels, microvessel depth, and the surrounding anatomy. Thus, the proposed multimodal ocular imaging platform may offer a potential equipment to enhance classification of microvasculature in a reliable and proficient manner in larger rabbit eyes.
Transcriptome profiling-based identification of prognostic subtypes and multi-omics signatures of glioblastoma
Authors: Park Junseong , Shim Jin-Kyoung , Yoon Seon-Jin , Kim Se Hoon , Chang Jong Hee , Kang Seok-Gu 
Published: July 2019

AbstractGlioblastoma (GBM) is a lethal tumor, but few biomarkers and molecular subtypes predicting prognosis are available. This study was aimed to identify prognostic subtypes and multi-omics signatures for GBM. Using oncopression and TCGA-GBM datasets, we identified 80 genes most associated with GBM prognosis using correlations between gene expression levels and overall survival of patients. The prognostic score of each sample was calculated using these genes, followed by assigning three prognostic subtypes. This classification was validated in two independent datasets (REMBRANDT and Severance). Functional annotation revealed that invasion- and cell cycle-related gene sets were enriched in poor and favorable group, respectively. The three GBM subtypes were therefore named invasive (poor), mitotic (favorable), and intermediate. Interestingly, invasive subtype showed increased invasiveness, and MGMT methylation was enriched in mitotic subtype, indicating need for different therapeutic strategies according to prognostic subtypes. For clinical convenience, we also identified genes that best distinguished the invasive and mitotic subtypes. Immunohistochemical staining showed that markedly higher expression of PDPN in invasive subtype and of TMEM100 in mitotic subtype (P < 0.001). We expect that this transcriptome-based classification, with multi-omics signatures and biomarkers, can improve molecular understanding of GBM, ultimately leading to precise stratification of patients for therapeutic interventions.
PIN1 transcript variant 2 acts as a long non-coding RNA that controls the HIF-1-driven hypoxic response
Authors: Choi Yong-Joon , Kim Iljin , Lee Jae Eun , Park Jong-Wan 
Published: July 2019

AbstractThe transcription factor HIF-1 induces the expression of genes that are essential for cell survival and oxygen homeostasis in hypoxic conditions. The prolyl isomerase Pin1 plays a role in the regulation of HIF-1α. However, the mechanism by which Pin1 controls HIF-1α remains controversial. Surprisingly, we here show that a PIN1 transcript downregulates HIF-1α as a long non-coding RNA. Pin1-silencing siRNAs augmented the hypoxia-induced expression of HIF-1α, thereby upregulating the expression of HIF-1 target genes. However, the overexpression of Pin1 protein did not inhibit the hypoxic expression of HIF-1α. Pin1 restoration in Pin1-depleted cells also failed to reverse the induction of HIF-1α by Pin1 knockdown. Unexpectedly, HIF-1α was found to be induced by both siRNAs for PIN1 transcript variants 1/2 and that for PIN1 transcript variants 2/3, indicating that the PIN1 transcript variant 2 (PIN1-v2) is responsible for HIF-1α induction. Mechanistically, PIN1-v2, which is classified as a long non-coding RNA due to early termination of translation, was evaluated to inhibit the transcription of HIF1A gene. In conclusion, PIN1-v2 may function in balancing the HIF-1-driven gene expression under hypoxia.
Higher soil fauna abundance accelerates litter carbon release across an alpine forest-tundra ecotone
Authors: Liu Yang , Wang Lifeng , He Runlian , Chen Yamei , Xu Zhenfeng , Tan Bo , Zhang Li , Xiao Jiujin , Zhu Peng , Chen Lianghua , Guo Li , Zhang Jian 
Published: July 2019

AbstractUpward shifts of alpine treelines and shrub expansion are occurring under climate change, and Abies faxoniana (AF) and Rhododendron lapponicum (RL) may become distributed at higher altitudes. How do abiotic factors and litter quality modulate the effects of soil fauna on carbon release in this context? A field decomposition experiment involving the foliar litter of AF and RL was conducted along an elevation gradient encompassing coniferous forest, alpine shrubland and alpine meadow by using litterbags with different mesh sizes (3 and 0.04 mm). The objective was to determine the influences of soil fauna, litter quality and abiotic factors on species-specific carbon release and their contributions during litter decomposition. Our findings demonstrated that higher soil fauna abundance and diversity facilitated litter carbon release. The contribution rates of soil fauna to carbon release (Cfau) decreased with elevation increasing and decomposition time. Cfau are influenced by soil faunal diversity, dominant fauna groups (Collembola, Oribatida, Mesostigmata), and abiotic factors (temperature). Soil fauna significantly and directly regulated carbon release, abiotic factors indirectly regulated carbon release via altering soil fauna community composition and litter quality. This study improve our understanding in the mechanisms of decomposer contributions to carbon cycling in the context of global climate change.
Asynchronous generation of oil droplets using a microfluidic flow focusing system
Authors: Thurgood Peter , Baratchi Sara , Arash Aram , Pirogova Elena , Jex Aaron R. , Khoshmanesh Khashayar 
Published: July 2019

AbstractHere, we show that long-term exposure of PDMS based microfluidic droplet generation systems to water can reverse their characteristics such that they generate oil-in-water droplets instead of water-in-oil droplets. The competition between two oil columns entering via the two side channels leads to asynchronous generation of oil droplets. We identify various modes of droplet generation, and study the size, gap and generation rate of droplets under different combinations of oil and water pressures. Oil droplets can also be generated using syringe pumps, various oil viscosities, and different combinations of immiscible liquids. We also demonstrate the ability to dynamically change the gap between the oil droplets from a few hundred microns to just a few microns in successive cycles using a latex balloon pressure pump. This method requires no special equipment or chemical treatments, and importantly can be reversed by long-term exposure of the PDMS surfaces to the ambient air.