bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long Range Correlation in Redox Potential Fluctuations Signals Energetic Efficiency of Bacterial Fe(II) Oxidation
Authors: Enright Allison M. L. , Edwards Brock A. , Ferris F. Grant 
Published: March 2019

AbstractDifferentiating biotic and abiotic processes in nature remains a persistent challenge, specifically in evaluating microbial contributions to geochemical processes through time. Building on previous work reporting that biologically-influenced systems exhibit stronger long-range correlation than abiotic systems, this study evaluated the relationship between long-range correlation of redox potential and oxidation rates of circumneutral microaerophilic bacterial Fe(II) oxidation using a series of batch microcosms with bacteriogenic iron oxides (BIOS). Initial detrended fluctuation analysis (DFA) scaling exponents of the abiotic microcosms were lower (ca. 1.20) than those of the biotic microcosms (ca. 1.80). As Fe(II) oxidation proceeded, correlation strength decayed as a logistic function of elapsed reaction time, exhibiting direct dependence on the free energy of reaction. Correlation strength for all microcosms decayed sharply from strong correlation to uncorrelated fluctuations. The decay rates are greater for abiotic microcosms than biotic microcosms. The ΔGm relaxation edges for biotic microcosms were lower, indicating less remaining free energy for Fe(II) oxidation than abiotic systems, with the implication that biologically-catalyzed reactions are likely more energetically efficient than abiotic reactions. These results strengthen the case for employing novel DFA techniques to distinguish in situ microbial metabolic activity from abiotic processes, as well as to potentially differentiate metabolisms among different chemoautotrophs.
Combined application of selected heavy metals and EDTA reduced the growth of Petunia hybrida L.
Authors: Khan Aqib Hassan Ali , Butt Tayyab Ashfaq , Mirza Cyrus Raza , Yousaf Sohail , Nawaz Ismat , Iqbal Mazhar 
Published: March 2019

AbstractUp till now, despite of well-developed ornamental market, very little information is available on Petunia hybrida L. tolerance against heavy metals (HMs), which can contribute in both beautification of urban dwellings, as well as potential in phytoremediation. Therefore, hydroponic study was conducted to check the effects of Cd, Cr, Cu, Ni and Pb individually (50 and 100 μM) and with co-application of EDTA (2.5 mM) in Hoagland’s nutrient solution. Results indicated higher uptake of Cd, Cr, Ni and Pb in above ground parts, and Cu in roots, further the co-application of EDTA enhanced HMs uptake in P. hybrida L. This uptake accompanied changes in biochemical stress indicators, included significantly higher MDA, H2O2 contents and electrolyte leakage with reduced chlorophyll a, chlorophyll b, total chlorophyll and carotenoid content. Upon exposure to HMs increased antioxidant enzyme activities (CAT, POX, GST, APX, and SOD) were noted. Though selected HMs can be removed by using P. hybrida L., the findings of current study indicated that the direct exposure of P. hybrida L. to Cd, Cr, Cu, Ni and Pb damaged the plant’s aesthetics, and to use P. hybrida L. for beautification of urban landscape or phytoremediation, appropriate soil modification should be included.
The In Vitro Biotransformation of the Fusion Protein Tetranectin-Apolipoprotein A1
Authors: Schadt Simone , Husser Christophe , Staack Roland F. , Ekiciler Aynur , Qiu Na Hong , Fowler Stephen , Funk Christoph , Kratochwil Nicole A. 
Published: March 2019

AbstractAs more and more protein biotherapeutics enter the drug discovery pipelines, there is an increasing interest in tools for mechanistic drug metabolism investigations of biologics in order to identify and prioritize the most promising candidates. Understanding or even predicting the in vivo clearance of biologics and to support translational pharmacokinetic modeling activities is essential, however there is a lack of effective and validated in vitro cellular tools. Although different mechanisms have to be adressed in the context of biologics disposition, the scope is not comparable to the nowadays widely established tools for early characterization of small molecule disposition. Here, we describe a biotransformation study of the fusion protein tetranectin apolipoprotein A1 by cellular systems. The in vivo biotransformation of tetranectin apolipoprotein A1 has been described previously, and the same major biotransformation product could also be detected in vitro, by a targeted and highly sensitive detection method based on chymotrypsin digest. In addition, the protease responsible for the formation of this biotransformation product could be elucidated to be DPP4. To our knowledge, this is one of the first reports of an in vitro biotransformation study by cells of a therapeutic protein.
Signs of biological activities of 28,000-year-old mammoth nuclei in mouse oocytes visualized by live-cell imaging
Authors: Yamagata Kazuo , Nagai Kouhei , Miyamoto Hiroshi , Anzai Masayuki , Kato Hiromi , Miyamoto Kei , Kurosaka Satoshi , Azuma Rika , Kolodeznikov Igor I. , Protopopov Albert V. , Plotnikov Valerii V. , Kobayashi Hisato , Kawahara-Miki Ryouka , Kono Tomohiro , Uchida Masao , Shibata Yasuyuki , Handa Tetsuya , Kimura Hiroshi , Hosoi Yoshihiko , Mitani Tasuku , Matsumoto Kazuya , Iritani Akira 
Published: March 2019

AbstractThe 28,000-year-old remains of a woolly mammoth, named ‘Yuka’, were found in Siberian permafrost. Here we recovered the less-damaged nucleus-like structures from the remains and visualised their dynamics in living mouse oocytes after nuclear transfer. Proteomic analyses demonstrated the presence of nuclear components in the remains. Nucleus-like structures found in the tissue homogenate were histone- and lamin-positive by immunostaining. In the reconstructed oocytes, the mammoth nuclei showed the spindle assembly, histone incorporation and partial nuclear formation; however, the full activation of nuclei for cleavage was not confirmed. DNA damage levels, which varied among the nuclei, were comparable to those of frozen-thawed mouse sperm and were reduced in some reconstructed oocytes. Our work provides a platform to evaluate the biological activities of nuclei in extinct animal species.
Cortical-like mini-columns of neuronal cells on zinc oxide nanowire surfaces
Authors: Onesto V. , Villani M. , Narducci R. , Malara N. , Imbrogno A. , Allione M. , Costa N. , Coppedè N. , Zappettini A. , Cannistraci C. V. , Cancedda L. , Amato F. , Di Fabrizio Enzo , Gentile F. 
Published: March 2019

AbstractA long-standing goal of neuroscience is a theory that explains the formation of the minicolumns in the cerebral cortex. Minicolumns are the elementary computational units of the mature neocortex. Here, we use zinc oxide nanowires with controlled topography as substrates for neural-cell growth. We observe that neuronal cells form networks where the networks characteristics exhibit a high sensitivity to the topography of the nanowires. For certain values of nanowires density and fractal dimension, neuronal networks express small world attributes, with enhanced information flows. We observe that neurons in these networks congregate in superclusters of approximately 200 neurons. We demonstrate that this number is not coincidental: the maximum number of cells in a supercluster is limited by the competition between the binding energy between cells, adhesion to the substrate, and the kinetic energy of the system. Since cortical minicolumns have similar size, similar anatomical and topological characteristics of neuronal superclusters on nanowires surfaces, we conjecture that the formation of cortical minicolumns is likewise guided by the interplay between energy minimization, information optimization and topology. For the first time, we provide a clear account of the mechanisms of formation of the minicolumns in the brain.
Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems
Authors: Mosqueira Maria J. , Marasco Ramona , Fusi Marco , Michoud Grégoire , Merlino Giuseppe , Cherif Ameur , Daffonchio Daniele 
Published: March 2019

AbstractHighly productive conventional agroecosystems are spatially embedded in resource-homogeneous systems and count on generally nutrient-rich soils. On the contrary, desert oases are isolated, the soil is relatively poor, but yet productivity is similar to conventional agroecosystems. Soil dominates over plant as the main factor shaping root-associated microbiomes in conventional agroecosystems. We hypothesize that in desert oasis, the environmental discontinuity, the resource paucity and limited microbial diversity of the soil make the plant a prevailing factor. We have examined the bacterial communities in the root system of date palm (Phoenix dactylifera), the iconic keystone species of the oases, grown in heterogeneous soils across a broad geographic range (22,200 km2 surface area) of the Sahara Desert in Tunisia. We showed that, regardless of the edaphic conditions and geographic location, the plant invariably selects similar Gammaproteobacteria- and Alphaproteobacteria-dominated bacterial communities. The phylogeny, networking properties and predicted functionalities of the bacterial communities indicate that these two phyla are performing the ecological services of biopromotion and biofertilization. We conclude that in a desert agroecosystem, regardless of the soil microbial diversity baseline, the plant, rather than soil type, is responsible of the bacterial community assembly in its root systems, reversing the pattern observed in conventional agroecosystem.
Size distributions of fractures, dykes, and eruptions on Etna, Italy: Implications for magma-chamber volume and eruption potential
Authors: Scudero Salvatore , De Guidi Giorgio , Gudmundsson Agust 
Published: March 2019

AbstractThe main magma source for eruptions on Etna (Italy) is poorly constrained. Here we use data on the size distributions of volcanic fissures/feeder-dykes, crater cones, dyke thicknesses, and lava flows to estimate the average magma volume flowing out of the chamber during eruptions and the volume of the chamber. For the past four centuries the average magma volume leaving the chamber during each eruption is estimated at 0.064 km3. From the theory of poroelasticity the estimated chamber volume is then between 69 and 206 km3. For comparison, a sill-like, circular chamber (an oblate ellipsoid) 1 km thick and 14 km in diameter would have a volume of about 154 km3. The elastic strain energy stored in the host rock during inflation of such a chamber is about 2.8 × 1014 J. Estimating the surface energy of a typical dyke-fracture as about 107 J m−2, the results suggest that the stored strain energy is sufficient to generate a dyke-fracture with an area of about 28 km2. The average strike-dimension of volcanic fissures/feeder-dykes in Etna is about 2.7 km. It follows that the estimated strain energy is sufficient to generate a feeder-dyke with a strike-dimension of 2–3 km and with a dip-dimension as great as 10 km, agreeing with the maximum estimated depth of the magma chamber.
Human melanoma brain metastases cell line MUG-Mel1, isolated clones and their detailed characterization
Authors: Heitzer Ellen , Groenewoud Arwin , Meditz Katharina , Lohberger Birgit , Liegl-Atzwanger Bernadette , Prokesch Andreas , Kashofer Karl , Behrens Diana , Haybaeck Johannes , Kolb-Lenz Dagmar , Koefeler Harald , Riedl Sabrina , Schaider Helmut , Fischer Carina , Snaar-Jagalska B. Ewa , de’Jong Danielle , Szuhai Karoly , Zweytick Dagmar , Rinner Beate 
Published: March 2019

AbstractMelanoma is a leading cause of high mortality that frequently spreads to the brain and is associated with deterioration in quality and quantity of life. Treatment opportunities have been restricted until now and new therapy options are urgently required. Our focus was to reveal the potential heterogeneity of melanoma brain metastasis. We succeeded to establish a brain melanoma metastasis cell line, namely MUG-Mel1 and two resulting clones D5 and C8 by morphological variety, differences in lipidome, growth behavior, surface, and stem cell markers. Mutation analysis by next-generation sequencing, copy number profiling, and cytogenetics demonstrated the different genetic profile of MUG-Mel1 and clones. Tumorigenicity was unsuccessfully tested in various mouse systems and finally established in a zebra fish model. As innovative treatment option, with high potential to pass the blood-brain barrier a peptide isolated from lactoferricin was studied in potential toxicity. Brain metastases are a major clinical challenge, therefore the development of relevant in vitro and in vivo models derived from brain melanoma metastases provides valuable information about tumor biology and offers great potential to screen for new innovative therapies.
Dual-energy CT for automatic organs-at-risk segmentation in brain-tumor patients using a multi-atlas and deep-learning approach
Authors: van der Heyden Brent , Wohlfahrt Patrick , Eekers Daniëlle B. P. , Richter Christian , Terhaag Karin , Troost Esther G. C. , Verhaegen Frank 
Published: March 2019

AbstractIn radiotherapy, computed tomography (CT) datasets are mostly used for radiation treatment planning to achieve a high-conformal tumor coverage while optimally sparing healthy tissue surrounding the tumor, referred to as organs-at-risk (OARs). Based on CT scan and/or magnetic resonance images, OARs have to be manually delineated by clinicians, which is one of the most time-consuming tasks in the clinical workflow. Recent multi-atlas (MA) or deep-learning (DL) based methods aim to improve the clinical routine by an automatic segmentation of OARs on a CT dataset. However, so far no studies investigated the performance of these MA or DL methods on dual-energy CT (DECT) datasets, which have been shown to improve the image quality compared to conventional 120 kVp single-energy CT. In this study, the performance of an in-house developed MA and a DL method (two-step three-dimensional U-net) was quantitatively and qualitatively evaluated on various DECT-derived pseudo-monoenergetic CT datasets ranging from 40 keV to 170 keV. At lower energies, the MA method resulted in more accurate OAR segmentations. Both the qualitative and quantitative metric analysis showed that the DL approach often performed better than the MA method.
Cellulose production increases sorghum colonization and the pathogenic potential of Herbaspirillum rubrisubalbicans M1
Authors: Tuleski Thalita Regina , Baura Valter Antônio de , Donatti Lucélia , Pedrosa Fabio de Oliveira , Souza Emanuel Maltempi de , Monteiro Rose Adele 
Published: March 2019

AbstractThree species of the β-Proteobacterial genus Herbaspirillum are able to fix nitrogen in endophytic associations with such important agricultural crops as maize, rice, sorghum, sugar-cane and wheat. In addition, Herbaspirillum rubrisubalbicans causes the mottled-stripe disease in susceptible sugar-cane cultivars as well as the red-stripe disease in some sorghum cultivars. The xylem of these cultivars exhibited a massive colonisation of mucus-producing bacteria leading to blocking the vessels. A cluster of eight genes (bcs) are involved in cellulose synthesis in Herbaspirillum rubrisubalbicans. Mutation of bcsZ, that encodes a 1,4-endoglucanase, impaired the exopolysaccharide production, the ability to form early biofilm and colonize sorghum when compared to the wild-type strain M1. This mutation also impaired the ability of Herbaspirillum rubrisubalbicans M1 to cause the red-stripe disease in Sorghum bicolor. We show cellulose synthesis is involved in the biofilm formation and as a consequence significantly modulates bacterial-plant interactions, indicating the importance of cellulose biosynthesis in this process.
Antibody and Memory B Cell Responses in Hepatitis E Recovered Individuals, 1–30 Years Post Hepatitis E Virus Infection
Authors: Kulkarni Shruti P. , Sharma Meenal , Tripathy Anuradha S. 
Published: March 2019

AbstractGeneration and persistence of anti-hepatitis E virus (HEV) antibodies are synonymous with the development of immunity and considered as correlates of protection against HEV infection. However, issues like longevity of immunological memory following recovery from hepatitis E still remains a puzzle. It is critical to understand whether anamnestic response exists for protection from HEV re-infection. The levels and persistence of anti-HEV antibodies were assessed in hepatitis E recovered individuals 1–30 years post HEV infection. The frequencies and functionality of recombinant HEV capsid protein (rORF2p)-stimulated memory B and T cells were also investigated 1–16 years post infection. Anti-HEV antibodies persisted in 91% of hepatitis E recovered individuals. HEV-specific memory B cell responses were detected in 95% of seropositive hepatitis E recovered individuals. CD4+ and CD8+ T cells displayed an effector memory cell phenotype in hepatitis E recovered individuals. In conclusion, long-lived anti-HEV antibodies and HEV-specific memory B cells are maintained for several years in hepatitis E recovered individuals. Involvement of CD4+ and CD8+ effector memory T cells is an important observation since it is inextricably linked to long-lasting protective immunity. In addition to anti-HEV antibodies, possible role of memory B cell response against HEV re-infection could also be considered.
TouchScreen-based phenotyping: altered stimulus/reward association and lower perseveration to gain a reward in mu opioid receptor knockout mice
Authors: Boulos Laura-Joy , Nasseef Md. Taufiq , McNicholas Michael , Mechling Anna , Harsan Laura Adela , Darcq Emmanuel , Ben Hamida Sami , Kieffer Brigitte Lina 
Published: March 2019

AbstractWhile the contribution of Mu Opioid Receptors (MORs) to hedonic aspects of reward processing is well-established, the notion that these receptors may also regulate motivation to gain a reward, and possibly other related cognitive dimensions, has been less investigated. The prefrontal cortex (PFC) is a critical site for these processes. Our previous functional magnetic resonance imaging study found alterations of functional connectivity (FC) in reward/aversion networks in MOR knockout mice. Here we pursued voxelwise seed-based FC analyses using the same dataset with a focus on the PFC. We observed significant reduction of PFC FC in mutant mice, predominantly with the nucleus accumbens, supporting the notion of altered reward-driven top-down controls. We tested motivation for palatable food in a classical operant self-administration paradigm, and found delayed performance for mutant mice. We then evaluated motivational and cognitive abilities of MOR knockout mice in TouchScreen-based behavioral tests. Learning was delayed and stimulus/reward association was impaired, suggesting lower hedonic reward value and reduced motivation. Perseverative responses were decreased, while discriminatory behavior and attention were unchanged, indicative of increased inhibitory controls with otherwise intact cognitive performance. Together, our data suggest that MORs contribute to enhance reward-seeking and facilitate perseverative behaviors. The possibility that MOR blockade could reduce maladaptive compulsivity deserves further investigation in addiction and self-control disorder research.
Andrographolide binds to ATP-binding pocket of VEGFR2 to impede VEGFA-mediated tumor-angiogenesis
Authors: Kajal Kirti , Panda Abir K. , Bhat Jyotsna , Chakraborty Dwaipayan , Bose Sayantan , Bhattacharjee Pushpak , Sarkar Tania , Chatterjee Subhrangsu , Kar Santosh K. , Sa Gaurisankar 
Published: March 2019

AbstractVasculogenesis and angiogenesis are process of formation of blood vessels. Blood vessels are evolved to distribute nutrients and oxygen to distant organs. These vessels are crucial for growth and repair of wounded tissue. During tumor condition there occurs imbalance in the growth of blood vessels which leads to neo-angiogenesis. Neo-angiogenesis is major perpetrator behind the establishment of tumor. Tumor cells secrete pro-angiogenic factor VEGFA which binds to VEGFR2 present over surface of endothelial cells and triggers formation of new blood vessels. To inhibit tumor-angiogenesis, a physiologically-safe small molecule inhibitor was screened which can potentially interact with kinase domain of VEGFR2 and inhibit its activity. Molecular-docking module and biochemical analysis identified andrographolide as one of the best docking molecules that binds to ATP-binding pocket of VEGFR2 and inhibits its kinase activity. Thus, for a more radical approach towards safe VEGFR2 inhibitor, andrographolide was repurposed to inhibit tumor-angiogenesis and reduce tumor burden.
H727 cells are inherently resistant to the proteasome inhibitor carfilzomib, yet require proteasome activity for cell survival and growth
Authors: Lee Min Jae , Miller Zachary , Park Ji Eun , Bhattarai Deepak , Lee Wooin , Kim Kyung Bo 
Published: March 2019

AbstractThe second-in-class proteasome inhibitor (PI) carfilzomib (Kyprolis, Cfz) has contributed to a substantial advancement in multiple myeloma treatment by improving patient survival and quality of life. A considerable portion of patients however display intrinsic resistance to Cfz. Our mechanistic understanding of intrinsic Cfz resistance is limited due to a lack of suitable cell-based models. We report that H727 human bronchial carcinoid cells are inherently resistant to Cfz, yet susceptible to other PIs and inhibitors targeting upstream components of the ubiquitin-proteasome system (UPS). These results indicate that H727 cells remain dependent on the UPS for cell survival and growth despite harboring intrinsic resistance to Cfz. Alterations in the composition of proteasome catalytic subunits via interferon-γ treatment or siRNA knockdown results in sensitization of H727 cells to Cfz. We postulate that a potential link may exist between the composition of proteasome catalytic subunits and the cellular response to Cfz. Overall, H727 cells may serve as a useful cell-based model for de novo Cfz resistance and our results suggest previously unexplored mechanisms of de novo PI resistance.
Plasma-activated medium triggers cell death and the presentation of immune activating danger signals in melanoma and pancreatic cancer cells
Authors: Azzariti Amalia , Iacobazzi Rosa Maria , Di Fonte Roberta , Porcelli Letizia , Gristina Roberto , Favia Pietro , Fracassi Francesco , Trizio Ilaria , Silvestris Nicola , Guida Gabriella , Tommasi Stefania , Sardella Eloisa 
Published: March 2019

AbstractOver the past decade, cold atmospheric plasmas have shown promising application in cancer therapy. The therapeutic use of plasma-activated media is a topic addressed in an emerging field known as plasma pharmacy. In oncology, plasma-activated media are used to harness the therapeutic effects of oxidant species when they come in contact with cancer cells. Among several factors that contribute to the anticancer effect of plasma-activated liquid media (PALM), H2O2 and NO derivatives likely play a key role in the apoptotic pathway. Despite the significant amount of literature produced in recent years, a full understanding of the mechanisms by which PALM exert their activity against cancer cells is limited. In this paper, a sealed dielectric-barrier discharge was used to disentangle the effect of reactive nitrogen species (RNS) from that of reactive oxygen species (ROS) on cancer cells. Two cancers characterized by poor prognosis have been investigated: metastatic melanoma and pancreatic cancer. Both tumour models exposed to PALM rich in H2O2 showed a reduction in proliferation and an increase in calreticulin exposure and ATP release, suggesting the potential use of activated media as an inducer of immunogenic cell death via activation of the innate immune system.