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Yuki Mitsuta, Takashi Kawakami, Mitsutaka Okumura, Shusuke Yamanaka
We present a new approach for automated exploration of free energy landscapes on the basis of the umbrella integration (UI) method. The method to search points in the landscape relies on the normal distributions and gradients of the potential of mean force (PMF) obtained from UI calculations. We applied this approach to the alanine dipeptide in solution and demonstrated that the equilibrium and the transition states were efficiently found in the ascending order of the PMF values.
March 21, 2018: International Journal of Molecular Sciences
Ni Fan, Yigui Tang, Zhiyuan Wu, Ming Guan, Bobin Chen, Xiaoping Xu, Weizhe Ma, Xiao Xu, Xinju Zhang
Primary myelofibrosis (PMF) is one of the BCR/ABL-negative myeloproliferative neoplasms (MPNs), characterized by the diffuse fibrous hyperproliferation, bone marrow osteosclerosis, extramedullary hematopoiesis, and marked splenomegaly. The patients with PMF have an insidious onset, a long duration of clinical course, and the deteriorated quality of life. It has been reported that the CALR gene 9 exon mutations were detected in 25-30% PMF patients, particularly as high as 80% in the JAK2/MPL-negative ones. As the second most common mutation in BCR/ABL-negative MPNs, CALR mutation has been included in the latest World Health Organization (WHO) classification criteria as one of the main diagnostic criteria for both essential thrombocythemia (ET) and PMF...
March 20, 2018: Annals of Hematology
Kimberly McCoy, Masaki Uchida, Byeongdu Lee, Trevor Douglas
Bottom-up construction of mesoscale materials using biologically derived nanoscale building blocks enables engineering of desired physical properties using green production methods. Virus-like particles (VLPs) are exceptional building blocks due to their monodispersed sizes, geometric shapes, production ease, proteinaceous composition, and our ability to independently functionalize the interior and exterior interfaces. Here a VLP, derived from bacteriophage P22, is used as a building block for the fabrication of a Protein Macromolecular Framework (PMF); a tightly-linked 3D network of functional protein cages that exhibit long-range order and catalytic activity...
March 20, 2018: ACS Nano
Yifeng Xue, Yong Wang, Xuefeng Li, Hezhong Tian, Lei Nie, Xiaoqing Wu, Junrui Zhou, Zhen Zhou
The mass concentration and major chemical components of fine particulate matter were measured before, during and after Beijing's massive parade commemorating 70th anniversary of the Chinese Victory in World War II on September 3, 2015. Regional emission inventory, positive matrix factorization (PMF), observations from space and backward air mass trajectories were jointly applied to identify the major pollution sources and their temporal and spatial variations. The contributions of emissions variations and the meteorological conditions related to the "parade blue" phenomenon in Beijing and its surrounding areas were investigated in detail...
March 2018: Journal of Environmental Sciences (China)
Qingfei Zeng, Erik Jeppesen, Xiaohong Gu, Zhigang Mao, Huihui Chen
The spatial-temporal distribution of polycyclic aromatic hydrocarbons (PAHs), their source, and potential health risks were determined in overlying water and surface sediments from Chinese Lake Guchenghu, adjacent commercial mitten crab ponds and the connected Wushen Canal to assess the contamination profile of the area. The total PAHs concentrations in sediment and water were 86.7-1790 ng g-1 dry weight (dw) and 184-365 ng L-1 in summer and 184-3140 ng g-1 dw and 410-1160 ng L-1 in winter. Two- and 3-ring PAHs were the predominant compounds in water, while PAHs with 4-6 rings dominated in the sediment at both upstream and downstream sites...
March 6, 2018: Chemosphere
Patrice Rassam, Kathleen R Long, Renata Kaminska, David J Williams, Grigorios Papadakos, Christoph G Baumann, Colin Kleanthous
Gram-negative bacteria depend on energised protein complexes that connect the two membranes of the cell envelope. However, β-barrel outer-membrane proteins (OMPs) and α-helical inner-membrane proteins (IMPs) display quite different organisation. OMPs cluster into islands that restrict their lateral mobility, while IMPs generally diffuse throughout the cell. Here, using live cell imaging of Escherichia coli, we demonstrate that when transient, energy-dependent transmembrane connections are formed, IMPs become subjugated by the inherent organisation of OMPs and that such connections impact IMP function...
March 14, 2018: Nature Communications
Wei Huang, Ying-Jie Yang, Shi-Bao Zhang, Tao Liu
In higher plants, moderate photoinhibition of photosystem II (PSII) leads to a stimulation of cyclic electron flow (CEF) at low light, which is accompanied by an increase in the P700 oxidation ratio. However, the specific role of CEF stimulation at low light is not well known. Furthermore, the mechanism underlying this increase in P700 oxidation ratio at low light is unclear. To address these questions, intact leaves of the shade-adapted plant Panax notoginseng were treated at 2258 μmol photons m-2 s-1 for 30 min to induce PSII photoinhibition...
2018: Frontiers in Plant Science
M Palova, T Szotkowski, A Hlusi, K Indrak, J Navratilova, M Divoka, T Papajik
Primary myelofibrosis (PMF) is a chronic clonal myeloid disorder. Together with essential thrombocythemia (ET) and polycythemia vera (PV), it belongs to a group of Philadelphia chromosome-negative myeloproliferative neoplasms. An integral part of laboratory tests carried out in this disease group is detecting the presence of mutations in the Janus kinase 2 gene at position 617 (JAK2 V617F) and in the gene encoding for the receptor for thrombopoietin (myeloproliferative leukemia virus oncogene, MPL) found in approximately 60% of PMF patients...
2018: Neoplasma
Zhaojie Lu, Qingyang Liu, Ying Xiong, Fan Huang, Jiabin Zhou, James J Schauer
The molecular marker-based chemical mass balance (MM-CMB) method performs well in the source apportionment of organic carbon (OC) but has some difficulty with contributions from primary sources to inorganic secondary ions when apportioning PM2.5 (particles with aerodynamic diameter of 2.5 μm or less) sources. Positive matrix factorization (PMF) with the input of inorganic and organic tracers can properly estimate the contributions of primary and secondary sources to inorganic secondary ions; however, PMF is unable to apportion several PM2...
March 10, 2018: Environmental Pollution
Sunhye Kim, Tae-Young Kim, Seung-Muk Yi, Jongbae Heo
The sources of different pollutants contributing to ambient fine particles (PM2.5 ) on Daebu Island, Korea, were estimated. Twenty four hour integrated filter samples were collected from May 21-November 1, 2016, and analyzed for organic carbon, elemental carbon, ions, and trace elements. Positive matrix factorization was conducted on the PM2.5 chemical speciation data from the samples to define the pathways and sources of PM2.5 at the sampling site. A total of 80 samples and 24 chemical species were used to run the model and a total of nine sources were identified: secondary sulfate (29...
March 10, 2018: Journal of Environmental Management
Md Aynul Bari, Warren B Kindzierski
Exposure to ambient volatile organic compound (VOCs) in urban areas is of interest because of their potential chronic and acute adverse effects to public health. Limited information is available about VOC sources in urban areas in Canada. An investigation of ambient VOCs levels, their potential sources and associated risks to public health was undertaken for the urban core of Alberta's largest city (downtown Calgary) for the period 2010-2015. Twenty-four hour arithmetic and geometric mean concentrations of total VOCs were 42μg/m3 and 39μg/m3 , respectively and ranged from 16 to 160μg/m3 , with winter levels about two-fold higher than summer...
March 10, 2018: Science of the Total Environment
Wenyou Hu, Huifeng Wang, Lurui Dong, Biao Huang, Ole K Borggaard, Hans Christian Bruun Hansen, Yue He, Peter E Holm
Intensive human activities, in particular agricultural and industrial production have led to heavy metal accumulation in the peri-urban agricultural soils of China threatening soil environmental quality and agricultural product security. A combination of spatial analysis (SA), Pb isotope ratio analysis (IRA), input fluxes analysis (IFA), and positive matrix factorization (PMF) model was successfully used to assess the status and sources of heavy metals in typical peri-urban agricultural soils from a rapidly developing region of China...
March 9, 2018: Environmental Pollution
Fengxia Li, Jürgen Schnelle-Kreis, Josef Cyrys, Kathrin Wolf, Erwin Karg, Jianwei Gu, Jürgen Orasche, Gülcin Abbaszade, Annette Peters, Ralf Zimmermann
OBJECTIVE: to study the sources contributing to quasi-ultrafine particle (UFP) organic carbon and the spatial temporal variability of the sources. METHOD: 24h quasi-UFP (particulate matter <0.36μm in this study) was sampled at a reference site continuously and at one of 5 other sites (T1, T2, T3, T4 and B1) in parallel in Augsburg, Germany from April 11th, 2014 to February 22nd, 2015, attempting to conduct 2-week campaigns at each site in 3 different seasons...
March 7, 2018: Science of the Total Environment
James C Gumbart, Martin B Ulmschneider, Anthony Hazel, Stephen H White, Jakob P Ulmschneider
We show that the free energy of inserting hydrophobic peptides into lipid bilayer membranes from surface-aligned to transmembrane inserted states can be reliably calculated using atomistic models. We use two entirely different computational methods: high temperature spontaneous peptide insertion calculations as well as umbrella sampling potential-of-mean-force (PMF) calculations, both yielding the same energetic profiles. The insertion free energies were calculated using two different protein and lipid force fields (OPLS protein/united-atom lipids and CHARMM36 protein/all-atom lipids) and found to be independent of the simulation parameters...
March 8, 2018: Journal of Membrane Biology
Jan C Peeken, Jonas S Jutzi, Julius Wehrle, Christoph Koellerer, Felix Staehle, Heiko Becker, Elias Schoenwandt, Thalia S Seeger, Daniel H Schanne, Monika Gothwal, Christopher J Ott, Albert Gründer, Heike L Pahl
The transcription factor "Nuclear Factor Erythroid 2" (NFE2) is overexpressed in the majority of patients with Myeloproliferative Neoplasms (MPN). In murine models, elevated NFE2 levels cause an MPN phenotype with spontaneous leukemic transformation. However, both the molecular mechanisms leading to NFE2 overexpression and its downstream targets remain incompletely understood. Here we show that the histone demethylase JMJD1C constitutes a novel NFE2 target gene. JMJD1C levels are significantly elevated in PV and PMF patients; concomitantly, global H3K9me1 and H3K9me2 levels are significantly decreased...
March 8, 2018: Blood
Zhen Li, Yonghui Zhang, Chun Chan, Chunyi Zhi, Xiaolin Cheng, Jun Fan
Two-dimensional (2D) materials can mechanically insert into cell membranes and extract lipids out, thus leading to the destruction of cell integrity. On the one hand, the cytotoxicity of 2D materials can be harnessed in surface engineering to resist biofouling; on the other hand, it causes great concern on in vivo biomedical applications ranging from drug delivery to nano-imaging. To understand the nature of this cytotoxic behavior and find strategies to control it, we performed molecular dynamics (MD) simulations on the lipid extraction of hexagonal boron nitride (BN) nanosheets from lipid membranes...
March 8, 2018: ACS Nano
Ibis M Agosto, Nicole L Nichols, Gordon S Mitchell
Although systemic inflammation induced by even a low dose of lipopolysaccharide (LPS, 100uL/kg) impairs respiratory motor plasticity, little is known concerning cellular mechanisms giving rise to this inhibition. Phrenic motor facilitation (pMF) is a form of respiratory motor plasticity elicited by pharmacological agents applied to the cervical spinal cord, or by acute intermittent hypoxia (AIH; 3, 5 min hypoxic episodes); when elicited by AIH, pMF is known as phrenic long-term facilitation (pLTF). AIH consisting of moderate hypoxic episodes (mAIH, PaO2 = 35-55 mmHg) elicits pLTF via the Q- pathway to pMF, a mechanism that requires spinal serotonin (5HT2) receptor activation and new BDNF protein synthesis...
March 7, 2018: Journal of Neurophysiology
Adeel Anwar, Zhen Zhang, Decheng Lv, Gang Lv, Zhi Zhao, Yanfeng Wang, Yue Cai, Wasim Qasim, Muhammad Umar Nazir, Ming Lu
BACKGROUND: Clinically there are different fixation methods used for fixation of the posterior malleolar fractures (PMF), but the best treatment modality is still not clear. Few studies have concentrated on this issue, least of all using a biomechanical comparison. The purpose of this study was to carry out a computational comparative biomechanics of three different commonly used fixation constructs for the fixation of PMF by finite element analysis (FEA). METHODS: Computed tomography (CT) images were used to reconstruct three dimensional (3D) model of the tibia...
March 6, 2018: BMC Musculoskeletal Disorders
K Lewandowski, M Gniot, M Wojtaszewska, Z Kanduła, R Becht, E Paczkowska, E Mędraś, E Wasilewska, M Iwoła
INTRODUCTION: There are 7 designated conditions under the category of myeloproliferative neoplasms (MPN), including chronic myelogenous leukemia (CML) and classical MPN, that is, polycythemia vera (PV), essential thrombocythaemia (ET), and primary myelofibrosis (PMF). Recently, reports about Philadelphia and JAK2 V617F-positive MPN cases have been described in literature. The coexistence of different molecular defects may change the clinical and laboratory manifestation of MPN and may result in an inappropriate interpretation of the response to treatment with tyrosine kinase inhibitors in CML patients...
March 6, 2018: International Journal of Laboratory Hematology
Reza Bashiri Khuzestani, James J Schauer, Jing Shang, Tianqi Cai, Dongqing Fang, Yongjie Wei, Lulu Zhang, Yuanxun Zhang
The Ordos region in the southwestern part of Inner Mongolia experiences frequent PM concentrations in excess of the national PM2.5 air quality standards. In order to determine the key sources of PM2.5 contributing to these pollution episodes, the main sources of PM2.5 OC during elevated PM episodes in the Inner Mongolia were analyzed and compared with non-polluted days. This will provide insight to the main sources of particulate matter pollution during the high-pollution episodes and the effective seasonal strategies to control sources of particulate matter during months and with the highest PM concentrations that need to be controlled...
February 28, 2018: Environmental Science and Pollution Research International
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