bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of Escherichia coli Phage vB_EcoM_Alf5
Authors: Alijošius Laurynas , Šimoliūnas Eugenijus , Kaliniene Laura , Meškys Rolandas , Truncaitė Lidija 
Published: May 2017

ABSTRACT

Here, we announce the complete genome sequence of the
Escherichia coli
myophage vB_EcoM_Alf5 belonging to the genus
Felixo1virus
, whose members have not been comprehensively studied at the molecular level. Phage vB_EcoM_Alf5 infects
E. coli
K-12-derived laboratory strains and therefore is well suited for functional studies.
Complete Genome Sequence of an Avian Paramyxovirus Type 4 Strain Isolated from Domestic Duck at a Live Bird Market in South Korea
Authors: Tseren-Ochir Erdene-Ochir , Yuk Seong-Su , Kwon Jung-Hoon , Noh Jin-Yong , Hong Woo-Tack , Jeong Jei-Hyun , Jeong Sol , Kim Yu-Jin , Kim Kyu-Jik , Lee Ji-Ho , Kim Jun-Beom , Lee Joong-Bok , Park Seung-Yong , Choi In-Soo , Lee Sang-Won , Song Chang-Seon 
Published: May 2017

ABSTRACT
We report here the first full-genome sequence of an avian paramyxovirus type 4 (APMV-4) strain isolated from a domestic mallard duck at a live bird market in South Korea. Phylogenetic analyses provide genetic information on a new genetic clade, APMV-4, isolated from a domestic duck and evidence of APMV-4 exchange between poultry and wild birds.
Draft Genome Sequences of Colistin-Resistant MCR-1-Producing Escherichia coli ST1850 and ST74 Strains Isolated from Commercial Chicken Meat
Authors: Monte Daniel F. , Fernandes Miriam R. , Cerdeira Louise , de Souza Tiago A. , Mem Andressa , Franco Bernadette D. G. M. , Landgraf Mariza , Lincopan Nilton 
Published: May 2017

ABSTRACT

We present here the draft genome sequences of two colistin-resistant
mcr-1
-carrying
Escherichia coli
strains belonging to sequence type 74 (ST74) and ST1850, isolated from commercial chicken meat in Brazil. Assembly of this draft genome resulted in 5,022,083 and 4,950,681 bp, respectively, revealing the presence of the IncX4 plasmid-mediated
mcr-1
gene responsible for resistance to colistin.
Identification of a Novel Hepatitis E Virus Genotype 3 Strain Isolated from a Chronic Hepatitis E Virus Infection in a Kidney Transplant Recipient in Switzerland
Authors: Wang Bo , Harms Dominik , Hofmann Jörg , Ciardo Diana , Kneubühl Agnes , Bock C.-Thomas 
Published: May 2017

ABSTRACT
Hepatitis E virus genotype 3 (HEV-3) is the causal pathogen of chronic hepatitis E. We report here the full-length genome sequence of an HEV-3 strain, isolated from a kidney transplant recipient in Switzerland (SW/16-0282). This HEV-3 strain showed less than 88% homology compared to known strains, suggesting a new HEV-3 strain.
Draft Genome Sequences of Five Brazilian Clostridium botulinum Group III Type D/C Strains
Authors: Woudstra Cédric , Brito Roseane B. , Fonseca Júnior Antônio A. , Silva Rodrigo O. S. , Lobato Francisco C. F. , Fach Patrick 
Published: May 2017

ABSTRACT

Animal botulism is mainly associated with
Clostridium botulinum
group III-producing neurotoxin types C, C/D, D, and D/C. In this report, we present the draft genome sequences of the first five strains of
Clostridium botulinum
type D/C isolated in Brazil and used for vaccination purposes.
Complete Genome Sequence of Undomesticated Bacillus subtilis Strain NCIB 3610
Authors: Nye Taylor M. , Schroeder Jeremy W. , Kearns Daniel B. , Simmons Lyle A. 
Published: May 2017

ABSTRACT

Bacillus subtilis
is a Gram-positive bacterium that serves as an important experimental system.
B. subtilis
NCIB 3610 is an undomesticated strain that exhibits phenotypes lost from the more common domesticated laboratory strains. Here, we announce the complete genome sequence of DK1042, a genetically competent derivative of NCIB 3610.
First Insight into the Genome Sequence of Clostridium thermobutyricum DSM 4928, a Butyrate-Producing Moderate Thermophile
Authors: Poehlein Anja , Anbalagan Abirami , Nagel Alexandra , Daniel Rolf 
Published: May 2017

ABSTRACT

The moderately thermophilic and Gram-positive bacterium
Clostridium thermobutyricum
is strictly anaerobic and forms subterminally located endospores. It was isolated from horse manure compost.
C. thermobutyricum
produces butyrate as the main fermentation product. The draft genome consists of one circular chromosome (3.425 Mb) and contains 3,201 predicted protein-coding genes.
Draft Genome Sequence of a Lipolytic Yeast,
Candida aaseri
SH-14
Authors: Lee Sun Hee , Jeong Haeyoung , Ko Hyeok-Jin , Bae Jung-Hoon , Ibrahim Zool Hilmi , Sung Bong Hyun , Sohn Jung-Hoon 
Published: May 2017

ABSTRACT

We report here the draft genome sequence of the lipolytic yeast
Candida aaseri
SH-14, isolated from the compost of oil palm empty fruit bunches, and the identification of eight putative lipase genes. This genome information will provide the opportunity to produce potential lipases for a variety of industrial applications.
Draft Genome Sequence of Staphylococcus epidermidis Clinical Strain GOI1153754-03-14 Isolated from an Infected Knee Prosthesis
Authors: Bottagisio Marta , Soggiu Alessio , Lovati Arianna B. , Toscano Marco , Piras Cristian , Romanò Carlo L. , Bonizzi Luigi , Roncada Paola , Drago Lorenzo 
Published: May 2017

ABSTRACT

We announce the draft genome sequence of
Staphylococcus epidermidis
clinical strain GOI1153754-03-14, isolated from an infected orthopedic prosthesis. The reported genomic sequence will provide valuable information concerning the mechanisms of the biofilm formation on metallic implants.
Draft Genome Sequences of Five
Enterococcus
Species Isolated from the Gut of Patients with Suspected Clostridium difficile Infection
Authors: Castro-Nallar Eduardo , Valenzuela Sandro L. , Baquedano Sebastián , Sánchez Carolina , Fernández Fabiola , Trombert Annette N. 
Published: May 2017

ABSTRACT

We present draft genome sequences of five
Enterococcus
species from patients suspected of
Clostridium difficile
infection. Genome completeness was confirmed by presence of bacterial orthologs (97%). Gene searches using Hidden-Markov models revealed that the isolates harbor between seven and 11 genes involved in antibiotic resistance to tetracyclines, beta-lactams, and vancomycin.
The Mycelium as a Network
Authors: Fricker Mark D. , Heaton Luke L. M. , Jones Nick S. , Boddy Lynne 
Published: May 2017

ABSTRACTThe characteristic growth pattern of fungal mycelia as an interconnected network has a major impact on how cellular events operating on a micron scale affect colony behavior at an ecological scale. Network structure is intimately linked to flows of resources across the network that in turn modify the network architecture itself. This complex interplay shapes the incredibly plastic behavior of fungi and allows them to cope with patchy, ephemeral resources, competition, damage, and predation in a manner completely different from multicellular plants or animals. Here, we try to link network structure with impact on resource movement at different scales of organization to understand the benefits and challenges of organisms that grow as connected networks. This inevitably involves an interdisciplinary approach whereby mathematical modeling helps to provide a bridge between information gleaned by traditional cell and molecular techniques or biophysical approaches at a hyphal level, with observations of colony dynamics and behavior at an ecological level.
An improved label propagation algorithm based on node importance and random walk for community detection
Authors: Ma Tianren , Xia Zhengyou 
Published: May 2017

Currently, with the rapid development of information technology, the electronic media for social communication is becoming more and more popular. Discovery of communities is a very effective way to understand the properties of complex networks. However, traditional community detection algorithms consider the structural characteristics of a social organization only, with more information about nodes and edges wasted. In the meanwhile, these algorithms do not consider each node on its merits.Label propagation algorithm (LPA) is a near linear time algorithm which aims to find the community in the network. It attracts many scholars owing to its high efficiency. In recent years, there are more improved algorithms that were put forward based on LPA. In this paper, an improved LPA based on random walk and node importance (NILPA) is proposed. Firstly, a list of node importance is obtained through calculation. The nodes in the network are sorted in descending order of importance. On the basis of random walk, a matrix is constructed to measure the similarity of nodes and it avoids the random choice in the LPA. Secondly, a new metric IAS (importance and similarity) is calculated by node importance and similarity matrix, which we can use to avoid the random selection in the original LPA and improve the algorithm stability.Finally, a test in real-world and synthetic networks is given. The result shows that this algorithm has better performance than existing methods in finding community structure.
Long non-coding RNA NEAT1 promotes hepatocellular carcinoma cell proliferation through the regulation of miR-129-5p-VCP-IκB
Authors: Fang Luo , Sun Jiao , Pan Zongfu , Song Yu , Zhong Like , Zhang Yiwen , Liu Yujia , Zheng Xiaowei , Huang Ping 
Published: May 2017

Long non-coding RNA nuclear-enriched abundant transcript 1 (NEAT1) plays an important role in the pathogenesis and development of several types of cancer. However, the functional mechanism of NEAT1 in hepatocellular carcinoma (HCC) remains unclear. NEAT1 and microRNA (miR)-129-5p expression in HCC tissues and cell lines was quantified by means of quantitative PCR. The effects of NEAT1 expression inhibition or upregulation in HCC cell lines were analyzed in terms of cell viability and apoptosis. Biological software was used to predict the binding sites of NEAT1 and miR-129-5p. The expression of the miR-129-5p target molecules valosin-containing protein (VCP) and IκB was detected using Western blotting. The effect of NEAT1 on tumor growth was observed in mouse models of transplanted hepatoma. In the present study, it was concluded that the expression of NEAT1 was significantly increased in the HCC tissues and cell lines. Meanwhile, after downregulating NEAT1 expression in HepG2/Huh7 cell lines, the cell viability was significantly lowered, whereas the corresponding rate of apoptosis was significantly increased. Additionally, it was found that the NEAT1 and miR-129-5p expression showed a negative correlation in HCC tissues. It was further proved that there was a certain negative regulatory mechanism between NEAT1 and miR-129-5p, which was related to the expression of VCP and IκB. The mouse model experiments confirmed that the interference with NEAT1 expression inhibited tumor growth. The study concluded that the overexpression of NEAT1 inhibited the expression of miR-129-5p by regulating VCP/IκB, thereby promoting the proliferation of HCC cells. This study provides new insights into the pathogenesis of HCC, as well as identifying new target genes for diagnosis and treatment. NEW & NOTEWORTHY The results provide strong evidence that upregulated NEAT1 promotes the proliferation of cancer cells in hepatocellular carcinoma (HCC) and this regulatory mechanism depends on the microRNA (miR)-129-5p-valosin-containing protein-IκB axis. The study also indicates that NEAT1 could be a potential therapeutic target for HCC.
Acetylation of mitochondrial proteins by GCN5L1 promotes enhanced fatty acid oxidation in the heart
Authors: Thapa Dharendra , Zhang Manling , Manning Janet R. , Guimarães Danielle A. , Stoner Michael W. , O’Doherty Robert M. , Shiva Sruti , Scott Iain 
Published: May 2017

Lysine acetylation is a reversible posttranslational modification and is particularly important in the regulation of mitochondrial metabolic enzymes. Acetylation uses acetyl-CoA derived from fuel metabolism as a cofactor, thereby linking nutrition to metabolic activity. In the present study, we investigated how mitochondrial acetylation status in the heart is controlled by food intake and how these changes affect mitochondrial metabolism. We found that there was a significant increase in cardiac mitochondrial protein acetylation in mice fed a long-term high-fat diet and that this change correlated with an increase in the abundance of the mitochondrial acetyltransferase-related protein GCN5L1. We showed that the acetylation status of several mitochondrial fatty acid oxidation enzymes (long-chain acyl-CoA dehydrogenase, short-chain acyl-CoA dehydrogenase, and hydroxyacyl-CoA dehydrogenase) and a pyruvate oxidation enzyme (pyruvate dehydrogenase) was significantly upregulated in high-fat diet-fed mice and that the increase in long-chain and short-chain acyl-CoA dehydrogenase acetylation correlated with increased enzymatic activity. Finally, we demonstrated that the acetylation of mitochondrial fatty acid oxidation proteins was decreased after GCN5L1 knockdown and that the reduced acetylation led to diminished fatty acid oxidation in cultured H9C2 cells. These data indicate that lysine acetylation promotes fatty acid oxidation in the heart and that this modification is regulated in part by the activity of GCN5L1. NEW & NOTEWORTHY Recent research has shown that acetylation of mitochondrial fatty acid oxidation enzymes has greatly contrasting effects on their activity in different tissues. Here, we provide new evidence that acetylation of cardiac mitochondrial fatty acid oxidation enzymes by GCN5L1 significantly upregulates their activity in diet-induced obese mice.
Ventricular action potential adaptation to regular exercise: role of β-adrenergic and KATPchannel function
Authors: Wang Xinrui , Fitts Robert H. 
Published: May 2017

Regular exercise training is known to affect the action potential duration (APD) and improve heart function, but involvement of β-adrenergic receptor (β-AR) subtypes and/or the ATP-sensitive K+(KATP) channel is unknown. To address this, female and male Sprague-Dawley rats were randomly assigned to voluntary wheel-running or control groups; they were anesthetized after 6–8 wk of training, and myocytes were isolated. Exercise training significantly increased APD of apex and base myocytes at 1 Hz and decreased APD at 10 Hz. Ca2+transient durations reflected the changes in APD, while Ca2+transient amplitudes were unaffected by wheel running. The nonselective β-AR agonist isoproterenol shortened the myocyte APD, an effect reduced by wheel running. The isoproterenol-induced shortening of APD was largely reversed by the selective β1-AR blocker atenolol, but not the β2-AR blocker ICI 118,551, providing evidence that wheel running reduced the sensitivity of the β1-AR. At 10 Hz, the KATPchannel inhibitor glibenclamide prolonged the myocyte APD more in exercise-trained than control rats, implicating a role for this channel in the exercise-induced APD shortening at 10 Hz. A novel finding of this work was the dual importance of altered β1-AR responsiveness and KATPchannel function in the training-induced regulation of APD. Of physiological importance to the beating heart, the reduced response to adrenergic agonists would enhance cardiac contractility at resting rates, where sympathetic drive is low, by prolonging APD and Ca2+influx; during exercise, an increase in KATPchannel activity would shorten APD and, thus, protect the heart against Ca2+overload or inadequate filling.NEW & NOTEWORTHY Our data demonstrated that regular exercise prolonged the action potential and Ca2+transient durations in myocytes isolated from apex and base regions at 1-Hz and shortened both at 10-Hz stimulation. Novel findings were that wheel running shifted the β-adrenergic receptor agonist dose-response curve rightward compared with controls by reducing β1-adrenergic receptor responsiveness and that, at the high activation rate, myocytes from trained animals showed higher KATPchannel function.
Ontogeny of myosin isoform expression and prehensile function in the tail of the gray short-tailed opossum (Monodelphis domestica)
Authors: Thomas Dylan R. , Chadwell Brad A. , Walker Gary R. , Budde Julio E. , VandeBerg John L. , Butcher Michael T. 
Published: May 2017

Terrestrial opossums use their semiprehensile tail for grasping nesting materials as opposed to arboreal maneuvering. We relate the development of this adaptive behavior with ontogenetic changes in myosin heavy chain (MHC) isoform expression from 21 days to adulthood. Monodelphis domestica is expected to demonstrate a progressive ability to flex the distal tail up to age 7 mo, when it should exhibit routine nest construction. We hypothesize that juvenile stages (3–7 mo) will be characterized by retention of the neonatal isoform (MHC-Neo), along with predominant expression of fast MHC-2X and -2B, which will transition into greater MHC-1β and -2A isoform content as development progresses. This hypothesis was tested using Q-PCR to quantify and compare gene expression of each isoform with its protein content determined by gel electrophoresis and densitometry. These data were correlated with nesting activity in an age-matched sample of each age group studied. Shifts in regulation of MHC gene transcripts matched well with isoform expression. Notably, mRNA for MHC-Neo and -2B decrease, resulting in little-to-no isoform translation after age 7 mo, whereas mRNA for MHC-1β and -2A increase, and this corresponds with subtle increases in content for these isoforms into late adulthood. Despite the tail remaining intrinsically fast-contracting, a critical growth period for isoform transition is observed between 7 and 13 mo, correlating primarily with use of the tail during nesting activities. Functional transitions in MHC isoforms and fiber type properties may be associated with muscle “tuning” repetitive nest remodeling tasks requiring sustained contractions of the caudal flexors.NEW & NOTEWORTHY Little is understood about skeletal muscle development as it pertains to tail prehensility in mammals. This study uses an integrative approach of relating both MHC gene and protein expression with behavioral and morphometric changes to reveal a predominant fast MHC expression with subtle isoform transitions in caudal muscle across ontogeny. The functional shifts observed are most notably correlated with increased tail grasping for nesting activities.
MET Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Authors: Lu Xinyuan , Peled Nir , Greer John , Wu Wei , Choi Peter , Berger Alice H. , Wong Sergio , Jen Kuang-Yu , Seo Youngho , Hann Byron , Brooks Angela , Meyerson Matthew , Collisson Eric A. 
Published: May 2017

Abstract
Targeting somatically activated oncogenes has revolutionized the treatment of non–small cell lung cancer (NSCLC). Mutations in the gene mesenchymal–epithelial transition (MET) near the exon 14 splice sites are recurrent in lung adenocarcinoma and cause exon skipping (METΔ14). Here, we analyzed 4,422 samples from 12 different malignancies to estimate the rate of said exon skipping. METΔ14 mutation and transcript were most common in lung adenocarcinoma. Endogenously expressed levels of METΔ14 transformed human epithelial lung cells in a hepatocyte growth factor–dependent manner. In addition, overexpression of the orthologous mouse allele induced lung adenocarcinoma in a novel, immunocompetent mouse model. Met inhibition showed clinical benefit in this model. In addition, we observed a clinical response to crizotinib in a patient with METΔ14-driven NSCLC, only to observe new missense mutations in the MET activation loop, critical for binding to crizotinib, upon clinical progression. These findings support genomically selected clinical trials directed toward METΔ14 in a fraction of NSCLC patients, confirm second-site mutations for further therapeutic targeting prior to and beyond acquired resistance, and provide an in vivo system for the study of METΔ14 in an immunocompetent host. Cancer Res; 77(16); 4498–505. ©2017 AACR.
Notch Inhibitor PF-03084014 Inhibits Hepatocellular Carcinoma Growth and Metastasis via Suppression of Cancer Stemness due to Reduced Activation of Notch1–Stat3
Authors: Wu Chuan Xing , Xu Aimin , Zhang Cathy C. , Olson Peter , Chen Lin , Lee Terence K. , Cheung Tan To , Lo Chung Mau , Wang Xiao Qi 
Published: May 2017

Abstract
Aberrant activation of the Notch signaling pathway is implicated in many solid tumors, including hepatocellular carcinoma, indicating a potential use of Notch inhibitors for treatment. In this study, we investigated the antitumor and antimetastasis efficacy of the novel Notch inhibitor (γ-secretase inhibitor) PF-03084014 in hepatocellular carcinoma. Hepatocellular carcinoma spherical cells (stem-like cancer cells), a sphere-derived orthotopic tumor model and one patient-derived xenograft (PDX) model were used in our experiment. We demonstrated that PF-03084014 inhibited the self-renewal and proliferation of cancer stem cells. PF-03084014 reduced the hepatocellular carcinoma sphere-derived orthotopic tumor and blocked the hepatocellular carcinoma tumor liver to lung metastasis. We further tested the PF-03084014 in PDX models and confirmed the inhibition tumor growth effect. In addition, a low dose of PF-03084014 induced hepatocellular carcinoma sphere differentiation, resulting in chemosensitization. Antitumor activity was associated with PF-03084014-induced suppression of Notch1 activity, decreased Stat3 activation and phosphorylation of the Akt signaling pathway, and reduced epithelial–mesenchymal transition. These are the key contributors to the maintenance of cancer stemness and the promotion of cancer metastasis. Moreover, the Notch–Stat3 association was implicated in the clinical hepatocellular carcinoma prognosis. Collectively, PF-03084014 revealed antitumor and antimetastatic effects in hepatocellular carcinoma, providing evidence for the potential use of gamma-secretase inhibitors as a therapeutic option for the treatment of hepatocellular carcinoma. Mol Cancer Ther; 16(8); 1531–43. ©2017 AACR.
Inhibition of Aurora A and Aurora B Is Required for the Sensitivity of HPV-Driven Cervical Cancers to Aurora Kinase Inhibitors
Authors: Martin David , Fallaha Sora , Proctor Martina , Stevenson Alexander , Perrin Lewis , McMillan Nigel , Gabrielli Brian 
Published: May 2017

Abstract
The activity and efficacy of Aurora inhibitors have been reported in a wide range of cancer types. The most prominent Aurora inhibitor is alisertib, an investigational Aurora inhibitor that has been the subject of more than 30 clinical trials. Alisertib has inhibitory activity against both Aurora A and B, although it is considered to be primarily an Aurora A inhibitor in vivo. Here, we show that alisertib inhibits both Aurora A and B in vivo in preclinical models of HPV-driven cervical cancer, and that it is the inhibition of Aurora A and B that provides the selectivity and efficacy of this drug in vivo in this disease setting. We also present formal evidence that alisertib requires progression through mitosis for its efficacy, and that it is unlikely to combine with drugs that promote a G2 DNA damage checkpoint response. This work demonstrates that inhibition of Aurora A and B is required for effective control of HPV-driven cancers by Aurora kinase inhibitors. Mol Cancer Ther; 16(9); 1934–41. ©2017 AACR.