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https://www.readbyqxmd.com/read/28088762/the-super-n-motifs-model-a-novel-alignment-free-approach-for-representing-and-comparing-rna-secondary-structures
#1
Jean-Pierre Séhi Glouzon, Jean-Pierre Perreault, Shengrui Wang
MOTIVATION: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take into account the RNA configuration (i.e. linear or circular), the presence of pseudoknot and G-quadruplex (G4) motifs and the increasing number of secondary structures generated by high-throughput probing techniques. To address this challenge, we propose the super-n-motifs model based on a latent analysis of enhanced motifs comprising not only basic motifs but also adjacency relations...
January 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28088586/a-case-control-study-of-risk-sources-for-severe-fever-with-thrombocytopenia-syndrome-in-hubei-province-china
#2
Xuesen Xing, Xuhua Guan, Li Liu, Junqiang Xu, Guoming Li, Jianbo Zhan, Gongping Liu, Xiaoqing Jiang, Xingfu Shen, Yongzhong Jiang, Yang Wu, Hao Zhang, Jing Huang, Fan Ding, Sha Sha, Man Liu, Faxian Zhan
BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS), an emerging infectious disease caused by a novel bunyavirus, was discovered in rural areas of Central China in 2009. METHODS: A case-control study based on hospital data was applied to detect the potential risk sources for SFTS in SFTS-endemic counties in Hubei Province. Cases were defined as hospitalized SFTSV confirmed patients. Controls were randomly selected from non-SFTSV patients in the same hospital ward within 2 weeks of inclusion of the cases, and they were matched by age (+/- 5 years) and gender according to 1:2 matching condition...
January 11, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28088462/activation-of-the-hypoxia-inducible-factor-1-alpha-subunit-pathway-in-steatotic-liver-contributes-to-formation-of-cholesterol-gallstones
#3
Yoichiro Asai, Tetsuya Yamada, Sohei Tsukita, Kei Takahashi, Masamitsu Maekawa, Midori Honma, Masanori Ikeda, Keigo Murakami, Yuichiro Munakata, Yuta Shirai, Shinjiro Kodama, Takashi Sugisawa, Yumiko Chiba, Yasuteru Kondo, Keizo Kaneko, Kenji Uno, Shojiro Sawada, Junta Imai, Yasuhiro Nakamura, Hiroaki Yamaguchi, Kozo Tanaka, Hironobu Sasano, Nariyasu Mano, Yoshiyuki Ueno, Tooru Shimosegawa, Hideki Katagiri
BACKGROUND AND AIMS: Hypoxia inducible factor 1 alpha subunit (HIF1A) is a transcription factor that controls the cellular response to hypoxia and is activated in hepatocytes of patients with non-alcoholic fatty liver disease (NAFLD). NAFLD increases risk for cholesterol gallstone disease by unclear mechanisms. We studied the relationship between HIF1A and gallstone formation associated with liver steatosis. METHODS: We performed studies with mice with inducible disruption of Hif1a in hepatocytes, via a Cre adenoviral vector (iH-HIFKO mice), and mice without disruption of Hif1a (control mice)...
January 11, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28088444/feeding-recombinant-e-coli-with-gst-mbmktx-fusion-protein-increases-the-fecundity-and-lifespan-of-caenorhabditis-elegans
#4
Jie Xu, Yajie Jiang, Lu Wan, Qi Wang, Zebo Huang, Yongmei Liu, Yingliang Wu, Zongyun Chen, Xin Liu
Scorpion venom could be a useful treatment for a variety of diseases, such as cancer, epilepsy and analgesia. BmKTX is a polypeptide extracts from scorpion venom (PESV), which have attracted much attention from researchers in recent years. mBmKTX is a mutant polypeptide according to the amino acid sequence of BmKTX. We expressed it with the vector pGEX-4T-1 in Escherichia coli, and Caenorhabditis elegans were used as the animal model and fed with the strains. In this study, the expression of pGEX-mBmKTX was analyzed by SDS-PAGE, and GST-mBmKTX purified from pGEX-mBmKTX as a glutathione S-transferase (GST)-tagged fusion protein is approximately 30kDa...
January 11, 2017: Peptides
https://www.readbyqxmd.com/read/28088356/advancing-the-prediction-accuracy-of-protein-protein-interactions-by-utilizing-evolutionary-information-from-position-specific-scoring-matrix-and-ensemble-classifier
#5
Lei Wang, Zhu-Hong You, Shi-Xiong Xia, Feng Liu, Xing Chen, Xin Yan, Yong Zhou
Protein-Protein Interactions (PPIs) are essential to most biological processes and play a critical role in most cellular functions. With the development of high-throughput biological techniques and in silico methods, a large number of PPI data have been generated for various organisms, but many problems remain unsolved. These factors promoted the development of the in silico methods based on machine learning to predict PPIs. In this study, we propose a novel method by combining ensemble Rotation Forest (RF) classifier and Discrete Cosine Transform (DCT) algorithm to predict the interactions among proteins...
January 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28088225/using-low-cost-drones-to-map-malaria-vector-habitats
#6
Andy Hardy, Makame Makame, Dónall Cross, Silas Majambere, Mwinyi Msellem
BACKGROUND: There is a growing awareness that if we are to achieve the ambitious goal of malaria elimination, we must compliment indoor-based vector control interventions (such as bednets and indoor spraying) with outdoor-based interventions such as larval source management (LSM). The effectiveness of LSM is limited by our capacity to identify and map mosquito aquatic habitats. This study provides a proof of concept for the use of a low-cost (< $1000) drone (DJI Phantom) for mapping water bodies in seven sites across Zanzibar including natural water bodies, irrigated and non-irrigated rice paddies, peri-urban and urban locations...
January 14, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28088191/predicting-probable-alzheimer-s-disease-using-linguistic-deficits-and-biomarkers
#7
Sylvester O Orimaye, Jojo S-M Wong, Karen J Golden, Chee P Wong, Ireneous N Soyiri
BACKGROUND: The manual diagnosis of neurodegenerative disorders such as Alzheimer's disease (AD) and related Dementias has been a challenge. Currently, these disorders are diagnosed using specific clinical diagnostic criteria and neuropsychological examinations. The use of several Machine Learning algorithms to build automated diagnostic models using low-level linguistic features resulting from verbal utterances could aid diagnosis of patients with probable AD from a large population...
January 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28087775/rapid-expansion-of-immune-related-gene-families-in-the-house-fly-musca-domestica
#8
Timothy B Sackton, Brian P Lazzaro, Clark G Andrew
The house fly, Musca domestica, occupies an unusual diversity of potentially septic niches compared to other sequenced Dipteran insects and is a vector of numerous diseases of humans and livestock. In the present study, we apply whole-transcriptome sequencing to identify genes whose expression is regulated in adult flies upon bacterial infection. We then combine the transcriptomic data with analysis of rates of gene duplication and loss to provide insight into the evolutionary dynamics of immune-related genes...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087631/papc-couples-the-segmentation-clock-to-somite-morphogenesis-by-regulating-n-cadherin-dependent-adhesion
#9
Jérome Chal, Charlène Guillot, Olivier Pourquié
Vertebrate segmentation is characterized by the periodic formation of epithelial somites from the mesenchymal presomitic mesoderm (PSM). How the rhythmic signaling pulse delivered by the Segmentation Clock is translated into the periodic morphogenesis of somites remains poorly understood. Here, we focused on the role of Paraxial protocadherin (PAPC/Pcdh8) in this process. We showed that in chicken and mouse embryos, PAPC expression is tightly regulated by the Clock and Wavefront system in the posterior PSM...
January 13, 2017: Development
https://www.readbyqxmd.com/read/28087534/mechanisms-of-horizontal-cell-to-cell-transfer-of-wolbachia-spp-in-drosophila-melanogaster
#10
Pamela M White, Jose E Pietri, Alain Debec, Shelbi Russell, Bhavin Patel, William Sullivan
: Wolbachia is an intracellular endosymbiont present in most arthropod and filarial nematode species. Transmission between hosts is primarily vertical, taking place exclusively through the female germline, though horizontal transmission has also been documented. Several studies indicate that Wolbachia is capable of transfer between somatic and germline cells during nematode development and in adult flies. However, the mechanisms underlying horizontal cell-to-cell transfer remain largely unexplored...
January 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28087528/engineering-mycobacteria-for-the-production-of-self-assembling-biopolyesters-displaying-mycobacterial-antigens-for-use-as-tuberculosis-vaccine
#11
Jason W Lee, Natalie A Parlane, Bernd H A Rehm, Bryce M Buddle, Axel Heiser
: Tuberculosis (TB) is a disease caused by Mycobacterium tuberculosis or Mycobacterium bovis and still remains one of the world's biggest global health burdens. Recently, engineered polyhydroxyalkanoate (PHA) biobeads produced in both E. coli and Lactococcus lactis displaying mycobacterial antigens were found to induce significant cell mediated immune responses in mice. We observed that such PHA beads contained host cell proteins as impurities which we hypothesized to have the potential to induce immunity...
January 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28087300/mutual-regulation-by-gnrh-and-kisspeptin-of-their-receptor-expression-and-its-impact-on-the-gene-expression-of-gonadotropin-subunits
#12
Tselmeg Mijiddorj, Haruhiko Kanasaki, Unurjargal Sukhbaatar, Aki Oride, Tomomi Hara, Satoru Kyo
Hypothalamic kisspeptin plays a pivotal role in the regulation of the hypothalamic-pituitary-gonadal axis by stimulating gonadotropin-releasing hormone (GnRH) release into the portal circulation, with the subsequent release of gonadotropins. Kisspeptin and its receptor, the kisspeptin 1 receptor (Kiss1R), are also expressed in the pituitary gland. This study demonstrates the interaction between GnRH and kisspeptin within the pituitary gonadotrophs by altering their individual receptor expression. Our results show that kisspeptin and Kiss1R are expressed in the mouse pituitary gonadotroph cell line LβT2...
January 10, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28087198/cloning-characterization-and-transmission-blocking-potential-of-midgut-carboxypeptidase-a-in-anopheles-stephensi
#13
V VenkatRao, Surendra K Kumar, P Sridevi, Vijaykumar Muley, R K Chaitanya
Transmission-blocking vaccines (TBV) interrupt malaria parasite transmission and hence form an important component for malaria eradication. Mosquito midgut exopeptidases such as aminopeptidase N & carboxypeptidase B have demonstrated TBV potential. In the present study, we cloned and characterized carboxypeptidase A (CPA) from the midgut of an important malarial vector, Anopheles stephensi. ClustalW amino acid alignment and in silico 3-dimensional structure analysis of CPA predicted the presence of active sites involved in zinc and substrate binding that are conserved among all the known mosquito species...
January 10, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28086964/anti-%C3%AE-synuclein-immunotherapy-reduces-%C3%AE-synuclein-propagation-in-the-axon-and-degeneration-in-a-combined-viral-vector-and-transgenic-model-of-synucleinopathy
#14
Brian Spencer, Elvira Valera, Edward Rockenstein, Cassia Overk, Michael Mante, Anthony Adame, Wagner Zago, Peter Seubert, Robin Barbour, Dale Schenk, Dora Games, Robert A Rissman, Eliezer Masliah
Neurodegenerative disorders such as Parkinson's Disease (PD), PD dementia (PDD) and Dementia with Lewy bodies (DLB) are characterized by progressive accumulation of α-synuclein (α-syn) in neurons. Recent studies have proposed that neuron-to-neuron propagation of α-syn plays a role in the pathogenesis of these disorders. We have previously shown that antibodies against the C-terminus of α-syn reduce the intra-neuronal accumulation of α-syn and related deficits in transgenic models of synucleinopathy, probably by abrogating the axonal transport and accumulation of α-syn in in vivo models...
January 13, 2017: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/28086941/diversity-in-breeding-sites-and-distribution-of-anopheles-mosquitoes-in-selected-urban-areas-of-southern-ghana
#15
Precious A Dzorgbe Mattah, Godfred Futagbi, Leonard K Amekudzi, Memuna M Mattah, Dziedzorm K de Souza, Worlasi D Kartey-Attipoe, Langbong Bimi, Michael D Wilson
BACKGROUND: Anopheles vectors of malaria are supposedly less common in urban areas as a result of pollution, but there is increasing evidence of their adaptation to organically polluted water bodies. This study characterized the breeding habitats of Anopheles mosquitoes in the two major urban areas in southern Ghana; Accra (AMA) and Sekondi-Takoradi (STMA) Metropolitan Areas, during dry and wet seasons. METHODS: Anopheles mosquito larvae were sampled using standard dipping methods to determine larval densities...
January 13, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28086902/exploiting-temporal-and-nonstationary-features-in-breathing-sound-analysis-for-multiple-obstructive-sleep-apnea-severity-classification
#16
Jaepil Kim, Taehoon Kim, Donmoon Lee, Jeong-Whun Kim, Kyogu Lee
BACKGROUND: Polysomnography (PSG) is the gold standard test for obstructive sleep apnea (OSA), but it incurs high costs, requires inconvenient measurements, and is limited by a one-night test. Thus, a repetitive OSA screening test using affordable data would be effective both for patients interested in their own OSA risk and in-hospital PSG. The purpose of this research was to develop a four-OSA severity classification model using a patient's breathing sounds. METHODS: Breathing sounds were recorded from 83 subjects during a PSG test...
January 7, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28086865/rnai-reveals-proteins-for-metabolism-and-protein-processing-associated-with-langat-virus-infection-in-ixodes-scapularis-black-legged-tick-ise6-cells
#17
Jeffrey M Grabowski, Monika Gulia-Nuss, Richard J Kuhn, Catherine A Hill
BACKGROUND: Tick-borne flaviviruses (TBFs) cause thousands of human cases of encephalitis worldwide each year, with some TBF infections progressing to hemorrhagic fever. TBFs are of medical and veterinary importance and strategies to reduce flavivirus transmission by the tick vector may have significant application. Analyses of the proteome of ISE6 cells derived from the black legged tick, Ixodes scapularis infected with the TBF, Langat virus (LGTV), have provided insights into proteins and cellular processes involved with LGTV infection...
January 13, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28086840/evidence-of-multiple-insecticide-resistance-mechanisms-in-anopheles-gambiae-populations-in-bangui-central-african-republic
#18
Marina Lidwine Olé Sangba, Aboubakar Sidick, Renaud Govoetchan, Christian Dide-Agossou, Razaki A Ossè, Martin Akogbeto, Mamadou Ousmane Ndiath
BACKGROUND: Knowledge of insecticide resistance status in the main malaria vectors is an essential component of effective malaria vector control. This study presents the first evaluation of the status of insecticide resistance in Anopheles gambiae populations from Bangui, the Central African Republic. METHODS: Anopheles mosquitoes were reared from larvae collected in seven districts of Bangui between September to November 2014. The World Health Organisation's bioassay susceptibility tests to lambda-cyhalothrin (0...
January 13, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28086776/comparison-of-two-adult-mosquito-sampling-methods-with-human-landing-catches-in-south-central-ethiopia
#19
Oljira Kenea, Meshesha Balkew, Habte Tekie, Teshome Gebre-Michael, Wakgari Deressa, Eskindir Loha, Bernt Lindtjørn, Hans J Overgaard
BACKGROUND: The human landing catch (HLC) is the standard reference method for measuring human exposure to mosquito bites. However, HLC is labour-intensive, exposes collectors to infectious mosquito bites and is subjected to collector bias. These necessitate local calibration and application of alternative methods. This study was undertaken to determine the relative sampling efficiency (RSE) of light traps with or without yeast-produced carbon dioxide bait vs. HLC in south-central Ethiopia...
January 13, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28086747/microrna-based-pan-cancer-diagnosis-and-treatment-recommendation
#20
Nikhil Cheerla, Olivier Gevaert
BACKGROUND: The current state-of-the-art in cancer diagnosis and treatment is not ideal; diagnostic tests are accurate but invasive, and treatments are "one-size fits-all" instead of being personalized. Recently, miRNA's have garnered significant attention as cancer biomarkers, owing to their ease of access (circulating miRNA in the blood) and stability. There have been many studies showing the effectiveness of miRNA data in diagnosing specific cancer types, but few studies explore the role of miRNA in predicting treatment outcome...
January 13, 2017: BMC Bioinformatics
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