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Piotr Klukowski, Michal Augoff, Maciej Zieba, Maciej Drwal, Adam Gonczarek, Michal J Walczak
Motivation: Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy...
March 14, 2018: Bioinformatics
Jiawei Wang, Bingjiao Yang, André Leier, Tatiana T Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Zhang Yanju, Tatsuya Akutsu, Kuo-Chen Chou, Richard A Strugnell, Jiangning Song, Trevor Lithgow
Motivation: Many Gram-negative bacteria use type VI secretion systems (T6SS) to export effector proteins into adjacent target cells. These secreted effectors (T6SEs) play vital roles in the competitive survival in bacterial populations, as well as pathogenesis of bacteria. Although various computational analyses have been previously applied to identify effectors secreted by certain bacterial species, there is no universal method available to accurately predict T6SS effector proteins from the growing tide of bacterial genome sequence data...
March 14, 2018: Bioinformatics
Ji-Eun Kang, Hyun-Do Kim, Soo-Young Park, Jae-Gu Pan, Jeong Hyun Kim, Do-Young Yum
Background and Aims: Commercial superoxide dismutase (SOD) is derived from melon extract and has a potential as a dietary supplement due to its beneficial anti-oxidative effects. We aimed to improve the productivity of SOD compared with plant SOD by using a generally-regarded-as-safe (GRAS) microorganism, Bacillus amyloliquefaciens, and assess its anti-oxidative effect using γ-radiation- and dextransulfate sodium (DSS)-induced oxidative models in mice. Methods: We identified the sodA gene encoding manganese-containing SODs (Mn-SOD) in B...
March 14, 2018: Journal of Crohn's & Colitis
Mingfei Zeng, Huachuan Cao
Short chain fatty acids (SCFA) and ketone bodies recently emerged as important physiological relevant metabolites because of their association with microbiota, immunology, obesity and other metabolic states. They were commonly analyzed by GC-MS with long run time and laborious sample preparation. In this study we developed a novel LC-MS/MS method using fast derivatization coupled with liquid-liquid extraction to detect SCFA and ketone bodies in plasma and feces. Several different derivatization reagents were evaluated to compare the efficiency, the sensitivity and chromatographic separation of structural isomers...
March 8, 2018: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
Alberto Gil de la Fuente, Joanna Godzien, Mariano Fernández López, Francisco J Rupérez, Coral Barbas, Abraham Otero
CEU Mass Mediator (CMM) is an on-line tool for aiding researchers when performing metabolite annotation. Its database is comprised of 279,318 real compounds integrated from several metabolomic databases including Human Metabolome Database (HMDB), KEGG and LipidMaps and 672,042 simulated compounds from MINE. In addition, CMM scores the annotations which matched the query parameters using 122 rules based on expert knowledge. This knowledge, obtained from the Centre for Metabolomics and Bioanalysis (CEMBIO) and from a literature review, enables CMM expert system to automatically extract evidence to support or refute the annotations by checking relationships among them...
February 23, 2018: Journal of Pharmaceutical and Biomedical Analysis
Aniko Krumbholz, Martin Schönfelder, Hande Hofmann, Detlef Thieme
BACKGROUND: The endogenous glucocorticosteroid cortisol (F) and its metabolite cortisone (E) are known to be involved in stress adaption and anti-inflammatory and immune regulatory effects. The ratios of F to E in the matrices serum, hair and saliva are different. The shift of this ratio by the enzyme activity of 11β-hydroxysteroid-dehydrogenase, which inactivates cortisol, was often discussed. The aim of our study was to calculate the contribution of the plasma protein binding (PPB) to this shift...
February 26, 2018: Forensic Science International
Samuel Mesihää, Ilpo Rasanen, Ilkka Ojanperä
Gas chromatography (GC) hyphenated with nitrogen chemiluminescence detection (NCD) and quadrupole time-of-flight mass spectrometry (QTOFMS) was applied for the first time to the quantitative analysis of new psychoactive substances (NPS) in urine, based on the N-equimolar response of NCD. A method was developed and validated to estimate the concentrations of three metabolites of the common stimulant NPS α-pyrrolidinovalerophenone (α-PVP) in spiked urine samples, simulating an analysis having no authentic reference standards for the metabolites and using the parent drug instead for quantitative calibration...
February 27, 2018: Forensic Science International
Teresa Morales-Ruiz, Álvaro C Romero-Valenzuela, Vanessa M Vázquez-Grande, Teresa Roldán-Arjona, Rafael R Ariza, Dolores Córdoba-Cañero
Base excision repair (BER) is a major defense pathway against spontaneous DNA damage. This multistep process is initiated by DNA glycosylases that recognise and excise the damaged base, and proceeds by the concerted action of additional proteins that perform incision of the abasic site, gap filling and ligation. BER has been extensively studied in bacteria, yeasts and animals. Although knowledge of this pathway in land plants is increasing, there are no reports detecting BER in algae. We describe here an experimental in vitro system allowing the specific analysis of BER in the model alga Chlamydomonas reinhardtii...
March 5, 2018: DNA Repair
Mohammad Hadi Karbalaie Niya, Hossein Keyvani, Fahimeh Safarnezhad Tameshkel, Mostafa Salehi-Vaziri, Sedigheh Teaghinezhad-S, Farah Bokharaei Salim, Seyed Hamid Reza Monavari, Davod Javanmard
Human papillomavirus (HPV) is a common viral infection worldwide associated with a variety of cancers. The integration of the HPV genome in these patients causes chromosomal instability and triggers carcinogenesis. The aim of this study was to investigate the HPV-16 genome physical status in four major cancers related to HPV infection. Formalin-fixed paraffin-embedded blocks from our previous projects on head and neck, colorectal, penile, and cervical cancers were collected, and HPV-16-positive specimens were used for further analysis...
March 13, 2018: Translational Oncology
Yasodha Maheshi Rohanachandra, Shamini Prathapan, Gampolage Swarna Wijetunge
INTRODUCTION: Maternal depression has been shown to be associated with neurodevelopmental, emotional and behavioural disorders in offspring. We aimed to describe the proportion of psychological problems among children of mothers with depression in Sri Lanka and to describe the association with the characteristics of the mothers' illness. METHODS: A cross-sectional descriptive study was conducted on 100 children and adolescents between 4-16 years whose mother has a diagnosis of depression and currently in remission...
March 3, 2018: Asian Journal of Psychiatry
Tao Wei, Lei Liu, Xiaoying Zhou
Airway smooth muscle (ASM) is a prominent effecter in maintaining bronchial muscle contraction and responsible for airway hyper-responsiveness (AHR); the phenotype change and over-proliferation of airway smooth muscle cells (ASMCs) play key roles in the pathogenesis of asthma. The aim of this study was to investigate the anti-proliferation effects of Cortex Dictamni aqueous extract (CDAE) and ethanol extract (CDE) on ASMCs and the possible underline mechanisms. Cell proliferation rates were determined by MTT assay; matrix metalloproteinases-2 (MMP-2) activity was examined by gelatin zymography; cell proliferation and migration were appraised by in-vitro cell-gap closure assessment; protein expressions of p38, Bcl-2 and FAK of ASMCs were evaluated by western blotting and Ca2+ influx of cells was measured by confocal laser microscope...
March 13, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Ipsita Subudhi, James Shorter
Ubiquilin 2 (UBQLN2) is an amyotrophic lateral sclerosis-linked molecular chaperone with a prion-like domain that directly engages ubiquitin to triage clients for proteasomal degradation. Dao et al. (2018) now establish that UBQLN2 forms ubiquitin-labile liquids, which may enable UBQLN2 to specifically extract ubiquitylated clients from stress granules for degradation.
March 15, 2018: Molecular Cell
Charalampos S Siristatidis, Eleni Sertedaki, Dennis Vaidakis, Christos Varounis, Marialena Trivella
BACKGROUND: In order to overcome the low effectiveness of assisted reproductive technologies (ART) and the high incidence of multiple births, metabolomics is proposed as a non-invasive method to assess oocyte quality, embryo viability, and endometrial receptivity, and facilitate a targeted subfertility treatment. OBJECTIVES: To evaluate the effectiveness and safety of metabolomic assessment of oocyte quality, embryo viability, and endometrial receptivity for improving live birth or ongoing pregnancy rates in women undergoing ART, compared to conventional methods of assessment...
March 16, 2018: Cochrane Database of Systematic Reviews
Annet Wijnen, Sjoukje E Bouma, Gesine H Seeber, Lucas H V van der Woude, Sjoerd K Bulstra, Djordje Lazovic, Martin Stevens, Inge van den Akker-Scheek
OBJECTIVE: To assess the therapeutic validity and effectiveness of physiotherapeutic exercise interventions following total hip arthroplasty (THA) for osteoarthritis. DATA SOURCES: The databases Embase, MEDLINE, Cochrane Library, CINAHL and AMED were searched from inception up to February 2017. ELIGIBILITY CRITERIA: Articles reporting results of randomized controlled trials in which physiotherapeutic exercise was compared with usual care or with a different type of physiotherapeutic exercise were included, with the applied interventions starting within six months after THA...
2018: PloS One
Michele Furlan, Laura Babcock, Antonino Vallesi
Traditionally, the left hemisphere has been thought to extract mainly verbal patterns of information, but recent evidence has shown that the left Inferior Frontal Gyrus (IFG) is active during inductive reasoning in both the verbal and spatial domains. We aimed to understand whether the left IFG supports inductive reasoning in a domain-specific or domain-general fashion. To do this we used Multi-Voxel Pattern Analysis to decode the representation of domain during a rule search task. Thirteen participants were asked to extract the rule underlying streams of letters presented in different spatial locations...
2018: PloS One
Hirofumi Chiba, Yoichi Kakuta, Yoshitaka Kinouchi, Yosuke Kawai, Kazuhiro Watanabe, Munenori Nagao, Takeo Naito, Motoyuki Onodera, Rintaro Moroi, Masatake Kuroha, Yoshitake Kanazawa, Tomoya Kimura, Hisashi Shiga, Katsuya Endo, Kenichi Negoro, Masao Nagasaki, Michiaki Unno, Tooru Shimosegawa
BACKGROUND: Inflammatory bowel disease (IBD) has an unknown etiology; however, accumulating evidence suggests that IBD is a multifactorial disease influenced by a combination of genetic and environmental factors. The influence of genetic variants on DNA methylation in cis and cis effects on expression have been demonstrated. We hypothesized that IBD susceptibility single-nucleotide polymorphisms (SNPs) regulate susceptibility gene expressions in cis by regulating DNA methylation around SNPs...
2018: PloS One
Fátima Higuera-de-la-Tijera
BACKGROUND: Proton pump inhibitors are the most effective medical therapy for gastroesophageal reflux disease, but their onset of action may be slow. OBJECTIVES: To assess the available literature regarding the efficacy of omeprazole/sodium bicarbonate in gastroesophageal reflux patients. METHODS: A systematic review was conducted. A systematic literature search starting from 2000. Reviewed manuscripts concerning the effectiveness of omeprazole/sodium bicarbonate treatment in gastroesophageal reflux disease were reviewed and the data were extracted...
March 14, 2018: Medwave
Mercedes Pérez-Bonilla, Daniel Oves-Costales, Mercedes de la Cruz, Maria Kokkini, Jesús Martín, Francisca Vicente, Olga Genilloud, Fernando Reyes
Phocoenamicins B and C ( 1 and 2 ), together with the known spirotetronate phocoenamicin ( 3 ), were isolated from cultures of Micromonospora sp. The acetone extract from a culture of this strain, isolated from marine sediments collected in the Canary Islands, displayed activity against methicillin-resistant Staphylococcus aureus (MRSA), Mycobacterium tuberculosis H37Ra and Mycobacterium bovis . Bioassay-guided fractionation of this extract using SP207ss column chromatography and preparative reversed-phased HPLC led to the isolation of the new compounds 1 and 2 belonging to the spirotetronate class of polyketides...
March 16, 2018: Marine Drugs
Sukyoung Choi, Soohan Jung, Kwang Suk Ko
Coffee roasting affects the taste, color, and aroma of coffee. The Maillard reaction, a major reaction during the roasting process, produces melanoidin, which affects the overall antioxidant capacity and anti-inflammatory effects of coffee. In this experiment, coffee roasting was divided into four degrees: Light, Medium, City, and French. To examine the in vivo antioxidant and anti-inflammatory effects of coffee extracts with different roasting degrees, we used 10-week-old male C57BL/6 mice. Mice were pre-treated with coffee extracts for 10 days by oral gavage (300 mg/Kg...
March 16, 2018: Nutrients
K D P P Gunathilake, K K D S Ranaweera, H P V Rupasinghe
The aim of the present study was to evaluate the effect of cooking (boiling, steaming, and frying) on anti-inflammation associated properties in vitro of six popularly consumed green leafy vegetables in Sri Lanka, namely: Centella asiatica , Cassia auriculata , Gymnema lactiferum , Olax zeylanica , Sesbania grnadiflora, and Passiflora edulis. The anti-inflammation associated properties of methanolic extracts of cooked leaves were evaluated using four in vitro biological assays, namely, hemolysis inhibition, proteinase inhibition, protein denaturation inhibition, and lipoxygenase inhibition...
March 16, 2018: Plants (Basel, Switzerland)
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